├── .devcontainer.json
├── .gitattributes
├── .github
    ├── ISSUE_TEMPLATE
    │   ├── bug.md
    │   ├── feature_request.md
    │   └── upgrade.md
    └── workflows
    │   ├── chatops.yaml
    │   ├── check_config.yaml
    │   ├── ci.yaml
    │   ├── docker-nbdev.yaml
    │   ├── docker.yaml
    │   ├── gh-page.yaml
    │   ├── issue_reminder.yaml
    │   ├── setup.yaml
    │   └── upgrade.yaml
├── .gitignore
├── Gemfile
├── Gemfile.lock
├── LICENSE
├── Makefile
├── README.md
├── _action_files
    ├── Dockerfile
    ├── __init__.py
    ├── action.yml
    ├── action_entrypoint.sh
    ├── fast_template.py
    ├── fastpages-jekyll.Dockerfile
    ├── fastpages-nbdev.Dockerfile
    ├── fastpages.tpl
    ├── hide.tpl
    ├── nb2post.py
    ├── parse_netlify.py
    ├── pr_comment.sh
    ├── settings.ini
    ├── word2post.py
    ├── word2post.sh
    └── word_front_matter.txt
├── _config.yml
├── _fastpages_docs
    ├── CONTRIBUTING.md
    ├── DEVELOPMENT.md
    ├── NOTEBOOK_FOOTNOTES.md
    ├── README_TEMPLATE.md
    ├── TROUBLESHOOTING.md
    ├── UPGRADE.md
    ├── _checkbox.png
    ├── _manual_setup.md
    ├── _paginate.png
    ├── _post_tags.png
    ├── _setup_pr_template.md
    ├── _show_image_true.png
    ├── _upgrade_pr.md
    ├── highlight_dracula.png
    ├── highlight_original.png
    ├── upgrade_step1.png
    ├── upgrade_step2.png
    ├── upgrade_step3.png
    └── version.txt
├── _includes
    ├── alert.html
    ├── custom-head.html
    ├── favicons.html
    ├── google-analytics.html
    ├── head.html
    ├── image-r
    ├── image.html
    ├── important.html
    ├── info.html
    ├── note.html
    ├── notebook_binder_link.html
    ├── notebook_colab_link.html
    ├── notebook_github_link.html
    ├── post_list.html
    ├── post_list_image_card.html
    ├── reading_time.html
    ├── screenshot
    ├── tip.html
    ├── toc.html
    ├── twitter.html
    ├── utterances.html
    ├── warning.html
    └── youtube.html
├── _layouts
    ├── categories.html
    ├── home.html
    ├── notebook.html
    └── post.html
├── _notebooks
    ├── 2020-04-28-Medical-Imaging-Using-Fastai.ipynb
    ├── 2020-04-29-Starting-With-Medical-Imaging.ipynb
    ├── 2020-05-12-Getting-To-Know-DICOMS.ipynb
    ├── 2020-06-16-Understanding-Photometric-Interpretation.ipynb
    ├── 2020-06-25-Selective-Mask.ipynb
    ├── 2020-11-04-A-Matter-Of-Grayscale-Understanding-Dicom-Windows.ipynb
    ├── 2021-01-03-Fmi-Additional-Functionality-For-Fastai-Medical-Imaging-Module.ipynb
    ├── 2021-08-17-Creating_Bounding-Boxes-From-Class-Activation-Maps.ipynb
    ├── README.md
    ├── my_icons
    │   ├── chest1.PNG
    │   ├── chest2.PNG
    │   ├── dicom.PNG
    │   ├── dicom_.PNG
    │   ├── dicom_wf.PNG
    │   ├── fastai_logo.png
    │   ├── glee.PNG
    │   ├── graphic6.png
    │   ├── gray.PNG
    │   ├── hist1.PNG
    │   ├── hist2.PNG
    │   ├── hist3.PNG
    │   ├── hist4.PNG
    │   ├── hu.PNG
    │   ├── post.PNG
    │   ├── pre.PNG
    │   ├── selective_msk.PNG
    │   ├── selective_msk2.PNG
    │   ├── tissues.png
    │   ├── typeerror.PNG
    │   └── view_.PNG
    └── test_df.csv
├── _pages
    ├── 404.html
    ├── about.md
    ├── search.html
    └── tags.html
├── _plugins
    ├── footnote-detail.rb
    └── footnote.rb
├── _posts
    └── README.md
├── _sass
    └── minima
    │   ├── custom-styles.scss
    │   ├── dark-mode.scss
    │   ├── fastpages-dracula-highlight.scss
    │   ├── fastpages-styles.scss
    │   ├── solarized.scss
    │   └── test-layout.scss
├── _word
    └── README.md
├── action.yml
├── assets
    ├── badges
    │   ├── binder.svg
    │   ├── colab.svg
    │   └── github.svg
    └── js
    │   ├── search-data.json
    │   ├── search.js
    │   └── vendor
    │       └── lunr.min.js
├── docker-compose.yml
├── images
    ├── bb.PNG
    ├── chart-preview.png
    ├── circle.PNG
    ├── copied_from_nb
    │   └── README.md
    ├── diagram.png
    ├── dicom.PNG
    ├── dicom_.PNG
    ├── dicom_wf.PNG
    ├── fastpages_posts
    │   └── actions
    │   │   ├── actions_logo.png
    │   │   ├── pr_1.png
    │   │   └── pr_2.png
    ├── favicon.ico
    ├── favicon_ORG.ico
    ├── fmi.png
    ├── gdicom.PNG
    ├── graphic6s.png
    ├── hist1.PNG
    ├── hist2.PNG
    ├── hist3.PNG
    ├── hist4.PNG
    ├── logo.png
    ├── med_pix.PNG
    ├── msk.PNG
    ├── part1.PNG
    ├── part3.PNG
    ├── width.PNG
    └── windowing.PNG
└── index.html


/.devcontainer.json:
--------------------------------------------------------------------------------
 1 | {
 2 |     "name": "fastpages-codespaces",
 3 |     "dockerComposeFile": "docker-compose.yml",
 4 |     "service": "watcher",
 5 |     "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ],
 6 |     "forwardPorts": [4000],
 7 |     "appPort": [4000],
 8 |     "extensions": ["ms-python.python",
 9 |                    "ms-azuretools.vscode-docker"],
10 |     "runServices": ["converter", "jekyll", "watcher"]
11 | }
12 | 
13 | 


--------------------------------------------------------------------------------
/.gitattributes:
--------------------------------------------------------------------------------
1 | # Set the default behavior, in case people don't have core.autocrlf set.
2 | * text=auto


--------------------------------------------------------------------------------
/.github/ISSUE_TEMPLATE/bug.md:
--------------------------------------------------------------------------------
 1 | ---
 2 | name: Bug
 3 | about: Use this template for filing bugs
 4 | title: ""
 5 | labels: bug
 6 | assignees: ''
 7 | 
 8 | ---
 9 | 
10 | ## Required Prerequisites for filing a bug
11 | 
12 | ### You must follow ALL the steps in the [troubleshooting guide](https://github.com/fastai/fastpages/blob/master/_fastpages_docs/TROUBLESHOOTING.md).  Not doing so may result in automatic closure of the issue.
13 | 
14 | 
15 | ## Required information
16 | 
17 | 1. Steps to reproduce the problem
18 | 2. A link to the notebook or markdown file where the error is occurring
19 | 3. If the error is happening in GitHub Actions, a link to the specific error along with how you are able to reproduce this error.  You must provide this **in addition to the link to the notebook or markdown file**.
20 | 4. A screenshot / dump of relevant logs or error messages you are receiving from your local development environment. Instructions of running a local development server is provided in the [development guide](https://github.com/fastai/fastpages/blob/master/_fastpages_docs/DEVELOPMENT.md).
21 | 


--------------------------------------------------------------------------------
/.github/ISSUE_TEMPLATE/feature_request.md:
--------------------------------------------------------------------------------
 1 | ---
 2 | name: Feature request
 3 | about: Suggest an idea for this project
 4 | title: ''
 5 | labels: enhancement
 6 | assignees: ''
 7 | 
 8 | ---
 9 | 
10 | **Is your feature request related to a problem? Please describe.**
11 | A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
12 | 
13 | **Describe the solution you'd like**
14 | A clear and concise description of what you want to happen.
15 | 
16 | **Describe alternatives you've considered**
17 | A clear and concise description of any alternative solutions or features you've considered.
18 | 
19 | **Additional context**
20 | Add any other context or screenshots about the feature request here.
21 | 


--------------------------------------------------------------------------------
/.github/ISSUE_TEMPLATE/upgrade.md:
--------------------------------------------------------------------------------
 1 | ---
 2 | name: "[fastpages] Automated Upgrade"
 3 | about: "Trigger a PR for upgrading fastpages"
 4 | title: "[fastpages] Automated Upgrade"
 5 | labels: fastpages-automation
 6 | assignees: ''
 7 | 
 8 | ---
 9 | 
10 | Opening this issue will trigger GitHub Actions to fetch the lastest version of [fastpages](https://github.com/fastai/fastpages).  More information will be provided in forthcoming comments below.
11 | 


--------------------------------------------------------------------------------
/.github/workflows/chatops.yaml:
--------------------------------------------------------------------------------
  1 | name: Chatops
  2 | on: [issue_comment]
  3 | 
  4 | jobs:
  5 |   trigger-chatops:
  6 |     if: (github.event.issue.pull_request != null) &&  contains(github.event.comment.body, '/preview') && (github.repository == 'fastai/fastpages')
  7 |     env:
  8 |       NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
  9 |       NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
 10 |       CHECK_RUN_NAME: "Draft-Site-Build"
 11 |     runs-on: ubuntu-latest
 12 |     steps:
 13 |           
 14 |       - name: see payload
 15 |         run: |
 16 |           echo "FULL PAYLOAD:\n${PAYLOAD}\n"
 17 |           echo "PR_PAYLOAD PAYLOAD:\n${PR_PAYLOAD}"
 18 |         env:
 19 |           PAYLOAD: ${{ toJSON(github.event) }}
 20 |           PR_PAYLOAD: ${{ github.event.pull_request }}
 21 |         
 22 |       - name: verify env exists
 23 |         id: get_status
 24 |         run:  |
 25 |           if [ -z ${NETLIFY_AUTH_TOKEN} ]; then echo "::set-output name=status::public"; else echo "::set-output name=status::private"; fi
 26 | 
 27 |       - name: make comment on PR if env does not exist
 28 |         if: steps.get_status.outputs.status == 'public'
 29 |         run: |
 30 |            ./_action_files/pr_comment.sh "Was not able to generate site preview due to absent credentials."
 31 |         env:
 32 |           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 33 |           ISSUE_NUMBER: ${{ github.event.issue.number }}
 34 | 
 35 |       - name: Fetch context about the PR that has been commented on
 36 |         id: chatops
 37 |         uses: machine-learning-apps/actions-chatops@master
 38 |         with:
 39 |           TRIGGER_PHRASE: "/preview"
 40 |         env: # you must supply GITHUB_TOKEN
 41 |           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 42 | 
 43 |       - name: Set up Python
 44 |         uses: actions/setup-python@v1
 45 |         with:
 46 |           python-version: 3.6
 47 |           
 48 |       - name: install requests
 49 |         run: pip3 install requests
 50 | 
 51 |       - name: add check run
 52 |         id: create_check
 53 |         if: steps.get_status.outputs.status == 'private'
 54 |         shell: python
 55 |         run: |
 56 |           import os, requests
 57 | 
 58 |           sha = os.getenv('SHA')
 59 |           token = os.getenv('GITHUB_TOKEN')
 60 |           nwo = os.getenv('GITHUB_REPOSITORY')
 61 |           name = os.getenv('CHECK_RUN_NAME')
 62 | 
 63 |           url = f'https://api.github.com/repos/{nwo}/check-runs'
 64 | 
 65 |           headers = {'authorization': f'token {token}',
 66 |            'accept': 'application/vnd.github.antiope-preview+json'}
 67 | 
 68 |           payload = {
 69 |             'name': f'{name}',
 70 |             'head_sha': f'{sha}',
 71 |             'status': 'in_progress',
 72 |             'output':{
 73 |                 'title': f'Building preview of site for {sha}.',
 74 |                 'summary': ' ',
 75 |                 'text': ' '
 76 |             },
 77 |           }
 78 |           response = requests.post(url=url, headers=headers, json=payload)
 79 |           print(response)
 80 |           id = response.json()['id']
 81 |           print(f"::set-output name=id::{id}")
 82 |         env:
 83 |           SHA: ${{ steps.chatops.outputs.SHA }}
 84 |           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 
 85 |           
 86 |       - name: add label
 87 |         if: steps.get_status.outputs.status == 'private'
 88 |         run: |
 89 |           import os, requests
 90 |           nwo = os.getenv('GITHUB_REPOSITORY')
 91 |           token = os.getenv('GITHUB_TOKEN')
 92 |           pr_num = os.getenv('PR_NUM')
 93 |           headers = {'Accept': 'application/vnd.github.symmetra-preview+json',
 94 |                      'Authorization': f'token {token}'}
 95 |           url = f"https://api.github.com/repos/{nwo}/issues/{pr_num}/labels"
 96 |           data = {"labels": ["draft build pending"]}
 97 |           result = requests.post(url=url, headers=headers, json=data)
 98 |           # assert response.status_code == 201, f"Received status code of {response.status_code}"
 99 |           print(result)
100 |         shell: python
101 |         env:
102 |           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
103 |           PR_NUM: ${{ steps.chatops.outputs.PULL_REQUEST_NUMBER }}
104 |           GITHUB_REPOSITORY: $GITHUB_REPOSITORY
105 |           
106 |       - name: Copy The PR's Branch Repository Contents
107 |         uses: actions/checkout@master
108 |         if: steps.get_status.outputs.status == 'private'
109 |         with:
110 |           ref: ${{ steps.chatops.outputs.SHA }}
111 |      
112 |       - name: convert notebooks and word docs to posts
113 |         uses: ./ # use the code in this repo to instead of fastai/fastpages@master
114 | 
115 |       - name: setup directories for Jekyll build
116 |         if: steps.get_status.outputs.status == 'private'
117 |         run: |
118 |           rm -rf _site
119 |           sudo chmod -R 777 .
120 |           
121 |       - name: Jekyll build with baseurl as root for netifly
122 |         if: steps.get_status.outputs.status == 'private'
123 |         uses: docker://hamelsmu/fastpages-jekyll
124 |         with:
125 |           args: bash -c "gem install bundler && jekyll build"
126 |      
127 |       - name: deploy to netlify
128 |         if: steps.get_status.outputs.status == 'private'
129 |         id: py
130 |         run: | 
131 |           sudo npm install netlify-cli -g
132 |           netlify deploy --dir _site | tee _netlify_logs.txt
133 |           cat _netlify_logs.txt | python _action_files/parse_netlify.py
134 | 
135 |       - name: make comment on PR 
136 |         if: steps.get_status.outputs.status == 'private'
137 |         run: |
138 |            MSG="A preview build of this branch has been generated for SHA: $SHA and can be viewed **live** at: ${URL}\n\nThe current fastpages site built from master can be viewed for comparison [here](https://fastpages.fast.ai/)"
139 |            echo "$MSG"
140 |            ./_action_files/pr_comment.sh "${MSG}"
141 |         env:
142 |            URL: ${{ steps.py.outputs.draft_url }}
143 |            SHA: ${{ steps.chatops.outputs.SHA }}
144 |            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
145 |            ISSUE_NUMBER: ${{ github.event.issue.number }}
146 |            
147 |       - name: remove label
148 |         if: always()
149 |         run: |
150 |           import os, requests
151 |           nwo = os.getenv('GITHUB_REPOSITORY')
152 |           token = os.getenv('GITHUB_TOKEN')
153 |           pr_num = os.getenv('PR_NUM')
154 |           headers = {'Accept': 'application/vnd.github.symmetra-preview+json',
155 |                      'Authorization': f'token {token}'}
156 |           url = f"https://api.github.com/repos/{nwo}/issues/{pr_num}/labels/draft%20build%20pending"
157 |           result = requests.delete(url=url, headers=headers)
158 |           print(result)
159 |         shell: python
160 |         env:
161 |           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
162 |           PR_NUM: ${{ steps.chatops.outputs.PULL_REQUEST_NUMBER }}
163 |           GITHUB_REPOSITORY: $GITHUB_REPOSITORY
164 | 
165 |       # defensively clear check run each time
166 |       - name: clear check run
167 |         if: always()
168 |         continue-on-error: true
169 |         shell: python
170 |         run: |
171 |           import os, requests
172 | 
173 |           sha = os.getenv('SHA')
174 |           conclusion = os.getenv('WORKFLOW_CONCLUSION').lower()
175 |           token = os.getenv('GITHUB_TOKEN')
176 |           nwo = os.getenv('GITHUB_REPOSITORY')
177 |           check_run_id = os.getenv('CHECK_RUN_ID')
178 |           if not check_run_id:
179 |             quit()
180 |           
181 |           url = f'https://api.github.com/repos/{nwo}/check-runs/{check_run_id}'
182 |           headers = {'authorization': f'token {token}',
183 |                      'accept': 'application/vnd.github.antiope-preview+json'}
184 |           
185 |           data = {
186 |               'conclusion': f'{conclusion}',
187 |           }
188 |           response = requests.patch(url=url, headers=headers, json=data)
189 |           print(response)
190 |         env:
191 |           SHA: ${{ steps.chatops.outputs.SHA }}
192 |           WORKFLOW_CONCLUSION: ${{ job.status }}
193 |           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
194 |           CHECK_RUN_ID: ${{ steps.create_check.outputs.id }}
195 | 
196 | 


--------------------------------------------------------------------------------
/.github/workflows/check_config.yaml:
--------------------------------------------------------------------------------
 1 | name: Check Configurations
 2 | on: push
 3 | 
 4 | jobs:
 5 |  check-config:
 6 |    runs-on: ubuntu-latest
 7 |    steps:
 8 |     - uses: actions/checkout@master
 9 | 
10 |     - name: Set up Python
11 |       uses: actions/setup-python@v1
12 |       with:
13 |         python-version: 3.7
14 | 
15 |     - name: install dependencies
16 |       run:  pip3 install pyyaml
17 | 
18 |     - name: check baseurl
19 |       id: baseurl
20 |       run: |
21 |         import yaml
22 |         from pathlib import Path
23 |         from configparser import ConfigParser
24 |         settings = ConfigParser()
25 |         
26 |         config_path = Path('_config.yml')
27 |         settings_path = Path('_action_files/settings.ini')
28 |         
29 |         assert config_path.exists(), 'Did not find _config.yml in the current directory!'
30 |         assert settings_path.exists(), 'Did not find _action_files/settings.ini in the current directory!'
31 |         
32 |         settings.read(settings_path)
33 |         with open('_config.yml') as f:
34 |             config = yaml.safe_load(f)
35 |             
36 |         errmsg = f"The value set for baseurl in _action_files/settings.ini and _config.yml are not identical. Please fix and try again."
37 |         assert config['baseurl'] == settings['DEFAULT']['baseurl'], errmsg
38 |       shell: python
39 | 
40 |     - name: Create issue if baseurl rule is violated
41 |       if: steps.baseurl.outcome == 'failure'
42 |       uses: actions/github-script@0.6.0
43 |       with:
44 |         github-token: ${{secrets.GITHUB_TOKEN}}
45 |         script: |
46 |           var err = process.env.ERROR_STRING;
47 |           var run_id = process.env.RUN_ID;
48 |           github.issues.create({
49 |             owner: context.repo.owner,
50 |             repo: context.repo.repo,
51 |             title: "Error with repository configuration: baseurl",
52 |             body: `${err}\n See run [${run_id}](https://github.com/${context.repo.owner}/${context.repo.repo}/actions/runs/${run_id}) for more details.`
53 |           })
54 |       env:
55 |         ERROR_STRING: "You have not configured your baseurl correctly, please read the instructions in _config.yml carefully."
56 |         RUN_ID: ${{ github.run_id	}}
57 | 
58 |     - name: check for User Pages
59 |       id: userpage
60 |       run: |
61 |         import os
62 |         nwo = os.getenv('GITHUB_REPOSITORY')
63 |         errmsg = "fastpages does not support User Pages or repo names that end with github.io, please see https://forums.fast.ai/t/fastpages-replacing-main-username-github-io-page-w-fastpages/64316/3 for more details."
64 |         assert ".github.io" not in nwo, errmsg
65 |       shell: python
66 | 
67 |     - name: Create Issue if User Pages rule is violated
68 |       if: steps.userpage.outcome == 'failure'
69 |       uses: actions/github-script@0.6.0
70 |       with:
71 |         github-token: ${{secrets.GITHUB_TOKEN}}
72 |         script: |
73 |           github.issues.create({
74 |             owner: context.repo.owner,
75 |             repo: context.repo.repo,
76 |             title: "Error with repository configuration: repo name",
77 |             body: 'fastpages does not support User Pages or repo names that end with github.io, please see https://forums.fast.ai/t/fastpages-replacing-main-username-github-io-page-w-fastpages/64316/3 for more details.'
78 |           })
79 | 


--------------------------------------------------------------------------------
/.github/workflows/ci.yaml:
--------------------------------------------------------------------------------
 1 | name: CI
 2 | on:
 3 |   push:
 4 |     branches:
 5 |       - master # need to filter here so we only deploy when there is a push to master
 6 |   # no filters on pull requests, so intentionally left blank
 7 |   pull_request: 
 8 | 
 9 | jobs:     
10 |   build-site:
11 |     if: ( github.event.commits[0].message != 'Initial commit' ) || github.run_number > 1
12 |     runs-on: ubuntu-latest
13 |     steps:
14 | 
15 |     - name: Copy Repository Contents
16 |       uses: actions/checkout@master
17 |       with:
18 |         persist-credentials: false
19 | 
20 |     - name: convert notebooks and word docs to posts
21 |       uses: ./_action_files
22 | 
23 |     - name: setup directories for Jekyll build
24 |       run: |
25 |         rm -rf _site
26 |         sudo chmod -R 777 .
27 | 
28 |     - name: Jekyll build
29 |       uses: docker://hamelsmu/fastpages-jekyll
30 |       with:
31 |         args: bash -c "gem install bundler && jekyll build -V --strict_front_matter --trace"
32 |       env:
33 |         JEKYLL_ENV: 'production'
34 |         
35 |     - name: copy CNAME file into _site if CNAME exists
36 |       run: |
37 |         sudo chmod -R 777 _site/
38 |         cp CNAME _site/ 2>/dev/null || :
39 | 
40 |     - name: Deploy
41 |       if: github.event_name	== 'push'
42 |       uses: peaceiris/actions-gh-pages@v3
43 |       with:
44 |         deploy_key: ${{ secrets.SSH_DEPLOY_KEY }}
45 |         publish_dir: ./_site
46 | 


--------------------------------------------------------------------------------
/.github/workflows/docker-nbdev.yaml:
--------------------------------------------------------------------------------
 1 | name: Build-Nbdev-Docker
 2 | on:
 3 |     schedule:
 4 |       - cron:  '0 */12 * * *'
 5 | 
 6 | jobs:
 7 |     nbdev-docker-fastpages:
 8 |         if: github.repository == 'fastai/fastpages'
 9 |         runs-on: ubuntu-latest
10 |         steps:
11 |             - uses: actions/checkout@master
12 |             
13 |             - name: build container
14 |               run: |
15 |                 docker build -t hamelsmu/fastpages-nbdev -f _action_files/fastpages-nbdev.Dockerfile ./_action_files
16 | 
17 |             - name: push container
18 |               run: |
19 |                 echo ${PASSWORD} | docker login -u $USERNAME --password-stdin
20 |                 docker push hamelsmu/fastpages-nbdev
21 |               env:
22 |                 USERNAME: ${{ secrets.DOCKER_USERNAME }}
23 |                 PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
24 | 


--------------------------------------------------------------------------------
/.github/workflows/docker.yaml:
--------------------------------------------------------------------------------
 1 | name: Build-Docker
 2 | on:
 3 |     push:
 4 |         paths:
 5 |             - Gemfile*
 6 |         branches:
 7 |             - master
 8 |     pull_request:
 9 |         paths:
10 |             - Gemfile*
11 | 
12 | jobs:
13 |     jekyll-fastpages:
14 |         if: github.repository == 'fastai/fastpages'
15 |         runs-on: ubuntu-latest
16 |         steps:
17 |             - uses: actions/checkout@master
18 |             
19 |             - name: setup directories for Jekyll build
20 |               run: sudo chmod -R 777 .
21 |               
22 |             - name: build container
23 |               run: |
24 |                 docker build -t hamelsmu/fastpages-jekyll -f _action_files/fastpages-jekyll.Dockerfile .
25 | 
26 |             - name: push container
27 |               if: github.event == 'push'
28 |               run: |
29 |                 echo ${PASSWORD} | docker login -u $USERNAME --password-stdin
30 |                 docker push hamelsmu/fastpages-jekyll
31 |               env:
32 |                 USERNAME: ${{ secrets.DOCKER_USERNAME }}
33 |                 PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
34 | 


--------------------------------------------------------------------------------
/.github/workflows/gh-page.yaml:
--------------------------------------------------------------------------------
 1 | name: GH-Pages Status
 2 | on:
 3 |   page_build
 4 |   
 5 | jobs:
 6 |   see-page-build-payload:
 7 |     runs-on: ubuntu-latest
 8 |     steps:      
 9 |       - name: check status
10 |         run: |
11 |           import os
12 |           status, errormsg = os.getenv('STATUS'), os.getenv('ERROR')
13 |           assert status == 'built', 'There was an error building the page on GitHub pages.\n\nStatus: {}\n\nError messsage: {}'.format(status, errormsg)
14 |         shell: python
15 |         env:
16 |           STATUS: ${{ github.event.build.status }}
17 |           ERROR: ${{ github.event.build.error.message }}
18 | 


--------------------------------------------------------------------------------
/.github/workflows/issue_reminder.yaml:
--------------------------------------------------------------------------------
 1 | 
 2 | name: Issue Reminder
 3 | on: 
 4 |   issues:
 5 |     types: [opened]
 6 | 
 7 | jobs:
 8 |   issue_comment:
 9 |     if: |
10 |       (github.repository == 'fastai/fastpages')
11 |     runs-on: ubuntu-latest
12 |     steps:
13 | 
14 |     - name: Comment on issue
15 |       uses: actions/github-script@0.6.0
16 |       with:
17 |         github-token: ${{secrets.GITHUB_TOKEN}}
18 |         script: |
19 |           var url = 'https://github.com/fastai/fastpages/blob/master/_fastpages_docs/TROUBLESHOOTING.md'
20 |           var msg = `Thank you for opening an issue.  If this issue is related to a bug, please follow the steps and provide the information outlined in the [Troubleshooting Guide](${url}).  Failure to follow these instructions may result in automatic closing of this issue.`
21 |           github.issues.createComment({
22 |             issue_number: context.issue.number,
23 |             owner: context.repo.owner,
24 |             repo: context.repo.repo,
25 |             body: msg
26 |           })
27 | 


--------------------------------------------------------------------------------
/.github/workflows/setup.yaml:
--------------------------------------------------------------------------------
  1 | name: Setup
  2 | on: push
  3 | 
  4 | jobs:
  5 |   setup:
  6 |     if: (github.event.commits[0].message == 'Initial commit') && (github.run_number == 1)
  7 |     runs-on: ubuntu-latest
  8 |     steps:
  9 | 
 10 |     - name: Set up Python
 11 |       uses: actions/setup-python@v1
 12 |       with:
 13 |         python-version: 3.6
 14 | 
 15 |     - name: Copy Repository Contents
 16 |       uses: actions/checkout@v2
 17 |         
 18 |     - name: modify files
 19 |       run: |
 20 |         import re, os
 21 |         from pathlib import Path
 22 |         from configparser import ConfigParser
 23 |         config = ConfigParser()
 24 | 
 25 |         nwo = os.getenv('GITHUB_REPOSITORY')
 26 |         username, repo_name = nwo.split('/')
 27 |         readme_template_path = Path('_fastpages_docs/README_TEMPLATE.md')
 28 |         readme_path = Path('README.md')
 29 |         config_path = Path('_config.yml')
 30 |         pr_msg_path = Path('_fastpages_docs/_setup_pr_template.md')
 31 |         settings = Path('_action_files/settings.ini')
 32 | 
 33 |         assert readme_template_path.exists(), 'Did not find _fastpages_docs/README_TEMPLATE.md in the current directory!'
 34 |         assert readme_path.exists(), 'Did not find README.md in the current directory!'
 35 |         assert config_path.exists(), 'Did not find _config.yml in the current directory!'
 36 |         assert pr_msg_path.exists(), 'Did not find _fastpages_docs/_setup_pr_template.md in the current directory!'
 37 |         assert settings.exists(), 'Did not find _action_files/settings.ini in the current directory!'
 38 |         
 39 |         # edit settings.ini file to inject baseurl
 40 |         config.read(settings)
 41 |         config['DEFAULT']['baseurl'] = f'/{repo_name}'
 42 |         with open('_action_files/settings.ini', 'w') as configfile:
 43 |           config.write(configfile)
 44 | 
 45 |         # replace content of README with template
 46 |         readme = readme_template_path.read_text().replace('{_username_}', username).replace('{_repo_name_}', repo_name)
 47 |         readme_path.write_text(readme)
 48 |         
 49 |         # update _config.yml
 50 |         cfg = config_path.read_text()
 51 |         cfg = re.sub(r'^(github_username: )(fastai)', fr'\g<1>{username}', cfg, flags=re.MULTILINE)
 52 |         cfg = re.sub(r'^(baseurl: )("")', r'\1"/{}"'.format(repo_name), cfg, flags=re.MULTILINE)
 53 |         cfg = re.sub(r'^(github_repo: ")(fastpages)', r'\1{}'.format(repo_name), cfg, flags=re.MULTILINE)
 54 |         cfg = re.sub(r'^(url: "https://)(fastpages.fast.ai)(")', fr'\g<1>{username}.github.io\3', cfg, flags=re.MULTILINE)
 55 |         cfg = re.sub('UA-57531313-5', '', cfg, flags=re.MULTILINE)
 56 |         config_path.write_text(cfg)
 57 | 
 58 |         # prepare the pr message
 59 |         pr = pr_msg_path.read_text().replace('{_username_}', username).replace('{_repo_name_}', repo_name)
 60 |         pr_msg_path.write_text(pr)
 61 |       shell: python
 62 | 
 63 |     - name: commit changes
 64 |       run: |
 65 |         git config --global user.email "${GH_EMAIL}"
 66 |         git config --global user.name "${GH_USERNAME}"
 67 |         git checkout -B fastpages-automated-setup
 68 |         git rm CNAME action.yml
 69 |         git rm _notebooks/2020-02-21-introducing-fastpages.ipynb
 70 |         git rm _posts/2020-03-06-fastpages-actions.md
 71 |         git rm -rf images/fastpages_posts
 72 |         git rm .github/workflows/chatops.yaml
 73 |         git rm .github/workflows/docker.yaml
 74 |         git rm .github/workflows/docker-nbdev.yaml
 75 |         git rm .github/ISSUE_TEMPLATE/bug.md
 76 |         git rm .github/ISSUE_TEMPLATE/feature_request.md
 77 |         git rm _word/*.docx
 78 |         git add _config.yml README.md _fastpages_docs/ _action_files/settings.ini
 79 |         git commit -m'setup repo'
 80 |         git push -f --set-upstream origin fastpages-automated-setup
 81 |       env: 
 82 |         GH_EMAIL: ${{ github.event.commits[0].author.email }}
 83 |         GH_USERNAME: ${{ github.event.commits[0].author.username }}
 84 | 
 85 |     - name: Open a PR
 86 |       uses: actions/github-script@0.5.0
 87 |       with:
 88 |         github-token: ${{secrets.GITHUB_TOKEN}}
 89 |         script: |
 90 |           var fs = require('fs');
 91 |           var contents = fs.readFileSync('_fastpages_docs/_setup_pr_template.md', 'utf8');
 92 |           github.pulls.create({
 93 |                         owner: context.repo.owner,
 94 |                         repo: context.repo.repo,
 95 |                         title: 'Initial Setup',
 96 |                         head: 'fastpages-automated-setup',
 97 |                         base: 'master',
 98 |                         body: `${contents}`
 99 |                         })
100 | 


--------------------------------------------------------------------------------
/.github/workflows/upgrade.yaml:
--------------------------------------------------------------------------------
  1 | name: Upgrade fastpages
  2 | on: 
  3 |   issues:
  4 |     types: [opened]
  5 | 
  6 | jobs:
  7 |   check_credentials:
  8 |     if: |
  9 |       (github.repository != 'fastai/fastpages') &&
 10 |       (github.event.issue.title == '[fastpages] Automated Upgrade')   
 11 |     runs-on: ubuntu-latest
 12 |     steps:
 13 | 
 14 |     - name: see payload
 15 |       run: |
 16 |         echo "FULL PAYLOAD:\n${PAYLOAD}\n"
 17 |         echo "PR_PAYLOAD PAYLOAD:\n${PR_PAYLOAD}"
 18 |       env:
 19 |         PAYLOAD: ${{ toJSON(github.event) }}
 20 |         PR_PAYLOAD: ${{ github.event.pull_request }}
 21 | 
 22 |     - name: Comment on issue if sufficient access does not exist
 23 |       if: |
 24 |         (github.event.issue.author_association != 'OWNER') && 
 25 |         (github.event.issue.author_association != 'COLLABORATOR') &&
 26 |         (github.event.issue.author_association != 'MEMBER')
 27 |       uses: actions/github-script@0.6.0
 28 |       with:
 29 |         github-token: ${{secrets.GITHUB_TOKEN}}
 30 |         script: |
 31 |           var permission_level = process.env.permission_level;
 32 |           var url = 'https://help.github.com/en/github/setting-up-and-managing-your-github-user-account/permission-levels-for-a-user-account-repository#collaborator-access-on-a-repository-owned-by-a-user-account'
 33 |           var msg = `You must have the [permission level](${url}) of either an **OWNER**, **COLLABORATOR** or **MEMBER** to instantiate an upgrade request.  Your permission level is ${permission_level}`
 34 |           github.issues.createComment({
 35 |             issue_number: context.issue.number,
 36 |             owner: context.repo.owner,
 37 |             repo: context.repo.repo,
 38 |             body: msg
 39 |           })
 40 |           github.issues.update({
 41 |             issue_number: context.issue.number,
 42 |             owner: context.repo.owner,
 43 |             repo: context.repo.repo,
 44 |             state: 'closed'
 45 |           })
 46 |           throw msg;
 47 |       env:
 48 |         permission_level: ${{ github.event.issue.author_association }}
 49 |           
 50 |   upgrade:
 51 |     needs: [check_credentials]
 52 |     if: |
 53 |       (github.repository != 'fastai/fastpages') &&
 54 |       (github.event.issue.title == '[fastpages] Automated Upgrade') &&
 55 |       (github.event.issue.author_association == 'OWNER' || github.event.issue.author_association == 'COLLABORATOR' || github.event.issue.author_association == 'MEMBER')
 56 |     runs-on: ubuntu-latest
 57 |     steps:
 58 |     
 59 |     - name: Set up Python
 60 |       uses: actions/setup-python@v1
 61 |       with:
 62 |         python-version: 3.7
 63 |     
 64 |     - name: checkout latest fastpages
 65 |       uses: actions/checkout@v2
 66 |       with:
 67 |         repository: 'fastai/fastpages'
 68 |         path: 'new_files'
 69 |         persist-credentials: false
 70 |         
 71 |     - name: copy this repo's contents
 72 |       uses: actions/checkout@v2
 73 |       with:
 74 |         path: 'current_files'
 75 |         persist-credentials: false
 76 | 
 77 |     - name: compare versions
 78 |       id: check_version
 79 |       run: |
 80 |         from pathlib import Path
 81 |         new_version = Path('new_files/_fastpages_docs/version.txt')
 82 |         old_version = Path('current_files/_fastpages_docs/version.txt')
 83 | 
 84 |         if old_version.exists():
 85 |           old_num = old_version.read_text().strip()
 86 |           new_num = new_version.read_text().strip()
 87 |           print(f'Old version: {old_num}')
 88 |           print(f'New version: {new_num}')
 89 |           if old_num == new_num:
 90 |             print('::set-output name=vbump::false')
 91 |           else:
 92 |             print('::set-output name=vbump::true')
 93 |         else:
 94 |           print('::set-output name=vbump::true')
 95 |       shell: python
 96 | 
 97 |     - name: copy new files
 98 |       if: steps.check_version.outputs.vbump == 'true'
 99 |       run: |
100 |         # remove files you don't want to copy from current version of fastpages
101 |         cd new_files        
102 |         rm -rf _posts _notebooks _word images
103 |         rm *.md CNAME action.yml _config.yml index.html LICENSE
104 |         rm _pages/*.md
105 |         rm .github/workflows/chatops.yaml
106 |         rm .github/workflows/docker-nbdev.yaml
107 |         rm .github/workflows/docker.yaml
108 |         rm .github/ISSUE_TEMPLATE/bug.md .github/ISSUE_TEMPLATE/feature_request.md
109 |         
110 |         # copy new files from fastpages into your repo
111 |         for file in $(ls | egrep -v "(assets|_sass)"); do 
112 |           if [[ -f "$file" ]] || [[ -d "$file" ]] 
113 |           then
114 |             echo "copying $file"; 
115 |             cp -r $file ../current_files;
116 |           fi
117 |         done
118 |         
119 |         # copy select files in assets and _sass
120 |         cp -r assets/js ../current_files/assets
121 |         cp -r assets/badges ../current_files/assets
122 |         cp _sass/minima/fastpages-styles.scss ../current_files/_sass/minima/
123 |         cp _sass/minima/fastpages-dracula-highlight.scss ../current_files/_sass/minima/
124 |         
125 |         # copy action workflows
126 |         cp -r .github ../current_files
127 |         
128 |         # install dependencies
129 |         pip3 install pyyaml
130 | 
131 |     - name: sync baseurl
132 |       if: steps.check_version.outputs.vbump == 'true'
133 |       run: |
134 |         import re, os, yaml
135 |         from pathlib import Path
136 |         from configparser import ConfigParser
137 |         settings = ConfigParser()
138 |         
139 |         # specify location of config files
140 |         nwo = os.getenv('GITHUB_REPOSITORY')
141 |         username, repo_name = nwo.split('/')
142 |         settings_path = Path('current_files/_action_files/settings.ini')
143 |         config_path = Path('current_files/_config.yml')
144 |         setup_pr_path = Path('current_files/_fastpages_docs/_setup_pr_template.md')
145 |         upgrade_pr_path = Path('current_files/_fastpages_docs/_upgrade_pr.md')
146 |         
147 |         assert settings_path.exists(), 'Did not find _action_files/settings.ini in your repository!'
148 |         assert config_path.exists(), 'Did not find _config.yml in your repository!'
149 |         assert setup_pr_path.exists(), 'Did not find_fastpages_docs/_setup_pr_template.md in the current directory!'
150 |         assert upgrade_pr_path.exists(), 'Did not find _fastpages_docs/_upgrade_pr.md in your repository!'
151 |         
152 |         # read data from config files
153 |         settings.read(settings_path)
154 |         with open(config_path, 'r') as cfg:
155 |           config = yaml.load(cfg)
156 |         
157 |         # sync value for baseurl b/w config.yml and settings.ini
158 |         settings['DEFAULT']['baseurl'] = config['baseurl']
159 |         with open(settings_path, 'w') as stg:
160 |           settings.write(stg)
161 |           
162 |         # update PR templates
163 |         setup_pr = setup_pr_path.read_text().replace('{_username_}', username).replace('{_repo_name_}', repo_name)
164 |         setup_pr_path.write_text(setup_pr)
165 |         upgrade_pr = upgrade_pr_path.read_text().replace('{_username_}', username).replace('{_repo_name_}', repo_name)
166 |         upgrade_pr_path.write_text(upgrade_pr)
167 |       shell: python
168 | 
169 |     - uses: webfactory/ssh-agent@v0.2.0
170 |       if: steps.check_version.outputs.vbump == 'true'
171 |       with:
172 |           ssh-private-key: ${{ secrets.SSH_DEPLOY_KEY }}
173 |                         
174 |     - name: push changes to branch
175 |       if: steps.check_version.outputs.vbump == 'true'
176 |       run: |
177 |         # commit changes
178 |         cd current_files
179 |         git config --global user.email "${GH_USERNAME}@users.noreply.github.com"
180 |         git config --global user.name "${GH_USERNAME}"
181 |         git remote remove origin
182 |         git remote add origin "git@github.com:${GITHUB_REPOSITORY}.git"
183 |         
184 |         git add _action_files/settings.ini
185 |         git checkout -b fastpages-automated-upgrade
186 |         git add -A
187 |         git commit -m'upgrade fastpages'
188 |         git push -f --set-upstream origin fastpages-automated-upgrade master
189 |       env: 
190 |         GH_USERNAME: ${{ github.event.issue.user.login }}
191 | 
192 |     - name: Open a PR
193 |       if: steps.check_version.outputs.vbump == 'true'
194 |       id: pr
195 |       uses: actions/github-script@0.6.0
196 |       with:
197 |         github-token: ${{secrets.GITHUB_TOKEN}}
198 |         script: |
199 |           var fs = require('fs');
200 |           var contents = fs.readFileSync('current_files/_fastpages_docs/_upgrade_pr.md', 'utf8');
201 |           github.pulls.create({
202 |                         owner: context.repo.owner,
203 |                         repo: context.repo.repo,
204 |                         title: '[fastpages] Update repo with changes from fastpages',
205 |                         head: 'fastpages-automated-upgrade',
206 |                         base: 'master',
207 |                         body: `${contents}`
208 |                         })
209 |                       .then(result => console.log(`::set-output name=pr_num::${result.data.number}`))
210 |   
211 |     - name: Comment on issue if failure
212 |       if: failure()  && (steps.check_version.outputs.vbump == 'true')
213 |       uses: actions/github-script@0.6.0
214 |       with:
215 |         github-token: ${{secrets.GITHUB_TOKEN}}
216 |         script: |
217 |           var pr_num = process.env.PR_NUM;
218 |           var repo = process.env.REPO
219 |           github.issues.createComment({
220 |             issue_number: context.issue.number,
221 |             owner: context.repo.owner,
222 |             repo: context.repo.repo,
223 |             body: `An error occurred when attempting to open a PR to update fastpages. See the [Actions tab of your repo](https://github.com/${repo}/actions) for more details.`
224 |           })
225 |       env:
226 |         PR_NUM: ${{ steps.pr.outputs.pr_num }}
227 |         REPO: ${{ github.repository }}
228 | 
229 |     - name: Comment on issue 
230 |       if: steps.check_version.outputs.vbump == 'true'    
231 |       uses: actions/github-script@0.6.0
232 |       with:
233 |         github-token: ${{secrets.GITHUB_TOKEN}}
234 |         script: |
235 |           var pr_num = process.env.PR_NUM;
236 |           var repo = process.env.REPO
237 |           github.issues.createComment({
238 |             issue_number: context.issue.number,
239 |             owner: context.repo.owner,
240 |             repo: context.repo.repo,
241 |             body: `Opened PR https://github.com/${repo}/pull/${pr_num} to assist with updating fastpages.`
242 |           })
243 |       env:
244 |         PR_NUM: ${{ steps.pr.outputs.pr_num }}
245 |         REPO: ${{ github.repository }}
246 | 
247 |     - name: Comment on issue if version has not changed
248 |       if: steps.check_version.outputs.vbump == 'false'    
249 |       uses: actions/github-script@0.6.0
250 |       with:
251 |         github-token: ${{secrets.GITHUB_TOKEN}}
252 |         script: |
253 |           github.issues.createComment({
254 |             issue_number: context.issue.number,
255 |             owner: context.repo.owner,
256 |             repo: context.repo.repo,
257 |             body: `Your version of fastpages is up to date.  There is nothing to change.`
258 |           })
259 |           
260 |     - name: Close Issue
261 |       if: always()
262 |       uses: actions/github-script@0.6.0
263 |       with:
264 |         github-token: ${{secrets.GITHUB_TOKEN}}
265 |         script: |
266 |           github.issues.update({
267 |             issue_number: context.issue.number,
268 |             owner: context.repo.owner,
269 |             repo: context.repo.repo,
270 |             state: 'closed'
271 |           })
272 | 


--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
 1 | *.swp
 2 | ~*
 3 | *~
 4 | _site
 5 | .sass-cache
 6 | .jekyll-cache
 7 | .jekyll-metadata
 8 | vendor
 9 | _notebooks/.ipynb_checkpoints
10 | # Local Netlify folder
11 | .netlify
12 | .tweet-cache
13 | __pycache__
14 | 


--------------------------------------------------------------------------------
/Gemfile:
--------------------------------------------------------------------------------
 1 | source "https://rubygems.org"
 2 | # Hello! This is where you manage which Jekyll version is used to run.
 3 | # When you want to use a different version, change it below, save the
 4 | # file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
 5 | #
 6 | #     bundle exec jekyll serve
 7 | #
 8 | # This will help ensure the proper Jekyll version is running.
 9 | # Happy Jekylling!
10 | gem "jekyll", "~> 4.0.0"
11 | # This is the default theme for new Jekyll sites. You may change this to anything you like.
12 | gem "minima"
13 | # To upgrade, run `bundle update github-pages`.
14 | # gem "github-pages", group: :jekyll_plugins
15 | # If you have any plugins, put them here!
16 | group :jekyll_plugins do
17 |   gem "jekyll-feed", "~> 0.12"
18 |   gem 'jekyll-octicons'
19 |   gem 'jekyll-remote-theme'
20 |   gem "jekyll-twitter-plugin"
21 |   gem 'jekyll-relative-links'
22 |   gem 'jekyll-seo-tag'
23 |   gem 'jekyll-toc'
24 |   gem 'jekyll-gist'
25 |   gem 'jekyll-paginate'
26 |   gem 'jekyll-sitemap'
27 | end
28 | 
29 | gem "kramdown-math-katex"
30 | gem "jemoji"
31 | 
32 | # Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
33 | # and associated library.
34 | install_if -> { RUBY_PLATFORM =~ %r!mingw|mswin|java! } do
35 |   gem "tzinfo", "~> 1.2"
36 |   gem "tzinfo-data"
37 | end
38 | 
39 | # Performance-booster for watching directories on Windows
40 | gem "wdm", "~> 0.1.1", :install_if => Gem.win_platform?
41 | 
42 | gem "faraday", "< 1.0"
43 | 
44 | 


--------------------------------------------------------------------------------
/Gemfile.lock:
--------------------------------------------------------------------------------
  1 | GEM
  2 |   remote: https://rubygems.org/
  3 |   specs:
  4 |     activesupport (6.0.3.1)
  5 |       concurrent-ruby (~> 1.0, >= 1.0.2)
  6 |       i18n (>= 0.7, < 2)
  7 |       minitest (~> 5.1)
  8 |       tzinfo (~> 1.1)
  9 |       zeitwerk (~> 2.2, >= 2.2.2)
 10 |     addressable (2.8.0)
 11 |       public_suffix (>= 2.0.2, < 5.0)
 12 |     colorator (1.1.0)
 13 |     concurrent-ruby (1.1.6)
 14 |     em-websocket (0.5.1)
 15 |       eventmachine (>= 0.12.9)
 16 |       http_parser.rb (~> 0.6.0)
 17 |     eventmachine (1.2.7)
 18 |     execjs (2.7.0)
 19 |     faraday (0.17.3)
 20 |       multipart-post (>= 1.2, < 3)
 21 |     ffi (1.12.2)
 22 |     forwardable-extended (2.6.0)
 23 |     gemoji (3.0.1)
 24 |     html-pipeline (2.12.3)
 25 |       activesupport (>= 2)
 26 |       nokogiri (>= 1.4)
 27 |     http_parser.rb (0.6.0)
 28 |     i18n (1.8.2)
 29 |       concurrent-ruby (~> 1.0)
 30 |     jekyll (4.0.0)
 31 |       addressable (~> 2.4)
 32 |       colorator (~> 1.0)
 33 |       em-websocket (~> 0.5)
 34 |       i18n (>= 0.9.5, < 2)
 35 |       jekyll-sass-converter (~> 2.0)
 36 |       jekyll-watch (~> 2.0)
 37 |       kramdown (~> 2.1)
 38 |       kramdown-parser-gfm (~> 1.0)
 39 |       liquid (~> 4.0)
 40 |       mercenary (~> 0.3.3)
 41 |       pathutil (~> 0.9)
 42 |       rouge (~> 3.0)
 43 |       safe_yaml (~> 1.0)
 44 |       terminal-table (~> 1.8)
 45 |     jekyll-feed (0.13.0)
 46 |       jekyll (>= 3.7, < 5.0)
 47 |     jekyll-gist (1.5.0)
 48 |       octokit (~> 4.2)
 49 |     jekyll-octicons (9.5.0)
 50 |       jekyll (>= 3.6, < 5.0)
 51 |       octicons (= 9.5.0)
 52 |     jekyll-paginate (1.1.0)
 53 |     jekyll-relative-links (0.6.1)
 54 |       jekyll (>= 3.3, < 5.0)
 55 |     jekyll-remote-theme (0.4.2)
 56 |       addressable (~> 2.0)
 57 |       jekyll (>= 3.5, < 5.0)
 58 |       jekyll-sass-converter (>= 1.0, <= 3.0.0, != 2.0.0)
 59 |       rubyzip (>= 1.3.0, < 3.0)
 60 |     jekyll-sass-converter (2.1.0)
 61 |       sassc (> 2.0.1, < 3.0)
 62 |     jekyll-seo-tag (2.6.1)
 63 |       jekyll (>= 3.3, < 5.0)
 64 |     jekyll-sitemap (1.4.0)
 65 |       jekyll (>= 3.7, < 5.0)
 66 |     jekyll-toc (0.13.1)
 67 |       jekyll (>= 3.7)
 68 |       nokogiri (~> 1.9)
 69 |     jekyll-twitter-plugin (2.1.0)
 70 |     jekyll-watch (2.2.1)
 71 |       listen (~> 3.0)
 72 |     jemoji (0.12.0)
 73 |       gemoji (~> 3.0)
 74 |       html-pipeline (~> 2.2)
 75 |       jekyll (>= 3.0, < 5.0)
 76 |     katex (0.6.0)
 77 |       execjs (~> 2.7)
 78 |     kramdown (2.3.1)
 79 |       rexml
 80 |     kramdown-math-katex (1.0.1)
 81 |       katex (~> 0.4)
 82 |       kramdown (~> 2.0)
 83 |     kramdown-parser-gfm (1.1.0)
 84 |       kramdown (~> 2.0)
 85 |     liquid (4.0.3)
 86 |     listen (3.2.1)
 87 |       rb-fsevent (~> 0.10, >= 0.10.3)
 88 |       rb-inotify (~> 0.9, >= 0.9.10)
 89 |     mercenary (0.3.6)
 90 |     mini_portile2 (2.8.0)
 91 |     minima (2.5.1)
 92 |       jekyll (>= 3.5, < 5.0)
 93 |       jekyll-feed (~> 0.9)
 94 |       jekyll-seo-tag (~> 2.1)
 95 |     minitest (5.14.1)
 96 |     multipart-post (2.1.1)
 97 |     nokogiri (1.13.6)
 98 |       mini_portile2 (~> 2.8.0)
 99 |       racc (~> 1.4)
100 |     octicons (9.5.0)
101 |       nokogiri (>= 1.6.3.1)
102 |     octokit (4.16.0)
103 |       faraday (>= 0.9)
104 |       sawyer (~> 0.8.0, >= 0.5.3)
105 |     pathutil (0.16.2)
106 |       forwardable-extended (~> 2.6)
107 |     public_suffix (4.0.7)
108 |     racc (1.6.0)
109 |     rb-fsevent (0.10.3)
110 |     rb-inotify (0.10.1)
111 |       ffi (~> 1.0)
112 |     rexml (3.2.5)
113 |     rouge (3.16.0)
114 |     rubyzip (2.2.0)
115 |     safe_yaml (1.0.5)
116 |     sassc (2.2.1)
117 |       ffi (~> 1.9)
118 |     sawyer (0.8.2)
119 |       addressable (>= 2.3.5)
120 |       faraday (> 0.8, < 2.0)
121 |     terminal-table (1.8.0)
122 |       unicode-display_width (~> 1.1, >= 1.1.1)
123 |     thread_safe (0.3.6)
124 |     tzinfo (1.2.6)
125 |       thread_safe (~> 0.1)
126 |     tzinfo-data (1.2019.3)
127 |       tzinfo (>= 1.0.0)
128 |     unicode-display_width (1.6.1)
129 |     wdm (0.1.1)
130 |     zeitwerk (2.3.0)
131 | 
132 | PLATFORMS
133 |   ruby
134 | 
135 | DEPENDENCIES
136 |   faraday (< 1.0)
137 |   jekyll (~> 4.0.0)
138 |   jekyll-feed (~> 0.12)
139 |   jekyll-gist
140 |   jekyll-octicons
141 |   jekyll-paginate
142 |   jekyll-relative-links
143 |   jekyll-remote-theme
144 |   jekyll-seo-tag
145 |   jekyll-sitemap
146 |   jekyll-toc
147 |   jekyll-twitter-plugin
148 |   jemoji
149 |   kramdown-math-katex
150 |   minima
151 |   tzinfo (~> 1.2)
152 |   tzinfo-data
153 |   wdm (~> 0.1.1)
154 | 
155 | BUNDLED WITH
156 |    2.1.4
157 | 


--------------------------------------------------------------------------------
/LICENSE:
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--------------------------------------------------------------------------------
/Makefile:
--------------------------------------------------------------------------------
 1 | help:
 2 | 	cat Makefile
 3 | 
 4 | # start (or restart) the services
 5 | server: .FORCE
 6 | 	docker-compose down --remove-orphans || true;
 7 | 	docker-compose up
 8 | 
 9 | # start (or restart) the services in detached mode
10 | server-detached: .FORCE
11 | 	docker-compose down || true;
12 | 	docker-compose up -d
13 | 
14 | # build or rebuild the services WITHOUT cache
15 | build: .FORCE
16 | 	chmod 777 Gemfile.lock
17 | 	docker-compose stop || true; docker-compose rm || true;
18 | 	docker build --no-cache -t hamelsmu/fastpages-nbdev -f _action_files/fastpages-nbdev.Dockerfile .
19 | 	docker build --no-cache -t hamelsmu/fastpages-jekyll -f _action_files/fastpages-jekyll.Dockerfile .
20 | 	docker-compose build --force-rm --no-cache
21 | 
22 | # rebuild the services WITH cache
23 | quick-build: .FORCE
24 | 	docker-compose stop || true;
25 | 	docker build -t hamelsmu/fastpages-nbdev -f _action_files/fastpages-nbdev.Dockerfile .
26 | 	docker build -t hamelsmu/fastpages-jekyll -f _action_files/fastpages-jekyll.Dockerfile .
27 | 	docker-compose build 
28 | 
29 | # convert word & nb without Jekyll services
30 | convert: .FORCE
31 | 	docker-compose up converter
32 | 
33 | # stop all containers
34 | stop: .FORCE
35 | 	docker-compose stop
36 | 	docker ps | grep fastpages | awk '{print $1}' | xargs docker stop
37 | 
38 | # remove all containers
39 | remove: .FORCE
40 | 	docker-compose stop  || true; docker-compose rm || true;
41 | 
42 | # get shell inside the notebook converter service (Must already be running)
43 | bash-nb: .FORCE
44 | 	docker-compose exec watcher /bin/bash
45 | 
46 | # get shell inside jekyll service (Must already be running)
47 | bash-jekyll: .FORCE
48 | 	docker-compose exec jekyll /bin/bash
49 | 
50 | # restart just the Jekyll server
51 | restart-jekyll: .FORCE
52 | 	docker-compose restart jekyll
53 | 
54 | .FORCE:
55 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | [//]: # (BADGES SECTION: change `fastai` with your GitHub username and `fastpages` with the name of your repo)
 2 | 
 3 | ![](https://github.com/asvcode/MedicalImaging/workflows/CI/badge.svg)
 4 | ![](https://github.com/asvcode/MedicalImaging/workflows/GH-Pages%20Status/badge.svg)
 5 | 
 6 | 
 7 | [![](https://img.shields.io/static/v1?label=Medical%20Imaging%20Tutorial&message=link&labelColor=2f363d&color=blue&style=flat&logo=github&logoColor=959da5)](https://asvcode.github.io/MedicalImaging/)
 8 | 
 9 | [//]: # (END OF BADGES SECTION)
10 | 
11 | Click on the link above to go to the tutorials
12 | 
13 | # Medical Imaging
14 | These tutorials take an in depth look at how to view DICOM images and what information is contained within the `head` of the DICOM. These tutorials also look at what considerations should be taken when evaluating models for medical diagnosis such as Positive and Negative Predictive values, Specificity, Sensitivity, what `RescaleSlope` and `RescaleIntercept` are and how to view diffent tissues densities, Windowing and how to normalize images using `bins`.  
15 | 
16 | These tutorials are based on the lastest release of `fastai` which was officially released in August 2020 and `Medical Imaging using Fastai` provides an in depth look at the `fastai's` `medical.imaging.module`.
17 | 
18 | Currently 3 easily accessible `datasets` are used for the tutorials.  These can be found in the `Getting to know DICOMS` tutorial
19 | 
20 | ### What are DICOMs?
21 | 
22 | **DICOM**(**D**igital **I**maging and **CO**mmunications in **M**edicine) is the de-facto standard that establishes rules that allow medical images(X-Ray, MRI, CT) and associated information to be exchanged between imaging equipment from different vendors, computers, and hospitals. The DICOM format provides a suitable means that meets [health infomation exchange](https://www.himss.org/interoperability-and-health-information-exchange) (HIE) standards for transmission of health related data among facilities and HL7 standards which is the messaging standard that enables clinical applications to exchange data.
23 | 
24 | <p align="center">
25 |   <img width="300" height="300" src="images/dicom_wf.PNG">
26 | </p>
27 | 
28 | DICOM files typically have a .dcm extension and provides a means of storing data in seperate **'tags'** such as patient information as well as image/pixel data. A DICOM file consists of a header and image data sets packed into a single file. The information within the header is organized as a constant and standardized series of tags. By extracting data from these tags one can access important information regarding the patient demographics, study parameters, etc
29 | 
30 | 16 bit DICOM images have values ranging from -32768 to 32768 while 8-bit greyscale images store values from 0 to 255. The value ranges in DICOM images are useful as they correlate with the [Hounsfield Scale](https://en.wikipedia.org/wiki/Hounsfield_scale) which is a quantitative scale for describing radiodensity
31 | 
32 | 
33 | <p align="center">
34 |   Parts of a DICOM
35 | </p>
36 | 
37 | 
38 | <p align="center">
39 |   <img width="208" height="388" src="images/dicom_.PNG">
40 | </p>
41 | 
42 | ### Requirements
43 | 
44 | Requires the most recent version of `fastai`, installation instructions can be viewed at [fastai](https://github.com/fastai/fastai)
45 | 
46 | Also requires installing `pydicom`
47 | 
48 | - `pip install pydicom`
49 | 
50 | and `scikit-image`
51 | 
52 | - `pip install scikit-image`
53 | 
54 | and `kornia`
55 | 
56 | - `pip install kornia===0.2.0`
57 | 
58 | (there is a current incompatability with the lastest version of `kornia`.  Installing version `0.2.0` solves this issue
59 | 
60 | ### Using with Google Colab:
61 | 
62 | Click on the link below for an example of loading the dependancies on `Colab`
63 | 
64 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/12yzCUieRREEb535XVbPzSzjv_7YUuTeb?usp=sharing)
65 | 
66 | 
67 | Fastai provides an easy to access slim dicom dataset (250 DICOM files, ~30MB) from the [SIIM-ACR Pneumothorax Segmentation dataset](https://doi.org/10.1007/s10278-019-00299-9) for us to experiment with dicom images.  The file structure of the dataset is as follows:
68 | 
69 | <p align="center">
70 |   <img width="600" height="284" src="images/dicom.PNG">
71 | </p>
72 | 
73 | ### Images from the notebooks
74 | 
75 | #### >hist_scaled(in Part1)
76 | `hist_scaled` provides a way to scale a tensor of pixels evenly using `freqhist_bins` to values between 0 and 1. This is the histogram of image pixel values scaled from 0 to 255.  As explained in this [notebook](https://www.kaggle.com/jhoward/don-t-see-like-a-radiologist-fastai)
77 | <p align="center">
78 |   <img width="436" height="288" src="images/hist1.PNG">
79 | </p>
80 | 
81 | Scaled histogram now has pixel values ranging from 0 to 1
82 | <p align="center">
83 |   <img width="436" height="288" src="images/hist2.PNG">
84 | </p>
85 | 
86 | 
87 | 


--------------------------------------------------------------------------------
/_action_files/Dockerfile:
--------------------------------------------------------------------------------
 1 | FROM hamelsmu/fastpages-nbdev
 2 | 
 3 | WORKDIR /fastpages
 4 | COPY . .
 5 | RUN chmod u+x action_entrypoint.sh
 6 | RUN chmod u+x word2post.sh
 7 | RUN dos2unix /fastpages/*.sh
 8 | 
 9 | CMD [ "/fastpages/action_entrypoint.sh" ]
10 | 


--------------------------------------------------------------------------------
/_action_files/__init__.py:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/asvcode/MedicalImaging/c615307dfca16f9c632dadf55572faa18f08d3ed/_action_files/__init__.py


--------------------------------------------------------------------------------
/_action_files/action.yml:
--------------------------------------------------------------------------------
 1 | name: 'fastpages: An easy to use blogging platform with support for Jupyter Notebooks.'
 2 | description: Converts Jupyter notebooks and Word docs into Jekyll blog posts.
 3 | author: Hamel Husain
 4 | inputs:
 5 |   BOOL_SAVE_MARKDOWN:
 6 |     description: Either 'true' or 'false'.  Whether or not to commit converted markdown files from notebooks and word documents into the _posts directory in your repo.  This is useful for debugging.
 7 |     required: false
 8 |     default: false
 9 |   SSH_DEPLOY_KEY:
10 |     description: a ssh deploy key is required if BOOL_SAVE_MARKDOWN = 'true'
11 |     required: false
12 | branding:
13 |   color: 'blue'
14 |   icon: 'book'
15 | runs:
16 |   using: 'docker'
17 |   image: 'Dockerfile'
18 | 


--------------------------------------------------------------------------------
/_action_files/action_entrypoint.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/bash
 2 | set -e
 3 | 
 4 | # setup ssh: allow key to be used without a prompt and start ssh agent
 5 | export GIT_SSH_COMMAND="ssh -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no"
 6 | eval "$(ssh-agent -s)"
 7 | 
 8 | ######## Run notebook/word converter ########
 9 | # word converter using pandoc
10 | /fastpages/word2post.sh
11 | # notebook converter using nbdev
12 | cp /fastpages/settings.ini .
13 | python /fastpages/nb2post.py
14 | 
15 | 
16 | ######## Optionally save files and build GitHub Pages ########
17 | if [[ "$INPUT_BOOL_SAVE_MARKDOWN" == "true" ]];then
18 | 
19 |     if [ -z "$INPUT_SSH_DEPLOY_KEY" ];then 
20 |         echo "You must set the SSH_DEPLOY_KEY input if BOOL_SAVE_MARKDOWN is set to true."; 
21 |         exit 1;
22 |     fi
23 | 
24 |     # Get user's email from commit history
25 |     if [[ "$GITHUB_EVENT_NAME" == "push" ]];then
26 |         USER_EMAIL=`cat $GITHUB_EVENT_PATH | jq '.commits | .[0] | .author.email'`
27 |     else
28 |         USER_EMAIL="actions@github.com"
29 |     fi
30 | 
31 |     # Setup Git credentials if we are planning to change the data in the repo
32 |     git config --global user.name "$GITHUB_ACTOR"
33 |     git config --global user.email "$USER_EMAIL"
34 |     git remote add fastpages-origin "git@github.com:$GITHUB_REPOSITORY.git"
35 |     echo "${INPUT_SSH_DEPLOY_KEY}" > _mykey
36 |     chmod 400 _mykey
37 |     ssh-add _mykey
38 | 
39 |     # Optionally save intermediate markdown
40 |     if [[ "$INPUT_BOOL_SAVE_MARKDOWN" == "true" ]]; then
41 |         git pull fastpages-origin ${GITHUB_REF} --ff-only
42 |         git add _posts
43 |         git commit -m "[Bot] Update $INPUT_FORMAT blog posts" --allow-empty
44 |         git push fastpages-origin HEAD:${GITHUB_REF}
45 |     fi
46 | fi
47 | 
48 | 
49 | 


--------------------------------------------------------------------------------
/_action_files/fast_template.py:
--------------------------------------------------------------------------------
 1 | from datetime import datetime
 2 | import re, os
 3 | from pathlib import Path
 4 | from typing import Tuple, Set
 5 | 
 6 | # Check for YYYY-MM-DD
 7 | _re_blog_date = re.compile(r'([12]\d{3}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])-)')
 8 | # Check for leading dashses or numbers
 9 | _re_numdash = re.compile(r'(^[-\d]+)')
10 | 
11 | def rename_for_jekyll(nb_path: Path, warnings: Set[Tuple[str, str]]=None) -> str:
12 |     """
13 |     Return a Path's filename string appended with its modified time in YYYY-MM-DD format.
14 |     """
15 |     assert nb_path.exists(), f'{nb_path} could not be found.'
16 | 
17 |     # Checks if filename is compliant with Jekyll blog posts
18 |     if _re_blog_date.match(nb_path.name): return nb_path.with_suffix('.md').name.replace(' ', '-')
19 |     
20 |     else:
21 |         clean_name = _re_numdash.sub('', nb_path.with_suffix('.md').name).replace(' ', '-')
22 | 
23 |         # Gets the file's last modified time and and append YYYY-MM-DD- to the beginning of the filename
24 |         mdate = os.path.getmtime(nb_path) - 86400 # subtract one day b/c dates in the future break Jekyll
25 |         dtnm = datetime.fromtimestamp(mdate).strftime("%Y-%m-%d-") + clean_name
26 |         assert _re_blog_date.match(dtnm), f'{dtnm} is not a valid name, filename must be pre-pended with YYYY-MM-DD-'
27 |         # push this into a set b/c _nb2htmlfname gets called multiple times per conversion
28 |         if warnings: warnings.add((nb_path, dtnm))
29 |         return dtnm
30 | 


--------------------------------------------------------------------------------
/_action_files/fastpages-jekyll.Dockerfile:
--------------------------------------------------------------------------------
 1 | # Defines https://hub.docker.com/repository/docker/hamelsmu/fastpages-jekyll
 2 | # FROM jekyll/jekyll:4.0.0 THIS IS BROKEN RIGHT NOW 
 3 | FROM hamelsmu/fastpages-jekyll
 4 | 
 5 | COPY . .
 6 | 
 7 | # Pre-load all gems into the environment
 8 | RUN chmod -R 777 .
 9 | RUN gem install bundler 
10 | RUN jekyll build


--------------------------------------------------------------------------------
/_action_files/fastpages-nbdev.Dockerfile:
--------------------------------------------------------------------------------
 1 | FROM python:3-slim-stretch
 2 | 
 3 | RUN pip install --upgrade pip
 4 | RUN apt-get update; apt-get -y install wget git jq dos2unix curl
 5 | RUN wget https://github.com/jgm/pandoc/releases/download/2.9.1.1/pandoc-2.9.1.1-1-amd64.deb
 6 | RUN dpkg -i pandoc-2.9.1.1-1-amd64.deb
 7 | RUN pip install jupyter watchdog[watchmedo] jupyter_client ipykernel jupyter
 8 | RUN python3 -m ipykernel install --user
 9 | RUN pip install nbdev==0.2.18
10 | 


--------------------------------------------------------------------------------
/_action_files/fastpages.tpl:
--------------------------------------------------------------------------------
 1 | {%- extends 'hide.tpl' -%}
 2 | {%- block body -%}
 3 | {%- set internals = ["metadata", "output_extension", "inlining", 
 4 |                     "raw_mimetypes", "global_content_filter"] -%}
 5 | ---
 6 | {%- for k in resources |reject("in", internals) %}
 7 | {% if k == "summary" and "description" not in resources %}description{% else %}{{ k }}{% endif %}: {{ resources[k] }}
 8 | {%- endfor %}
 9 | layout: notebook
10 | ---
11 | 
12 | <!--
13 | #################################################
14 | ### THIS FILE WAS AUTOGENERATED! DO NOT EDIT! ###
15 | #################################################
16 | # file to edit: {{ resources.nb_path }}
17 | -->
18 | 
19 | <div class="container" id="notebook-container">
20 |         {{ super()  }}
21 | </div>
22 | {%- endblock body %}


--------------------------------------------------------------------------------
/_action_files/hide.tpl:
--------------------------------------------------------------------------------
 1 | {%- extends 'basic.tpl' -%}
 2 | 
 3 | {% block codecell %}
 4 |     {{ "{% raw %}" }}
 5 |     {{ super() }}
 6 |     {{ "{% endraw %}" }}
 7 | {% endblock codecell %}
 8 | 
 9 | {% block input_group -%}
10 | {%- if cell.metadata.collapse_show -%}
11 |     <details class="description" open>
12 |       <summary class="btn btn-sm" data-open="Hide Code" data-close="Show Code"></summary>
13 |         <p>{{ super() }}</p>
14 |     </details>
15 | {%- elif cell.metadata.collapse_hide -%}
16 |     <details class="description">
17 |       <summary class="btn btn-sm" data-open="Hide Code" data-close="Show Code"></summary>
18 |         <p>{{ super() }}</p>
19 |     </details>
20 | {%- elif cell.metadata.hide_input or nb.metadata.hide_input -%}
21 | {%- else -%}
22 |     {{ super()  }}
23 | {%- endif -%}
24 | {% endblock input_group %}
25 | 
26 | {% block output_group -%}
27 | {%- if cell.metadata.hide_output -%}
28 | {%- else -%}
29 |     {{ super()  }}
30 | {%- endif -%}
31 | {% endblock output_group %}
32 | 
33 | {% block output_area_prompt %}
34 | {%- if cell.metadata.hide_input or nb.metadata.hide_input -%}
35 |    <div class="prompt"> </div>
36 | {%- else -%}
37 |     {{ super()  }}
38 | {%- endif -%}
39 | {% endblock output_area_prompt %}


--------------------------------------------------------------------------------
/_action_files/nb2post.py:
--------------------------------------------------------------------------------
 1 | """Converts Jupyter Notebooks to Jekyll compliant blog posts"""
 2 | from datetime import datetime
 3 | import re, os, logging
 4 | from nbdev import export2html
 5 | from nbdev.export2html import Config, Path, _re_digits, _to_html, _re_block_notes
 6 | from fast_template import rename_for_jekyll
 7 | 
 8 | warnings = set()
 9 |     
10 | # Modify the naming process such that destination files get named properly for Jekyll _posts
11 | def _nb2htmlfname(nb_path, dest=None): 
12 |     fname = rename_for_jekyll(nb_path, warnings=warnings)
13 |     if dest is None: dest = Config().doc_path
14 |     return Path(dest)/fname
15 | 
16 | # TODO: Open a GitHub Issue in addition to printing warnings
17 | for original, new in warnings:
18 |     print(f'{original} has been renamed to {new} to be complaint with Jekyll naming conventions.\n')
19 |     
20 | ## apply monkey patches
21 | export2html._nb2htmlfname = _nb2htmlfname
22 | export2html.notebook2html(fname='_notebooks/*.ipynb', dest='_posts/', template_file='/fastpages/fastpages.tpl')
23 | 


--------------------------------------------------------------------------------
/_action_files/parse_netlify.py:
--------------------------------------------------------------------------------
1 | import sys, re
2 | logs = sys.stdin.read()
3 | 
4 | draft_url = re.findall(r'Website Draft URL: .*(https://.*)', logs)[0]
5 | assert draft_url, 'Was not able to find Draft URL in the logs:\n{}'.format(logs)
6 | print("::set-output name=draft_url::{}".format(draft_url))
7 | 
8 | 


--------------------------------------------------------------------------------
/_action_files/pr_comment.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/sh
 2 | 
 3 | # Make a comment on a PR.
 4 | # Usage:
 5 | # > pr_comment.sh <<Text Comment>>
 6 | 
 7 | set -e
 8 | 
 9 | # This is populated by our secret from the Workflow file.
10 | if [[ -z "${GITHUB_TOKEN}" ]]; then
11 | 	echo "Set the GITHUB_TOKEN env variable."
12 | 	exit 1
13 | fi
14 | 
15 | if [[ -z "${ISSUE_NUMBER}" ]]; then
16 | 	echo "Set the ISSUE_NUMBER env variable."
17 | 	exit 1
18 | fi
19 | 
20 | if [ -z "$1" ]
21 |   then
22 |     echo "No MESSAGE argument supplied.  Usage: issue_comment.sh <message>"
23 |     exit 1
24 | fi
25 | 
26 | MESSAGE=$1
27 | 
28 | ## Set Vars
29 | URI=https://api.github.com
30 | API_VERSION=v3
31 | API_HEADER="Accept: application/vnd.github.${API_VERSION}+json"
32 | AUTH_HEADER="Authorization: token ${GITHUB_TOKEN}"
33 | 
34 | # Create a comment with APIv3 # POST /repos/:owner/:repo/issues/:issue_number/comments
35 | curl -XPOST -sSL \
36 |     -d "{\"body\": \"$MESSAGE\"}" \
37 |     -H "${AUTH_HEADER}" \
38 |     -H "${API_HEADER}" \
39 |     "${URI}/repos/${GITHUB_REPOSITORY}/issues/${ISSUE_NUMBER}/comments"
40 | 


--------------------------------------------------------------------------------
/_action_files/settings.ini:
--------------------------------------------------------------------------------
 1 | [DEFAULT]
 2 | lib_name = nbdev
 3 | user = fastai
 4 | branch = master
 5 | version = 0.2.10
 6 | description = Writing a library entirely in notebooks
 7 | keywords = jupyter notebook
 8 | author = Amrit Virdee
 9 | author_email = amrit@pillview.com
10 | baseurl = /MedicalImaging
11 | title = nbdev
12 | copyright = fast.ai
13 | license = apache2
14 | status = 2
15 | min_python = 3.6
16 | audience = Developers
17 | language = English
18 | requirements = nbformat>=4.4.0 nbconvert>=5.6.1 pyyaml fastscript packaging
19 | console_scripts = nbdev_build_lib=nbdev.cli:nbdev_build_lib
20 | 	nbdev_update_lib=nbdev.cli:nbdev_update_lib
21 | 	nbdev_diff_nbs=nbdev.cli:nbdev_diff_nbs
22 | 	nbdev_test_nbs=nbdev.cli:nbdev_test_nbs
23 | 	nbdev_build_docs=nbdev.cli:nbdev_build_docs
24 | 	nbdev_nb2md=nbdev.cli:nbdev_nb2md
25 | 	nbdev_trust_nbs=nbdev.cli:nbdev_trust_nbs
26 | 	nbdev_clean_nbs=nbdev.clean:nbdev_clean_nbs
27 | 	nbdev_read_nbs=nbdev.cli:nbdev_read_nbs
28 | 	nbdev_fix_merge=nbdev.cli:nbdev_fix_merge
29 | 	nbdev_install_git_hooks=nbdev.cli:nbdev_install_git_hooks
30 | 	nbdev_bump_version=nbdev.cli:nbdev_bump_version
31 | 	nbdev_new=nbdev.cli:nbdev_new
32 | 	nbdev_detach=nbdev.cli:nbdev_detach
33 | nbs_path = nbs
34 | doc_path = images/copied_from_nb
35 | doc_host = https://nbdev.fast.ai
36 | doc_baseurl = %(baseurl)s/images/copied_from_nb/
37 | git_url = https://github.com/fastai/nbdev/tree/master/
38 | lib_path = nbdev
39 | tst_flags = fastai2
40 | custom_sidebar = False
41 | cell_spacing = 1
42 | monospace_docstrings = False
43 | jekyll_styles = note,warning,tip,important,youtube,twitter
44 | 


--------------------------------------------------------------------------------
/_action_files/word2post.py:
--------------------------------------------------------------------------------
1 | import sys
2 | from pathlib import Path
3 | from fast_template import rename_for_jekyll
4 | 
5 | if __name__ == '__main__':
6 |     file_path = Path(sys.argv[1])
7 |     new_name = rename_for_jekyll(file_path)
8 |     print(new_name)
9 | 


--------------------------------------------------------------------------------
/_action_files/word2post.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/sh
 2 | 
 3 | # This sets the environment variable when testing locally and not in a GitHub Action
 4 | if [ -z "$GITHUB_ACTIONS" ]; then
 5 |     GITHUB_WORKSPACE='/data'
 6 |     echo "=== Running Locally: All assets expected to be in the directory /data ==="
 7 | fi
 8 | 
 9 | # Loops through directory of *.docx files and converts to markdown
10 | # markdown files are saved in _posts, media assets are saved in assets/img/<filename>/media
11 | for FILENAME in ${GITHUB_WORKSPACE}/_word/*.docx; do
12 |     [ -e "$FILENAME" ] || continue # skip when glob doesn't match
13 |     NAME=${FILENAME##*/} # Get filename without the directory
14 |     NEW_NAME=`python3 "/fastpages/word2post.py" "${FILENAME}"` # clean filename to be Jekyll compliant for posts
15 |     BASE_NEW_NAME=${NEW_NAME%.md}  # Strip the file extension
16 | 
17 |     if [ -z "$NEW_NAME" ]; then
18 |         echo "Unable To Rename: ${FILENAME} to a Jekyll complaint filename for blog posts"
19 |         exit 1
20 |     fi
21 |     
22 |     echo "Converting: ${NAME}  ---to--- ${NEW_NAME}"
23 |     cd ${GITHUB_WORKSPACE}
24 |     pandoc --from docx --to gfm --output "${GITHUB_WORKSPACE}/_posts/${NEW_NAME}" --columns 9999 \
25 |     --extract-media="assets/img/${BASE_NEW_NAME}" --standalone "${FILENAME}"
26 | 
27 |     # Inject correction to image links in markdown
28 |     sed -i.bak 's/!\[\](assets/!\[\]({{ site.url }}{{ site.baseurl }}\/assets/g' "_posts/${NEW_NAME}"
29 |     # Remove intermediate files
30 |     rm _posts/*.bak 2> /dev/null || true
31 | 
32 |     cat "${GITHUB_WORKSPACE}/_action_files/word_front_matter.txt" "_posts/${NEW_NAME}" > temp && mv temp "_posts/${NEW_NAME}"
33 | done
34 | 


--------------------------------------------------------------------------------
/_action_files/word_front_matter.txt:
--------------------------------------------------------------------------------
1 | ---
2 | layout: post
3 | ---
4 | 


--------------------------------------------------------------------------------
/_config.yml:
--------------------------------------------------------------------------------
  1 | # Welcome to Jekyll!
  2 | #
  3 | # This config file is meant for settings that affect your whole blog.
  4 | #
  5 | # If you need help with YAML syntax, here are some quick references for you:
  6 | # https://learn-the-web.algonquindesign.ca/topics/markdown-yaml-cheat-sheet/#yaml
  7 | # https://learnxinyminutes.com/docs/yaml/
  8 | 
  9 | title: Medical Imaging
 10 | description: Tutorials to help with using DICOM images for medical imaging.
 11 | github_username: asvcode
 12 | # you can comment the below line out if your repo name is not different than your baseurl
 13 | github_repo: "MedicalImaging"
 14 | 
 15 | # OPTIONAL: override baseurl and url if using a custom domain
 16 | # Note: leave out the trailing / from this value.
 17 | url: "https://asvcode.github.io" # the base hostname & protocol for your site, e.g. http://example.com
 18 | 
 19 | ###########################################################
 20 | #########  Special Instructions for baseurl ###############
 21 | #
 22 | #### Scenario One: If you do not have a Custom Domain #####
 23 | #    -  if you are not using a custom domain, the baseurl *must* be set to your repo name
 24 | #
 25 | ####  Scenario Two: If you have a Custom Domain #####
 26 | # 1. If your domain does NOT have a subpath, this leave this value as ""
 27 | # 2. If your domain does have a subpath, you must preceed the value with a / and NOT have a / at the end.
 28 | #      For example:
 29 | #           "" is valid
 30 | #           "/blog"        is valid
 31 | #            "/blog/site/" is invalid  ( / at the end)
 32 | #            "/blog/site"  is valid
 33 | #            "blog/site"   is invalid  ( because doesn't begin with a /)
 34 | #
 35 | # 3. You must replace the parameter `baseurl` in _action_files/settings.ini with the same value as you set here but WITHOUT QUOTES.
 36 | #
 37 | baseurl: "/MedicalImaging" # the subpath of your site, e.g. "/blog".
 38 | 
 39 | # Github and twitter are optional:
 40 | minima:
 41 |   social_links:
 42 |     twitter: _AVirdee
 43 |     github: asvcode
 44 | 
 45 | # Set this to true to get LaTeX math equation support
 46 | use_math: true
 47 | 
 48 | # Set this to true to display the summary of your blog post under your title on the Home page.
 49 | show_description: true
 50 | 
 51 | # Set this to true to display image previews on home page, if they exist
 52 | show_image: true
 53 | 
 54 | # Set this to true to display tags on each post
 55 | show_tags: true
 56 | 
 57 | # Add your Google Analytics ID here if you have one and want to use it
 58 | google_analytics: UA-78184009-1
 59 | 
 60 | exclude:
 61 |   - docker-compose.yml
 62 |   - action.yml
 63 |   - Makefile
 64 | 
 65 | # this setting allows you to keep pages organized in the _pages folder
 66 | include:
 67 |   - _pages
 68 | 
 69 | # This specifies what badges are turned on by default for notebook posts.
 70 | default_badges:
 71 |   github: true
 72 |   binder: false
 73 |   colab: true
 74 | 
 75 | # Escape HTML in post descriptions
 76 | html_escape:
 77 |   description: false
 78 | 
 79 | # Everything below here should be left alone. Modifications may break fastpages
 80 | future: true
 81 | theme: minima
 82 | plugins:
 83 |   - jekyll-feed
 84 |   - jekyll-gist
 85 |   - jekyll-octicons
 86 |   - jekyll-toc
 87 |   - jekyll-twitter-plugin
 88 |   - jekyll-relative-links
 89 |   - jekyll-seo-tag
 90 |   - jekyll-remote-theme
 91 |   - jekyll-paginate
 92 |   - jekyll-sitemap
 93 |   - jemoji
 94 | 
 95 | # See https://jekyllrb.com/docs/pagination/
 96 | # For pagination to work, you cannot have index.md at the root of your repo, instead you must rename this file to index.html
 97 | paginate: 15
 98 | paginate_path: /page:num/
 99 | 
100 | remote_theme: jekyll/minima
101 | 
102 | titles_from_headings:
103 |   enabled:     true
104 |   strip_title: true
105 |   collections: true
106 | 
107 | highlighter: rouge
108 | markdown: kramdown
109 | kramdown:
110 |   math_engine: katex
111 |   input: GFM
112 |   auto_ids: true
113 |   hard_wrap: false
114 |   syntax_highlighter: rouge
115 | 


--------------------------------------------------------------------------------
/_fastpages_docs/CONTRIBUTING.md:
--------------------------------------------------------------------------------
 1 | _Adapted from [fastai/nbdev/CONTRIBUTING.md](https://github.com/fastai/nbdev/blob/master/CONTRIBUTING.md)_
 2 | 
 3 | # How to contribute to fastpages
 4 | 
 5 | First, thanks a lot for wanting to help! Some things to keep in mind:
 6 | 
 7 | - The jupyter to blog post conversion functionality relies on [fastai/nbdev](https://github.com/fastai/nbdev).  For idiosyncratic uses of nbdev that only apply to blogs that would require a large refactor to nbdev, it might be acceptable to apply a [monkey patch](https://stackoverflow.com/questions/5626193/what-is-monkey-patching) in `fastpages`.  However, it is encouraged to contribute to `nbdev` where possible if there is a change that could unlock a new feature.  If you are unsure, please open an issue in this repo to discuss.
 8 | 
 9 | 
10 | ## Note for new contributors from Jeremy
11 | 
12 | It can be tempting to jump into a new project by questioning the stylistic decisions that have been made, such as naming, formatting, and so forth. This can be especially so for python programmers contributing to this project, which is unusual in following a number of conventions that are common in other programming communities, but not in Python. However, please don’t do this, for (amongst others) the following reasons:
13 | 
14 | - Contributing to [Parkinson’s law of triviality](https://www.wikiwand.com/en/Law_of_triviality) has negative consequences for a project. Let’s focus on deep learning!
15 | - It’s exhausting to repeat the same discussion over and over again, especially when it’s been well documented already. When you have a question about the project, please check the pages in the docs website linked here.
16 | - You’re likely to get a warmer welcome from the community if you start out by contributing something that’s been requested on the forum, since you’ll be solving someone’s current problem.
17 | - If you start out by just telling us your point of view, rather than studying the background behind the decisions that have been made, you’re unlikely to be contributing anything new or useful.
18 | - I’ve been writing code for nearly 40 years now, across dozens of languages, and other folks involved have quite a bit of experience too - the approaches used are based on significant experience and research. Whilst there’s always room for improvement, it’s much more likely you’ll be making a positive contribution if you spend a few weeks studying and working within the current framework before suggesting wholesale changes.
19 | 
20 | 
21 | ## Did you find a bug?
22 | 
23 | * Nobody is perfect, especially not us. But first, please double-check the bug doesn't come from something on your side. The [forum](http://forums.fast.ai/) is a tremendous source for help, and we'd advise to use it as a first step. Be sure to include as much code as you can so that other people can easily help you.
24 | * Then, ensure the bug was not already reported by searching on GitHub under [Issues](https://github.com/fastai/fastpages/issues).
25 | * If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/fastai/fastpages/issues/new). Be sure to include a title and clear description, as much relevant information as possible, and a code sample or an executable test case demonstrating the expected behavior that is not occurring.
26 | * Be sure to add the complete error messages.
27 | 
28 | #### Did you write a patch that fixes a bug?
29 | 
30 | * Open a new GitHub pull request with the patch.
31 | * Ensure that your PR includes a test that fails without your patch, and pass with it.
32 | * Ensure the PR description clearly describes the problem and solution. Include the relevant issue number if applicable.
33 | * Before submitting, please be sure you abide by our [coding style](https://docs.fast.ai/dev/style.html) (where appropriate) and [the guide on abbreviations](https://docs.fast.ai/dev/abbr.html) and clean-up your code accordingly.
34 | 
35 | ## Do you intend to add a new feature or change an existing one?
36 | 
37 | * You can suggest your change on the [fastai forum](http://forums.fast.ai/) to see if others are interested or want to help. 
38 | * Once your approach has been discussed and confirmed on the forum, you are welcome to push a PR, including a complete description of the new feature and an example of how it's used. Be sure to document your code in the notebook.
39 | * Ensure that your code includes tests that exercise not only your feature, but also any other code that might be impacted.
40 | 
41 | ## PR submission guidelines
42 | 
43 | Some general rules of thumb that will make your life easier.
44 | 
45 | * Test locally before opening a pull request. See [the development guide](_fastpages_docs/DEVELOPMENT.md) for instructions on how to run fastpages on your local machine.
46 | * When you do open a pull request, please request a draft build of your PR by making a **comment with the magic command `/preview` in the pull request.**  This will allow reviewers to see a live-preview of your changes without having to clone your branch.
47 |     * You can do this multiple times, if necessary, to rebuild your preview due to changes.  But please do not abuse this and test locally before doing this.
48 | 
49 | * Keep each PR focused. While it's more convenient, do not combine several unrelated fixes together. Create as many branches as needing to keep each PR focused.
50 | * Do not mix style changes/fixes with "functional" changes. It's very difficult to review such PRs and it most likely get rejected.
51 | * Do not add/remove vertical whitespace. Preserve the original style of the file you edit as much as you can.
52 | * Do not turn an already submitted PR into your development playground. If after you submitted PR, you discovered that more work is needed - close the PR, do the required work and then submit a new PR. Otherwise each of your commits requires attention from maintainers of the project.
53 | * If, however, you submitted a PR and received a request for changes, you should proceed with commits inside that PR, so that the maintainer can see the incremental fixes and won't need to review the whole PR again. In the exception case where you realize it'll take many many commits to complete the requests, then it's probably best to close the PR, do the work and then submit it again. Use common sense where you'd choose one way over another.
54 | * When you open a pull request, you can generate a live preview build of how the blog site will look by making a comment in the PR that contains this command: `/preview`.  GitHub will build your site and drop a temporary link for everyone to review.  You can do this as multiple times if necessary, however, as mentioned previously do not turn an already submitted  PR into a development playground.
55 | 
56 | ## Do you have questions about the source code?
57 | 
58 | * Please ask it on the [fastai forum](http://forums.fast.ai/) (after searching someone didn't ask the same one before with a quick search). We'd rather have the maximum of discussions there so that the largest number can benefit from it.
59 | 
60 | ## Do you want to contribute to the documentation?
61 | 
62 | * PRs are welcome for this.  For any confusion about the documentation, please feel free to open an issue on this repo.
63 | 
64 | 


--------------------------------------------------------------------------------
/_fastpages_docs/DEVELOPMENT.md:
--------------------------------------------------------------------------------
  1 | # Development Guide
  2 |   - [Seeing All Options From the Terminal](#seeing-all-commands-in-the-terminal)
  3 |   - [Basic usage: viewing your blog](#basic-usage-viewing-your-blog)
  4 |   - [Converting the pages locally](#converting-the-pages-locally)
  5 |   - [Visual Studio Code integration](#visual-studio-code-integration)
  6 |   - [Advanced usage](#advanced-usage)
  7 |     - [Rebuild all the containers](#rebuild-all-the-containers)
  8 |     - [Removing all the containers](#removing-all-the-containers)
  9 |     - [Attaching a shell to a container](#attaching-a-shell-to-a-container)
 10 |   - [Running a Jupyter Server](#running-a-jupyter-server)
 11 | 
 12 | You can run your fastpages blog on your local machine, and view any changes you make to your posts, including Jupyter Notebooks and Word documents, live.
 13 | The live preview requires that you have Docker installed on your machine. [Follow the instructions on this page if you need to install Docker.](https://www.docker.com/products/docker-desktop)
 14 | 
 15 | ## Seeing All Commands In The Terminal
 16 | 
 17 | There are many different `docker-compose` commands that are necessary to manage the lifecycle of the fastpages Docker containers.  To make this easier, we aliased common commands in a [Makefile](https://www.gnu.org/software/make/manual/html_node/Introduction.html).  
 18 | 
 19 | You can quickly see all available commands by running this command in the root of your repository:
 20 | 
 21 | `make`
 22 | 
 23 | ## Basic usage: viewing your blog
 24 | 
 25 | All of the commands in this block assume that you're in your blog root directory.
 26 | To run the blog with live preview:
 27 | 
 28 | ```bash
 29 | make server
 30 | ```
 31 | 
 32 | When you run this command for the first time, it'll build the required Docker images, and the process might take a couple minutes.
 33 | 
 34 | This command will build all the necessary containers and run the following services:
 35 | 1. A service that monitors any changes in `./_notebooks/*.ipynb/` and `./_word/*.docx;*.doc` and rebuild the blog on change.
 36 | 2. A Jekyll server on https://127.0.0.1:4000 — use this to preview your blog.
 37 | 
 38 | The services will output to your terminal. If you close the terminal or hit `Ctrl-C`, the services will stop.
 39 | If you want to run the services in the background:
 40 | 
 41 | ```bash
 42 | # run all services in the background
 43 | make server-detached
 44 | 
 45 | # stop the services
 46 | make stop
 47 | ```
 48 | 
 49 | If you need to restart just the Jekyll server, and it's running in the background — you can do `make restart-jekyll`.
 50 | 
 51 | _Note that the blog won't autoreload on change, you'll have to refresh your browser manually._
 52 | 
 53 | **If containers won't start**: try `make build` first, this would rebuild all the containers from scratch, This might fix the majority of update problems.
 54 | 
 55 | ## Converting the pages locally
 56 | 
 57 | If you just want to convert your notebooks and word documents to `.md` posts in `_posts`, this command will do it for you:
 58 | 
 59 | ```bash
 60 | make convert
 61 | ```
 62 | 
 63 | You can launch just the jekyll server with `make server`.
 64 | 
 65 | ## Visual Studio Code integration
 66 | 
 67 | If you're using VSCode with the Docker extension, you can run these containers from the sidebar: `fastpages_watcher_1` and `fastpages_jekyll_1`.
 68 | The containers will only show up in the list after you run or build them for the first time. So if they're not in the list — try `make build` in the console.
 69 | 
 70 | ## Advanced usage
 71 | 
 72 | ### Rebuild all the containers
 73 | If you changed files in `_action_files` directory, you might need to rebuild the containers manually, without cache.
 74 | 
 75 | ```bash
 76 | make build
 77 | ```
 78 | 
 79 | ### Removing all the containers
 80 | Want to start from scratch and remove all the containers?
 81 | 
 82 | ```
 83 | make remove
 84 | ```
 85 | 
 86 | ### Attaching a shell to a container
 87 | You can attach a terminal to a running service:
 88 | 
 89 | ```bash
 90 | 
 91 | # If the container is already running:
 92 | 
 93 | # attach to a bash shell in the jekyll service
 94 | make bash-jekyll
 95 | 
 96 | # attach to a bash shell in the watcher service.
 97 | make bash-nb
 98 | ```
 99 | 
100 | _Note: you can use `docker-compose run` instead of `make bash-nb` or `make bash-jekyll` to start a service and then attach to it.
101 | Or you can run all your services in the background, `make server-detached`, and then use `make bash-nb` or `make bash-jekyll` as in the examples above._
102 | 
103 | ## Running A Jupyter Server
104 | 
105 | The fastpages development environment does not provide a Jupyter server for you.  This is intentional so that you are free to run Jupyter Notebooks or Jupyter Lab in a manner that is familiar to you, and manage dependencies (requirements.txt, conda, etc) in the way you wish.  Some tips that may make your life easier:
106 | 
107 | - Provide instructions in your README and your blog posts on how to install the dependencies required to run your notebooks.  This will make it easier for your audience to reproduce your notebooks.
108 | - Do not edit the Dockerfile in `/_action_files`, as that may interfere with the blogging environment.  Furthermore, any changes you make to these files may get lost in future upgrades, if [upgrading automatically](UGPRADE.md).  Instead, if you wish to manage your Jupyter server with Docker, we recommend that you maintain a seperate Dockerfile at the root of your repository.
109 | 


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/_fastpages_docs/NOTEBOOK_FOOTNOTES.md:
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 1 | # Detailed Guide To Footnotes in Notebooks
 2 | 
 3 | Notebook -> HTML Footnotes don't work the same as Markdown. There isn't a good solution, so made these Jekyll plugins as a workaround
 4 | 
 5 | ```
 6 | This adds a linked superscript {% fn 15 %}
 7 | 
 8 | {{ "This is the actual footnote" | fndetail: 15 }}
 9 | ```
10 | 
11 | ![image](https://user-images.githubusercontent.com/1483922/76640645-83e49f80-650d-11ea-8f8a-01ee6eba91e1.png)
12 | 
13 | You can have links, but then you have to use **single quotes** to escape the link.  
14 | ```
15 | This adds a linked superscript {% fn 20 %}
16 | 
17 | {{ 'This is the actual footnote with a [link](www.github.com) as well!'  | fndetail: 20 }}
18 | ```
19 | ![image](https://user-images.githubusercontent.com/1483922/76640916-f9e90680-650d-11ea-88e2-039394d741f7.png)
20 | 
21 | However, what if you want a single quote in your footnote?  There is not an easy way  to escape that.  Fortunately, you can use the special HTML character `&#39;` (you must keep the semicolon!).  For example, you can include a single quote like this:
22 | 
23 | 
24 | ```
25 | This adds a linked superscript {% fn 20 %}
26 | 
27 | {{ 'This is the actual footnote; with a [link](www.github.com) as well! and a single quote &#39; too!'  | fndetail: 20 }}
28 | ```
29 | 
30 | ![image](https://user-images.githubusercontent.com/1483922/76641725-45e87b00-650f-11ea-9bf3-6839717cac2a.png)
31 | 


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/_fastpages_docs/README_TEMPLATE.md:
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 1 | [//]: # (This template replaces README.md when someone creates a new repo with the fastpages template.)
 2 | 
 3 | ![](https://github.com/{_username_}/{_repo_name_}/workflows/CI/badge.svg) 
 4 | ![](https://github.com/{_username_}/{_repo_name_}/workflows/GH-Pages%20Status/badge.svg) 
 5 | [![](https://img.shields.io/static/v1?label=fastai&message=fastpages&color=57aeac&labelColor=black&style=flat&logo=data:image/png;base64,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)](https://github.com/fastai/fastpages)
 6 | 
 7 | https://{_username_}.github.io/{_repo_name_}/
 8 | 
 9 | # My Blog
10 | 
11 | 
12 | _powered by [fastpages](https://github.com/fastai/fastpages)_
13 | 
14 | 
15 | ## What To Do Next?
16 | 
17 | Great!  You have setup your repo.  Now its time to start writing content.  Some helpful links:
18 | 
19 | - [Writing Blogs With Jupyter](https://github.com/fastai/fastpages#writing-blog-posts-with-jupyter)
20 | 
21 | - [Writing Blogs With Markdown](https://github.com/fastai/fastpages#writing-blog-posts-with-markdown)
22 | 
23 | - [Writing Blog Posts With Word](https://github.com/fastai/fastpages#writing-blog-posts-with-microsoft-word)
24 | 
25 | - [(Optional) Preview Your Blog Locally](_fastpages_docs/DEVELOPMENT.md)
26 | 
27 | Note: you may want to remove example blog posts from the `_posts`,  `_notebooks` or `_word` folders (but leave them empty, don't delete these folders) if you don't want these blog posts to appear on your site.
28 | 
29 | Please use the [nbdev & blogging channel](https://forums.fast.ai/c/fastai-users/nbdev/48) in the fastai forums for any questions or feature requests.
30 | 


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/_fastpages_docs/TROUBLESHOOTING.md:
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 1 | # Filing Bugs & Troubleshooting
 2 | 
 3 | These are required prerequisites before filing an issue on GitHub or on the [fastai forums](https://forums.fast.ai/)
 4 | 
 5 | ## Step 1: Attempt To Upgrade fastpages
 6 | 
 7 | See the [Upgrading guide](https://github.com/fastai/fastpages/blob/master/_fastpages_docs/UPGRADE.md).
 8 | 
 9 | **In addition to upgrading**, if developing locally, refresh your Docker containers with the following commands from the root of your repo:
10 | 
11 | `make remove` followed by `make build`
12 | 
13 | ## Step 2: Search Relevant Places For Similar Issues
14 | 
15 | - [ ] Search the [fastai forums](https://forums.fast.ai/) for similar problems.
16 | - [ ] Search issues on the [fastpages repo](https://github.com/fastai/fastpages/) for a similar problems?
17 | - [ ] Read the [README of the repo](https://github.com/fastai/fastpages/blob/master/README.md) carefully
18 | 
19 | 
20 | ## Step 3: Observe Build Logs When Developing Locally
21 |  
22 | - [ ] Run the [fastpages blog server locally](DEVELOPMENT.md)
23 |     - Pay attention to the emitted logs when you save your notebooks or files. Often, you will see errors here that will give you important clues.
24 | - [ ] When developing locally, you will notice that Jupyter notebooks are converted to corresponding markdown files in the `_posts` folder.  Take a look at the problematic blog posts and see if you can spot the offending HTML or markdown in that code.
25 | - Use your browser's developer tools to see if there are any errors.  Common errors are (1) not able to find images because they have not been saved into the right folder, (2) javascript or other errors.
26 | - If you receive a Jekyll build error or a Liquid error, search for this error on Stack Overflow to provide more insight on the problem.
27 | 
28 | ## Step 4: See if there are errors in the build process of GitHub Actions.
29 | 
30 | - [ ] In your GitHub repository, you will have a tab called **Actions**.  To find build errors, click on the `Event` dropdown list and select `push`.  Browse through tthe logs to see if you can find an error.  If you receive an error, read the error message and try to debug.
31 | 
32 | ## Step 5: Once you have performed all the above steps, post your issue in the fastai formus or a GitHub Issue.
33 | 
34 | - [ ] Use the [nbdev & blogging category](https://forums.fast.ai/c/fastai-users/nbdev/48) to specify your problem if posting on the fastpages forums.
35 | - [ ] If you cannot find a similar issue create a new thread instead of commenting on an unrelated one.
36 | - When reporting a bug, provide this information:
37 | 
38 |     1. Steps to reproduce the problem
39 |     2. **A link to the notebook or markdown file** where the error is occuring
40 |     3. If the error is happening in GitHub Actions, a link to the specific error along with how you are able to reproduce this error.  You must provide this **in addition to the link to the notebook or markdown file**.
41 |     4. A screenshot / dump of relevant logs or error messages you are receiving from your local development environment. the local development server as indicated in the [development guide](https://github.com/fastai/fastpages/blob/master/_fastpages_docs/DEVELOPMENT.md).
42 | 
43 | 
44 | **You must provide ALL of the above information**.
45 | 
46 | # Frequent Errors
47 | 
48 | 1. Malformed front matter.  Note that anything defined in front matter must be valid YAML.  **Failure to provide valid YAML could result in your page not rendering** in your blog.  For example, if you want a colon in your title you must escape it with double quotes like this:
49 | 
50 |     ` - title: "Deep learning: A tutorial"`
51 |     
52 |     or in a notebook
53 | 
54 |     `# "Deep learning: A tutorial"`
55 | 
56 |     See this [tutorial on YAML](https://rollout.io/blog/yaml-tutorial-everything-you-need-get-started/) for more information.
57 | 
58 |     **Colons, tilda, asteriks and other characters may cause your front matter to break and for your posts to not render.**  If you violoate these conventions you often get an error that looks something like this:
59 | 
60 |     ```bash
61 |     Error: YAML Exception reading ... (<unknown>): mapping values are not allowed
62 |     ```
63 | 
64 | 2. Can you customize the styling or theme of fastpages?  **A**: See [Customizing Fastpages](https://github.com/fastai/fastpages#customizing-fastpages)
65 | 
66 | See the [FAQ](https://github.com/fastai/fastpages#faq) for frequently asked questions.
67 | 


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/_fastpages_docs/UPGRADE.md:
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 1 | # Upgrading fastpages
 2 | 
 3 | <!-- TOC depthFrom:1 depthTo:6 withLinks:1 updateOnSave:1 orderedList:0 -->
 4 | 
 5 | - [Automated Upgrade](#automated-upgrade)
 6 |     - [Step 1: Open An Issue With The Upgrade Template.](#step-1-open-an-issue-with-the-upgrade-template)
 7 |     - [Step 2: Click `Submit new issue`](#step-2-click-submit-new-issue)
 8 |     - [Step 3: A Link to Pull Request Will Appaer](#step-3-a-link-to-pull-request-will-appaer)
 9 |     - [Step 4: Review & Merge PR](#step-4-review-merge-pr)
10 | - [Manual Upgrade](#manual-upgrade)
11 |     - [Easy Way (Recommended)](#easy-way-recommended)
12 |     - [Advanced](#advanced)
13 | - [Additional Resources](#additional-resources)
14 | <!-- /TOC -->
15 | 
16 | There are two ways to upgrade fastpages.  One is an automated way that assumes you have made no changes to the HTML of your site. Alternatively, you may [upgrade manually](#manual-upgrade) and determine which changes to accept or reject.  For most people we recommend upgrading fastpages automatically.
17 | 
18 | ## Automated Upgrade
19 | 
20 |  - This method is appropriate for those who have not customized the HTML of their site.  
21 |  - **If you are unsure, try the Automated approach and review which files are changed in the automated PR** to see if this appropriate for you.
22 | 
23 | ### Step 1: Open An Issue With The Upgrade Template.
24 | 
25 | - Open a new issue in your repository, and push the "Get Started" button for the `[fastpages] Automated Upgrade` Issue template, which looks like this:
26 |     - **IF YOU DON'T SEE THIS**: you have an older version of fastpages and you **must [manually upgrade](#manual-upgrade) once** to get this new functionality.
27 | 
28 |     ![](upgrade_step1.png)
29 | 
30 | ### Step 2: Click `Submit new issue`
31 | 
32 | - Be careful not to change anything before clicking the button.
33 | 
34 |     ![](upgrade_step2.png)
35 | 
36 | ### Step 3: A Link to Pull Request Will Appaer
37 | 
38 | - This issue will trigger GitHub to open a PR making changes to your repository for the upgrade to take palce.  A comment with the link to the PR will be made in the issue, and will look like this:
39 | 
40 |     ![](upgrade_step3.png)
41 | 
42 |     It is possible that you might receive an error message instead of this command.  You can follow the instructions in the comment to troubleshoot the issue.  Common reasons for receiving an error are:
43 | 
44 |     - You are up to date, therefore no upgrade is possible.  You will see an error that there is "nothing to commit".
45 |     - You already have a PR from a prevoius upgrade open that you never merged.
46 | 
47 |     Please [ask on the forums](https://forums.fast.ai/) if you have encounter another problem that is unclear.
48 | 
49 | ### Step 4: Review & Merge PR
50 | 
51 | - Ensure that you read the instructions in the PR carefully.  Furthermore, carefully review which files will be changed to determine if this interferes with any customizations you have mades to your site.  When ready, select `Merge pull request`.  
52 | - If the PR is making undesired changes to files you can use the manual upgrade approach instead.
53 | 
54 | ## Manual Upgrade
55 | 
56 | ### Easy Way (Recommended)
57 | 
58 | Create a new repo with the current `fastpages` template by following the [setup instructions](https://github.com/fastai/fastpages#setup-instructions) in the README, and copy all of your blog posts from `_notebooks`, `_word`, and `_posts` into the new template.  This is very similar to what the automated process is doing.
59 | 
60 | ### Advanced
61 | 
62 | - This method is appropriate for those who made customizations to the HTML of fastpages.  
63 | - You must proceed with caution, as new versions of fastpages may not be compatible with your customizations.
64 | - You can use git to perform the upgrade by [following this approach](https://stackoverflow.com/questions/56577184/github-pull-changes-from-a-template-repository/56577320) instead.  A step-by-step companion to this stack overflow post with screenshots is [written up here](https://github.com/fastai/fastpages/issues/163#issuecomment-593766189).
65 | - Be careful to not duplicate files, as files in fastpages have been reorganized several times.
66 | 
67 | 
68 | ## Additional Resources
69 | 
70 | - [This Actions workflow](/.github/workflows/upgrade.yaml) defines the automated upgrade process.
71 | - You can get more help with upgrading in the [fastai forums - nbdev & blogging category](https://forums.fast.ai/c/fastai-users/nbdev/48).
72 | 


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 1 | # Manual Setup Instructions
 2 | 
 3 | These are the setup steps that are automated by [setup.yaml](.github/workflows/setup.yaml)
 4 | 
 5 | 1. Click the [![](https://img.shields.io/static/v1?label=&message=Use%20this%20template&color=brightgreen&style=flat)](https://github.com/fastai/fastpages/generate) button to create a copy of this repo in your account.
 6 | 
 7 | 2. [Follow these instructions to create an ssh-deploy key](https://developer.github.com/v3/guides/managing-deploy-keys/#deploy-keys).  Make sure you **select Allow write access** when adding this key to your GitHub account.
 8 | 
 9 | 3. [Follow these instructions to upload your deploy key](https://help.github.com/en/actions/configuring-and-managing-workflows/creating-and-storing-encrypted-secrets#creating-encrypted-secrets) as an encrypted secret on GitHub.  Make sure you name your key `SSH_DEPLOY_KEY`.  Note: The deploy key secret is your **private key** (NOT the public key).
10 | 
11 | 4. [Create a branch](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-and-deleting-branches-within-your-repository#creating-a-branch) named `gh-pages`.
12 | 
13 | 5. Change the badges on this README to point to **your** repository instead of `fastai/fastpages`.  Badges are organized in a section at the beginning of this README.  For example, you should replace `fastai` and `fastpages` in the below url:
14 | 
15 |     `![](https://github.com/fastai/fastpages/workflows/CI/badge.svg)`
16 | 
17 |       to
18 | 
19 |     `![](https://github.com/{your-username}/{your-repo-name}/workflows/CI/badge.svg)`
20 | 
21 | 6. Change `baseurl:` in `_config.yaml` to the name of your repository. For example, instead of 
22 | 
23 |     `baseurl: "/fastpages"`
24 | 
25 |     this should be
26 | 
27 |     `baseurl: "/your-repo-name"`
28 | 
29 | 7. Similarly, change the `url:` parameter in `_config.yaml` to the url your blog will be served on.  For example, instead of
30 | 
31 |     `url: "https://fastpages.fast.ai/"`
32 | 
33 |     this should be 
34 | 
35 |     `url: "https://<your-user-name>.github.io"`
36 | 
37 | 8. Read through `_config.yaml` carefully as there may be other options that must be set.  The comments in this file will provide instructions. 
38 | 
39 | 9. Delete the `CNAME` file from the root of your `master` branch (or change it if you are using a custom domain)
40 | 
41 | 10. Go to your [repository settings and enable GitHub Pages](https://help.github.com/en/enterprise/2.13/user/articles/configuring-a-publishing-source-for-github-pages) with the `gh-pages` branch you created earlier.


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/_fastpages_docs/_setup_pr_template.md:
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 1 | Hello :wave: @{_username_}!  Thank you for using fastpages!  
 2 | 
 3 | ## Before you merge this PR
 4 | 
 5 | 1. Create an ssh key-pair.  Open <a href="https://8gwifi.org/sshfunctions.jsp" target="_blank">this utility</a>. Select: `RSA` and `4096` and leave `Passphrase` blank.  Click the blue button `Generate-SSH-Keys`.
 6 | 
 7 | 2. Navigate to <a href="https://github.com/{_username_}/{_repo_name_}/settings/secrets" target="_blank">this link</a> and click `Add a new secret`.  Copy and paste the **Private Key** into the `Value` field. This includes the "---BEGIN RSA PRIVATE KEY---" and "--END RSA PRIVATE KEY---" portions. In the `Name` field, name the secret `SSH_DEPLOY_KEY`.  
 8 | 
 9 | 3. Navigate to <a href="https://github.com/{_username_}/{_repo_name_}/settings/keys" target="_blank">this link</a> and click the `Add deploy key` button.  Paste your **Public Key** from step 1 into the `Key` box.  In the `Title`, name the key anything you want, for example `fastpages-key`.  Finally, **make sure you click the checkbox next to `Allow write access`** (pictured below), and click `Add key` to save the key.
10 | 
11 | ![](https://raw.githubusercontent.com/fastai/fastpages/master/_fastpages_docs/_checkbox.png)
12 | 
13 | 
14 | ### What to Expect After Merging This PR
15 | 
16 | - GitHub Actions will build your site, which will take 2-3 minutes to complete.  **This will happen anytime you push changes to the master branch of your repository.**  You can monitor the logs of this if you like on the [Actions tab of your repo](https://github.com/{_username_}/{_repo_name_}/actions).
17 | - Your GH-Pages Status badge on your README will eventually appear and be green, indicating your first sucessfull build.
18 | - You can monitor the status of your site in the GitHub Pages section of your [repository settings](https://github.com/{_username_}/{_repo_name_}/settings).
19 | 
20 | If you are not using a custom domain, your website will appear at: 
21 | 
22 | #### https://{_username_}.github.io/{_repo_name_}
23 | 
24 | 
25 | ## Optional: Using a Custom Domain
26 | 
27 | 1. After merging this PR, add a file named `CNAME` at the root of your repo.  For example, the `fastpages` blog is hosted at `https://fastpages.fast.ai`, which means [our CNAME](https://github.com/fastai/fastpages/blob/master/CNAME) contains the following contents: 
28 | 
29 |         
30 |     >`fastpages.fast.ai`
31 | 
32 | 
33 | 2. Change the `url` and `baseurl` parameters in your `/_config.yml` file to reflect your custom domain.
34 | 
35 | 
36 |     Wondering how to setup a custom domain?  See [this article](https://dev.to/trentyang/how-to-setup-google-domain-for-github-pages-1p58).  You must add a CNAME file to the root of your master branch for the intructions in the article to work correctly.
37 | 
38 | 
39 | ## Questions
40 | 
41 | Please use the [nbdev & blogging channel](https://forums.fast.ai/c/fastai-users/nbdev/48) in the fastai forums for any questions or feature requests.
42 | 


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/_fastpages_docs/_show_image_true.png:
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https://raw.githubusercontent.com/asvcode/MedicalImaging/c615307dfca16f9c632dadf55572faa18f08d3ed/_fastpages_docs/_show_image_true.png


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/_fastpages_docs/_upgrade_pr.md:
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 1 | Hello :wave: @{_username_}! 
 2 | 
 3 | This PR pulls the most recent files from [fastpages](https://github.com/fastai/fastpages), and attempts to replace relevant files in your repository, without changing the content of your blog posts.  This allows you to receive bug fixes and feature updates.
 4 | 
 5 | ## Warning
 6 | 
 7 | If you have applied  **customizations to the HTML or styling of your site, they may be lost if you merge this PR.  Please review the changes this PR makes carefully before merging!.**  However, for people who only write content and don't change the styling of their site, this method is recommended.
 8 | 
 9 | If you would like more fine-grained control over what changes to accept or decline, consider [following this approach](https://stackoverflow.com/questions/56577184/github-pull-changes-from-a-template-repository/56577320) instead.  
10 | 
11 | ### What to Expect After Merging This PR
12 | 
13 | - GitHub Actions will build your site, which will take 3-4 minutes to complete.  **This will happen anytime you push changes to the master branch of your repository.**  You can monitor the logs of this if you like on the [Actions tab of your repo](https://github.com/{_username_}/{_repo_name_}/actions).
14 | - You can monitor the status of your site in the GitHub Pages section of your [repository settings](https://github.com/{_username_}/{_repo_name_}/settings).
15 | 


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/_fastpages_docs/highlight_dracula.png:
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/_fastpages_docs/highlight_original.png:
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/_fastpages_docs/upgrade_step2.png:
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/_fastpages_docs/version.txt:
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1 | 2.1.29
2 | 


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/_includes/alert.html:
--------------------------------------------------------------------------------
1 | <div class="Toast Toast--warning googoo">
2 |    <span class="Toast-icon">{% octicon alert %}</span>
3 |    <span class="Toast-content">{{include.text}}</span>
4 | </div>
5 | 


--------------------------------------------------------------------------------
/_includes/custom-head.html:
--------------------------------------------------------------------------------
 1 | {% comment %}
 2 |   Placeholder to allow defining custom head, in principle, you can add anything here, e.g. favicons:
 3 | 
 4 |   1. Head over to https://realfavicongenerator.net/ to add your own favicons.
 5 |   2. Customize default _includes/custom-head.html in your source directory and insert the given code snippet.
 6 | {% endcomment %}
 7 | 
 8 | 
 9 | {%- include favicons.html -%}
10 | {% seo %}
11 | <link href="https://unpkg.com/@primer/css/dist/primer.css" rel="stylesheet" />
12 | <link rel="stylesheet" href="//use.fontawesome.com/releases/v5.0.7/css/all.css">
13 | {%- feed_meta -%}
14 | {%- if jekyll.environment == 'production' and site.google_analytics -%}
15 |     {%- include google-analytics.html -%}
16 | {%- endif -%}
17 | 
18 | {% if site.use_math %}
19 |     <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.11.1/dist/katex.min.css" integrity="sha384-zB1R0rpPzHqg7Kpt0Aljp8JPLqbXI3bhnPWROx27a9N0Ll6ZP/+DiW/UqRcLbRjq" crossorigin="anonymous">
20 |     <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-MML-AM_CHTML"> </script>
21 |     <script src="https://cdn.jsdelivr.net/npm/katex@0.11.1/dist/katex.min.js" integrity="sha384-y23I5Q6l+B6vatafAwxRu/0oK/79VlbSz7Q9aiSZUvyWYIYsd+qj+o24G5ZU2zJz" crossorigin="anonymous"></script>
22 |     <script src="https://cdn.jsdelivr.net/npm/katex@0.11.1/dist/contrib/auto-render.min.js" integrity="sha384-kWPLUVMOks5AQFrykwIup5lo0m3iMkkHrD0uJ4H5cjeGihAutqP0yW0J6dpFiVkI" crossorigin="anonymous"></script>
23 |     <script>
24 |     document.addEventListener("DOMContentLoaded", function() {
25 |         renderMathInElement( document.body, {
26 |         delimiters: [
27 |             {left: "$$", right: "$$", display: true},
28 |             {left: "[%", right: "%]", display: true},
29 |             {left: "$", right: "$", display: false}
30 |         ]}
31 |         );
32 |     });
33 |     </script>
34 | {% endif %}
35 | 
36 | <script>
37 | function wrap_img(fn) {
38 |     if (document.attachEvent ? document.readyState === "complete" : document.readyState !== "loading") {
39 |         var elements = document.querySelectorAll(".post img");
40 |         Array.prototype.forEach.call(elements, function(el, i) {
41 |             if (el.getAttribute("title") && (el.className != "emoji")) {
42 |                 const caption = document.createElement('figcaption');
43 |                 var node = document.createTextNode(el.getAttribute("title"));
44 |                 caption.appendChild(node);
45 |                 const wrapper = document.createElement('figure');
46 |                 wrapper.className = 'image';
47 |                 el.parentNode.insertBefore(wrapper, el);
48 |                 el.parentNode.removeChild(el);
49 |                 wrapper.appendChild(el);
50 |                 wrapper.appendChild(caption);
51 |             }
52 |         });
53 |     } else { document.addEventListener('DOMContentLoaded', fn); }
54 | }
55 | window.onload = wrap_img;
56 | </script>
57 | 
58 | <script>
59 |     document.addEventListener("DOMContentLoaded", function(){
60 |     // add link icon to anchor tags
61 |     var elem = document.querySelectorAll(".anchor-link")
62 |     elem.forEach(e => (e.innerHTML = '<i class="fas fa-link fa-xs"></i>'));
63 |     });
64 | </script>
65 | 


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/_includes/favicons.html:
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1 | <link rel="shortcut icon" type="image/x-icon" href="{{ "images/favicon.ico" | relative_url }}">


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/_includes/google-analytics.html:
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1 | <!-- the google_analytics_id gets auto inserted from the config file -->
2 | 
3 | {% if site.google_analytics %}
4 | 
5 | <script>(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)})(window,document,'script','//www.google-analytics.com/analytics.js','ga');ga('create','{{site.google_analytics}}','auto');ga('require','displayfeatures');ga('send','pageview');</script>
6 | {% endif %}
7 | 


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/_includes/head.html:
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 1 | <head>
 2 |   <meta charset="utf-8">
 3 |   <meta http-equiv="X-UA-Compatible" content="IE=edge">
 4 |   <meta name="viewport" content="width=device-width, initial-scale=1">
 5 |   {%- seo -%}
 6 |   <link rel="stylesheet" href="{{ "/assets/css/style.css" | relative_url }}">
 7 |   {%- feed_meta -%}
 8 |   {%- if jekyll.environment == 'production' and site.google_analytics -%}
 9 |     {%- include google-analytics.html -%}
10 |   {%- endif -%}
11 | 
12 |   {%- include custom-head.html -%}
13 |   
14 | </head>


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/_includes/image-r:
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 1 | <figure style="float: right;">
 2 |   <img class="image" width="{{ include.w }}" src="/images/{{ include.url }}"
 3 |     {% if include.caption %}
 4 |     alt="{{ include.caption }}"
 5 |     {% endif %}
 6 |   >
 7 |   {% if include.caption %}
 8 |   <figcaption class="image-caption">{{ include.caption }}</figcaption>
 9 |   {% endif %}
10 | </figure>
11 | 
12 | 


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/_includes/image.html:
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1 | <figure>
2 |   {% if {{include.url}} %}<a class="no_icon" target="_blank" href="{{include.url}}">{% endif %}
3 |     <img class="docimage" src="{{include.file}}" alt="{{include.alt}}" {% if {{include.max-width}} %}style="max-width: {{include.max-width}}px"{% endif %} />
4 |     {% if {{include.url}} %}</a>{% endif %}
5 |     {% if {{include.caption}} %}
6 |       <figcaption>{{include.caption}}</figcaption>
7 |     {% endif %}
8 | </figure>
9 | 


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/_includes/important.html:
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1 | <div class="flash flash-warn">
2 |     {% octicon zap %}
3 |     <strong>Important: </strong>{{ include.content }}
4 | </div>


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/_includes/info.html:
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1 | <div class="Toast">
2 |    <span class="Toast-icon">{% octicon info %}</span>
3 |    <span class="Toast-content">{{include.text}}</span>
4 | </div>
5 | 


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/_includes/note.html:
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1 | <div class="flash">
2 |     {% octicon info %}
3 |     <strong>Note: </strong>{{ include.content }}
4 | </div>


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/_includes/notebook_binder_link.html:
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1 | <div class="px-2">
2 |     <a href="https://mybinder.org/v2/gh/{{site.github_username}}/{{site.github_repo | default: site.baseurl | remove: "/" }}/{{page.branch | default: "master"}}?filepath={{page.nb_path | url_encode }}" target="_blank">
3 |         <img class="notebook-badge-image" src="{{ "assets/badges/binder.svg" | relative_url }}" alt="Open In Binder"/>
4 |     </a>
5 | </div>
6 | 


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/_includes/notebook_colab_link.html:
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1 | <div class="px-2">
2 |     <a href="https://colab.research.google.com/github/{{site.github_username}}/{{site.github_repo | default: site.baseurl | remove: "/" }}/blob/{{page.branch | default: "master"}}/{{page.nb_path}}" target="_blank">
3 |         <img class="notebook-badge-image" src="{{ "assets/badges/colab.svg" | relative_url }}" alt="Open In Colab"/>
4 |     </a>
5 | </div>


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/_includes/notebook_github_link.html:
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 1 | <div class="px-2">
 2 | {% if page.layout == 'notebook' %}
 3 |     <a href="https://github.com/{{site.github_username}}/{{site.github_repo | default: site.baseurl | remove: "/" }}/tree/{{page.branch | default: "master" }}/{{page.nb_path}}" role="button" target="_blank">
 4 | {% elsif page.layout == 'post' %}
 5 |     <a href="https://github.com/{{site.github_username}}/{{site.github_repo | default: site.baseurl | remove: "/" }}/tree/{{page.branch | default: "master" }}/{{page.path}}" role="button" target="_blank">
 6 | {% endif -%}
 7 |         <img class="notebook-badge-image" src="{{ "assets/badges/github.svg" | relative_url }}" alt="View On GitHub">
 8 |     </a>
 9 | </div>
10 | 


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/_includes/post_list.html:
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 1 | <h3>
 2 |     <a class="post-link" href="{{ post.url | relative_url }}">
 3 |     {{ post.title | escape }}
 4 |     </a>
 5 | </h3>
 6 | {%- if site.show_description and post.description  -%}
 7 | <p class="post-meta-description">{{ post.description }}</p>
 8 | {%- endif -%}
 9 | <p class="post-meta">{{ post.date | date: date_format }}</p>
10 | 


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/_includes/post_list_image_card.html:
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 1 | <div class="Box box-shadow-medium rounded-1 col-12">
 2 |     {%- if post.image -%}
 3 |     <div class="col-4 d-table-cell p-3 v-align-middle">
 4 |         <img class="image-preview " src="{{ post.image | relative_url }}" />
 5 |       </div>
 6 |     {%- endif -%}
 7 |     <div class="col-8 d-table-cell p-3">
 8 |         <h3>
 9 |           <a class="post-link" href="{{ post.url | relative_url }}">
10 |             {{ post.title | escape }}
11 |           </a>
12 |         </h3>
13 |         <p class="post-meta-description">{{ post.description }}</p>
14 |           <p class="post-meta">{{ post.date | date: date_format }}</p>
15 |       </div>
16 |   </div>


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/_includes/reading_time.html:
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1 | <span class="read-time" title="Estimated read time">
2 |     {% assign words = content | strip_html | number_of_words %}
3 |     {% if words < 360 %}
4 |       1 min read
5 |     {% else %}
6 |       {{ words | divided_by:180 }} min read
7 |     {% endif %}
8 | </span>


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/_includes/screenshot:
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1 | <figure>
2 |   <img class="image" srcset="/images/{{ include.url }} 2w" sizes="1px" src="/images/{{ include.url }}">
3 |   {% if include.caption %}
4 |   <figcaption class="image-caption">{{ include.caption }}</figcaption>
5 |   {% endif %}
6 | </figure>
7 | 
8 | 


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/_includes/tip.html:
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1 | <div class="flash flash-success">
2 |     {% octicon checklist %}
3 |     <strong>Tip: </strong>{{ include.content }}
4 | </div>


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/_includes/toc.html:
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 1 | <!-- this handles the automatic toc. use ## for subheads to auto-generate the on-page minitoc. if you use html tags, you must supply an ID for the heading element in order for it to appear in the minitoc. -->
 2 | <script>
 3 |     $( document ).ready(function() {
 4 |       // Handler for .ready() called.
 5 |     
 6 |     $('#toc').toc({ minimumHeaders: 0, listType: 'ul', showSpeed: 0, headers: 'h2,h3,h4' });
 7 |     
 8 |     /* this offset helps account for the space taken up by the floating toolbar. */
 9 |     $('#toc').on('click', 'a', function() {
10 |       var target = $(this.getAttribute('href'))
11 |         , scroll_target = target.offset().top
12 |     
13 |       $(window).scrollTop(scroll_target - 10);
14 |       return false
15 |     })
16 |       
17 |     });
18 | </script>
19 |     
20 | <div id="toc"></div>
21 | 


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/_includes/twitter.html:
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1 | {% if include.content contains  "<code>" %}
2 |     {% assign url = include.content | remove: "<code>" | remove: "</code>" %}
3 | {% else %}
4 |     {% assign url = include.content | remove: "</a>" | split: ">" | last %}
5 | {% endif %}
6 | <center>
7 |     {% twitter url %}
8 | </center>
9 | 


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/_includes/utterances.html:
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1 | <!-- from https://github.com/utterance/utterances -->
2 | <script src="https://utteranc.es/client.js"
3 |         repo="{{ site.github_username }}/{{ site.github_repo | default: site.baseurl | remove: "/" }}"
4 |         issue-term="title"
5 |         label="blogpost-comment"
6 |         theme="github-light"
7 |         crossorigin="anonymous"
8 |         async>
9 | </script>


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/_includes/warning.html:
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1 | <div class="flash flash-error">
2 |     {% octicon alert %}
3 |     <strong>Warning: </strong>{{ include.content }}
4 | </div>


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/_includes/youtube.html:
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 1 | {% if include.content contains  "<code>" %}
 2 |     {% assign base_url = include.content | remove: "<code>" | remove: "</code>" |  split: "/" | last %}
 3 | {% else %}
 4 |     {% assign url = include.content | remove: "</a>" | split: ">" | last %}
 5 |     {% assign base_url = url |  split: "/" | last %}
 6 | {% endif %}
 7 | <center>
 8 |     <iframe width="560" height="315" src="https://www.youtube.com/embed/{{base_url}}" frameborder="0" allowfullscreen></iframe>
 9 | </center>
10 | 


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/_layouts/categories.html:
--------------------------------------------------------------------------------
1 | ---
2 | layout: default
3 | ---
4 | 
5 | <div class="home">
6 | 
7 | {{ content }}
8 | 
9 | </div>


--------------------------------------------------------------------------------
/_layouts/home.html:
--------------------------------------------------------------------------------
 1 | ---
 2 | layout: default
 3 | ---
 4 | 
 5 | <div class="home">
 6 |   {%- if page.title -%}
 7 |     <h1 class="page-heading">{{ page.title }}</h1>
 8 |   {%- endif -%}
 9 | 
10 |   {{ content | markdownify }}
11 | 
12 | 
13 |   {% if site.paginate %}
14 |     {% assign rawposts = paginator.posts %}
15 |   {% else %}
16 |     {% assign rawposts = site.posts %}
17 |   {% endif %}
18 | 
19 |   <!-- Hide posts if front matter flag hide:true -->
20 |   {% assign posts = ''|split:'' %}
21 |   {% for post in rawposts %}
22 |     {% if post.hide != true %}
23 |       {% assign posts = posts|push:post%}
24 |     {% endif %}
25 |   {% endfor %}
26 | 
27 |   <!-- Sort posts by rank, then date -->
28 |   {% assign grouped_posts = posts | group_by: "sticky_rank" | sort: "name", "last" %}
29 |   {% assign sticky_posts = ''|split:'' %}
30 |   {% assign non_sticky_posts = '' | split:'' %}
31 | 
32 |  
33 |   {% for gp in grouped_posts %}
34 |     {%- if gp.name == "" -%}
35 |       {% assign non_sticky_posts = gp.items | sort: "date" | reverse %}
36 |     {%- else %}
37 |       {% assign sticky_posts = sticky_posts | concat: gp.items %}
38 |     {%- endif -%}
39 |   {% endfor %}
40 | 
41 |    <!-- Assemble final sorted posts array -->
42 |   {% assign sticky_posts = sticky_posts | sort: "sticky_rank", "last" %}
43 |   {% assign posts = sticky_posts | concat: non_sticky_posts %}
44 | 
45 |   {%- if posts.size > 0 -%}
46 |     {%- if page.list_title -%}
47 |       <h2 class="post-list-heading">{{ page.list_title }}</h2>
48 |     {%- endif -%}
49 |     <ul class="post-list">
50 |       {%- assign date_format = site.minima.date_format | default: "%b %-d, %Y" -%}
51 |       {%- for post in posts -%}
52 |       <li>
53 |         {%- if site.show_image -%}
54 |             {%- include post_list_image_card.html -%}
55 |         {% else %}
56 |             {%- include post_list.html -%}
57 |         {%- endif -%}
58 |       </li>
59 |       {%- endfor -%}
60 |     </ul>
61 | 
62 |     {% if site.paginate and site.posts.size > site.paginate %}
63 |       <div class="pager">
64 |         <ul class="pagination">
65 |         {%- if paginator.previous_page %}
66 |           <li><a href="{{ paginator.previous_page_path | relative_url }}" class="previous-page">{{ paginator.previous_page }}</a></li>
67 |         {%- else %}
68 |           <li><div class="pager-edge">•</div></li>
69 |         {%- endif %}
70 |           <li><div class="current-page">{{ paginator.page }}</div></li>
71 |         {%- if paginator.next_page %}
72 |           <li><a href="{{ paginator.next_page_path | relative_url }}" class="next-page">{{ paginator.next_page }}</a></li>
73 |         {%- else %}
74 |           <li><div class="pager-edge">•</div></li>
75 |         {%- endif %}
76 |         </ul>
77 |       </div>
78 |     {%- endif %}
79 | 
80 |   {%- endif -%}
81 | 
82 | </div>


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/_layouts/notebook.html:
--------------------------------------------------------------------------------
1 | ---
2 | layout: post
3 | ---
4 | 
5 | {{ content }}
6 | 


--------------------------------------------------------------------------------
/_layouts/post.html:
--------------------------------------------------------------------------------
 1 | ---
 2 | layout: default
 3 | ---
 4 | <article class="post h-entry" itemscope itemtype="http://schema.org/BlogPosting">
 5 | 
 6 |   <header class="post-header">
 7 |     <h1 class="post-title p-name" itemprop="name headline">{{ page.title | escape }}</h1>
 8 |     {%- if page.description -%}
 9 |       {%- if site.html_escape.description -%}
10 |         <p class="page-description">{{ page.description | escape }}</p>
11 |       {%- else -%}
12 |         <p class="page-description">{{ page.description }}</p>
13 |       {%- endif -%}
14 |     {%- endif -%}
15 |     <p class="post-meta post-meta-title">
16 |       {%- assign date_format = site.minima.date_format | default: "%b %-d, %Y" -%}
17 |       <time class="dt-published" datetime="{{ page.date | date_to_xmlschema }}" itemprop="datePublished">
18 |         {{ page.date | date: date_format }}
19 |       </time>
20 |       {%- if page.modified_date -%}
21 |         ~ 
22 |         {%- assign mdate = page.modified_date | date_to_xmlschema -%}
23 |         <time class="dt-modified" datetime="{{ mdate }}" itemprop="dateModified">
24 |           {{ mdate | date: date_format }}
25 |         </time>
26 |       {%- endif -%}
27 |       {%- if page.author -%}
28 |         • {% for author in page.author %}
29 |           <span itemprop="author" itemscope itemtype="http://schema.org/Person">
30 |             <span class="p-author h-card" itemprop="name">{{ author }}</span></span>
31 |             {%- if forloop.last == false %}, {% endif -%}
32 |         {% endfor %}
33 |       {%- endif %}
34 |        • {% include reading_time.html -%}
35 |     </p>
36 | 
37 |     {% if page.categories.size > 0 and site.show_tags %}
38 |       <p class="category-tags"><i class="fas fa-tags category-tags-icon"></i></i> 
39 |       {% for category in  page.categories  %}
40 |         <a class="category-tags-link" href="{{site.baseurl}}/categories/#{{category|slugize}}">{{category}}</a>
41 |         {% unless forloop.last %}&nbsp;{% endunless %}
42 |       {% endfor %}
43 |       </p>
44 |     {% endif %}
45 | 
46 |     {% if page.layout == 'notebook' %}
47 |       {% if page.badges or page.badges == nil %}
48 |         <div class="pb-5 d-flex flex-wrap flex-justify-end">
49 |           {% unless page.hide_github_badge or site.default_badges.github != true %}{% include notebook_github_link.html %}{% endunless %}
50 |           {% unless page.hide_binder_badge or site.default_badges.binder != true  %}{% include notebook_binder_link.html %}{% endunless %}
51 |           {% unless page.hide_colab_badge or site.default_badges.colab != true %}{% include notebook_colab_link.html %}{% endunless %}
52 |         </div>
53 |       {% endif -%}
54 |     {% endif -%}
55 |   </header>
56 | 
57 |   <div class="post-content e-content" itemprop="articleBody">
58 |     {{ content | toc  }}
59 |   </div>
60 |   {%- if page.comments -%}
61 |     {%- include utterances.html -%}
62 |   {%- endif -%}
63 |   {%- if site.disqus.shortname -%}
64 |     {%- include disqus_comments.html -%}
65 |   {%- endif -%}
66 |   <a class="u-url" href="{{ page.url | relative_url }}" hidden></a>
67 | </article>


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/_notebooks/2021-01-03-Fmi-Additional-Functionality-For-Fastai-Medical-Imaging-Module.ipynb:
--------------------------------------------------------------------------------
  1 | {
  2 |  "cells": [
  3 |   {
  4 |    "cell_type": "markdown",
  5 |    "metadata": {},
  6 |    "source": [
  7 |     "# \"Fmi: Additional Functionality For Fastai's Medical Imaging Module \"\n",
  8 |     "> \"fmi is a library built on top of fastai and adds additional functionality to fastai's medical imaging module\"\n",
  9 |     "- toc: true\n",
 10 |     "- branch: master\n",
 11 |     "- badges: true\n",
 12 |     "- comments: true\n",
 13 |     "- categories: [fmi, medical_imaging, dicoms, wearable]\n",
 14 |     "- image: images/circle.PNG"
 15 |    ]
 16 |   },
 17 |   {
 18 |    "cell_type": "markdown",
 19 |    "metadata": {},
 20 |    "source": [
 21 |     "### About"
 22 |    ]
 23 |   },
 24 |   {
 25 |    "cell_type": "markdown",
 26 |    "metadata": {},
 27 |    "source": [
 28 |     "`fmi` is a library built on top of `fastai` and adds additional functionality to fastai's medical imaging module.  This project is still a work in progress. \n",
 29 |     "\n",
 30 |     "> View the library on [Github](https://github.com/asvcode/fmi)"
 31 |    ]
 32 |   },
 33 |   {
 34 |    "cell_type": "markdown",
 35 |    "metadata": {},
 36 |    "source": [
 37 |     "### Installation"
 38 |    ]
 39 |   },
 40 |   {
 41 |    "cell_type": "markdown",
 42 |    "metadata": {},
 43 |    "source": [
 44 |     "`git clone https://github.com/asvcode/fmi.git`"
 45 |    ]
 46 |   },
 47 |   {
 48 |    "cell_type": "markdown",
 49 |    "metadata": {},
 50 |    "source": [
 51 |     "### Tutorials"
 52 |    ]
 53 |   },
 54 |   {
 55 |    "cell_type": "markdown",
 56 |    "metadata": {},
 57 |    "source": [
 58 |     "Here is a list of tutorials to get you stated with the `fmi` library\n",
 59 |     "\n",
 60 |     "[Create Bounding Boxes from Class Activation Maps](https://github.com/asvcode/fmi/blob/master/tutorial_nbs/bounding_box_generation.ipynb) - **New**\n",
 61 |     "\n",
 62 |     "[Medical Imaging Tutorial](https://github.com/asvcode/fmi/blob/master/tutorial_nbs/medical_imaging_tutorial.ipynb) - **Updated**\n",
 63 |     "\n",
 64 |     "[Explore & Preprocessing Tutorial](https://github.com/asvcode/fmi/blob/master/tutorial_nbs/explore_preprocessing_tutorial.ipynb)\n",
 65 |     "\n",
 66 |     "[Dicom Splitter Examples](https://github.com/asvcode/fmi/blob/master/tutorial_nbs/dicom_splitter_examples.ipynb)\n",
 67 |     "\n",
 68 |     "[Signal Processing Tutorial](https://github.com/asvcode/fmi/blob/master/tutorial_nbs/Signal_Processing_Tutorial.ipynb) - **Not Complete**"
 69 |    ]
 70 |   },
 71 |   {
 72 |    "cell_type": "code",
 73 |    "execution_count": null,
 74 |    "metadata": {},
 75 |    "outputs": [],
 76 |    "source": []
 77 |   }
 78 |  ],
 79 |  "metadata": {
 80 |   "kernelspec": {
 81 |    "display_name": "Python 3",
 82 |    "language": "python",
 83 |    "name": "python3"
 84 |   },
 85 |   "language_info": {
 86 |    "codemirror_mode": {
 87 |     "name": "ipython",
 88 |     "version": 3
 89 |    },
 90 |    "file_extension": ".py",
 91 |    "mimetype": "text/x-python",
 92 |    "name": "python",
 93 |    "nbconvert_exporter": "python",
 94 |    "pygments_lexer": "ipython3",
 95 |    "version": "3.8.10"
 96 |   }
 97 |  },
 98 |  "nbformat": 4,
 99 |  "nbformat_minor": 4
100 | }
101 | 


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/_notebooks/README.md:
--------------------------------------------------------------------------------
 1 | # Auto-convert Jupyter Notebooks To Posts
 2 | 
 3 | [`fastpages`](https://github.com/fastai/fastpages) will automatically convert [Jupyter](https://jupyter.org/) Notebooks saved into this directory as blog posts!
 4 | 
 5 | You must save your notebook with the naming convention `YYYY-MM-DD-*.ipynb`.  Examples of valid filenames are:
 6 | 
 7 | ```shell
 8 | 2020-01-28-My-First-Post.ipynb
 9 | 2012-09-12-how-to-write-a-blog.ipynb
10 | ```
11 | 
12 | If you fail to name your file correctly, `fastpages` will automatically attempt to fix the problem by prepending the last modified date of your notebook. However, it is recommended that you name your files properly yourself for more transparency.
13 | 
14 | See [Writing Blog Posts With Jupyter](https://github.com/fastai/fastpages#writing-blog-posts-with-jupyter) for more details.


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/_notebooks/test_df.csv:
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 1 | ,file,PatientID,Age,Sex,Rows,Cols
 2 | 0,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000000 - Copy.dcm,16d7f894-55d7-4d95-8957-d18987f0e981,62,M,1024,1024
 3 | 1,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000000.dcm,16d7f894-55d7-4d95-8957-d18987f0e981,62,M,1024,1024
 4 | 2,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000002.dcm,850ddeb3-73ac-45e0-96bf-7d275bc83782,52,F,1024,1024
 5 | 3,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000005.dcm,e0fd6161-2b8d-4757-96bc-6cf620a993d5,65,F,1024,1024
 6 | 4,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000006 - Copy.dcm,99171908-3665-48e8-82c8-66d0098ce209,52,F,1024,1024
 7 | 5,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000006.dcm,99171908-3665-48e8-82c8-66d0098ce209,52,F,1024,1024
 8 | 6,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000007.dcm,7fbf0ea0-5f00-469e-94da-fca797948237,15,M,1024,1024
 9 | 7,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000008.dcm,9e3a536f-a85c-4963-a28e-77583f934b4a,31,M,1024,1024
10 | 8,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000009.dcm,e55b3354-2030-456f-acd3-45f341ee8b94,61,F,1024,1024
11 | 9,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000011.dcm,6633c659-9249-443e-9851-b83782d1b111,21,M,1024,1024
12 | 10,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000012.dcm,9cc01bd4-5924-4b3f-8486-dc6151e4e8ae,55,F,1024,1024
13 | 11,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000014.dcm,50b20b04-2bef-47d2-a303-841730ae11fd,61,M,1024,1024
14 | 12,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000015.dcm,13f40bdc-803d-4fe0-b008-21234c2be1c3,74,F,1024,1024
15 | 13,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000017.dcm,b8cfe098-f592-4eb1-8396-9ebfdba5a075,66,M,1024,1024
16 | 14,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000018.dcm,81551598-ab51-4e57-a4de-8d0b03993c55,66,F,1024,1024
17 | 15,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\000019.dcm,6da2e64b-b97f-45e7-958c-18996e3a9cdd,68,M,1024,1024
18 | 16,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\C000013 - Copy.dcm,6224213b-a185-4821-8490-c9cba260a959,42,F,1024,1024
19 | 17,C:\Users\avird\.fastai\data\siim_small\sm\No Pneumothorax\C000013.dcm,6224213b-a185-4821-8490-c9cba260a959,42,F,1024,1024
20 | 18,C:\Users\avird\.fastai\data\siim_small\sm\Pneumothorax\000001 - Copy.dcm,a98e23a3-b096-4ec0-91ec-a4727ea6b375,34,M,1024,1024
21 | 19,C:\Users\avird\.fastai\data\siim_small\sm\Pneumothorax\000001.dcm,a98e23a3-b096-4ec0-91ec-a4727ea6b375,34,M,1024,1024
22 | 20,C:\Users\avird\.fastai\data\siim_small\sm\Pneumothorax\000003.dcm,9ed3a0bf-7cf1-4fe6-9ddd-7a895e691181,30,F,1024,1024
23 | 21,C:\Users\avird\.fastai\data\siim_small\sm\Pneumothorax\000004.dcm,c844072c-3ba6-48d2-b009-4eb329fecd26,57,F,1024,1024
24 | 22,C:\Users\avird\.fastai\data\siim_small\sm\Pneumothorax\000010.dcm,d6547f8c-6ef7-4b60-85e5-116c4f846209,41,M,1024,1024
25 | 23,C:\Users\avird\.fastai\data\siim_small\sm\Pneumothorax\000013 - Copy.dcm,6224213b-a185-4821-8490-c9cba260a959,42,F,1024,1024
26 | 24,C:\Users\avird\.fastai\data\siim_small\sm\Pneumothorax\000013.dcm,6224213b-a185-4821-8490-c9cba260a959,42,F,1024,1024
27 | 25,C:\Users\avird\.fastai\data\siim_small\sm\Pneumothorax\000016.dcm,8954624c-be17-45fb-b6b7-c305a5f5589b,45,F,1024,1024
28 | 


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/_pages/404.html:
--------------------------------------------------------------------------------
 1 | ---
 2 | permalink: /404.html
 3 | layout: default
 4 | search_exclude: true
 5 | ---
 6 | 
 7 | <style type="text/css" media="screen">
 8 |   .container {
 9 |     margin: 10px auto;
10 |     max-width: 600px;
11 |     text-align: center;
12 |   }
13 |   h1 {
14 |     margin: 30px 0;
15 |     font-size: 4em;
16 |     line-height: 1;
17 |     letter-spacing: -1px;
18 |   }
19 | </style>
20 | 
21 | <div class="container">
22 |   <h1>404</h1>
23 |   <p><strong>Page not found :(</strong></p>
24 |   <p>The requested page could not be found.</p>
25 | </div>
26 | 


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/_pages/about.md:
--------------------------------------------------------------------------------
 1 | ---
 2 | layout: page
 3 | title: About
 4 | permalink: /about/
 5 | ---
 6 | 
 7 | Amrit Virdee
 8 | 
 9 | I am a prior Insight Data Science AI Fellow, pharmacist with a Masters in Health Informatics, presented and moderated at HIMSS, pitched at AWS Startups and Startup SanDiego and proud father of 2.
10 | 
11 | [![](https://img.shields.io/static/v1?label=LinkedIn&message=link&labelColor=2f363d&color=blue&style=flat&logo=linkedin&logoColor=959da5)](https://www.linkedin.com/in/amritvirdee/)
12 | 
13 | [![](https://img.shields.io/static/v1?label=Twitter&message=link&labelColor=2f363d&color=green&style=flat&logo=twitter&logoColor=959da5)](https://twitter.com/_AVirdee)
14 | 
15 | [![](https://img.shields.io/static/v1?label=GitHub&message=link&labelColor=2f363d&color=red&style=flat&logo=github&logoColor=959da5)](https://github.com/asvcode)
16 | 


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/_pages/search.html:
--------------------------------------------------------------------------------
 1 | ---
 2 | layout: default
 3 | permalink: /search/
 4 | title: Search
 5 | search_exclude: true
 6 | ---
 7 | 
 8 | <!-- adapted from https://github.com/pmarsceill/just-the-docs -->
 9 | <script type="text/javascript" src="{{ '/assets/js/search.js' | relative_url }}"></script>
10 | <script type="text/javascript" src="{{ '/assets/js/vendor/lunr.min.js' | relative_url }}"></script>
11 | 
12 | <div class="search">
13 |     <div class="search-input-wrap">
14 |     <input type="text" class="js-search-input search-input input-block form-control" tabindex="0" placeholder="Search {{ site.title }}" aria-label="Search {{ site.title }}" autocomplete="off">
15 |     </div>
16 |     <br>
17 |     <div class="js-search-results search-results-wrap"></div>
18 | </div>
19 | 


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/_pages/tags.html:
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 1 | ---
 2 | layout: categories
 3 | permalink: /categories/
 4 | title: Tags
 5 | search_exclude: true
 6 | ---
 7 | 
 8 | {% if site.categories.size > 0 %}
 9 | <h2>Contents</h2>
10 | 
11 |   {% assign categories = "" | split:"" %}
12 |   {% for c in site.categories %}
13 |     {% assign categories = categories | push: c[0] %}
14 |   {% endfor %}
15 |   {% assign categories = categories | sort_natural %}
16 | 
17 |   <ul>
18 |   {% for category in categories %}
19 |     <li><a href="#{{ category }}">{{ category }}</a></li>
20 |   {% endfor %}
21 |   </ul>
22 | 
23 |   {% for category in categories %}
24 |       <h3 id ="{{ category }}"><i class="fas fa-tags category-tags-icon"></i></i> {{ category }}</h3>
25 |       <a name="{{ category | slugize }}"></a>
26 |       {% for post in site.categories[category] %}
27 |       {%- assign date_format = site.minima.date_format | default: "%b %-d, %Y" -%}
28 |       <article class="archive-item">
29 |         <p class="post-meta post-meta-title"><a class="page-meta" href="{{ site.baseurl }}{{ post.url }}">{{post.title}}</a>  • {{ post.date | date: date_format }}</p>
30 |       </article>
31 |       {% endfor %}
32 |   {% endfor %}
33 | 
34 | {% endif %}
35 | 


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/_plugins/footnote-detail.rb:
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 1 | module Jekyll
 2 |     module AssetFilter
 3 |       def fndetail(input, id)
 4 |         "<div class='footnotes'><p id='fn-#{id}'>#{id}. #{input}<a href='#fnref-#{id}' class='footnote footnotes'>↩</a></p></div>"
 5 |       end
 6 |     end
 7 |   end
 8 |   
 9 | Liquid::Template.register_filter(Jekyll::AssetFilter)
10 | 


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/_plugins/footnote.rb:
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 1 | module Jekyll
 2 |     class FootNoteTag < Liquid::Tag
 3 |   
 4 |       def initialize(tag_name, text, tokens)
 5 |         super
 6 |         @text = text.strip
 7 |       end
 8 |   
 9 |       def render(context)
10 |         "<sup id='fnref-#{@text}' class='footnote-ref'><a href='#fn-#{@text}'>#{@text}</a></sup>"
11 |       end
12 |     end
13 |   end
14 |   
15 | Liquid::Template.register_tag('fn', Jekyll::FootNoteTag)
16 | 


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/_posts/README.md:
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 1 | # Auto-convert markdown files To Posts
 2 | 
 3 | [`fastpages`](https://github.com/fastai/fastpages) will automatically convert markdown files saved into this directory as blog posts!
 4 | 
 5 | You must save your notebook with the naming convention `YYYY-MM-DD-*.md`.  Examples of valid filenames are:
 6 | 
 7 | ```shell
 8 | 2020-01-28-My-First-Post.md
 9 | 2012-09-12-how-to-write-a-blog.md
10 | ```
11 | 
12 | # Resources
13 | 
14 | - [Jekyll posts](https://jekyllrb.com/docs/posts/)
15 | - [Example markdown post](https://github.com/fastai/fastpages/blob/master/_posts/2020-01-14-test-markdown-post.md)
16 | 


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/_sass/minima/custom-styles.scss:
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 1 | /*-----------------------------------*/
 2 | /*--- IMPORT STYLES FOR FASTPAGES ---*/
 3 | @import "minima/fastpages-styles";   
 4 | //@import "minima/test-layout";
 5 | //@import "minima/dark-mode";
 6 | 
 7 | 
 8 | 
 9 | /*-----------------------------------*/
10 | /*----- ADD YOUR STYLES BELOW -------*/
11 | 
12 | // If you want to turn off dark background for syntax highlighting, comment or delete the below line.
13 | //@import "minima/fastpages-dracula-highlight"; 
14 | //@import "minima/solarized"; 
15 | 


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/_sass/minima/dark-mode.scss:
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 1 | //credit: https://gist.github.com/prampey/aac8f8436827ea09f53a67873142706c
 2 | 
 3 | $high-emph: rgba(white, 0.87);
 4 | $med-emph: rgba(white, 0.69); //Noicee
 5 | $low-emph: rgba(white, 0.38);
 6 | $dark-grey : #121212; 
 7 | // $dark-grey : #1F1B24;
 8 | $overlay: mix($dark-grey, white, 95%);
 9 | $overlay-light: mix($dark-grey, white, 86%);
10 | 
11 | html, body, input, textarea, select, button {   
12 |   color: $high-emph !important;
13 |   background-color: $dark-grey !important;
14 | }
15 | 
16 | a {
17 |     color: rgb(75, 186, 255) !important;
18 | }
19 | 
20 | a:hover {
21 |     color:$high-emph !important;
22 | }
23 | 
24 | .site-title, .site-title:visited, .site-nav, .page-link {
25 |     color: $high-emph !important;
26 | }
27 | 
28 | .site-nav {
29 |     background-color: $dark-grey;
30 |     border-color: $overlay-light;
31 | }
32 | 
33 | * {
34 |     scrollbar-color: $dark-grey $overlay-light;
35 | }
36 | 
37 | pre, code {
38 |     // BVas a lighter colour to better highlight short code words
39 |     border-color: $overlay-light;
40 |     background-color: $overlay;
41 | }
42 | 
43 | .page-description {
44 |     color: $med-emph;
45 | }
46 | 
47 | .post-meta {
48 |     color: $low-emph;
49 | }
50 | 
51 | .post-content p, .post-content li {
52 |     color: $med-emph;
53 | }
54 | 
55 | .btn {
56 |     background-color: $overlay !important;
57 |     color: $high-emph !important;
58 |     border-color: $overlay-light !important;
59 | }
60 | 
61 | .btn:hover {
62 |     background-color: $dark-grey !important;
63 | }
64 | 
65 | table th{
66 |     background-color: $overlay;
67 |     border-color: $overlay-light;
68 |     color: $high-emph;
69 | }
70 | 
71 | table td{
72 |     background-color: $dark-grey;
73 |     border-color: $overlay-light;
74 |     color: $med-emph;
75 | }
76 | 
77 | .flash {
78 |     color: $dark-grey !important;
79 |     filter: brightness(80%);
80 | }
81 | 
82 | canvas {
83 |     filter: invert(100%);
84 | }
85 | 


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/_sass/minima/fastpages-dracula-highlight.scss:
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  1 | // Override Syntax Highlighting In Minima With the Dracula Theme: https://draculatheme.com/
  2 | // If you wish to override any of this CSS, do so in _sass/minima/custom-styles.css
  3 |  
  4 | $dt-gray-dark: #282a36;  // Background
  5 | $dt-code-cell-background: #323443;
  6 | $dt-gray: #44475a;       // Current Line & Selection
  7 | $dt-gray-light: #f8f8f2; // Foreground
  8 | $dt-blue: #6272a4;       // Comment
  9 | $dt-cyan: #8be9fd;
 10 | $dt-green: #50fa7b;
 11 | $dt-orange: #ffb86c;
 12 | $dt-pink: #ff79c6;
 13 | $dt-purple: #bd93f9;
 14 | $dt-red: #ff5555;
 15 | $dt-yellow: #f1fa8c;
 16 | $dt-green-light: rgb(172, 229, 145);
 17 | 
 18 | .language-python + .language-plaintext {
 19 |     border-left: 1px solid grey;
 20 |     margin-left: 1rem !important;
 21 | }
 22 | 
 23 | // ensure dark background for code in markdown
 24 | [class^="language-"]:not(.language-plaintext) pre,
 25 | [class^="language-"]:not(.language-plaintext) code {
 26 |     background-color: $dt-code-cell-background !important;
 27 |     color: $dt-gray-light;
 28 | }
 29 | 
 30 | .language-python + .language-plaintext code { background-color: white !important; }
 31 | .language-python + .language-plaintext pre  { background-color: white !important; }
 32 | 
 33 | // for Jupyter Notebook HTML Code Cells modified from https://www.fast.ai/public/css/hyde.css
 34 | 
 35 | .input_area pre, .input_area div {
 36 |     margin-bottom:2rem !important;
 37 |     margin-top:1.5rem !important;
 38 |     padding-bottom:0 !important;
 39 |     padding-top:0 !important;
 40 |     background: #323443 !important;
 41 |     -webkit-font-smoothing: antialiased;
 42 |     text-rendering: optimizeLegibility;
 43 |     font-family: Menlo, Monaco, Consolas, "Lucida Console", Roboto, Ubuntu, monospace;
 44 |     border-radius: 5px;
 45 |     font-size: 100%;
 46 | }
 47 | .output_area pre, .output_area div {
 48 |     margin-bottom:1rem !important;
 49 |     margin-top:1rem !important;
 50 |     padding-bottom:0 !important;
 51 |     padding-top:0 !important;
 52 | }
 53 | .input_area pre {
 54 |     border-left: 1px solid lightcoral;
 55 | }
 56 | .output_area pre {
 57 |     border-left: 1px solid grey;
 58 |     margin-left: 1rem !important;
 59 | }
 60 | 
 61 | .code_cell table { width: auto; }
 62 | 
 63 | /* Dracula Theme v1.2.5
 64 |  *
 65 |  * https://github.com/zenorocha/dracula-theme
 66 |  *
 67 |  * Copyright 2016, All rights reserved
 68 |  *
 69 |  * Code licensed under the MIT license
 70 |  *
 71 |  */
 72 | 
 73 | .highlight {
 74 |     background: $dt-code-cell-background !important;
 75 |     color: $dt-gray-light !important;
 76 |     pre, code {
 77 |      background: $dt-code-cell-background;
 78 |      color: $dt-gray-light;
 79 |     }
 80 |    
 81 |     .hll,
 82 |     .s,
 83 |     .sa,
 84 |     .sb,
 85 |     .sc,
 86 |     .dl,
 87 |     .sd,
 88 |     .s2,
 89 |     .se,
 90 |     .sh,
 91 |     .si,
 92 |     .sx,
 93 |     .sr,
 94 |     .s1,
 95 |     .ss {
 96 |          color:rgb(231, 153, 122);
 97 |     }
 98 |   
 99 |     .go {
100 |       color: $dt-gray;
101 |     }
102 |   
103 |     .err,
104 |     .g,
105 |     .l,
106 |     .n,
107 |     .x,
108 |     .ge,
109 |     .gr,
110 |     .gh,
111 |     .gi,
112 |     .gp,
113 |     .gs,
114 |     .gu,
115 |     .gt,
116 |     .ld,
117 |     .no,
118 |     .nd,
119 |     .pi,
120 |     .ni,
121 |     .ne,
122 |     .nn,
123 |     .nx,
124 |     .py,
125 |     .w,
126 |     .bp {
127 |       color: $dt-gray-light;
128 |       background-color: $dt-code-cell-background !important;
129 |     }
130 |  
131 |     .p {
132 |          font-weight: bold;
133 |          color: rgb(102, 217, 239);
134 |  }
135 |   
136 |     .ge {
137 |       text-decoration: underline;
138 |     }
139 |   
140 |     .bp {
141 |       font-style: italic;
142 |     }
143 |   
144 |     .c,
145 |     .ch,
146 |     .cm,
147 |     .cpf,
148 |     .c1,
149 |     .cs {
150 |       color: $dt-blue;
151 |     }
152 |   
153 |     .kd,
154 |     .kt,
155 |     .nb,
156 |     .nl,
157 |     .nv,
158 |     .vc,
159 |     .vg,
160 |     .vi,
161 |     .vm {
162 |       color: $dt-cyan;
163 |     }
164 |   
165 |     .kd,
166 |     .nb,
167 |     .nl,
168 |     .nv,
169 |     .vc,
170 |     .vg,
171 |     .vi,
172 |     .vm {
173 |       font-style: italic;
174 |     }
175 |   
176 |     .fm,
177 |     .na,
178 |     .nc,
179 |     .nf
180 |      {
181 |       color: $dt-green-light;
182 |     }
183 |   
184 |     .k,
185 |     .o,
186 |     .cp,
187 |     .kc,
188 |     .kn,
189 |     .kp,
190 |     .kr,
191 |     .nt,
192 |     .ow {
193 |       color: $dt-pink;
194 |     }
195 |  
196 |     .kc {
197 |          color: $dt-green-light;   
198 |     }
199 |   
200 |     .m,
201 |     .mb,
202 |     .mf,
203 |     .mh,
204 |     .mi,
205 |     .mo,
206 |     .il {
207 |       color: $dt-purple;
208 |     }
209 |   
210 |     .gd {
211 |       color: $dt-red;
212 |     }
213 | }
214 | 


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/_sass/minima/fastpages-styles.scss:
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  1 | //Default Overrides For Styles In Minima 
  2 | // If you wish to override any of this CSS, do so in _sass/minima/custom-styles.css
  3 | 
  4 | .post img {
  5 |         display: block;
  6 |         // border:1px solid #021a40;
  7 |         vertical-align: top;
  8 |         margin-left: auto;
  9 |         margin-right: auto;
 10 | }
 11 | 
 12 | img.emoji{
 13 |       display: inline !important;
 14 |       vertical-align: baseline !important;
 15 | }
 16 | 
 17 | .post figcaption {
 18 |   text-align: center;
 19 |   font-size: .8rem;
 20 |   font-style: italic;
 21 |   color: light-grey;
 22 | }
 23 | 
 24 | .page-content {
 25 |         -webkit-font-smoothing: antialiased !important;
 26 |         text-rendering: optimizeLegibility !important;
 27 |         font-family: "Segoe UI", SegoeUI, Roboto, "Segoe WP", "Helvetica Neue", "Helvetica", "Tahoma", "Arial", sans-serif !important;
 28 | }
 29 | 
 30 | // make non-headings slightly lighter
 31 | .post-content p, .post-content li {
 32 |    font-size: 20px;
 33 |    color: #515151;
 34 | }
 35 | 
 36 | .post-link{
 37 |     font-weight: normal;
 38 | }
 39 | 
 40 | // change padding of headings
 41 | h1 {
 42 |     margin-top:2.5rem !important;
 43 | }
 44 | 
 45 | h2 {
 46 |     margin-top:2rem !important;      
 47 | }
 48 | 
 49 | h3, h4 {
 50 |     margin-top:1.5rem !important;      
 51 | }
 52 | 
 53 | p {
 54 |     margin-top:1rem !important; 
 55 |     margin-bottom:1rem !important;   
 56 | }
 57 | 
 58 | h1, h2, h3, h4 {
 59 |     font-weight: normal !important;
 60 |     margin-bottom:0.5rem !important;  
 61 |     code {
 62 |       font-size: 100%;
 63 |     }
 64 | }
 65 | 
 66 | pre {
 67 |     margin-bottom:1.5rem !important; 
 68 | }
 69 | 
 70 | // make sure the post title doesn't have too much spacing
 71 | .post-title { margin-top: .5rem !important; }
 72 | 
 73 | li {
 74 |   h3, h4 {
 75 |   margin-top:.05rem !important;
 76 |   margin-bottom:.05rem !important;
 77 |   }
 78 |   .post-meta-description {
 79 |     color: rgb(88, 88, 88);
 80 |     font-size: 15px;
 81 |     margin-top:.05rem !important;
 82 |     margin-bottom:.05rem !important;
 83 |   }
 84 | }
 85 | 
 86 | 
 87 | 
 88 | //  Code Folding
 89 |  details.description[open] summary::after {
 90 |   content: attr(data-open);
 91 | }
 92 | 
 93 | details.description:not([open]) summary::after {
 94 |   content: attr(data-close);
 95 | }
 96 | 
 97 | // Notebook badges
 98 | .notebook-badge-image {
 99 |   border:0 !important;
100 | }
101 | 
102 | // Adjust font size for footnotes.
103 | .footnotes {
104 |   font-size: 12px !important;
105 |   p, li{
106 |     font-size: 12px !important;
107 |  } 
108 | }
109 | 
110 | // Adjust with of social media icons were getting cut off
111 | .social-media-list{
112 |   .svg-icon {
113 |     width: 25px !important;
114 |     height: 23px !important;
115 |   }
116 | }
117 | 
118 | // Make Anchor Links Appear Only on Hover
119 | 
120 | .anchor-link {
121 |   opacity: 0;
122 |   padding-left: 0.375em;
123 |   \-webkit-text-stroke: 1.75px white;
124 |   \-webkit-transition: opacity 0.2s ease-in-out 0.1s;
125 |   \-moz-transition: opacity 0.2s ease-in-out 0.1s;
126 |   \-ms-transition: opacity 0.2s ease-in-out 0.1s;
127 | }
128 | 
129 | h1:hover .anchor-link,
130 | h2:hover .anchor-link,
131 | h3:hover .anchor-link,
132 | h4:hover .anchor-link,
133 | h5:hover .anchor-link,
134 | h6:hover .anchor-link {
135 |   opacity: 1;
136 | }
137 | 
138 | 
139 | // category tags
140 | .category-tags {
141 |   margin-top: .25rem !important;
142 |   margin-bottom: .25rem !important;
143 |   font-size: 105%;
144 | }
145 | 
146 | // Custom styling for homepage post previews
147 | .post-meta-title, .post-meta{
148 |   margin-top: .25em !important;
149 |   margin-bottom: .25em !important;
150 |   font-size: 105%;
151 | }
152 | 
153 | .page-description {
154 |   margin-top: .5rem !important;
155 |   margin-bottom: .5rem !important;
156 |   color: #585858;
157 |   font-size: 115%;
158 | }
159 | 
160 | // Custom styling for category tags
161 | .category-tags-icon {
162 |   font-size: 75% !important;
163 |   padding-left: 0.375em;
164 |   opacity: 35%;
165 | }
166 | .category-tags-link {
167 |   color:rgb(187, 129, 129) !important;
168 |   font-size: 13px !important;
169 | }
170 | 
171 | // Search Page Styles
172 | .js-search-results {padding-top: 0.2rem;}
173 | .search-results-list-item {padding-bottom: 1rem;}
174 | .search-results-list-item .search-result-title {
175 |   font-size: 16px;
176 |   color: #d9230f;
177 | }
178 | .search-result-rel-url {color: silver;}
179 | .search-results-list-item a {display: block; color: #777;}
180 | .search-results-list-item a:hover, .search-results-list-item a:focus {text-decoration: none;}
181 | .search-results-list-item a:hover .search-result-title {text-decoration: underline;}
182 | 
183 | .search-result-rel-date {
184 |   color: rgb(109, 120, 138);
185 |   font-size: 14px;
186 | }
187 | 
188 | .search-result-preview {
189 |   color: #777;
190 |   font-size: 16px;
191 |   margin-top:.02rem !important;
192 |   margin-bottom:.02rem !important;
193 | }
194 | .search-result-highlight {
195 |   color: #2e0137;
196 |   font-weight:bold;
197 | }
198 | 
199 | // Handle Overflow With Table Output
200 | 
201 | table {
202 |   display: block !important;
203 |   overflow-x: auto;
204 |   white-space: nowrap;
205 |   font-size: 75%;
206 |   border:none;
207 |   th{
208 |     text-align: center! important;
209 |   }
210 |   td{
211 |     text-overflow:ellipsis;
212 |     overflow:hidden;
213 |     max-width: 15em;
214 |   }
215 | }
216 | 
217 | // customize scrollbars
218 | ::-webkit-scrollbar {
219 |   width: 14px;
220 |   height: 18px;
221 | }
222 | ::-webkit-scrollbar-thumb {
223 |   height: 6px;
224 |   border: 4px solid rgba(0, 0, 0, 0);
225 |   background-clip: padding-box;
226 |   -webkit-border-radius: 7px;
227 |   background-color: #9D9D9D;
228 |   -webkit-box-shadow: inset -1px -1px 0px rgba(0, 0, 0, 0.05), inset 1px 1px 0px rgba(0, 0, 0, 0.05);
229 | }
230 | ::-webkit-scrollbar-button {
231 |   width: 0;
232 |   height: 0;
233 |   display: none;
234 | }
235 | ::-webkit-scrollbar-corner {
236 |   background-color: transparent;
237 | }
238 | 
239 | // Wrap text outputs instead of horizontal scroll
240 | .output_text.output_execute_result {
241 |   pre{
242 |     white-space: pre-wrap;
243 |   }
244 | }
245 | 
246 | 
247 | // Handling large charts on mobile devices
248 | @media only screen and (max-width: 900px) {
249 |   /* for mobile phone and tablet devices */
250 |   .output_wrapper{
251 |     overflow: scroll;
252 |   }
253 | }
254 | 


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/_sass/minima/solarized.scss:
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  1 | @charset "utf-8";
  2 | 
  3 | // Solarized skin
  4 | // ==============
  5 | // Created by Sander Voerman <mailto:sander@savoerman.nl> using the Solarized
  6 | // color scheme by Ethan Schoonover <https://ethanschoonover.com/solarized>.
  7 | 
  8 | // This style sheet implements two options for the minima.skin setting:
  9 | // "solarized" for light mode and "solarized-dark" for dark mode.
 10 | $sol-is-dark: true !default;
 11 | 
 12 | 
 13 | // Color scheme
 14 | // ------------
 15 | // The inline comments show the canonical L*a*b values for each color.
 16 | 
 17 | $sol-base03:   #002b36;  // 15 -12 -12
 18 | $sol-base02:   #073642;  // 20 -12 -12
 19 | $sol-base01:   #586e75;  // 45 -07 -07
 20 | $sol-base00:   #657b83;  // 50 -07 -07
 21 | $sol-base0:    #839496;  // 60 -06 -03
 22 | $sol-base1:    #93a1a1;  // 65 -05 -02
 23 | $sol-base2:    #eee8d5;  // 92 -00  10
 24 | $sol-base3:    #fdf6e3;  // 97  00  10
 25 | $sol-yellow:   #b58900;  // 60  10  65
 26 | $sol-orange:   #cb4b16;  // 50  50  55
 27 | $sol-red:      #dc322f;  // 50  65  45
 28 | $sol-magenta:  #d33682;  // 50  65 -05
 29 | $sol-violet:   #6c71c4;  // 50  15 -45
 30 | $sol-blue:     #268bd2;  // 55 -10 -45
 31 | $sol-cyan:     #2aa198;  // 60 -35 -05
 32 | $sol-green:    #859900;  // 60 -20  65
 33 | 
 34 | $sol-mono3:    $sol-base3;
 35 | $sol-mono2:    $sol-base2;
 36 | $sol-mono1:    $sol-base1;
 37 | $sol-mono00:   $sol-base00;
 38 | $sol-mono01:   $sol-base01;
 39 | 
 40 | @if $sol-is-dark {
 41 |   $sol-mono3:  $sol-base03;
 42 |   $sol-mono2:  $sol-base02;
 43 |   $sol-mono1:  $sol-base01;
 44 |   $sol-mono00: $sol-base0;
 45 |   $sol-mono01: $sol-base1;
 46 | }
 47 | 
 48 | 
 49 | // Minima color variables
 50 | // ----------------------
 51 | 
 52 | $brand-color:           $sol-mono1 !default;
 53 | $brand-color-light:     mix($sol-mono1, $sol-mono3) !default;
 54 | $brand-color-dark:      $sol-mono00 !default;
 55 | 
 56 | $site-title-color:      $sol-mono00 !default;
 57 | 
 58 | $text-color:            $sol-mono01 !default;
 59 | $background-color:      $sol-mono3 !default;
 60 | $code-background-color: $sol-mono2 !default;
 61 | 
 62 | $link-base-color:       $sol-blue !default;
 63 | $link-visited-color:    mix($sol-blue, $sol-mono00) !default;
 64 | $link-hover-color:      $sol-mono00 !default;
 65 | 
 66 | $border-color-01:       $brand-color-light !default;
 67 | $border-color-02:       $sol-mono1 !default;
 68 | $border-color-03:       $sol-mono00 !default;
 69 | 
 70 | $table-text-color:      $sol-mono00 !default;
 71 | $table-zebra-color:     mix($sol-mono2, $sol-mono3) !default;
 72 | $table-header-bg-color: $sol-mono2 !default;
 73 | $table-header-border:   $sol-mono1 !default;
 74 | $table-border-color:    $sol-mono1 !default;
 75 | 
 76 | 
 77 | // Syntax highlighting styles
 78 | // --------------------------
 79 | 
 80 | .highlight {
 81 |   .c     { color: $sol-mono1; font-style: italic } // Comment
 82 |   .err   { color: $sol-red } // Error
 83 |   .k     { color: $sol-mono01; font-weight: bold } // Keyword
 84 |   .o     { color: $sol-mono01; font-weight: bold } // Operator
 85 |   .cm    { color: $sol-mono1; font-style: italic } // Comment.Multiline
 86 |   .cp    { color: $sol-mono1; font-weight: bold } // Comment.Preproc
 87 |   .c1    { color: $sol-mono1; font-style: italic } // Comment.Single
 88 |   .cs    { color: $sol-mono1; font-weight: bold; font-style: italic } // Comment.Special
 89 |   .gd    { color: $sol-red } // Generic.Deleted
 90 |   .gd .x { color: $sol-red } // Generic.Deleted.Specific
 91 |   .ge    { color: $sol-mono00; font-style: italic } // Generic.Emph
 92 |   .gr    { color: $sol-red } // Generic.Error
 93 |   .gh    { color: $sol-mono1 } // Generic.Heading
 94 |   .gi    { color: $sol-green } // Generic.Inserted
 95 |   .gi .x { color: $sol-green } // Generic.Inserted.Specific
 96 |   .go    { color: $sol-mono00 } // Generic.Output
 97 |   .gp    { color: $sol-mono00 } // Generic.Prompt
 98 |   .gs    { color: $sol-mono01; font-weight: bold } // Generic.Strong
 99 |   .gu    { color: $sol-mono1 } // Generic.Subheading
100 |   .gt    { color: $sol-red } // Generic.Traceback
101 |   .kc    { color: $sol-mono01; font-weight: bold } // Keyword.Constant
102 |   .kd    { color: $sol-mono01; font-weight: bold } // Keyword.Declaration
103 |   .kp    { color: $sol-mono01; font-weight: bold } // Keyword.Pseudo
104 |   .kr    { color: $sol-mono01; font-weight: bold } // Keyword.Reserved
105 |   .kt    { color: $sol-violet; font-weight: bold } // Keyword.Type
106 |   .m     { color: $sol-cyan } // Literal.Number
107 |   .s     { color: $sol-magenta } // Literal.String
108 |   .na    { color: $sol-cyan } // Name.Attribute
109 |   .nb    { color: $sol-blue } // Name.Builtin
110 |   .nc    { color: $sol-violet; font-weight: bold } // Name.Class
111 |   .no    { color: $sol-cyan } // Name.Constant
112 |   .ni    { color: $sol-violet } // Name.Entity
113 |   .ne    { color: $sol-violet; font-weight: bold } // Name.Exception
114 |   .nf    { color: $sol-blue; font-weight: bold } // Name.Function
115 |   .nn    { color: $sol-mono00 } // Name.Namespace
116 |   .nt    { color: $sol-blue } // Name.Tag
117 |   .nv    { color: $sol-cyan } // Name.Variable
118 |   .ow    { color: $sol-mono01; font-weight: bold } // Operator.Word
119 |   .w     { color: $sol-mono1 } // Text.Whitespace
120 |   .mf    { color: $sol-cyan } // Literal.Number.Float
121 |   .mh    { color: $sol-cyan } // Literal.Number.Hex
122 |   .mi    { color: $sol-cyan } // Literal.Number.Integer
123 |   .mo    { color: $sol-cyan } // Literal.Number.Oct
124 |   .sb    { color: $sol-magenta } // Literal.String.Backtick
125 |   .sc    { color: $sol-magenta } // Literal.String.Char
126 |   .sd    { color: $sol-magenta } // Literal.String.Doc
127 |   .s2    { color: $sol-magenta } // Literal.String.Double
128 |   .se    { color: $sol-magenta } // Literal.String.Escape
129 |   .sh    { color: $sol-magenta } // Literal.String.Heredoc
130 |   .si    { color: $sol-magenta } // Literal.String.Interpol
131 |   .sx    { color: $sol-magenta } // Literal.String.Other
132 |   .sr    { color: $sol-green } // Literal.String.Regex
133 |   .s1    { color: $sol-magenta } // Literal.String.Single
134 |   .ss    { color: $sol-magenta } // Literal.String.Symbol
135 |   .bp    { color: $sol-mono1 } // Name.Builtin.Pseudo
136 |   .vc    { color: $sol-cyan } // Name.Variable.Class
137 |   .vg    { color: $sol-cyan } // Name.Variable.Global
138 |   .vi    { color: $sol-cyan } // Name.Variable.Instance
139 |   .il    { color: $sol-cyan } // Literal.Number.Integer.Long
140 | }
141 | 


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/_sass/minima/test-layout.scss:
--------------------------------------------------------------------------------
  1 | $dt-gray-dark: #e01b14;  // Background
  2 | $dt-code-cell-background: #ffffff; //
  3 | $dt-gray: #44475a;       // Current Line & Selection
  4 | $dt-gray-light: #6666c2; // bulk area of code #6666c2 is currently blue 
  5 | $dt-blue: #0d0d0d;       // Comment
  6 | $dt-cyan: #0d0d0d;
  7 | $dt-green: #050505; //original #50fa7b def
  8 | $dt-orange: #1a1a1c; //original #ffb86c
  9 | $dt-pink: #0d0d0d;
 10 | $dt-purple: #0d0d0d;
 11 | $dt-red: #0d0d0d;
 12 | $dt-yellow: #0d0d0d; //original #f1fa8c
 13 | $dt-green-light: rgb(255,0,0); //172, 229, 145 //after def
 14 | 
 15 | .post img {
 16 |         display: block;
 17 |         // border:1px solid #021a40;
 18 |         vertical-align: top;
 19 |         margin-left: auto;
 20 |         margin-right: auto;
 21 | }
 22 | 
 23 | .post figcaption {
 24 |   text-align: center;
 25 |   font-size: .8rem;
 26 |   font-style: italic;
 27 |   color: light-grey;
 28 | }
 29 | 
 30 | .language-python + .language-plaintext {
 31 |         border-left: 1px solid grey;
 32 |         margin-left: 1rem !important;
 33 | }
 34 | 
 35 | // ensure dark background for code in markdown
 36 | [class^="language-"]:not(.language-plaintext) pre,
 37 | [class^="language-"]:not(.language-plaintext) code
 38 | // .highlight.[class^="h1-"]
 39 | {
 40 |   background-color: $dt-code-cell-background !important;
 41 |   color: $dt-gray-light;
 42 | }
 43 | 
 44 | .language-python + .language-plaintext code { background-color: white !important; }
 45 | .language-python + .language-plaintext pre  { background-color: white !important; }
 46 | 
 47 | // for Jupyter Notebook HTML Code Cells modified from https://www.fast.ai/public/css/hyde.css
 48 | 
 49 | .input_area pre, .input_area div {
 50 |         margin-bottom:2rem !important;
 51 |         margin-top:1.5rem !important;
 52 |         padding-bottom:0 !important;
 53 |         padding-top:0 !important;
 54 |         background: #ffffff !important; //original #323443
 55 |         -webkit-font-smoothing: antialiased;
 56 |         text-rendering: optimizeLegibility;
 57 |         font-family: Menlo, Monaco, Consolas, "Lucida Console", Roboto, Ubuntu, monospace;
 58 |         border-radius: 5px;
 59 |         font-size: 100%; // background code cell area
 60 | }
 61 | .output_area pre, .output_area div {
 62 |         margin-bottom:1rem !important;
 63 |         margin-top:1rem !important;
 64 |         padding-bottom:0 !important;
 65 |         padding-top:0 !important;
 66 |         background: #c6edf7 !important; // background output cell code #a1e2f7
 67 | }
 68 | .input_area pre {
 69 |         border-left: 1px solid lightcoral;
 70 | }
 71 | .output_area pre {
 72 |         border-left: 1px solid grey;
 73 |         margin-left: 1rem !important;
 74 | }
 75 | 
 76 | .code_cell table { width: auto; }
 77 | 
 78 | .page-content {
 79 |         -webkit-font-smoothing: antialiased !important;
 80 |         text-rendering: optimizeLegibility !important;
 81 |         font-family: "Segoe UI", SegoeUI, Roboto, "Segoe WP", "Helvetica Neue", "Helvetica", "Tahoma", "Arial", sans-serif !important;
 82 |         background: #a1e2f7 !important; //background page content
 83 | }
 84 | 
 85 | // make non-headings slightly lighter
 86 | .post-content p, .post-content li {
 87 |    font-size: 20px;
 88 |    color: #515151;
 89 | }
 90 | 
 91 | .post-link{
 92 |     font-weight: normal;
 93 | }
 94 | 
 95 | // change padding of headings
 96 | h1 {
 97 |     margin-top:2.5rem !important;
 98 | }
 99 | 
100 | h2 {
101 |     margin-top:2rem !important;
102 | }
103 | 
104 | h3, h4 {
105 |     margin-top:1.5rem !important;
106 | }
107 | 
108 | p {
109 |     margin-top:1rem !important;
110 |     margin-bottom:1rem !important;
111 | }
112 | 
113 | h1, h2, h3, h4 {
114 |     font-weight: normal !important;
115 |     margin-bottom:0.5rem !important;
116 | }
117 | 
118 | pre {
119 |     margin-bottom:1.5rem !important;
120 | }
121 | 
122 | // make sure the post title doesn't have too much spacing
123 | .post-title { margin-top: .5rem !important; }
124 | 
125 | li {
126 |   h3, h4 {
127 |   margin-top:.05rem !important;
128 |   margin-bottom:.05rem !important;
129 |   }
130 |   .post-meta-description {
131 |     color: rgb(100, 100, 100); //88 88 88
132 |     font-size: 15px;
133 |     margin-top:.05rem !important;
134 |     margin-bottom:.05rem !important;
135 |   }
136 | }
137 | 
138 | /* Dracula Theme v1.2.5
139 |  *
140 |  * https://github.com/zenorocha/dracula-theme
141 |  *
142 |  * Copyright 2016, All rights reserved
143 |  *
144 |  * Code licensed under the MIT license
145 |  *
146 |  */
147 | 
148 |  /*
149 |   * Styles
150 |   */
151 | 
152 |  .highlight {
153 |    background: $dt-code-cell-background !important;
154 |    color: $dt-orange !important; //$dt-gray-light
155 |    pre, code {
156 |     background: $dt-code-cell-background;
157 |     color: $dt-yellow; //dt=$dt-gray-light
158 |    }
159 | 
160 |    .hll,
161 |    .s,
162 |    .sa,
163 |    .sb,
164 |    .sc,
165 |    .dl,
166 |    .sd,
167 |    .s2,
168 |    .se,
169 |    .sh,
170 |    .si,
171 |    .sx,
172 |    .sr,
173 |    .s1,
174 |    .ss {
175 |         color:rgb(255, 102, 153); // 231, 153, 122 for color betwween '' ""
176 |    }
177 | 
178 |    .go {
179 |      color: $dt-gray;
180 |    }
181 | 
182 |    .err,
183 |    .g,
184 |    .l,
185 |    .n,
186 |    .x,
187 |    .ge,
188 |    .gr,
189 |    .gh,
190 |    .gi,
191 |    .gp,
192 |    .gs,
193 |    .gu,
194 |    .gt,
195 |    .ld,
196 |    .no,
197 |    .nd,
198 |    .pi,
199 |    .ni,
200 |    .ne,
201 |    .nn,
202 |    .nx,
203 |    .py,
204 |    .w,
205 |    .bp {
206 |      color: $dt-gray-light;
207 |      background-color: $dt-code-cell-background !important;
208 |    }
209 | 
210 |    .p {
211 |         font-weight: bold;
212 |         color: rgb(51, 153, 255); //102 127 239 will color the color of the brackets [] ()
213 | }
214 | 
215 | //    .gh,
216 | //    .gi,
217 | //    .gu {
218 | //      font-weight: bold;
219 | //    }
220 | 
221 |    .ge {
222 |      text-decoration: underline;
223 |    }
224 | 
225 |    .bp {
226 |      font-style: italic;
227 |    }
228 | 
229 |    .c,
230 |    .ch,
231 |    .cm,
232 |    .cpf,
233 |    .c1,
234 |    .cs {
235 |      color: $dt-blue;
236 |    }
237 | 
238 |    .kd,
239 |    .kt,
240 |    .nb,
241 |    .nl,
242 |    .nv,
243 |    .vc,
244 |    .vg,
245 |    .vi,
246 |    .vm {
247 |      color: $dt-cyan;
248 |    }
249 | 
250 |    .kd,
251 |    .nb,
252 |    .nl,
253 |    .nv,
254 |    .vc,
255 |    .vg,
256 |    .vi,
257 |    .vm {
258 |      font-style: italic;
259 |    }
260 | 
261 |    .fm,
262 |    .na,
263 |    .nc,
264 |    .nf
265 |     {
266 |      color: $dt-green-light;
267 |    }
268 | 
269 |    .k,
270 |    .o,
271 |    .cp,
272 |    .kc,
273 |    .kn,
274 |    .kp,
275 |    .kr,
276 |    .nt,
277 |    .ow {
278 |      color: $dt-green; //prior dt-pink
279 |    }
280 | 
281 |    .kc {
282 |         color: $dt-green-light;
283 |    }
284 | 
285 |    .m,
286 |    .mb,
287 |    .mf,
288 |    .mh,
289 |    .mi,
290 |    .mo,
291 |    .il {
292 |      color: $dt-green; //prior dt-purple
293 |    }
294 | 
295 |    .gd {
296 |      color: $dt-red;
297 |    }
298 |  }
299 | 
300 | //  Code Folding
301 |  details.description[open] summary::after {
302 |   content: attr(data-open);
303 | }
304 | 
305 | details.description:not([open]) summary::after {
306 |   content: attr(data-close);
307 | }
308 | 
309 | // Notebook badges
310 | .notebook-badge-image {
311 |   border:0 !important;
312 | }
313 | 
314 | // Adjust font size for footnotes.
315 | .footnotes {
316 |   font-size: 12px !important;
317 |   p, li{
318 |     font-size: 12px !important;
319 |  }
320 | }
321 | 
322 | // Adjust with of social media icons were getting cut off
323 | .social-media-list{
324 |   .svg-icon {
325 |     width: 25px !important;
326 |     height: 23px !important;
327 |   }
328 | }
329 | 
330 | // Make Anchor Links Appear Only on Hover
331 | 
332 | .anchor-link {
333 |   opacity: 0;
334 |   padding-left: 0.375em;
335 |   \-webkit-text-stroke: 1.75px white;
336 |   \-webkit-transition: opacity 0.2s ease-in-out 0.1s;
337 |   \-moz-transition: opacity 0.2s ease-in-out 0.1s;
338 |   \-ms-transition: opacity 0.2s ease-in-out 0.1s;
339 | }
340 | 
341 | h1:hover .anchor-link,
342 | h2:hover .anchor-link,
343 | h3:hover .anchor-link,
344 | h4:hover .anchor-link,
345 | h5:hover .anchor-link,
346 | h6:hover .anchor-link {
347 |   opacity: 1;
348 | }
349 | 
350 | 
351 | // category tags
352 | .category-tags {
353 |   margin-top: .25rem !important;
354 |   margin-bottom: .25rem !important;
355 |   font-size: 105%;
356 | }
357 | 
358 | // Custom styling for homepage post previews
359 | .post-meta-title, .post-meta{
360 |   margin-top: .25em !important;
361 |   margin-bottom: .25em !important;
362 |   font-size: 105%;
363 | }
364 | 
365 | .page-description {
366 |   margin-top: .5rem !important;
367 |   margin-bottom: .5rem !important;
368 |   color: #585858;
369 |   font-size: 115%;
370 | }
371 | 
372 | // Custom styling for category tags
373 | .category-tags-icon {
374 |   font-size: 75% !important;
375 |   padding-left: 0.375em;
376 |   opacity: 35%;
377 | }
378 | .category-tags-link {
379 |   color:rgb(187, 129, 129) !important;
380 |   font-size: 13px !important;
381 | }
382 | 
383 | // Search Page Styles
384 | .js-search-results {padding-top: 0.2rem;}
385 | .search-results-list-item {padding-bottom: 1rem;}
386 | .search-results-list-item .search-result-title {
387 |   font-size: 16px;
388 |   color: #d9230f;
389 | }
390 | .search-result-rel-url {color: silver;}
391 | .search-results-list-item a {display: block; color: #777;}
392 | .search-results-list-item a:hover, .search-results-list-item a:focus {text-decoration: none;}
393 | .search-results-list-item a:hover .search-result-title {text-decoration: underline;}
394 | 
395 | .search-result-rel-date {
396 |   color: rgb(109, 120, 138);
397 |   font-size: 14px;
398 | }
399 | 
400 | .search-result-preview {
401 |   color: #777;
402 |   font-size: 16px;
403 |   margin-top:.02rem !important;
404 |   margin-bottom:.02rem !important;
405 | }
406 | .search-result-highlight {
407 |   color: #2e0137;
408 |   font-weight:bold;
409 | }
410 | 
411 | // Handle Overflow With Table Output
412 | 
413 | table {
414 |   display: block !important;
415 |   overflow-x: auto;
416 |   white-space: nowrap;
417 |   font-size: 75%;
418 |   border:none;
419 |   th{
420 |     text-align: center! important;
421 |   }
422 |   td{
423 |     text-overflow:ellipsis;
424 |     overflow:hidden;
425 |     max-width: 15em;
426 |   }
427 | }
428 | 
429 | // customize scrollbars
430 | ::-webkit-scrollbar {
431 |   width: 14px;
432 |   height: 18px;
433 | }
434 | ::-webkit-scrollbar-thumb {
435 |   height: 6px;
436 |   border: 4px solid rgba(0, 0, 0, 0);
437 |   background-clip: padding-box;
438 |   -webkit-border-radius: 7px;
439 |   background-color: #9D9D9D;
440 |   -webkit-box-shadow: inset -1px -1px 0px rgba(0, 0, 0, 0.05), inset 1px 1px 0px rgba(0, 0, 0, 0.05);
441 | }
442 | ::-webkit-scrollbar-button {
443 |   width: 0;
444 |   height: 0;
445 |   display: none;
446 | }
447 | ::-webkit-scrollbar-corner {
448 |   background-color: transparent;
449 | }
450 | 
451 | // Wrap text outputs instead of horizontal scroll
452 | .output_text.output_execute_result {
453 |   pre{
454 |     white-space: pre-wrap;
455 |   }
456 | }
457 | 


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/_word/README.md:
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 1 | # Automatically Convert MS Word (*.docx) Documents To Blog Posts
 2 | 
 3 | _Note: You can convert Google Docs to Word Docs by navigating to the File menu, and selecting Download > Microsoft Word (.docx)_
 4 | 
 5 | [`fastpages`](https://github.com/fastai/fastpages) will automatically convert Word Documents (.docx) saved into this directory as blog posts!.  Furthermore, images in your document are saved and displayed as you would expect on your blog post automatically.
 6 | 
 7 | ## Usage
 8 | 
 9 | 1. Create a Word Document (must be .docx) with the contents of your blog post.
10 | 
11 | 2. Save your file with the naming convention `YYYY-MM-DD-*.docx` into the `/_word` folder of this repo.  For example `2020-01-28-My-First-Post.docx`.  This [naming convention is required by Jekyll](https://jekyllrb.com/docs/posts/) to render your blog post.
12 |     - Be careful to name your file correctly!  It is easy to forget the last dash in `YYYY-MM-DD-`. Furthermore, the character immediately following the dash should only be an alphabetical letter.  Examples of valid filenames are:
13 | 
14 |         ```shell
15 |         2020-01-28-My-First-Post.docx
16 |         2012-09-12-how-to-write-a-blog.docx
17 |         ```
18 | 
19 |     - If you fail to name your file correctly, `fastpages` will automatically attempt to fix the problem by prepending the last modified date of your notebook to your generated blog post. However, it is recommended that you name your files properly yourself for more transparency.
20 | 
21 | 3. Synchronize your files with GitHub by [following the instructions in this blog post](https://www.fast.ai/2020/01/18/gitblog/).
22 | 


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/action.yml:
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 1 | name: 'fastpages: An easy to use blogging platform with support for Jupyter Notebooks.'
 2 | description: Converts Jupyter notebooks and Word docs into Jekyll blog posts.
 3 | author: Hamel Husain
 4 | inputs:
 5 |   BOOL_SAVE_MARKDOWN:
 6 |     description: Either 'true' or 'false'.  Whether or not to commit converted markdown files from notebooks and word documents into the _posts directory in your repo.  This is useful for debugging.
 7 |     required: false
 8 |     default: false
 9 |   SSH_DEPLOY_KEY:
10 |     description: a ssh deploy key is required if BOOL_SAVE_MARKDOWN = 'true'
11 |     required: false
12 | branding:
13 |   color: 'blue'
14 |   icon: 'book'
15 | runs:
16 |   using: 'docker'
17 |   image: '_action_files/Dockerfile'
18 | 


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/assets/badges/binder.svg:
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/assets/badges/colab.svg:
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1 | <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="117" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="117" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#555" d="M0 0h30v20H0z"/><path fill="#007ec6" d="M30 0h87v20H30z"/><path fill="url(#b)" d="M0 0h117v20H0z"/></g><g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"><svg x="4px" y="0px" width="22px" height="20px" viewBox="-2 0 28 24" style="background-color: #fff;border-radius: 1px;"><path style="fill:#ef9008;" d="M1.977,16.77c-2.667-2.277-2.605-7.079,0-9.357C2.919,8.057,3.522,9.075,4.49,9.691c-1.152,1.6-1.146,3.201-0.004,4.803C3.522,15.111,2.918,16.126,1.977,16.77z"/><path style="fill:#fdba18;" d="M12.257,17.114c-1.767-1.633-2.485-3.658-2.118-6.02c0.451-2.91,2.139-4.893,4.946-5.678c2.565-0.718,4.964-0.217,6.878,1.819c-0.884,0.743-1.707,1.547-2.434,2.446C18.488,8.827,17.319,8.435,16,8.856c-2.404,0.767-3.046,3.241-1.494,5.644c-0.241,0.275-0.493,0.541-0.721,0.826C13.295,15.939,12.511,16.3,12.257,17.114z"/><path style="fill:#ef9008;" d="M19.529,9.682c0.727-0.899,1.55-1.703,2.434-2.446c2.703,2.783,2.701,7.031-0.005,9.764c-2.648,2.674-6.936,2.725-9.701,0.115c0.254-0.814,1.038-1.175,1.528-1.788c0.228-0.285,0.48-0.552,0.721-0.826c1.053,0.916,2.254,1.268,3.6,0.83C20.502,14.551,21.151,11.927,19.529,9.682z"/><path style="fill:#fdba18;" d="M4.49,9.691C3.522,9.075,2.919,8.057,1.977,7.413c2.209-2.398,5.721-2.942,8.476-1.355c0.555,0.32,0.719,0.606,0.285,1.128c-0.157,0.188-0.258,0.422-0.391,0.631c-0.299,0.47-0.509,1.067-0.929,1.371C8.933,9.539,8.523,8.847,8.021,8.746C6.673,8.475,5.509,8.787,4.49,9.691z"/><path style="fill:#fdba18;" d="M1.977,16.77c0.941-0.644,1.545-1.659,2.509-2.277c1.373,1.152,2.85,1.433,4.45,0.499c0.332-0.194,0.503-0.088,0.673,0.19c0.386,0.635,0.753,1.285,1.181,1.89c0.34,0.48,0.222,0.715-0.253,1.006C7.84,19.73,4.205,19.188,1.977,16.77z"/></svg><text x="245" y="140" transform="scale(.1)" textLength="30"> </text><text x="725" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="770">Open in Colab</text><text x="725" y="140" transform="scale(.1)" textLength="770">Open in Colab</text></g> </svg>
2 | 


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/assets/badges/github.svg:
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1 | <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="122" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="122" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#2f363d" d="M0 0h25v20H0z"/><path fill="#586069" d="M25 0h97v20H25z"/><path fill="url(#b)" d="M0 0h122v20H0z"/></g><g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"><image x="5" y="3" width="14" height="14" xlink:href="data:image/svg+xml;base64,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"/> <text x="735" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="870">View On GitHub</text><text x="735" y="140" transform="scale(.1)" textLength="870">View On GitHub</text></g> </svg>


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/assets/js/search-data.json:
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 1 | ---
 2 | ---
 3 | {
 4 |   {% assign comma = false %}
 5 |   {%- assign date_format = site.minima.date_format | default: "%b %-d, %Y" -%}
 6 |   {% for post in site.posts %}
 7 |     {% if post.search_exclude != true %}
 8 |         {% if comma == true%},{% endif %}"post{{ forloop.index0 }}": {
 9 |             "title": "{{ post.title | replace: '&amp;', '&' }}",
10 |             "content": "{{ post.content | markdownify | replace: '</h', ' . </h' | replace: '<hr', ' . <hr' | replace: '</p', ' . </p' | replace: '</ul', ' . </ul' | replace: '</tr', ' . </tr' | replace: '</li', ' | </li' | replace: '</td', ' | </td' | strip_html | escape_once | remove: 'Table of contents' | remove: '```'  | remove: '---' | replace: '\', ' ' | replace: ' .  .  . ', ' . ' | replace: ' .  . ', ' . ' | normalize_whitespace }}",
11 |             "url": "{{ post.url | absolute_url }}",
12 |             "relUrl": "{{ post.url }}",
13 |             "date": " • {{ post.date | date: date_format }}"
14 |         }
15 |         {% assign comma = true %}
16 |     {% endif %}
17 |   {% endfor %}
18 | 
19 |   {% for page in site.pages %}
20 |   {% if page.url contains '.xml' or page.url contains 'assets'%}
21 |   {% elsif page.search_exclude != true %}
22 |       {% if comma == true%},{% endif %}"page{{ forloop.index0 }}": {
23 |           "title": "{{ page.title | replace: '&amp;', '&' }}",
24 |           "content": "{{ page.content | markdownify | replace: '</h', ' . </h' | replace: '<hr', ' . <hr' | replace: '</p', ' . </p' | replace: '</ul', ' . </ul' | replace: '</tr', ' . </tr' | replace: '</li', ' | </li' | replace: '</td', ' | </td' | strip_html | escape_once | remove: 'Table of contents' | remove: '```'  | remove: '---' | replace: '\', ' ' | replace: ' .  .  . ', ' . ' | replace: ' .  . ', ' . ' | normalize_whitespace }}",
25 |           "url": "{{ page.url | absolute_url }}",
26 |           "relUrl": "{{ page.url }}",
27 |           "date": ""
28 |       }
29 |       {% assign comma = true %}
30 |   {% endif %}
31 | {% endfor %}
32 | }


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/assets/js/search.js:
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  1 | ---
  2 | ---
  3 | // from https://github.com/pmarsceill/just-the-docs/blob/master/assets/js/just-the-docs.js#L47
  4 | 
  5 | (function (jtd, undefined) {
  6 | 
  7 | // Event handling
  8 | 
  9 | jtd.addEvent = function(el, type, handler) {
 10 |   if (el.attachEvent) el.attachEvent('on'+type, handler); else el.addEventListener(type, handler);
 11 | }
 12 | jtd.removeEvent = function(el, type, handler) {
 13 |   if (el.detachEvent) el.detachEvent('on'+type, handler); else el.removeEventListener(type, handler);
 14 | }
 15 | jtd.onReady = function(ready) {
 16 |   // in case the document is already rendered
 17 |   if (document.readyState!='loading') ready();
 18 |   // modern browsers
 19 |   else if (document.addEventListener) document.addEventListener('DOMContentLoaded', ready);
 20 |   // IE <= 8
 21 |   else document.attachEvent('onreadystatechange', function(){
 22 |       if (document.readyState=='complete') ready();
 23 |   });
 24 | }
 25 | 
 26 | // Show/hide mobile menu
 27 | 
 28 | // function initNav() {
 29 | //     const mainNav = document.querySelector('.js-main-nav');
 30 | //     const pageHeader = document.querySelector('.js-page-header');
 31 | //     const navTrigger = document.querySelector('.js-main-nav-trigger');
 32 |   
 33 | //     jtd.addEvent(navTrigger, 'click', function(e){
 34 | //       e.preventDefault();
 35 | //       var text = navTrigger.innerText;
 36 | //       var textToggle = navTrigger.getAttribute('data-text-toggle');
 37 |   
 38 | //       mainNav.classList.toggle('nav-open');
 39 | //       pageHeader.classList.toggle('nav-open');
 40 | //       navTrigger.classList.toggle('nav-open');
 41 | //       navTrigger.innerText = textToggle;
 42 | //       navTrigger.setAttribute('data-text-toggle', text);
 43 | //       textToggle = text;
 44 | //     })
 45 | //   }
 46 | 
 47 | 
 48 | // Site search
 49 | 
 50 | function initSearch() {
 51 |     var request = new XMLHttpRequest();
 52 |     request.open('GET', '{{ "assets/js/search-data.json" | relative_url }}', true);
 53 |   
 54 |     request.onload = function(){
 55 |       if (request.status >= 200 && request.status < 400) {
 56 |         // Success!
 57 |         var data = JSON.parse(request.responseText);
 58 |         
 59 |         {% if site.search_tokenizer_separator != nil %}
 60 |         lunr.tokenizer.separator = {{ site.search_tokenizer_separator }}
 61 |         {% else %}
 62 |         lunr.tokenizer.separator = /[\s\-/]+/
 63 |         {% endif %}
 64 |         
 65 |         var index = lunr(function () {
 66 |           this.ref('id');
 67 |           this.field('title', { boost: 200 });
 68 |           this.field('content', { boost: 2 });
 69 |           this.field('url');
 70 |           this.metadataWhitelist = ['position']
 71 |   
 72 |           for (var i in data) {
 73 |             this.add({
 74 |               id: i,
 75 |               title: data[i].title,
 76 |               content: data[i].content,
 77 |               url: data[i].url
 78 |             });
 79 |           }
 80 |         });
 81 |   
 82 |         searchResults(index, data);
 83 |       } else {
 84 |         // We reached our target server, but it returned an error
 85 |         console.log('Error loading ajax request. Request status:' + request.status);
 86 |       }
 87 |     };
 88 |   
 89 |     request.onerror = function(){
 90 |       // There was a connection error of some sort
 91 |       console.log('There was a connection error');
 92 |     };
 93 |   
 94 |     request.send();
 95 |   
 96 |     function searchResults(index, data) {
 97 |       var index = index;
 98 |       var docs = data;
 99 |       var searchInput = document.querySelector('.js-search-input');
100 |       var searchResults = document.querySelector('.js-search-results');
101 |   
102 |       function hideResults() {
103 |         searchResults.innerHTML = '';
104 |         searchResults.classList.remove('active');
105 |       }
106 |   
107 |       jtd.addEvent(searchInput, 'keydown', function(e){
108 |         switch (e.keyCode) {
109 |           case 38: // arrow up
110 |             e.preventDefault();
111 |             var active = document.querySelector('.search-result.active');
112 |             if (active) {
113 |               active.classList.remove('active');
114 |               if (active.parentElement.previousSibling) {
115 |                 var previous = active.parentElement.previousSibling.querySelector('.search-result');
116 |                 previous.classList.add('active');
117 |               }
118 |             }
119 |             return;
120 |           case 40: // arrow down
121 |             e.preventDefault();
122 |             var active = document.querySelector('.search-result.active');
123 |             if (active) {
124 |               if (active.parentElement.nextSibling) {
125 |                 var next = active.parentElement.nextSibling.querySelector('.search-result');
126 |                 active.classList.remove('active');
127 |                 next.classList.add('active');
128 |               }
129 |             } else {
130 |               var next = document.querySelector('.search-result');
131 |               if (next) {
132 |                 next.classList.add('active');
133 |               }
134 |             }
135 |             return;
136 |           case 13: // enter
137 |             e.preventDefault();
138 |             var active = document.querySelector('.search-result.active');
139 |             if (active) {
140 |               active.click();
141 |             } else {
142 |               var first = document.querySelector('.search-result');
143 |               if (first) {
144 |                 first.click();
145 |               }
146 |             }
147 |             return;
148 |         }
149 |       });
150 |   
151 |       jtd.addEvent(searchInput, 'keyup', function(e){
152 |         switch (e.keyCode) {
153 |           case 27: // When esc key is pressed, hide the results and clear the field
154 |             hideResults();
155 |             searchInput.value = '';
156 |             return;
157 |           case 38: // arrow up
158 |           case 40: // arrow down
159 |           case 13: // enter
160 |             e.preventDefault();
161 |             return;
162 |         }
163 |   
164 |         hideResults();
165 |   
166 |         var input = this.value;
167 |         if (input === '') {
168 |           return;
169 |         }
170 |   
171 |         var results = index.query(function (query) {
172 |           var tokens = lunr.tokenizer(input)
173 |           query.term(tokens, {
174 |             boost: 10
175 |           });
176 |           query.term(tokens, {
177 |             wildcard: lunr.Query.wildcard.TRAILING
178 |           });
179 |         });
180 |   
181 |         if (results.length > 0) {
182 |           searchResults.classList.add('active');
183 |           var resultsList = document.createElement('ul');
184 |           resultsList.classList.add('search-results-list');
185 |           searchResults.appendChild(resultsList);
186 |   
187 |           for (var i in results) {
188 |             var result = results[i];
189 |             var doc = docs[result.ref];
190 |   
191 |             var resultsListItem = document.createElement('li');
192 |             resultsListItem.classList.add('search-results-list-item');
193 |             resultsList.appendChild(resultsListItem);
194 |   
195 |             var resultLink = document.createElement('a');
196 |             resultLink.classList.add('search-result');
197 |             resultLink.setAttribute('href', doc.url);
198 |             resultsListItem.appendChild(resultLink);
199 |   
200 |             var resultTitle = document.createElement('div');
201 |             resultTitle.classList.add('search-result-title');
202 |             resultTitle.innerText = doc.title;
203 |             resultLink.appendChild(resultTitle);
204 |   
205 |             var resultRelUrl = document.createElement('span');
206 |             resultRelUrl.classList.add('search-result-rel-date');
207 |             resultRelUrl.innerText = doc.date;
208 |             resultTitle.appendChild(resultRelUrl);
209 |   
210 |             var metadata = result.matchData.metadata;
211 |             var contentFound = false;
212 |             for (var j in metadata) {
213 |               if (metadata[j].title) {
214 |                 var position = metadata[j].title.position[0];
215 |                 var start = position[0];
216 |                 var end = position[0] + position[1];
217 |                 resultTitle.innerHTML = doc.title.substring(0, start) + '<span class="search-result-highlight">' + doc.title.substring(start, end) + '</span>' + doc.title.substring(end, doc.title.length)+'<span class="search-result-rel-date">'+doc.date+'</span>';
218 |   
219 |               } else if (metadata[j].content && !contentFound) {
220 |                 contentFound = true;
221 |   
222 |                 var position = metadata[j].content.position[0];
223 |                 var start = position[0];
224 |                 var end = position[0] + position[1];
225 |                 var previewStart = start;
226 |                 var previewEnd = end;
227 |                 var ellipsesBefore = true;
228 |                 var ellipsesAfter = true;
229 |                 for (var k = 0; k < 3; k++) {
230 |                   var nextSpace = doc.content.lastIndexOf(' ', previewStart - 2);
231 |                   var nextDot = doc.content.lastIndexOf('.', previewStart - 2);
232 |                   if ((nextDot > 0) && (nextDot > nextSpace)) {
233 |                     previewStart = nextDot + 1;
234 |                     ellipsesBefore = false;
235 |                     break;
236 |                   }
237 |                   if (nextSpace < 0) {
238 |                     previewStart = 0;
239 |                     ellipsesBefore = false;
240 |                     break;
241 |                   }
242 |                   previewStart = nextSpace + 1;
243 |                 }
244 |                 for (var k = 0; k < 10; k++) {
245 |                   var nextSpace = doc.content.indexOf(' ', previewEnd + 1);
246 |                   var nextDot = doc.content.indexOf('.', previewEnd + 1);
247 |                   if ((nextDot > 0) && (nextDot < nextSpace)) {
248 |                     previewEnd = nextDot;
249 |                     ellipsesAfter = false;
250 |                     break;
251 |                   }
252 |                   if (nextSpace < 0) {
253 |                     previewEnd = doc.content.length;
254 |                     ellipsesAfter = false;
255 |                     break;
256 |                   }
257 |                   previewEnd = nextSpace;
258 |                 }
259 |                 var preview = doc.content.substring(previewStart, start);
260 |                 if (ellipsesBefore) {
261 |                   preview = '... ' + preview;
262 |                 }
263 |                 preview += '<span class="search-result-highlight">' + doc.content.substring(start, end) + '</span>';
264 |                 preview += doc.content.substring(end, previewEnd);
265 |                 if (ellipsesAfter) {
266 |                   preview += ' ...';
267 |                 }
268 |   
269 |                 var resultPreview = document.createElement('div');
270 |                 resultPreview.classList.add('search-result-preview');
271 |                 resultPreview.innerHTML = preview;
272 |                 resultLink.appendChild(resultPreview);
273 |               }
274 |             }
275 |           }
276 |         }
277 |       });
278 |   
279 |       // jtd.addEvent(searchInput, 'blur', function(){
280 |       //   setTimeout(function(){ hideResults() }, 300);
281 |       // });
282 |     }
283 |   }
284 |   
285 | //   function pageFocus() {
286 | //     var mainContent = document.querySelector('.js-main-content');
287 | //     mainContent.focus();
288 | //   }
289 |   
290 |   // Document ready
291 |   
292 |   jtd.onReady(function(){
293 |     // initNav();
294 |     // pageFocus();
295 |     if (typeof lunr !== 'undefined') {
296 |       initSearch();
297 |     }
298 |   });
299 |   
300 |   })(window.jtd = window.jtd || {});


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/docker-compose.yml:
--------------------------------------------------------------------------------
 1 | version: "3"
 2 | services:
 3 |   fastpages: &fastpages
 4 |     working_dir: /data
 5 |     environment:
 6 |         - INPUT_BOOL_SAVE_MARKDOWN=false
 7 |     build:
 8 |       context: ./_action_files
 9 |       dockerfile: ./Dockerfile
10 |     image: fastpages-dev
11 |     logging:
12 |       driver: json-file
13 |       options:
14 |         max-size: 50m
15 |     stdin_open: true
16 |     tty: true
17 |     volumes:
18 |       - .:/data/
19 | 
20 |   converter:
21 |     <<: *fastpages
22 |     command: /fastpages/action_entrypoint.sh
23 | 
24 |   watcher:
25 |     <<: *fastpages
26 |     command: watchmedo shell-command --command /fastpages/action_entrypoint.sh --pattern *.ipynb --recursive --drop
27 |     network_mode: host # for GitHub Codespaces https://github.com/features/codespaces/
28 | 
29 |   jekyll:
30 |     working_dir: /data
31 |     image: hamelsmu/fastpages-jekyll
32 |     restart: unless-stopped
33 |     ports:
34 |       - "4000:4000"
35 |     volumes:
36 |       - .:/data/
37 |     command: >
38 |      bash -c "gem install bundler
39 |      && jekyll serve --trace --strict_front_matter"
40 | 
41 | 


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/images/bb.PNG:
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https://raw.githubusercontent.com/asvcode/MedicalImaging/c615307dfca16f9c632dadf55572faa18f08d3ed/images/bb.PNG


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/images/chart-preview.png:
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https://raw.githubusercontent.com/asvcode/MedicalImaging/c615307dfca16f9c632dadf55572faa18f08d3ed/images/chart-preview.png


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/images/circle.PNG:
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/images/copied_from_nb/README.md:
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1 | <center><h1>Warning</h1></center>
2 | 
3 | Do not manually save images into this folder. This is used by GitHub Actions to automatically copy images.  Any images you save into this folder could be deleted at build time.


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/images/diagram.png:
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https://raw.githubusercontent.com/asvcode/MedicalImaging/c615307dfca16f9c632dadf55572faa18f08d3ed/images/diagram.png


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/images/dicom.PNG:
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https://raw.githubusercontent.com/asvcode/MedicalImaging/c615307dfca16f9c632dadf55572faa18f08d3ed/images/dicom.PNG


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/images/dicom_.PNG:
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https://raw.githubusercontent.com/asvcode/MedicalImaging/c615307dfca16f9c632dadf55572faa18f08d3ed/images/dicom_.PNG


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/images/dicom_wf.PNG:
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https://raw.githubusercontent.com/asvcode/MedicalImaging/c615307dfca16f9c632dadf55572faa18f08d3ed/images/dicom_wf.PNG


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/images/fastpages_posts/actions/actions_logo.png:
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https://raw.githubusercontent.com/asvcode/MedicalImaging/c615307dfca16f9c632dadf55572faa18f08d3ed/images/fastpages_posts/actions/actions_logo.png


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/images/fastpages_posts/actions/pr_1.png:
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https://raw.githubusercontent.com/asvcode/MedicalImaging/c615307dfca16f9c632dadf55572faa18f08d3ed/images/fastpages_posts/actions/pr_1.png


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/images/fastpages_posts/actions/pr_2.png:
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https://raw.githubusercontent.com/asvcode/MedicalImaging/c615307dfca16f9c632dadf55572faa18f08d3ed/images/fastpages_posts/actions/pr_2.png


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/index.html:
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 1 | ---
 2 | layout: home
 3 | search_exclude: true
 4 | ---
 5 | 
 6 | [![](https://img.shields.io/static/v1?label=View%20On%20Github&message=link&labelColor=2f363d&color=red&style=flat&logo=github&logoColor=959da5)](https://github.com/asvcode)
 7 | 
 8 | <!-- Place this tag where you want the button to render. -->
 9 | <a class="github-button" href="https://github.com/asvcode/MedicalImaging" data-color-scheme="no-preference: dark; light: dark; dark: dark;" data-icon="octicon-star" data-size="large" data-show-count="true" aria-label="Star asvcode/MedicalImaging on GitHub">Star</a>
10 | 
11 | <!-- Place this tag in your head or just before your close body tag. -->
12 | <script async defer src="https://buttons.github.io/buttons.js"></script>
13 | 
14 | Tutorials are listed at the bottom of the page
15 | 
16 | ### What are DICOMs?
17 | 
18 | **DICOM**(**D**igital **I**maging and **CO**mmunications in **M**edicine) is the de-facto standard that establishes rules that allow medical images(X-Ray, MRI, CT) and associated information to be exchanged between imaging equipment from different vendors, computers, and hospitals. The DICOM format provides a suitable means that meets [health infomation exchange](https://www.himss.org/interoperability-and-health-information-exchange) (HIE) standards for transmision of health related data among facilites and HL7 standards which is the messaging standard that enables clinical applications to exchange data.
19 | 
20 | <p align="center">
21 |   <img width="300" height="300" src="{{site.baseurl}}/images/dicom_wf.PNG">
22 | </p>
23 | 
24 | 
25 | DICOM files typically have a .dcm extension and provides a means of storing data in seperate **'tags'** such as patient information as well as image/pixel data. A DICOM file consists of a header and image data sets packed into a single file. The information within the header is organized as a constant and standardized series of tags. By extracting data from these tags one can access important information regarding the patient demographics, study parameters, etc
26 | 
27 | 16 bit DICOM images have values ranging from -32768 to 32768 while 8-bit greyscale images store values from 0 to 255. The value ranges in DICOM images are useful as they correlate with the [Hounsfield Scale](https://en.wikipedia.org/wiki/Hounsfield_scale) which is a quantitative scale for describing radiodensity
28 | 
29 | 
30 | <p align="center">
31 |   Parts of a DICOM
32 | </p>
33 | 
34 | 
35 | <p align="center">
36 |   <img width="208" height="388" src="{{site.baseurl}}/images/dicom_.PNG">
37 | </p>
38 | 
39 | ### Requirements
40 | 
41 | These tutorials are based on the most recent release of [fastai](https://github.com/fastai/fastai) which was officially released in August 2020 and hence will require
42 | installation of `fastai`
43 | 
44 | Also requires installing `pydicom`
45 | 
46 | - `pip install pydicom`
47 | 
48 | and `scikit-image`
49 | 
50 | - `pip install scikit-image`
51 | 
52 | and `kornia`
53 | 
54 | - `pip install kornia===0.2.0`
55 | 
56 | (there is a current incompatability with the lastest version of `kornia`.  Installing version `0.2.0` solves this issue
57 | 
58 | ### Using with Google Colab:
59 | 
60 | Click on the link below for an example of loading the dependancies on `Colab`
61 | 
62 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/12yzCUieRREEb535XVbPzSzjv_7YUuTeb?usp=sharing)
63 | 
64 | 
65 | # Posts
66 | 


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