├── .gitignore ├── .vscode ├── tasks.json └── tasks │ ├── code-generation.sh │ ├── publish-pypi.sh │ └── publish-pypi.sh.j2 ├── LICENSE ├── README.md ├── devel └── zenodo_figure.html ├── doc ├── embedded_figure_protocol.md ├── intro.md └── intro_old.md ├── examples ├── altair_example.py ├── markdown_example.py ├── old │ ├── markdown_electron.py │ └── markdown_local.py ├── plotly_example.py └── report_example.py ├── figurl.png ├── figurl ├── __init__.py ├── cli.py ├── core │ ├── Figure.py │ ├── __init__.py │ └── serialize_wrapper.py ├── plugins │ ├── __init__.py │ └── builtin │ │ ├── __init__.py │ │ ├── altair │ │ ├── Altair.py │ │ └── __init__.py │ │ ├── markdown │ │ ├── Markdown.py │ │ └── __init__.py │ │ ├── plotly │ │ ├── Plotly.py │ │ └── __init__.py │ │ └── report │ │ ├── Report.py │ │ └── __init__.py ├── preserve │ ├── __init__.py │ ├── preserve.py │ └── templates │ │ └── index.html ├── version.py └── version.py.j2 ├── jinjaroot.yaml ├── setup.cfg ├── setup.cfg.j2 └── setup.py /.gitignore: -------------------------------------------------------------------------------- 1 | tmp 2 | dask-worker-space 3 | 4 | # Byte-compiled / optimized / DLL files 5 | __pycache__/ 6 | *.py[cod] 7 | *$py.class 8 | 9 | # C extensions 10 | *.so 11 | 12 | # Distribution / packaging 13 | .Python 14 | build/ 15 | develop-eggs/ 16 | dist/ 17 | downloads/ 18 | eggs/ 19 | .eggs/ 20 | lib/ 21 | lib64/ 22 | parts/ 23 | sdist/ 24 | var/ 25 | wheels/ 26 | pip-wheel-metadata/ 27 | share/python-wheels/ 28 | *.egg-info/ 29 | .installed.cfg 30 | *.egg 31 | MANIFEST 32 | 33 | # PyInstaller 34 | # Usually these files are written by a python script from a template 35 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 36 | *.manifest 37 | *.spec 38 | 39 | # Installer logs 40 | pip-log.txt 41 | pip-delete-this-directory.txt 42 | 43 | # Unit test / coverage reports 44 | htmlcov/ 45 | .tox/ 46 | .nox/ 47 | .coverage 48 | .coverage.* 49 | .cache 50 | nosetests.xml 51 | coverage.xml 52 | *.cover 53 | *.py,cover 54 | .hypothesis/ 55 | .pytest_cache/ 56 | 57 | # Translations 58 | *.mo 59 | *.pot 60 | 61 | # Django stuff: 62 | *.log 63 | local_settings.py 64 | db.sqlite3 65 | db.sqlite3-journal 66 | 67 | # Flask stuff: 68 | instance/ 69 | .webassets-cache 70 | 71 | # Scrapy stuff: 72 | .scrapy 73 | 74 | # Sphinx documentation 75 | docs/_build/ 76 | 77 | # PyBuilder 78 | target/ 79 | 80 | # Jupyter Notebook 81 | .ipynb_checkpoints 82 | 83 | # IPython 84 | profile_default/ 85 | ipython_config.py 86 | 87 | # pyenv 88 | .python-version 89 | 90 | # pipenv 91 | # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. 92 | # However, in case of collaboration, if having platform-specific dependencies or dependencies 93 | # having no cross-platform support, pipenv may install dependencies that don't work, or not 94 | # install all needed dependencies. 95 | #Pipfile.lock 96 | 97 | # PEP 582; used by e.g. github.com/David-OConnor/pyflow 98 | __pypackages__/ 99 | 100 | # Celery stuff 101 | celerybeat-schedule 102 | celerybeat.pid 103 | 104 | # SageMath parsed files 105 | *.sage.py 106 | 107 | # Environments 108 | .env 109 | .venv 110 | env/ 111 | venv/ 112 | ENV/ 113 | env.bak/ 114 | venv.bak/ 115 | 116 | # Spyder project settings 117 | .spyderproject 118 | .spyproject 119 | 120 | # Rope project settings 121 | .ropeproject 122 | 123 | # mkdocs documentation 124 | /site 125 | 126 | # mypy 127 | .mypy_cache/ 128 | .dmypy.json 129 | dmypy.json 130 | 131 | # Pyre type checker 132 | .pyre/ 133 | -------------------------------------------------------------------------------- /.vscode/tasks.json: -------------------------------------------------------------------------------- 1 | { 2 | // See https://go.microsoft.com/fwlink/?LinkId=733558 3 | // for the documentation about the tasks.json format 4 | // The "bash -ic" is needed here so that our ~/.bashrc gets sourced. See: https://github.com/microsoft/vscode/issues/29412 5 | "version": "2.0.0", 6 | "tasks": [ 7 | { 8 | "label": "Code generation", 9 | "type": "shell", 10 | "command": "bash -ic .vscode/tasks/code-generation.sh", 11 | "presentation": { 12 | "clear": true 13 | }, 14 | "detail": "Run code generation" 15 | }, 16 | { 17 | "label": "Publish PyPI", 18 | "type": "shell", 19 | "command": "bash -ic .vscode/tasks/publish-pypi.sh", 20 | "presentation": { 21 | "clear": true 22 | }, 23 | "detail": "Publish package to PyPI" 24 | } 25 | ] 26 | } -------------------------------------------------------------------------------- /.vscode/tasks/code-generation.sh: -------------------------------------------------------------------------------- 1 | set -ex 2 | 3 | jinjaroot generate 4 | # exec .vscode/tasks/create_gen_ts_files.py -------------------------------------------------------------------------------- /.vscode/tasks/publish-pypi.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # This file was automatically generated by jinjaroot. Do not edit directly. 3 | 4 | 5 | set -e 6 | 7 | # check that we have a clean working directory 8 | if [ -z "$(git status --porcelain)" ]; then 9 | echo "Working directory is clean" 10 | else 11 | echo "Working directory is not clean (use git status)" 12 | exit 1 13 | fi 14 | 15 | # verify that code generation is up-to-date (if not throws an error) 16 | jinjaroot verify 17 | 18 | # run pre-publish-tasks.sh 19 | # .vscode/tasks/pre-publish-tasks.sh 20 | 21 | cd . 22 | 23 | # remove the dist folder 24 | rm -rf dist 25 | # create the package for dist 26 | python setup.py sdist 27 | # Show size of dist 28 | du -sh dist 29 | 30 | pip install -e . 31 | 32 | # Confirm publish 33 | while true; do 34 | read -p "Publish version (y/n)?" yn 35 | case $yn in 36 | [Yy]* ) break;; 37 | [Nn]* ) echo "aborting"; exit;; 38 | * ) echo "Please answer yes or no.";; 39 | esac 40 | done 41 | 42 | 43 | # upload the package to pypi 44 | twine upload ./dist/* 45 | 46 | # Tag this commit 47 | git tag v0.3.0a1 48 | 49 | echo "Tagged as v0.3.0a1" -------------------------------------------------------------------------------- /.vscode/tasks/publish-pypi.sh.j2: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | set -e 4 | 5 | # check that we have a clean working directory 6 | if [ -z "$(git status --porcelain)" ]; then 7 | echo "Working directory is clean" 8 | else 9 | echo "Working directory is not clean (use git status)" 10 | exit 1 11 | fi 12 | 13 | # verify that code generation is up-to-date (if not throws an error) 14 | jinjaroot verify 15 | 16 | # run pre-publish-tasks.sh 17 | # .vscode/tasks/pre-publish-tasks.sh 18 | 19 | cd {{ pythonPackageDir }} 20 | 21 | # remove the dist folder 22 | rm -rf dist 23 | # create the package for dist 24 | python setup.py sdist 25 | # Show size of dist 26 | du -sh dist 27 | 28 | pip install -e . 29 | 30 | # Confirm publish 31 | while true; do 32 | read -p "Publish version {{ projectVersion }} (y/n)?" yn 33 | case $yn in 34 | [Yy]* ) break;; 35 | [Nn]* ) echo "aborting"; exit;; 36 | * ) echo "Please answer yes or no.";; 37 | esac 38 | done 39 | 40 | 41 | # upload the package to pypi 42 | twine upload ./dist/* 43 | 44 | # Tag this commit 45 | git tag v{{ pythonProjectVersion }} 46 | 47 | echo "Tagged as v{{ pythonProjectVersion }}" -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Apache License 2 | Version 2.0, January 2004 3 | http://www.apache.org/licenses/ 4 | 5 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 6 | 7 | 1. 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We also recommend that a 185 | file or class name and description of purpose be included on the 186 | same "printed page" as the copyright notice for easier 187 | identification within third-party archives. 188 | 189 | Copyright [yyyy] [name of copyright owner] 190 | 191 | Licensed under the Apache License, Version 2.0 (the "License"); 192 | you may not use this file except in compliance with the License. 193 | You may obtain a copy of the License at 194 | 195 | http://www.apache.org/licenses/LICENSE-2.0 196 | 197 | Unless required by applicable law or agreed to in writing, software 198 | distributed under the License is distributed on an "AS IS" BASIS, 199 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 200 | See the License for the specific language governing permissions and 201 | limitations under the License. 202 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | 3 | # figurl 4 | 5 | Figurl is a framework for creating browser-based, shareable, interactive views of scientific datasets in the cloud. It is designed to be used in collaborative environments, such as scientific research teams, and is built on top of [Kachery cloud](https://github.com/flatironinstitute/kachery-cloud). 6 | 7 | [Introduction to Figurl](./doc/intro.md) 8 | 9 | [Gallery of examples](https://magland.github.io/figurl-gallery-viewer/) 10 | 11 | > This package is intended for collaborative sharing of data for scientific research. It should not be used for other purposes. At this point, uploaded files are not guaranteed to be available for ever. Contact us if you are interested storing files using your own cloud resources. 12 | 13 | ## Installation and setup 14 | 15 | > Note: most of the time, you will be using a different Python package that includes figurl as a dependency. But you can also install figurl directly and use the basic static functionality (Altair charts, markdown documents, reports). 16 | 17 | It is recommended that you use a conda environment with Python >= 3.8 and numpy. 18 | 19 | ```bash 20 | pip install --upgrade figurl 21 | ``` 22 | 23 | Configure your [kachery-cloud](https://github.com/flatironinstitute/kachery-cloud) client 24 | 25 | ```bash 26 | kachery-cloud-init 27 | # follow the instructions to associate your client with your GitHub user name on kachery-cloud 28 | ``` 29 | 30 | ## Static examples 31 | 32 | To test the system, try running the scripts in the [examples/](./examples/) folder. Here are the example (static) figures: 33 | 34 | * [Altair chart](https://figurl.org/f?v=gs://figurl/vegalite-2&d=sha1://0369af9f1a54a5a410f99e63cb08b6b899d1c92f&label=stocks%20chart) 35 | * [Markdown document](https://figurl.org/f?v=gs://figurl/markdown-1&d=sha1://9fe1d643f883e1676f70082b679c8a825b879041&label=Example%20markdown) 36 | * [Report](https://figurl.org/f?v=gs://figurl/figurl-report&d=sha1://e0f267258f432adcb89c5379c4136c3f00fbce78&label=Example%20report) 37 | 38 | Each of these links pair a visualization plugin (`v` query parameter) with a piece of data (`d` query parameter). For example, the Altair chart figURL: 39 | 40 | https://figurl.org/f?v=gs://figurl/vegalite-2&d=sha1://0369af9f1a54a5a410f99e63cb08b6b899d1c92f&label=stocks%20chart 41 | 42 | ## Interactive examples 43 | 44 | For examples of interactive figures, see [intro to Figurl](./doc/intro.md). 45 | 46 | ## How it works 47 | 48 | ![image](https://user-images.githubusercontent.com/3679296/201342587-b1af33bd-ac2b-4f9f-9cfa-3a0c0ce6d23b.png) 49 | 50 | * Python script assembles the data and figure specifications. 51 | * Data are uploaded to a content-addressable storage database in the cloud ([Kachery](https://github.com/flatironinstitute/kachery-cloud)). 52 | * Python script generates a URL that pairs a visualization plugin (hosted in a cloud storage bucket) and the uploaded data. 53 | * The shareable URL takes the user to figurl.org where the data is downloaded and sent to the visualization plugin for display. 54 | 55 | ## Cloud storage 56 | 57 | By default, your data files will be stored using our cloud resources, and they are not guaranteed to be available forever. You can also configure figurl to use your own resources by [creating a Kachery zone](https://github.com/flatironinstitute/kachery-cloud/blob/main/doc/create_kachery_zone.md). 58 | 59 | ## Contributing 60 | 61 | * Star us on GitHub 62 | * Provide feedback 63 | * Contact us if you would like to help develop and maintain this open source project 64 | 65 | ## For developers 66 | 67 | [Embedded figure protocol](./doc/embedded_figure_protocol.md) 68 | 69 | ## Authors 70 | 71 | Jeremy Magland and Jeff Soules, [Center for Computational Mathematics, Flatiron Institute](https://www.simonsfoundation.org/flatiron/center-for-computational-mathematics) 72 | 73 | ## License 74 | 75 | Apache 2.0 76 | -------------------------------------------------------------------------------- /devel/zenodo_figure.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Figurl zenodo example 5 | 212 | 277 | 278 | 279 | 286 | 287 | -------------------------------------------------------------------------------- /doc/embedded_figure_protocol.md: -------------------------------------------------------------------------------- 1 | # Embedded figure protocol (v1) 2 | 3 | The figURL is of the form 4 | 5 | ```html 6 | https://figurl.org/f?v=&d=&label=