├── envs └── environment.yml ├── notebooks ├── util.py └── Notebook_Template.ipynb ├── LICENSE ├── README.md └── .gitignore /envs/environment.yml: -------------------------------------------------------------------------------- 1 | name: analysis 2 | channels: 3 | - conda-forge 4 | - nodefaults 5 | dependencies: 6 | - bokeh 7 | - bottleneck 8 | -------------------------------------------------------------------------------- /notebooks/util.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | def some_calc(ds): 4 | """ 5 | Insert docstring here 6 | """ 7 | 8 | # Do some sort of calculation 9 | out = ds.some_variable * equation 10 | return out 11 | # ----------------------------------- 12 | # REMOVE ABOVE THIS LINE 13 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2021 National Center for Atmospheric Research 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /notebooks/Notebook_Template.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "# Sample Notebook\n", 8 | "\n", 9 | "Once you copy this repository, feel free to delete this notebook!" 10 | ] 11 | }, 12 | { 13 | "cell_type": "markdown", 14 | "metadata": {}, 15 | "source": [ 16 | "### Imports" 17 | ] 18 | }, 19 | { 20 | "cell_type": "code", 21 | "execution_count": null, 22 | "metadata": {}, 23 | "outputs": [], 24 | "source": [ 25 | "#Import something here\n", 26 | "import xarray as xr\n", 27 | "import matplotlib.pyplot as plt" 28 | ] 29 | }, 30 | { 31 | "cell_type": "markdown", 32 | "metadata": {}, 33 | "source": [ 34 | "### Data Ingest" 35 | ] 36 | }, 37 | { 38 | "cell_type": "code", 39 | "execution_count": null, 40 | "metadata": {}, 41 | "outputs": [], 42 | "source": [ 43 | "# Read in the data using xarray or some other package\n", 44 | "ds = xr.open_dataset('some_file.nc')" 45 | ] 46 | }, 47 | { 48 | "cell_type": "markdown", 49 | "metadata": {}, 50 | "source": [ 51 | "### Data Operation" 52 | ] 53 | }, 54 | { 55 | "cell_type": "code", 56 | "execution_count": null, 57 | "metadata": {}, 58 | "outputs": [], 59 | "source": [ 60 | "# Do some sort of calculation on the data\n", 61 | "some_calc = ds.temp * some_equation" 62 | ] 63 | }, 64 | { 65 | "cell_type": "markdown", 66 | "metadata": {}, 67 | "source": [ 68 | "### Data Visualization" 69 | ] 70 | }, 71 | { 72 | "cell_type": "code", 73 | "execution_count": null, 74 | "metadata": {}, 75 | "outputs": [], 76 | "source": [ 77 | "# Plot the data\n", 78 | "plt.plot(x, y)" 79 | ] 80 | } 81 | ], 82 | "metadata": { 83 | "kernelspec": { 84 | "display_name": "Python 3", 85 | "language": "python", 86 | "name": "python3" 87 | }, 88 | "language_info": { 89 | "codemirror_mode": { 90 | "name": "ipython", 91 | "version": 3 92 | }, 93 | "file_extension": ".py", 94 | "mimetype": "text/x-python", 95 | "name": "python", 96 | "nbconvert_exporter": "python", 97 | "pygments_lexer": "ipython3", 98 | "version": "3.8.5" 99 | } 100 | }, 101 | "nbformat": 4, 102 | "nbformat_minor": 4 103 | } 104 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # analysis_project_template 2 | This is a sample template meant to be used for workflows centered around notebooks 3 | 4 | ## Why you should use this template 5 | This template is meant to give you the basic setup of an "analysis" repository, focused on storing notebooks or other pieces of scientific code/documentation. This repository is not meant to be a "one size fits all" repository, but rather, a starting point from which the user can build upon. 6 | 7 | ## Essential checklist for your repository 8 | - [ ] Software license 9 | - [ ] Detailed readme 10 | - [ ] Update the environment.yml file in include the required libraries/packages 11 | - [ ] Your analysis code/notebooks! 12 | 13 | ## Choosing a license for this repository 14 | There are a variety of software licenses to choose from. The default for this 15 | repository is the [MIT License](https://opensource.org/licenses/MIT) which is short 16 | and to the point. If you are interested in learning more about which license is 17 | best for you, check out [this resource](https://choosealicense.com/) to help you 18 | determine which is best for your specific needs, or consult [UCAR Legal](https://internal.ucar.edu/counsel/about) 19 | 20 | ## What to include in your README (README.md) 21 | Once you copy over this template and choose your license, you should populate your README file. This file serves as a landing page for your repository and should provide the following: 22 | - Title of the project 23 | - Introduction and overview of what the analysis covers 24 | - How to contribute 25 | - How to reproduce the conda environment 26 | 27 | An example of this is given below 28 | ``` 29 | # Climate-Analysis 30 | This is a repository meant to show how to do climate analysis. 31 | 32 | ## Contributing 33 | Clone this repository to your account, then create your own branch to work in 34 | 35 | "git checkout -b " 36 | 37 | 38 | ## Reproducing the environment 39 | 40 | "conda env create -f envs/environment.yml" 41 | "conda activate environment_name" 42 | 43 | 44 | ``` 45 | 46 | ## The importance of software citation and minting a DOI 47 | Once your repository is built and you have added your analysis, you may want to mint a DOI for your project, so you can share your work with the community AND receive credit for doing so. 48 | 49 | Directions on how to mint a DOI for your project can be found on the [NCAR Software Citation Documentation](https://ncar.github.io/software-citation/pages/recommendation/mint-doi.html) 50 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | build/ 12 | develop-eggs/ 13 | dist/ 14 | downloads/ 15 | eggs/ 16 | .eggs/ 17 | lib/ 18 | lib64/ 19 | parts/ 20 | sdist/ 21 | var/ 22 | wheels/ 23 | pip-wheel-metadata/ 24 | share/python-wheels/ 25 | *.egg-info/ 26 | .installed.cfg 27 | *.egg 28 | MANIFEST 29 | 30 | # PyInstaller 31 | # Usually these files are written by a python script from a template 32 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 33 | *.manifest 34 | *.spec 35 | 36 | # Installer logs 37 | pip-log.txt 38 | pip-delete-this-directory.txt 39 | 40 | # Unit test / coverage reports 41 | htmlcov/ 42 | .tox/ 43 | .nox/ 44 | .coverage 45 | .coverage.* 46 | .cache 47 | nosetests.xml 48 | coverage.xml 49 | *.cover 50 | *.py,cover 51 | .hypothesis/ 52 | .pytest_cache/ 53 | 54 | # Translations 55 | *.mo 56 | *.pot 57 | 58 | # Django stuff: 59 | *.log 60 | local_settings.py 61 | db.sqlite3 62 | db.sqlite3-journal 63 | 64 | # Flask stuff: 65 | instance/ 66 | .webassets-cache 67 | 68 | # Scrapy stuff: 69 | .scrapy 70 | 71 | # Sphinx documentation 72 | docs/_build/ 73 | 74 | # PyBuilder 75 | target/ 76 | 77 | # Jupyter Notebook 78 | .ipynb_checkpoints 79 | 80 | # IPython 81 | profile_default/ 82 | ipython_config.py 83 | 84 | # pyenv 85 | .python-version 86 | 87 | # pipenv 88 | # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. 89 | # However, in case of collaboration, if having platform-specific dependencies or dependencies 90 | # having no cross-platform support, pipenv may install dependencies that don't work, or not 91 | # install all needed dependencies. 92 | #Pipfile.lock 93 | 94 | # PEP 582; used by e.g. github.com/David-OConnor/pyflow 95 | __pypackages__/ 96 | 97 | # Celery stuff 98 | celerybeat-schedule 99 | celerybeat.pid 100 | 101 | # SageMath parsed files 102 | *.sage.py 103 | 104 | # Environments 105 | .env 106 | .venv 107 | env/ 108 | venv/ 109 | ENV/ 110 | env.bak/ 111 | venv.bak/ 112 | 113 | # Spyder project settings 114 | .spyderproject 115 | .spyproject 116 | 117 | # Rope project settings 118 | .ropeproject 119 | 120 | # mkdocs documentation 121 | /site 122 | 123 | # mypy 124 | .mypy_cache/ 125 | .dmypy.json 126 | dmypy.json 127 | 128 | # Pyre type checker 129 | .pyre/ 130 | --------------------------------------------------------------------------------