diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 648639d..dc30e9e 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -49,6 +49,11 @@ jobs: run: | make + - name: Check for dead links + working-directory: book + run: | + make linkcheck + - name: Move built HTML book if: github.event_name == 'release' working-directory: book @@ -86,3 +91,4 @@ jobs: GITHUB_TOKEN: ${{ secrets.ACTIONS }} with: build_dir: book_output/ + diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml deleted file mode 100644 index c3af10e..0000000 --- a/.github/workflows/tests.yml +++ /dev/null @@ -1,44 +0,0 @@ -name: Tests - -on: - pull_request: - push: - branches: [main, next_release] - -jobs: - test: - name: Ubuntu - runs-on: ${{ matrix.os }} - strategy: - matrix: - python: [ 3.8 ] - os: [ ubuntu-20.04 ] - defaults: - run: - shell: bash - steps: - - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python }} - - name: Cancel Previous Runs - uses: styfle/cancel-workflow-action@0.6.0 - with: - access_token: ${{ secrets.GITHUB_TOKEN }} - - - name: Checkout - uses: actions/checkout@v2 - with: - submodules: true - - - name: Edit PATH - run: | - echo "$HOME/.local/bin" >> $GITHUB_PATH - - - name: Install pip dependencies - run: | - python -m pip install --user --upgrade setuptools wheel - python -m pip install --user -r requirements.txt - - - name: Run Python tests - run: | - python -m pytest tests diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..a73481c --- /dev/null +++ b/LICENSE @@ -0,0 +1,428 @@ +Attribution-ShareAlike 4.0 International + +======================================================================= + +Creative Commons Corporation ("Creative Commons") is not a law firm and +does not provide legal services or legal advice. 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Except for the limited purpose of indicating that +material is shared under a Creative Commons public license or as +otherwise permitted by the Creative Commons policies published at +creativecommons.org/policies, Creative Commons does not authorize the +use of the trademark "Creative Commons" or any other trademark or logo +of Creative Commons without its prior written consent including, +without limitation, in connection with any unauthorized modifications +to any of its public licenses or any other arrangements, +understandings, or agreements concerning use of licensed material. For +the avoidance of doubt, this paragraph does not form part of the +public licenses. + +Creative Commons may be contacted at creativecommons.org. + diff --git a/README.md b/README.md new file mode 100644 index 0000000..1800fd1 --- /dev/null +++ b/README.md @@ -0,0 +1,9 @@ +# README + +## License + +The license is [CC-BY-SA-4](https://creativecommons.org/licenses/by-sa/4.0/). + +Some of the code blocks have dependencies licensed as [GPL3](https://opensource.org/licenses/gpl-3.0.html). + +See [here](https://creativecommons.org/2015/10/08/cc-by-sa-4-0-now-one-way-compatible-with-gplv3/) for a statement on the compatibility of the `GPL` and Creative Commons licenses. diff --git a/book/Makefile b/book/Makefile index 62c3fc1..aa1a6ca 100644 --- a/book/Makefile +++ b/book/Makefile @@ -7,4 +7,8 @@ all: $(INDEX) clean: rm -rf _build +linkcheck: + jupyter-book build . --builder linkcheck + + $(INDEX): $(MDFILE) _config.yml _toc.yml build.sh references.bib diff --git a/book/_toc.yml b/book/_toc.yml index b6d612a..833da68 100644 --- a/book/_toc.yml +++ b/book/_toc.yml @@ -22,4 +22,8 @@ parts: - caption: Appendix chapters: - file: markdown/appendix/interactive.md + - file: markdown/appendix/holoviews_in_slides + - file: markdown/appendix/observable_in_slides + - file: markdown/appendix/python_dependencies + - file: markdown/appendix/acknowledgements - file: markdown/bibliography diff --git a/book/build.sh b/book/build.sh index 13302d2..cc84bd3 100644 --- a/book/build.sh +++ b/book/build.sh @@ -1,5 +1,5 @@ REPORTDIR=_build/html/reports -jupyter-book build -W . +jupyter-book build -n -W --keep-going . RV=$? if [ $RV -ne 0 ]; then diff --git a/book/intro.md b/book/intro.md index e10b99d..801bfb3 100644 --- a/book/intro.md +++ b/book/intro.md @@ -1 +1,32 @@ # Introduction + +This book is a collection of visualisations developed for teaching population genetics. +The goal is to create a collection of interactive content that can be remixed alongside existing course material. + +The icons near the top right of this page will take you to the `GitHub` repository for this book. + +## Technologies used + +* [Jupyter book](https://www.jupyterbook.org) +* [Observable](https://www.observablehq.com) notebooks. + These are pure JavaScript inserted into the book via [embedding](https://observablehq.com/@observablehq/introduction-to-embedding). +* [Holoviews](https://www.holoviews.org) creates interactive JavaScript applications that require Python. + These pages require [MyBinder](https://mybinder.readthedocs.io/) to function, which just takes a few mouse clicks!. + See {ref}`here ` for details. + +## Integrating the information into existing courses. + +* Direct links to the many of the pages "just work" in "learning management" systems such as [Canvas](https://www.instructure.com/canvas). + The exception is the pages requiring `MyBinder`. + These pages need to be launched in the binder, or... +* ...you can use them in slides as described {ref}`here `. +* The Observable content can also be used in slides. + See {ref}`here ` for instructions for `Jupyter` . + +## License + +The license is [CC-BY-SA-4](https://creativecommons.org/licenses/by-sa/4.0/). + +Some of the code blocks have dependencies licensed as [GPL3](https://opensource.org/licenses/gpl-3.0.html). + +See [here](https://creativecommons.org/2015/10/08/cc-by-sa-4-0-now-one-way-compatible-with-gplv3/) for a statement on the compatibility of the `GPL` and Creative Commons licenses. diff --git a/book/markdown/appendix/acknowledgements.md b/book/markdown/appendix/acknowledgements.md new file mode 100644 index 0000000..06f414e --- /dev/null +++ b/book/markdown/appendix/acknowledgements.md @@ -0,0 +1,5 @@ +# Acknowledgements + +* David Kirby, UCI +* Aaron Ragsdale, U. Wisconsin +* The `tskit` and `msprime` communities diff --git a/book/markdown/appendix/holoviews_in_slides.md b/book/markdown/appendix/holoviews_in_slides.md new file mode 100644 index 0000000..57d84c4 --- /dev/null +++ b/book/markdown/appendix/holoviews_in_slides.md @@ -0,0 +1,39 @@ +(interactive_python_in_slides)= + +# Using interactive Python applets in slideshow presentations + +It is possible to use the interactive Python applications in slideshows. +Doing this makes this content available for lectures, etc.. +You *do not* need internet access for the applets to function. + +You need the following tools, all of which can be installed using `pip`: + +* [jupyter](https://www.jupyter.org) notebook +* [RISE](https://rise.readthedocs.io/en/stable/) +* [hide_code](https://github.com/kirbs-/hide_code) + +We highly recommend using a `virtualenv` + +```{note} +The installation and setup instructions for `hide_code` did not "just work" for the author. +Each command needs a `--user` flag. + +`RISE` is not compatible with `jupyter-lab`. +You must use the classic notebook interface. +``` + +Once the above are installed, you can generate slides, hide the code, and the slide will contain a working applet. + +## Additional hints + +* You may want to redefine the `height` and `width` output of the plots in order to better fill the slides. + Doing so will cause the images to be far too big in the regular notebook view, but they will look good in the slide view. +* The pages of this book allow the Python code to be copied. + If you mouse over a code block, a "page" icon appears in the top right. + Click it, and the code block will be copied to your clip board. + This copy method is the simplest way to get the examples into your own slideshows. + +## Caveats and limitations + +* Using this type of content in lecture slides basically commits you to bringing your own laptop to class. + You need a fully-functional Python environment, etc., and you are unlikely to find such a thing on the ancient Windows PC at the podium in your classroom. diff --git a/book/markdown/appendix/observable_in_slides.md b/book/markdown/appendix/observable_in_slides.md new file mode 100644 index 0000000..8072473 --- /dev/null +++ b/book/markdown/appendix/observable_in_slides.md @@ -0,0 +1,29 @@ +(observable_in_slides)= + +# Using Observable content in Jupyter presentations + +You can display the observable content in Jupyter notebooks (and slideshows). +Note that you *do need* internet access for the content to display! + +The following Python code will display {ref}`this ` Observable widget in a Jupyter output cell: + +``` python +from IPython.core.display import display, HTML +script=""" + +""" +display(HTML(script)) +``` + +Using the tools described {ref}`here `, you can hide the Python code needed to display the applet. + +## Additional hints + +* The `iframe` code needed to embed the Observable content can be copied from the source code for this project. + Alternately, you can generate your own embed code manually from the [author's collection](https://www.observablehq.com/@molpopgen). + +## Limitations + +* The applications may be quite small in the slides. + We are currently not sure if there is a way to rescale them. diff --git a/book/markdown/appendix/python_dependencies.md b/book/markdown/appendix/python_dependencies.md new file mode 100644 index 0000000..bc666e1 --- /dev/null +++ b/book/markdown/appendix/python_dependencies.md @@ -0,0 +1,40 @@ +--- +jupytext: + formats: md:myst + text_representation: + extension: .md + format_name: myst +kernelspec: + display_name: Python 3 + language: python + name: python3 +--- + +# Python dependencies + +The Python requirements for this book are: + +```{code-cell} +--- +tags: ['remove-input'] +--- + +with open("../../../requirements.txt", "r") as f: + x = f.readlines() + print(''.join(x)) +``` + +The above list is defined in `requirements.txt` in the `GitHub` repository. + +The precise versions of all packages used to create this book are: + +```{code-cell} +--- +tags: ['remove-input'] +--- + +import subprocess + +lockfile = subprocess.run(["pip", "freeze"], stdout=subprocess.PIPE) +print(lockfile.stdout.decode('utf-8')) +``` diff --git a/book/markdown/classic_selection_drift/diploid_fixation.md b/book/markdown/classic_selection_drift/diploid_fixation.md index 688165f..3dff5a1 100644 --- a/book/markdown/classic_selection_drift/diploid_fixation.md +++ b/book/markdown/classic_selection_drift/diploid_fixation.md @@ -1,3 +1,5 @@ +(fixation_in_diploid_population)= + # Fixation in a diploid population