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| Here is an extra conda environment, `bookbuilder`, that provides tools for executing the notebooks and assembling the html site using jupyter-book. They are kept separate from the notebook kernel for easier maintenance. | ||
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| Example steps for local use: | ||
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| 1. Create the environment from the lockfile: | ||
| ``` | ||
| conda create --name bookbuilder --file .bookbuilder/conda-linux-64.lock | ||
| ``` | ||
| 2. Configure the jupyter kernel for the existing `igrf` environment if necessary: | ||
| ``` | ||
| conda run --no-capture-output -n igrf python -m ipykernel install --user --name igrf | ||
| ``` | ||
| 3. Execute the notebooks against the `igrf` kernel: | ||
| ``` | ||
| conda run -n bookbuilder pytest --numprocesses auto --nbmake --overwrite --nbmake-kernel=igrf notebooks/*.ipynb | ||
| ``` | ||
| 4. Build the jupyter book: | ||
| ``` | ||
| conda run -n bookbuilder jupyter-book build . | ||
| ``` | ||
| Notes: | ||
| - jupyter-book is configured via `_config.yml` and `_toc.yml` | ||
| - We use pytest and the [nbmake plugin](https://github.com/treebeardtech/nbmake) to execute the notebooks first before running jupyter-book. This means that we can separate the steps for easier debugging (notebooks may fail to execute, or jupyter-book may fail to build). It also enables parallel execution for faster builds. | ||
| - `.github/workflows/publish.yml` configures the book building and push to github pages in CI | ||
| - Github settings are at https://github.com/IAGA-VMOD/IGRF14eval/settings/pages | ||
| - By default the site can only be published from the `main` branch. Alter the deployment protection rules in https://github.com/IAGA-VMOD/IGRF14eval/settings/environments to change this. |
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| # Generated by conda-lock. | ||
| # platform: linux-64 | ||
| # input_hash: 86adb8acb7c5102c87a8ac5d378f9de22ab7a870695e9f1a0208f7a315732beb | ||
| @EXPLICIT | ||
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| https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.21.1-pyhd8ed1ab_0.conda#8a3a3d01629da20befa340919e3dd2c4 | ||
| https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.6.0-pyhd8ed1ab_0.conda#6bd3f1069cdebb44c7ae9efb900e312d | ||
| https://conda.anaconda.org/conda-forge/linux-64/pybtex-docutils-1.0.3-py311h38be061_1.conda#137a63bd93d3e1a2b6812119b671f44e | ||
| https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.29.0-pyhd33586a_0.conda#10915bfa94b94f4ad0f347efd124a339 | ||
| https://conda.anaconda.org/conda-forge/noarch/nbformat-5.9.2-pyhd8ed1ab_0.conda#61ba076de6530d9301a0053b02f093d2 | ||
| https://conda.anaconda.org/conda-forge/noarch/nbclient-0.6.8-pyhd8ed1ab_0.tar.bz2#f052376c70c9d6a8e783e8e7c56b5f82 | ||
| https://conda.anaconda.org/conda-forge/noarch/jupyter-cache-0.6.1-pyhd8ed1ab_0.conda#2e360820ae68e3d28e1a5a9d2714ca5c | ||
| https://conda.anaconda.org/conda-forge/noarch/nbmake-1.4.6-pyhd8ed1ab_0.conda#3be14349b3fb2dfbf72baa59d8148e64 | ||
| https://conda.anaconda.org/conda-forge/noarch/myst-parser-0.18.1-pyhd8ed1ab_0.tar.bz2#bcfdf5c7d8bf5c6f6be7b4c66fff2eca | ||
| https://conda.anaconda.org/conda-forge/noarch/myst-nb-0.17.2-pyhd8ed1ab_0.conda#40190b7d06f86b63d28fa78aaa39c023 | ||
| https://conda.anaconda.org/conda-forge/noarch/pydata-sphinx-theme-0.15.2-pyhd8ed1ab_0.conda#ce99859070b0e17ccc63234ca58f3ed8 | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinx-book-theme-1.0.1-pyhd8ed1ab_0.conda#1ef419576de2c51b6e3a5a393eb35cda | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinx-comments-0.0.3-pyh9f0ad1d_0.tar.bz2#2ae3ce35de0c1cec45c94182694f8d1b | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinx-copybutton-0.5.2-pyhd8ed1ab_0.conda#ac832cc43adc79118cf6e23f1f9b8995 | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinx-design-0.3.0-pyhd8ed1ab_0.tar.bz2#83d1a712e6d2bab6b298b1d2f42ad355 | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinx-external-toc-0.3.1-pyhd8ed1ab_1.conda#d9a56bf4dce363e8e7e2466691668895 | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinx-jupyterbook-latex-0.5.2-pyhd8ed1ab_0.tar.bz2#88fc7863c8675f297b03e0ca50500b7f | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinx-multitoc-numbering-0.1.3-pyhd8ed1ab_0.tar.bz2#40749a4d0f0d2e11c65fb26c1cd16a90 | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinx-thebe-0.2.1-pyhd8ed1ab_0.conda#8a4151bde2af98c6cbc42ee12b48eb7f | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinx-togglebutton-0.3.2-pyhd8ed1ab_0.tar.bz2#382738101934261ea7931d1460e64868 | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-1.0.8-pyhd8ed1ab_0.conda#611a35a27914fac3aa37611a6fe40bb5 | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-bibtex-2.5.0-pyhd8ed1ab_0.tar.bz2#b2e5c9aece936ebf9f26abdf71ddd74b | ||
| https://conda.anaconda.org/conda-forge/noarch/jupyter-book-0.15.1-pyhd8ed1ab_0.conda#f10d556d3b3dc0aeae6aee37c412ea60 | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-1.0.6-pyhd8ed1ab_0.conda#d7e4954df0d3aea2eacc7835ad12671d | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.5-pyhd8ed1ab_0.conda#7e1e7437273682ada2ed5e9e9714b140 | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.7-pyhd8ed1ab_0.conda#26acae54b06f178681bfb551760f5dd1 | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinx-5.0.2-pyh6c4a22f_0.tar.bz2#d4eaa1f50733a377480ce1d5aac556c7 | ||
| https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_0.conda#e507335cb4ca9cff4c3d0fa9cdab255e |
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|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| name: bookbuilder | ||
| channels: | ||
| - conda-forge | ||
| dependencies: | ||
| - python=3.11 | ||
| - pip | ||
| - pytest | ||
| - pytest-xdist | ||
| - nbmake | ||
| - jupyter-book |
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|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| name: Build and Deploy GitHub Pages | ||
|
|
||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| workflow_dispatch: | ||
|
|
||
| jobs: | ||
| build: | ||
| name: Build Jupyter Book | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
| - name: Initialise conda | ||
| uses: conda-incubator/setup-miniconda@v3 | ||
| with: | ||
| auto-activate-base: true | ||
| - name: Setup conda environments from lock files | ||
| shell: bash -el {0} | ||
| run: | | ||
| conda create --name bookbuilder --file .bookbuilder/conda-linux-64.lock | ||
| conda create --name igrf --file binder/lockfiles/conda-linux-64.lock | ||
| conda run --no-capture-output -n igrf python -m ipykernel install --user --name igrf | ||
| - name: Execute notebooks against igrf python kernel | ||
| shell: bash -el {0} | ||
| run: | | ||
| conda run -n bookbuilder \ | ||
| pytest --numprocesses auto --nbmake --overwrite --nbmake-kernel=igrf notebooks/*.ipynb | ||
| - name: Build jupyter book | ||
| shell: bash -el {0} | ||
| run: conda run -n bookbuilder jupyter-book build . | ||
| - name: Upload artifact to pass to GitHub Pages | ||
| uses: actions/upload-pages-artifact@v3 | ||
| with: | ||
| path: _build/html | ||
| deploy: | ||
| name: Deploy to GitHub Pages | ||
| needs: build | ||
| # Grant GITHUB_TOKEN the permissions required to make a Pages deployment | ||
| permissions: | ||
| pages: write # to deploy to Pages | ||
| id-token: write # to verify the deployment originates from an appropriate source | ||
| # Deploy to the github-pages environment | ||
| environment: | ||
| name: github-pages | ||
| url: ${{ steps.deployment.outputs.page_url }} | ||
| # Specify runner + deployment step | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Deploy to GitHub Pages | ||
| id: deployment | ||
| uses: actions/deploy-pages@v4 |
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| # Book settings | ||
| # Learn more at https://jupyterbook.org/customize/config.html | ||
| title: IGRF-14 Evaluation | ||
| author: "IAGA V MOD" | ||
| logo: "" | ||
| only_build_toc_files: true | ||
|
|
||
| execute: | ||
| execute_notebooks: off | ||
|
|
||
| launch_buttons: | ||
| notebook_interface : jupyterlab | ||
| jupyterhub_url : "https://vre.vires.services" | ||
| binderhub_url : "https://mybinder.org" | ||
|
|
||
| repository: | ||
| url: https://github.com/IAGA-VMOD/IGRF14eval/ | ||
| branch: main |
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