Add building notebooks and a github-page (#29)

* Test notebook building + deployment on gh-pages

* Fix branch name

* Make sure jupyter is installed

* Comment out change checks while testing

* Try setting the kernel name

* Update deployment version?

* test set up using deployment with pages and jekyll

* Avoid mkdir for docs

* Try setting the folder to deploy

* First attempt to link to built notebook and binder

* Bump python version now that casa works with >3.6

* Attempt to install without libgfortran3 in binder

* Initial working version of decent enough formatting per tutorial

* Move all logos to images

* Test executing multiple notebooks

* Previously working build now fails? Revert as a quick check

* Issue from the pipe for some reason?

* Skip matplotlib style for 2nd notebook build

* Remove old build

* Add casadata to requirements

* CASA's plotbandpass function calls a deprecated matplotlib warning. Pin to older version

* Causes other issues. Pin to last matplotlib version before warning was removed

* Copy all generated html files to the site

* Download the data for the Dame map in the notebook

* Ensure PV example from MAPS is still running and clear outputs

* Clear all outputs

* Add all notebooks to pages and build them

* Clear notebook outputs

* Missing import

* Add regions to requirements

* Add astroquery to requirements.txt

* Known issue with the reprojection tutorials. Ensure rest of builds work for now

* Fix copy cmd

.github/workflows/build_and_deploy_site.yml

@@ -0,0 +1,78 @@
+name: Github Pages
+
+on:
+ push:
+ branches:
+ - master
+ # paths:
+ # - 'spectral_fitting/*.ipynb'
+ # - '*.json'
+ # - '.github/**'
+
+jobs:
+ build:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+
+ - name: Set up python
+ id: setup-python
+ uses: actions/setup-python@v2
+ with:
+ python-version: '3.10'
+ cache: 'pip'
+
+ - name: Install requirements
+ run: pip install -r requirements.txt
+
+ - name: Export notebooks
+ run: |
+ JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert spectral_fitting/*.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
+ JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert casa_to_spectralcube_guide/*.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
+ JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert masking_and_moments/*.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
+ JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert parallel_spectral_fitting/*.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
+ JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert DameCube.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
+ JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert PVDiagramPlotting.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
+ JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert DiskPVExample.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
+ # JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert SpectralCubeReprojectExample.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
+ # JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert SpectralCubeReprojectMaskExample_v4p1.ipynb.ipynb --execute --to html --ExecutePreprocessor.kerne]l_name=python
+
+ - name: Prepare public folder
+ id: folder
+ run: |
+ cp spectral_fitting/*.html docs
+ cp casa_to_spectralcube_guide/*.html docs
+ cp masking_and_moments/*.html docs
+ cp parallel_spectral_fitting/*.html docs
+ cp *.html docs
+
+ - name: Build with Jekyll
+ uses: actions/jekyll-build-pages@v1
+ with:
+ source: docs
+ destination: docs/_site
+
+ - name: Setup Pages
+ id: pages
+ uses: actions/configure-pages@v3
+
+ - name: Upload artifact
+ uses: actions/upload-pages-artifact@v2
+ with:
+ path: docs
+
+ deploy:
+ permissions:
+ pages: write
+ id-token: write
+
+ environment:
+ name: github-pages
+ url: ${{ steps.deployment.outputs.page_url }}
+
+ runs-on: ubuntu-latest
+ needs: build
+ steps:
+ - name: Deploy to GitHub Pages
+ id: deployment
+ uses: actions/deploy-pages@v2

.jupyter/custom/custom.css

@@ -0,0 +1,14 @@
+/**
+For this file to be processed by jupyter,
+ensure you export JUPYTER_CONFIG_DIR, for example:
+ JUPYTER_CONFIG_DIR=jupyter jupyter nbconvert --to html
+ https://blog.derlin.ch/share-your-jupyter-notebooks-like-a-pro
+*/
+
+/** Make jupyter HTML export more responsive. */
+@media (max-width: 600px) {
+ .jp-InputPrompt.jp-InputArea-prompt,
+ .jp-OutputPrompt.jp-OutputArea-prompt {
+ display: none !important;
+ }
+}

PVDiagramPlotting.ipynb

@@ -531,9 +531,9 @@
  ],
  "metadata": {
  "kernelspec": {
- "display_name": "py39",
+ "display_name": "Python 3 (ipykernel)",
  "language": "python",
- "name": "py39"
+ "name": "python3"
  },
  "language_info": {
  "codemirror_mode": {
@@ -545,7 +545,7 @@
  "name": "python",
  "nbconvert_exporter": "python",
  "pygments_lexer": "ipython3",
- "version": "3.9.6"
+ "version": "3.8.10"
  }
  },
  "nbformat": 4,

SpectralCubeReprojectExample.ipynb

@@ -468,7 +468,11 @@
  "outputs": [],
  "source": [
  "import radio_beam\n",
- "common_beam = radio_beam.commonbeam.common_2beams(radio_beam.Beams(beams=[cube1vel.beam, cube2vel.beam]))\n",
+ "common_beam = cube1vel.beam.commonbeam_with(cube2vel.beam)\n",
+ "\n",
+ "# This works with older versions of radio-beam:\n",
+ "# common_beam = radio_beam.commonbeam.common_2beams(radio_beam.Beams(beams=[cube1vel.beam, cube2vel.beam]))\n",
+ "\n",
  "common_beam"
  ]
  },
@@ -618,9 +622,9 @@
  ],
  "metadata": {
  "kernelspec": {
- "display_name": "Py 3.9",
+ "display_name": "Python 3 (ipykernel)",
  "language": "python",
- "name": "python39"
+ "name": "python3"
  },
  "language_info": {
  "codemirror_mode": {
@@ -632,7 +636,7 @@
  "name": "python",
  "nbconvert_exporter": "python",
  "pygments_lexer": "ipython3",
- "version": "3.9.2"
+ "version": "3.8.10"
  }
  },
  "nbformat": 4,