🚇 Add pipeline to create PDFs from notebooks (#3)

Since we remove the output of notebooks before committing them
(`pre-commit`+`nbstripout` to reduce git cluttering) we can't directly
compare differences in plots. This PR adds a pipeline to run the
notebooks and generate PDFs from them so we can compare proposed changes
with the current state in an easier fashion.

See [this CI run on my
fork](https://github.com/s-weigand/pyglotaran-release-paper-supplementary-information/actions/runs/4276690589)
for a preview.

Note that the changes to the notebooks are caused by `papermill` running
the notebook which adds additional `tags` metadata to each cell and the
now required `id` field due to upgrading the `nbformat` version.

### Change summary

- [🔧 Remove papermill generated metadata from
notebook](dc722c4)
- [🧹 Add pdf build folder to
gitignore](a999ca8)
- [👌 Added custom template to avoid missing utf8 chars in code
cells](d21360e)
- [✨ Added script to build PDFs from
notebooks](b362ef8)
- [🔧 Added conda env
file](6288233)
- [🚇 Added pipeline to build
pdfs](1e4c7ab)
- [🩹 Added jpg to resource copy
pattern](aa02bc3)
- [🧹 Cleanup mention of master thesis is build
pipeline](626749d)
- [🧹 Notebooks after running them with papermill with added
metadata](1b2790c)

.github/workflows/build-pdfs.yml

@@ -0,0 +1,50 @@
+name: Build-PDFs
+
+on:
+  # For now commented out since private repositories only have a limited amount of CI time
+  # push:
+  # pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: 🚀 Compile PDFs ${{ matrix.case_study }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        case_study: [4TT, dPSI, rc]
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      - uses: actions/cache@v3
+        name: Tectonic Cache
+        with:
+          path: ~/.cache/Tectonic
+          key: ${{ runner.os }}-tectonic-${{ hashFiles('**/_preamble*.tex') }}
+          restore-keys: |
+            ${{ runner.os }}-tectonic-
+
+      - name: Install Conda environment with Micromamba
+        uses: mamba-org/provision-with-micromamba@v15
+        with:
+          cache-env: true
+
+      - name: Setup tectonic and biber
+        uses: wtfjoke/setup-tectonic@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          biber-version: "2.17"
+
+      - name: Run notebooks and build PDFs
+        run: |
+          python scripts/create_notebook_pdf.py ${{ matrix.case_study }}
+
+      - name: Upload PDFs
+        uses: actions/upload-artifact@v3
+        with:
+          name: pdfs
+          path: pdfs/*.pdf

.gitignore

@@ -138,3 +138,6 @@ guide/
 
 # Corrected 4TT data generate after the first analysis step
 4TT/data/corr4TT.ascii
+
+# Generated PDFs and tex source
+pdfs

.pre-commit-config.yaml

@@ -31,7 +31,7 @@ repos:
         args:
           - "--drop-empty-cells"
           - "--extra-keys"
-          - "metadata.vscode metadata.language_info.version"
+          - "metadata.vscode metadata.language_info.version cell.metadata.papermill metadata.papermill"
 
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.6.1