test example in CI (new) (#579)

* test example CI * try to correct path * update * update test * add to tox * rename * fix tox * add to tox * update * update path * add kernel * fix deps * readd deps * add env * update * update ci * add submodules * add recursive * change command to build the docs * new name just to test CI * specify kernel * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove display name * rename kernel * fix tox env * use jupytext * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * print notebook name * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Arina Danilina <[email protected]> Co-authored-by: giovp <[email protected]> Co-authored-by: Giovanni Palla <[email protected]> Co-authored-by: Dominik Klein <[email protected]> Co-authored-by: selmanozleyen <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Selman Özleyen <[email protected]>
theislab · Mar 26, 2024 · d79c18c · d79c18c
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commit d79c18c
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diff --git a/.github/workflows/test-examples.yml b/.github/workflows/test-examples.yml
@@ -0,0 +1,41 @@
+name: Test examples
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: recursive
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install pip dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+      - name: Test examples
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          tox -e examples-docs
diff --git a/pyproject.toml b/pyproject.toml
@@ -282,7 +282,6 @@ commands =
 
 [testenv:lint-docs]
 description = Lint the documentation.
-deps =
 extras = docs
 ignore_errors = true
 allowlist_externals = make
@@ -294,6 +293,22 @@ commands =
     # TODO(michalk8): uncomment after https://github.com/theislab/moscot/issues/490
     # make spelling {posargs}
 
+[testenv:examples-docs]
+allowlist_externals = bash
+description = Run the notebooks.
+use_develop = true
+deps =
+    ipykernel
+    jupytext
+    nbconvert
+    leidenalg
+extras = docs
+changedir = {tox_root}{/}docs
+commands =
+    python -m ipykernel install --user --name=moscot
+    bash -c "for nb in notebooks/examples/plotting/*.ipynb notebooks/examples/problems/*ipynb notebooks/examples/solvers/*ipynb; do echo Running $nb; jupytext -k moscot --execute $nb; done"
+
+
 [testenv:clean-docs]
 description = Remove the documentation.
 deps =