ci: run notebooks with pytest

ComPWA · May 7, 2021 · 982aa21 · 982aa21
1 parent f0cbcaa
commit 982aa21
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Showing 8 changed files with 67 additions and 44 deletions.
diff --git a/.constraints/py3.6.txt b/.constraints/py3.6.txt
@@ -19,7 +19,7 @@ attrs==20.3.0
 babel==2.9.1
 backcall==0.2.0
 beautifulsoup4==4.9.3
-black==21.4b2
+black==21.5b0
 bleach==3.3.0
 cachetools==4.2.2
 certifi==2020.12.5
@@ -46,10 +46,10 @@ flake8-blind-except==0.2.0
 flake8-bugbear==21.4.3
 flake8-builtins==1.5.3
 flake8-comprehensions==3.4.0
-flake8-plugin-utils==1.3.1
+flake8-plugin-utils==1.3.2
 flake8-polyfill==1.0.2
 flake8-pytest-style==1.4.1
-flake8-rst-docstrings==0.2.2
+flake8-rst-docstrings==0.2.3
 flake8-use-fstring==1.1
 flake8==3.9.1
 flatbuffers==1.12
@@ -73,12 +73,12 @@ immutables==0.15
 importlib-metadata==4.0.1
 importlib-resources==3.0.0
 iniconfig==1.1.1
-ipykernel==5.5.3
+ipykernel==5.5.4
 ipython-genutils==0.2.0
 ipython==7.16.1
 ipywidgets==7.6.3
 isort==5.8.0
-jax==0.2.12
+jax==0.2.13
 jaxlib==0.1.65
 jedi==0.18.0
 jinja2==2.11.3
@@ -88,7 +88,7 @@ jupyter-cache==0.4.2
 jupyter-client==6.1.12
 jupyter-console==6.4.0
 jupyter-core==4.7.1
-jupyter-packaging==0.9.2
+jupyter-packaging==0.10.1
 jupyter-server-mathjax==0.2.2
 jupyter-server==1.6.4
 jupyter-sphinx==0.3.2
@@ -143,7 +143,7 @@ pluggy==0.13.1
 pre-commit==2.12.1
 prometheus-client==0.10.1
 prompt-toolkit==3.0.18
-protobuf==3.15.8
+protobuf==3.16.0
 ptyprocess==0.7.0
 py==1.10.0
 pyasn1-modules==0.2.8
@@ -153,16 +153,17 @@ pycparser==2.20
 pydata-sphinx-theme==0.6.3
 pydocstyle==6.0.0
 pyflakes==2.3.1
-pygments==2.8.1
+pygments==2.9.0
 pylint==2.8.2
 pyparsing==2.4.7
 pyrsistent==0.17.3
 pytest-cov==2.11.1
 pytest-forked==1.3.0
-pytest-mock==3.6.0
+pytest-mock==3.6.1
+pytest-notebook==0.6.1
 pytest-profiling==1.7.0
 pytest-xdist==2.2.1
-pytest==6.2.3
+pytest==6.2.4
 python-constraint==1.4.0
 python-dateutil==2.8.1
 pytz==2021.1
@@ -199,7 +200,7 @@ sphinxcontrib-serializinghtml==1.1.4
 sphobjinv==2.1
 sqlalchemy==1.3.24
 sympy==1.8
-tensorboard-data-server==0.6.0
+tensorboard-data-server==0.6.1
 tensorboard-plugin-wit==1.8.0
 tensorboard==2.5.0
 tensorflow-estimator==2.4.0
@@ -211,13 +212,13 @@ testpath==0.4.4
 toml==0.10.2
 tomlkit==0.7.0
 tornado==6.1
-tox==3.23.0
+tox==3.23.1
 tqdm==4.60.0
 traitlets==4.3.3
 typed-ast==1.4.3
 typing-extensions==3.7.4.3 ; python_version < "3.8.0"
 urllib3==1.26.4
-virtualenv==20.4.4
+virtualenv==20.4.6
 wcwidth==0.2.5
 webencodings==0.5.1
 werkzeug==1.0.1

diff --git a/.constraints/py3.7.txt b/.constraints/py3.7.txt
@@ -19,7 +19,7 @@ attrs==20.3.0
 babel==2.9.1
 backcall==0.2.0
 beautifulsoup4==4.9.3
-black==21.4b2
+black==21.5b0
 bleach==3.3.0
 cachetools==4.2.2
 certifi==2020.12.5
@@ -44,10 +44,10 @@ flake8-blind-except==0.2.0
 flake8-bugbear==21.4.3
 flake8-builtins==1.5.3
 flake8-comprehensions==3.4.0
-flake8-plugin-utils==1.3.1
+flake8-plugin-utils==1.3.2
 flake8-polyfill==1.0.2
 flake8-pytest-style==1.4.1
-flake8-rst-docstrings==0.2.2
+flake8-rst-docstrings==0.2.3
 flake8-use-fstring==1.1
 flake8==3.9.1
 flatbuffers==1.12
@@ -68,13 +68,14 @@ idna==2.10
 imagesize==1.2.0
 iminuit==2.6.0
 importlib-metadata==4.0.1
+importlib-resources==5.1.2
 iniconfig==1.1.1
-ipykernel==5.5.3
+ipykernel==5.5.4
 ipython-genutils==0.2.0
-ipython==7.23.0
+ipython==7.23.1
 ipywidgets==7.6.3
 isort==5.8.0
-jax==0.2.12
+jax==0.2.13
 jaxlib==0.1.65
 jedi==0.18.0
 jinja2==2.11.3
@@ -84,7 +85,7 @@ jupyter-cache==0.4.2
 jupyter-client==6.1.12
 jupyter-console==6.4.0
 jupyter-core==4.7.1
-jupyter-packaging==0.9.2
+jupyter-packaging==0.10.1
 jupyter-server-mathjax==0.2.2
 jupyter-server==1.6.4
 jupyter-sphinx==0.3.2
@@ -140,7 +141,7 @@ pluggy==0.13.1
 pre-commit==2.12.1
 prometheus-client==0.10.1
 prompt-toolkit==3.0.18
-protobuf==3.15.8
+protobuf==3.16.0
 ptyprocess==0.7.0
 py==1.10.0
 pyasn1-modules==0.2.8
@@ -150,16 +151,17 @@ pycparser==2.20
 pydata-sphinx-theme==0.6.3
 pydocstyle==6.0.0
 pyflakes==2.3.1
-pygments==2.8.1
+pygments==2.9.0
 pylint==2.8.2
 pyparsing==2.4.7
 pyrsistent==0.17.3
 pytest-cov==2.11.1
 pytest-forked==1.3.0
-pytest-mock==3.6.0
+pytest-mock==3.6.1
+pytest-notebook==0.6.1
 pytest-profiling==1.7.0
 pytest-xdist==2.2.1
-pytest==6.2.3
+pytest==6.2.4
 python-constraint==1.4.0
 python-dateutil==2.8.1
 pytz==2021.1
@@ -196,7 +198,7 @@ sphinxcontrib-serializinghtml==1.1.4
 sphobjinv==2.1
 sqlalchemy==1.3.24
 sympy==1.8
-tensorboard-data-server==0.6.0
+tensorboard-data-server==0.6.1
 tensorboard-plugin-wit==1.8.0
 tensorboard==2.5.0
 tensorflow-estimator==2.4.0
@@ -208,13 +210,13 @@ testpath==0.4.4
 toml==0.10.2
 tomlkit==0.7.0
 tornado==6.1
-tox==3.23.0
+tox==3.23.1
 tqdm==4.60.0
 traitlets==5.0.5
 typed-ast==1.4.3
 typing-extensions==3.7.4.3 ; python_version < "3.8.0"
 urllib3==1.26.4
-virtualenv==20.4.4
+virtualenv==20.4.6
 wcwidth==0.2.5
 webencodings==0.5.1
 werkzeug==1.0.1

diff --git a/.constraints/py3.8.txt b/.constraints/py3.8.txt
@@ -19,7 +19,7 @@ attrs==20.3.0
 babel==2.9.1
 backcall==0.2.0
 beautifulsoup4==4.9.3
-black==21.4b2
+black==21.5b0
 bleach==3.3.0
 cachetools==4.2.2
 certifi==2020.12.5
@@ -44,10 +44,10 @@ flake8-blind-except==0.2.0
 flake8-bugbear==21.4.3
 flake8-builtins==1.5.3
 flake8-comprehensions==3.4.0
-flake8-plugin-utils==1.3.1
+flake8-plugin-utils==1.3.2
 flake8-polyfill==1.0.2
 flake8-pytest-style==1.4.1
-flake8-rst-docstrings==0.2.2
+flake8-rst-docstrings==0.2.3
 flake8-use-fstring==1.1
 flake8==3.9.1
 flatbuffers==1.12
@@ -68,13 +68,14 @@ idna==2.10
 imagesize==1.2.0
 iminuit==2.6.0
 importlib-metadata==4.0.1
+importlib-resources==5.1.2
 iniconfig==1.1.1
-ipykernel==5.5.3
+ipykernel==5.5.4
 ipython-genutils==0.2.0
-ipython==7.23.0
+ipython==7.23.1
 ipywidgets==7.6.3
 isort==5.8.0
-jax==0.2.12
+jax==0.2.13
 jaxlib==0.1.65
 jedi==0.18.0
 jinja2==2.11.3
@@ -84,7 +85,7 @@ jupyter-cache==0.4.2
 jupyter-client==6.1.12
 jupyter-console==6.4.0
 jupyter-core==4.7.1
-jupyter-packaging==0.9.2
+jupyter-packaging==0.10.1
 jupyter-server-mathjax==0.2.2
 jupyter-server==1.6.4
 jupyter-sphinx==0.3.2
@@ -140,7 +141,7 @@ pluggy==0.13.1
 pre-commit==2.12.1
 prometheus-client==0.10.1
 prompt-toolkit==3.0.18
-protobuf==3.15.8
+protobuf==3.16.0
 ptyprocess==0.7.0
 py==1.10.0
 pyasn1-modules==0.2.8
@@ -150,16 +151,17 @@ pycparser==2.20
 pydata-sphinx-theme==0.6.3
 pydocstyle==6.0.0
 pyflakes==2.3.1
-pygments==2.8.1
+pygments==2.9.0
 pylint==2.8.2
 pyparsing==2.4.7
 pyrsistent==0.17.3
 pytest-cov==2.11.1
 pytest-forked==1.3.0
-pytest-mock==3.6.0
+pytest-mock==3.6.1
+pytest-notebook==0.6.1
 pytest-profiling==1.7.0
 pytest-xdist==2.2.1
-pytest==6.2.3
+pytest==6.2.4
 python-constraint==1.4.0
 python-dateutil==2.8.1
 pytz==2021.1
@@ -196,7 +198,7 @@ sphinxcontrib-serializinghtml==1.1.4
 sphobjinv==2.1
 sqlalchemy==1.3.24
 sympy==1.8
-tensorboard-data-server==0.6.0
+tensorboard-data-server==0.6.1
 tensorboard-plugin-wit==1.8.0
 tensorboard==2.5.0
 tensorflow-estimator==2.4.0
@@ -208,13 +210,13 @@ testpath==0.4.4
 toml==0.10.2
 tomlkit==0.7.0
 tornado==6.1
-tox==3.23.0
+tox==3.23.1
 tqdm==4.60.0
 traitlets==5.0.5
 typed-ast==1.4.3
 typing-extensions==3.7.4.3
 urllib3==1.26.4
-virtualenv==20.4.4
+virtualenv==20.4.6
 wcwidth==0.2.5
 webencodings==0.5.1
 werkzeug==1.0.1

diff --git a/.flake8 b/.flake8
@@ -34,6 +34,4 @@ rst-directives =
     deprecated,
     envvar,
     exception,
-    glue:figure,
-    glue:math,
     seealso,
diff --git a/pyrightconfig.json b/pyrightconfig.json
@@ -1,6 +1,6 @@
 {
   "exclude": [".git", ".tox", "docs/_build"],
-  "include": ["docs/conf.py", "src", "tests"],
+  "include": ["docs", "src", "tests"],
   "reportGeneralTypeIssues": false,
   "reportUnboundVariable": false,
   "reportUnusedClass": true,

diff --git a/pytest.ini b/pytest.ini
@@ -8,9 +8,17 @@ addopts =
     --doctest-continue-on-failure
     --doctest-modules
     --durations=3
+    --ignore=docs/abbreviate_signature.py
+    --ignore=docs/conf.py
 filterwarnings =
     ignore:.*Using or importing the ABCs.*:DeprecationWarning
     ignore:.*the imp module is deprecated in favour of importlib.*:DeprecationWarning
+nb_diff_ignore =
+    /cells/*/execution_count
+    /cells/*/outputs
+    /metadata/widgets
+norecursedirs =
+    _build
 markers =
     slow: marks tests as slow (deselect with '-m "not slow"')
 testpaths =

diff --git a/setup.cfg b/setup.cfg
@@ -72,6 +72,7 @@ doc =
     %(all)s
     jupyter
     matplotlib
+    mdit-py-plugins < 0.2.7  # temporary fix
     myst-nb >= 0.11  # myst_enable_extensions
     pandas
     Sphinx >= 3
@@ -86,6 +87,7 @@ test =
     pytest
     pytest-cov
     pytest-mock >= 3.3.0
+    pytest-notebook
     pytest-profiling
     pytest-xdist
 format =

diff --git a/tox.ini b/tox.ini
@@ -108,3 +108,13 @@ allowlist_externals =
 commands =
     mypy src tests # run separately because of potential caching problems
     pre-commit run {posargs} -a
+
+[testenv:testnb]
+description =
+    Run all notebooks with pytest
+allowlist_externals =
+    pytest
+passenv =
+    EXECUTE_NB
+commands =
+    pytest {posargs:docs} --nb-test-files