DX: add test stage to GitLab CI (#253)

* DX: always upload GitLab CI caches
* DX: cache Julia packages
* DX: cache `julia` binary
* DX: define GitLab CI stages
* DX: print `julia` version
* DX: run `pre-commit` on GitLab CI
* DX: run `pytest` on GitLab CI
* FIX: add JAX to package dependencies
* FIX: add `matplotlib` to package dependencies
* FIX: add `tensorwaves` to package dependencies
* FIX: list `pytest` under `sty` dependencies
* MAINT: address pre-commit issues
* MAINT: reduce cache sizes
* MAINT: remove deprecated `set-output`
  https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
* MAINT: set `JULIA_CI` to `true`
  https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_CI
* MAINT: update hashes in `test_get_readable_hash_large`
* MAINT: update pip constraints and pre-commit

Co-authored-by: GitHub <[email protected]>

.constraints/py3.10.txt

@@ -56,15 +56,15 @@ ipywidgets==8.0.2
 isort==5.10.1
 jax==0.3.25
 jaxlib==0.3.25
-jedi==0.18.1
+jedi==0.18.2
 jinja2==3.1.2
 json5==0.9.10
 jsonschema==4.17.0
 jupyter-cache==0.5.0
 jupyter-client==7.4.7
 jupyter-core==5.0.0
 jupyter-resource-usage==0.6.4
-jupyter-server==1.23.2
+jupyter-server==1.23.3
 jupyterlab==3.5.0
 jupyterlab-code-formatter==1.5.3
 jupyterlab-markup==1.1.0
@@ -97,7 +97,7 @@ nest-asyncio==1.5.6
 nodeenv==1.7.0
 notebook==6.5.2
 notebook-shim==0.2.2
-numpy==1.23.4
+numpy==1.23.5
 opt-einsum==3.3.0
 packaging==21.3
 pandas==1.5.1
@@ -113,7 +113,7 @@ plotly==5.11.0
 pluggy==1.0.0
 pre-commit==2.20.0
 prometheus-client==0.15.0
-prompt-toolkit==3.0.32
+prompt-toolkit==3.0.33
 psutil==5.9.4
 ptyprocess==0.7.0
 pure-eval==0.2.2

.constraints/py3.7.txt

@@ -54,15 +54,15 @@ ipywidgets==8.0.2
 isort==5.10.1
 jax==0.3.25
 jaxlib==0.3.25
-jedi==0.18.1
+jedi==0.18.2
 jinja2==3.1.2
 json5==0.9.10
 jsonschema==4.17.0
 jupyter-cache==0.5.0
 jupyter-client==7.4.7
 jupyter-core==4.11.2
 jupyter-resource-usage==0.6.4
-jupyter-server==1.23.2
+jupyter-server==1.23.3
 jupyterlab==3.5.0
 jupyterlab-code-formatter==1.5.3
 jupyterlab-markup==1.1.0
@@ -112,7 +112,7 @@ plotly==5.11.0
 pluggy==1.0.0
 pre-commit==2.20.0
 prometheus-client==0.15.0
-prompt-toolkit==3.0.32
+prompt-toolkit==3.0.33
 psutil==5.9.4
 ptyprocess==0.7.0
 py==1.11.0

.constraints/py3.8.txt

@@ -57,15 +57,15 @@ ipywidgets==8.0.2
 isort==5.10.1
 jax==0.3.25
 jaxlib==0.3.25
-jedi==0.18.1
+jedi==0.18.2
 jinja2==3.1.2
 json5==0.9.10
 jsonschema==4.17.0
 jupyter-cache==0.5.0
 jupyter-client==7.4.7
 jupyter-core==5.0.0
 jupyter-resource-usage==0.6.4
-jupyter-server==1.23.2
+jupyter-server==1.23.3
 jupyterlab==3.5.0
 jupyterlab-code-formatter==1.5.3
 jupyterlab-markup==1.1.0
@@ -98,7 +98,7 @@ nest-asyncio==1.5.6
 nodeenv==1.7.0
 notebook==6.5.2
 notebook-shim==0.2.2
-numpy==1.23.4
+numpy==1.23.5
 opt-einsum==3.3.0
 packaging==21.3
 pandas==1.5.1
@@ -115,7 +115,7 @@ plotly==5.11.0
 pluggy==1.0.0
 pre-commit==2.20.0
 prometheus-client==0.15.0
-prompt-toolkit==3.0.32
+prompt-toolkit==3.0.33
 psutil==5.9.4
 ptyprocess==0.7.0
 pure-eval==0.2.2

.constraints/py3.9.txt

@@ -56,15 +56,15 @@ ipywidgets==8.0.2
 isort==5.10.1
 jax==0.3.25
 jaxlib==0.3.25
-jedi==0.18.1
+jedi==0.18.2
 jinja2==3.1.2
 json5==0.9.10
 jsonschema==4.17.0
 jupyter-cache==0.5.0
 jupyter-client==7.4.7
 jupyter-core==5.0.0
 jupyter-resource-usage==0.6.4
-jupyter-server==1.23.2
+jupyter-server==1.23.3
 jupyterlab==3.5.0
 jupyterlab-code-formatter==1.5.3
 jupyterlab-markup==1.1.0
@@ -97,7 +97,7 @@ nest-asyncio==1.5.6
 nodeenv==1.7.0
 notebook==6.5.2
 notebook-shim==0.2.2
-numpy==1.23.4
+numpy==1.23.5
 opt-einsum==3.3.0
 packaging==21.3
 pandas==1.5.1
@@ -113,7 +113,7 @@ plotly==5.11.0
 pluggy==1.0.0
 pre-commit==2.20.0
 prometheus-client==0.15.0
-prompt-toolkit==3.0.32
+prompt-toolkit==3.0.33
 psutil==5.9.4
 ptyprocess==0.7.0
 pure-eval==0.2.2

.cspell/python.txt

@@ -47,6 +47,7 @@ linewidth
 linspace
 makedirs
 matplotlib
+maxsize
 meshgrid
 nbconvert
 ncols
@@ -66,6 +67,7 @@ pyplot
 pyright
 pytest
 rcdefaults
+repr
 scipy
 seealso
 sharey

.cspell/this-project.txt

@@ -22,6 +22,7 @@ nbformat
 pdfnb
 phsp
 pushd
+pytest
 PYTHONHASHSEED
 Remco
 texlive

.github/workflows/requirements-pr.yml

@@ -18,8 +18,9 @@ jobs:
           fetch-depth: 0
       - name: Determine dependency changes
         run: |
-          DIFF="$(git diff origin/main --color -- .constraints .pre-commit-config.yaml setup.cfg)"
-          echo ::set-output name=diff::"${DIFF}"
+          echo 'diff<<EOF' >> $GITHUB_OUTPUT
+          git diff origin/main --color -- .constraints .pre-commit-config.yaml setup.cfg >> $GITHUB_OUTPUT
+          echo 'EOF' >> $GITHUB_OUTPUT
         id: diff
     outputs:
       diff: ${{ steps.diff.outputs.diff }}
@@ -80,7 +81,7 @@ jobs:
             cd artifact
             ls -A
             [[ -f .pre-commit-config.yaml ]] && mv -f .pre-commit-config.yaml ..
-            [[ "$(ls)" != "" ]] && mkdir -p ../.constraints/ && mv -f * ../.constraints/
+            [[ "$(ls)" != "" ]] && mv -f * ../.constraints/
           fi
       - run: git status -s
       - name: Commit and push changes
@@ -91,7 +92,7 @@ jobs:
           git checkout -b ${GITHUB_HEAD_REF}
           if [[ $(git status -s) ]]; then
             git add -A
-            git commit -m "MAINT: update pip constraints and pre-commit config"
+            git commit -m "MAINT: update pip constraints and pre-commit"
             git config pull.rebase true
             git pull origin ${GITHUB_HEAD_REF}
             git push origin HEAD:${GITHUB_HEAD_REF}

.gitlab-ci.yml

@@ -1,9 +1,37 @@
 image: python:3.8
 
-cache:
-  - paths:
-      - .cache/pip
-  - key:
+.cache-definitions:
+  - &julia
+    key:
+      prefix: julia
+      files:
+        - julia/Manifest.toml
+        - julia/Project.toml
+    paths:
+      - .julia/
+      - julia-*/
+    when: always
+
+  - &pip
+    key:
+      prefix: pip
+      files:
+        - .constraints/*.txt
+    paths:
+      - .cache/pip/
+    when: always
+
+  - &pre-commit
+    key:
+      prefix: pre-commit
+      files:
+        - .pre-commit-config.yaml
+    paths:
+      - .cache/pre-commit/
+    when: always
+
+  - &sphinx
+    key:
       prefix: myst-nb
       files:
         - .constraints/*.txt
@@ -17,39 +45,105 @@ cache:
       - docs/_static/export
       - docs/_static/images
       - docs/appendix/export
-  - key:
+    when: always
+
+  - &sympy
+    key:
       prefix: sympy
       files:
         - .constraints/*.txt
     paths:
       - .sympy-cache-jax
       - .sympy-cache
+    when: always
 
-pages:
-  only:
-    - main
-    - tags
+pre-commit:
+  stage: test
+  cache:
+    - *pip
+    - *pre-commit
+  before_script:
+    - python3 -m pip install -e .[sty] -c .constraints/py3.8.txt
+  script:
+    - pre-commit run -a --color always
+
+pytest:
+  stage: test
+  cache:
+    - *pip
+    - *sympy
+  before_script:
+    - python3 -m pip install .[test] -c .constraints/py3.8.txt
+  script:
+    - pytest -n auto
+
+pytest-slow:
+  stage: build
+  cache:
+    - *pip
+    - *sympy
+  before_script:
+    - python3 -m pip install .[test] -c .constraints/py3.8.txt
+  script:
+    - pytest -n auto -m slow
+
+documentation:
+  stage: build
+  cache:
+    - *julia
+    - *pip
+    - *sphinx
+    - *sympy
   before_script:
     - apt-get update
     - apt-get install -y cm-super dvipng inkscape latexmk texlive-fonts-extra texlive-latex-extra texlive-xetex xindy
     - python3 -m pip install .[doc] tox -c .constraints/py3.8.txt
-    - wget -q https://julialang-s3.julialang.org/bin/linux/x64/1.7/julia-1.7.3-linux-x86_64.tar.gz
-    - tar xzf julia-1.7.3-linux-x86_64.tar.gz
-    - mv julia-1.7.3 /opt/
-    - ln -s /opt/julia-1.7.3/bin/julia /usr/local/bin/julia
+    - version=$(sed -n '3p' julia/Manifest.toml)
+    - version=${version:17:-1}
+    - major_version=${version:0:-2}
+    - filename=julia-${version}-linux-x86_64.tar.gz
+    - |
+      if [ ! -d julia-${version} ]; then
+        wget -q https://julialang-s3.julialang.org/bin/linux/x64/${major_version}/${filename}
+        tar xzf ${filename}
+      fi
+    - mv julia-${version} /opt/
+    - ln -s /opt/julia-${version}/bin/julia /usr/local/bin/julia
+    - julia --version
     - julia --project=./julia -e 'import Pkg; Pkg.instantiate()'
   script:
     - tox -e pdfnb
     - EXECUTE_PLUTO="YES" tox -e docnb
+  artifacts:
+    paths:
+      - docs/_build/html
+      - docs/_build/latex
+    when: always
+
+pages:
+  stage: deploy
+  dependencies:
+    - documentation
+  only:
+    - main
+    - tags
+  script:
     - mv docs/_build/html/ public/
-    - tar czf public/latex.tar.gz -C docs/_build/ latex/
   artifacts:
     paths:
       - public
     when: always
 
+stages:
+  - test
+  - build
+  - deploy
+
 # https://docs.gitlab.com/ee/ci/caching/#cache-python-dependencies
 variables:
+  JULIA_CI: "true"
+  JULIA_DEPOT_PATH: "$CI_PROJECT_DIR/.julia/"
   PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+  PRE_COMMIT_HOME: "$CI_PROJECT_DIR/.cache/pre-commit"
   PYTHONHASHSEED: "0"
   SYMPY_CACHE_DIR: "$CI_PROJECT_DIR"

docs/extensions/relink_references.py

@@ -1,4 +1,6 @@
 # cspell:ignore refdomain refspecific reftarget reftype
+# pyright: reportMissingImports=false
+# pyright: reportMissingModuleSource=false
 """Abbreviated the annotations generated by sphinx-autodoc.
 
 It's not necessary to generate the full path of type hints, because they are

docs/extensions/support_bibtex_math.py

@@ -1,4 +1,6 @@
 # cspell:ignore bibtex latexcodec pybtex sphinxcontrib ulatex
+# pyright: reportMissingImports=false
+# pyright: reportMissingModuleSource=false
 """Enable math mode in `sphinxcontrib-bibtex`.
 
 .. note:: The source code below is inspired by

docs/extensions/unsrt_et_al.py

@@ -1,3 +1,5 @@
+# pyright: reportMissingImports=false
+# pyright: reportMissingModuleSource=false
 from pybtex.database import Entry
 from pybtex.plugin import register_plugin
 from pybtex.richtext import Tag, Text

pyproject.toml

@@ -44,8 +44,7 @@ black = [
 ]
 flake8 = [
     "--extend-ignore=E501,E731",
-    "--per-file-ignores=docs/appendix/homomorphism*:E402",
-    "--per-file-ignores=docs/zz.polarization-fit*:E741",
+    "--per-file-ignores=docs/appendix/homomorphism*:E402,docs/zz.polarization-fit*:E741",
 ]
 isort = [
     "--line-length=85",