Fix/tests (#57)

* Fix linter

* Fix docs linter

* Fix stacklevel in warnings

* Update pre-commits

* Fix linkcheck 403

* Remove unused `jinja2` requirement

* Use new GA features

* Upgrade PETSc python version

* Drop Python3.7 support

* Remove `pip install petsc slepc`

* Enable and switch to `tox-conda`

* Install libenchant, use fetch-depth=0

Author: michalk8

.github/workflows/ci.yml

@@ -12,30 +12,32 @@ on:
         branches:
         -   main
 
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+
 jobs:
     lint:
         runs-on: ubuntu-latest
         steps:
         -   uses: actions/checkout@v3
-            with:
-                fetch-depth: 0
         -   name: Set up Python
             uses: actions/setup-python@v4
             with:
-                python-version: 3.8
+                python-version: '3.10'
 
         -   uses: actions/cache@v3
             with:
                 path: ~/.cache/pre-commit
                 key: precommit-${{ env.pythonLocation }}-${{ hashFiles('**/.pre-commit-config.yaml') }}
-                restore-keys: |
-                    precommit-${{ env.pythonLocation }}-
 
         -   name: Install dependencies
             run: |
-                sudo apt install pandoc
+                sudo apt-get update -y
+                sudo apt install libenchant-2-dev pandoc
                 python -m pip install --upgrade pip
-                pip install tox
+                python -m pip install tox
 
         -   name: Linting
             run: |
@@ -47,80 +49,41 @@ jobs:
             fail-fast: false
             max-parallel: 5
             matrix:
-                python: [3.7, 3.9]
+                python: ['3.8', '3.10', '3.11']
                 os: [ubuntu-latest]
-                use_slepc: [false]
+                slepc: ['noslepc']
                 include:
                 -   os: ubuntu-latest
-                    python: 3.8
-                    use_slepc: true
-                -   os: macos-latest
-                    python: 3.9
-                    # TODO(michalk8): enable this in the future (problem/missing mpif90)
-                    use_slepc: false
+                    python: '3.9'
+                    slepc: 'slepc'
                 -   os: macos-latest
-                    python: 3.8
-                    use_slepc: false
-        env:
-            # make sure to pin this in tox.ini as well
-            PC_VERSION: 3.18.0  # PETSc version
-            SC_VERSION: 3.18.0  # SLEPc version
+                    python: '3.10'
+                    slepc: 'slepc'
 
         steps:
         -   uses: actions/checkout@v3
-            with:
-                fetch-depth: 0
         -   name: Set up Python ${{ matrix.python }}
             uses: actions/setup-python@v4
             with:
                 python-version: ${{ matrix.python }}
 
-        -   name: Export environment variables
-            if: matrix.use_slepc == true
-            run: |
-                echo "PETSC_DIR=$HOME/petsc-$PC_VERSION" >> $GITHUB_ENV
-                echo "SLEPC_DIR=$HOME/slepc-$SC_VERSION" >> $GITHUB_ENV
-                echo "PETSC_ARCH=arch-$RUNNER_OS-c-opt" >> $GITHUB_ENV
-        -   name: Install PETSc/SLEPc dev dependencies
-            if: matrix.use_slepc == true
-            run: |
-                ./.scripts/ci/install_dependencies.sh
-
-        -   name: Get pip cache dir
-            id: pip-cache-dir
-            run: |
-                echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
-        -   name: Restore pip cache
-            uses: actions/cache@v3
-            with:
-                path: ${{ steps.pip-cache-dir.outputs.dir }}
-                key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/requirements.txt') }}
-
         -   name: Install pip dependencies
             run: |
                 python -m pip install --upgrade pip
-                pip install tox tox-gh-actions codecov
-
-        -   name: Restore PETSc/SLEPc tox cache
-            if: matrix.use_slepc == true
-            uses: actions/cache@v3
-            with:
-                path: .tox
-                key: tox-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/install_dependencies.sh', '**/requirements.txt', '**/setup.py', '**/tox.ini') }}
+                pip install tox codecov
 
         -   name: Test
             run: |
-                tox -vv
+                tox -e py${{ matrix.python }}-${{ matrix.slepc }} -vv
             env:
                 PLATFORM: ${{ matrix.os }}
-                USE_SLEPC: ${{ matrix.use_slepc }}
 
         -   name: Upload coverage
             uses: codecov/codecov-action@v3
             with:
                 files: ./coverage.xml
                 flags: unittests
-                name: ${{ matrix.os }}-${{ matrix.python }}-{{ matrix.use_slepc }}
+                name: ${{ matrix.os }}-${{ matrix.python }}-${{ matrix.slepc }}
                 env_vars: OS,PYTHON
                 fail_ci_if_error: false
                 verbose: true
@@ -131,12 +94,10 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         -   uses: actions/checkout@v3
-            with:
-                fetch-depth: 0
         -   name: Set up Python
             uses: actions/setup-python@v4
             with:
-                python-version: 3.8
+                python-version: '3.10'
         -   name: Install pypa/build
             run: |
                 python -m pip install --upgrade pip
@@ -146,9 +107,10 @@ jobs:
                 python -m build --sdist --wheel --outdir dist/
 
         -   name: Publish package on PyPI
-            uses: pypa/gh-action-pypi-publish@master
+            uses: pypa/gh-action-pypi-publish@release/v1
             with:
                 user: __token__
                 password: ${{ secrets.PYPI_PASSWORD }}
                 skip_existing: true
+                verify-metadata: true
                 verbose: true

.pre-commit-config.yaml

@@ -7,12 +7,12 @@ default_stages:
 minimum_pre_commit_version: 2.9.0
 repos:
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.0.1
+    rev: v1.3.0
     hooks:
     -   id: mypy
-        additional_dependencies: [numpy==1.20.0, scipy>=1.6.0]
+        additional_dependencies: [numpy>=1.20.0, scipy>=1.6.0]
 -   repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
     -   id: black
         additional_dependencies: [toml]
@@ -28,7 +28,7 @@ repos:
     -   id: yesqa
         additional_dependencies: [flake8-tidy-imports, flake8-docstrings, flake8-rst-docstrings, flake8-comprehensions, flake8-bugbear, flake8-logging-format, flake8-blind-except, flake8-builtins, flake8-pytest-style, flake8-string-format]
 -   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-    rev: v2.7.0
+    rev: v2.9.0
     hooks:
     -   id: pretty-format-yaml
         args: [--autofix, --indent, '4', --preserve-quotes]
@@ -61,7 +61,7 @@ repos:
     -   id: flake8
         additional_dependencies: [flake8-tidy-imports, flake8-docstrings, flake8-rst-docstrings, flake8-comprehensions, flake8-bugbear, flake8-logging-format, flake8-blind-except, flake8-builtins, flake8-pytest-style, flake8-string-format]
 -   repo: https://github.com/myint/autoflake
-    rev: v2.0.1
+    rev: v2.1.1
     hooks:
     -   id: autoflake
         args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
@@ -77,7 +77,7 @@ repos:
     -   id: blacken-docs
         additional_dependencies: [black==23.1.0]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.4.0
     hooks:
     -   id: pyupgrade
         args: [--py3-plus, --py37-plus]

.scripts/ci/install_dependencies.sh

@@ -45,7 +45,6 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.mathjax",
     "sphinx_autodoc_typehints",
-    "sphinx_last_updated_by_git",
     "sphinx_copybutton",
     "typed_returns",
     "nbsphinx",
@@ -115,7 +114,11 @@
 
 # linkcheck
 linkcheck_anchors = False  # problem with specifying lines on GitHub in `acknowledgments.rst`
-linkcheck_ignore = ["https://doi.org/10.1021/acs.jctc.8b00079", "https://pubs.acs.org/doi/abs/10.1021/acs.jctc.8b00079"]
+linkcheck_ignore = [
+    "https://doi.org/10.1021/acs.jctc.8b00079",
+    "https://pubs.acs.org/doi/abs/10.1021/acs.jctc.8b00079",
+    "https://doi.org/10.1063/1.5064530",
+]
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

docs/source/conf.py

@@ -1,6 +1,6 @@
 Installation
 ============
-*pyGPCCA* requires Python >= 3.6 to run. If any problems arise, please consult the
+*pyGPCCA* requires Python >= 3.8 to run. If any problems arise, please consult the
 `Troubleshooting`_ section.
 
 Methods

docs/source/installation.rst

@@ -1,33 +1,42 @@
-scipy
-docstring
+Eq
+Fackeldey
+Freie
+G-PCCA
+GPCCA
+Konstantin
+Perron
+Reuter
+Röblitz
+Schur
+Sikorski
+Universitaet
+Zenodo
+Zuse
+brandts
+clusterings
+coarsegrain
 conda
-pygpcca
-pyGPCCA
+conformational
+cubically
+decompositions
+docstring
 gpcca
-GPCCA
-G-PCCA
-minChi
+graining
+intersphinx
 krylov
-brandts
-Schur
-schur
-microstate
-microstates
+macOS
 macrostate
 macrostates
-graining
-coarsegrain
-clusterings
-Freie
-Universitaet
-macOS
-Fackeldey
-Röblitz
-Sikorski
-Zuse
+metastable
+microstate
+microstates
+minChi
 mypy
 numpy
-Zenodo
-Konstantin
+optimality
+orthonormal
 pre
-intersphinx
+pyGPCCA
+pygpcca
+schur
+scipy