Fix using .A instead of .toarray() (#61)

* Fix using `.A` instead of `.toarray()`

* Fix typos

* Fix class template in the docs

* Use BLAS/LAPACK from conda

* Update GA's versions

* Update pre-commits

* Fix `pyproject.toml`

* Switch to `myst-nb`

* Use amsmath

* Remove `enviroment.yaml`

* Drop `tox-conda`

* Use conda in CI

* Remove `tox` from CI

* Don't skip on `mpi4py`

* Install petsc/slepc

* Specify correct shell

* Change env name

* Fix conda CI

* Update codecov action

* Update coverage

* Add codecov token to CI

Author: michalk8

.github/workflows/ci.yml

@@ -30,29 +30,36 @@ jobs:
                     slepc: 'slepc'
 
         steps:
-        -   uses: actions/checkout@v3
-        -   name: Set up Python ${{ matrix.python }}
-            uses: actions/setup-python@v4
+        -   uses: actions/checkout@v4
+        -   name: Set up Conda
+            uses: conda-incubator/setup-miniconda@v3.1.0
             with:
                 python-version: ${{ matrix.python }}
+                auto-update-conda: true
+                channels: conda-forge,defaults
 
         -   name: Install pip dependencies
+            shell: bash -el {0}
             run: |
                 python -m pip install --upgrade pip
-                pip install tox codecov
+                pip install '.[test]'
+
+        -   name: Install conda dependencies
+            if: ${{ matrix.slepc == 'slepc' }}
+            shell: bash -el {0}
+            run: |
+                conda install petsc slepc petsc4py slepc4py mpi4py
 
         -   name: Test
+            shell: bash -el {0}
             run: |
-                tox -e py${{ matrix.python }}-${{ matrix.slepc }} -vv
-            env:
-                PLATFORM: ${{ matrix.os }}
+                python -m pytest --cov --cov-config=tox.ini --no-cov-on-fail --cov-report=xml --cov-report=term-missing:skip-covered -vv
 
         -   name: Upload coverage
-            uses: codecov/codecov-action@v3
+            uses: codecov/codecov-action@v4
             with:
+                fail_ci_if_error: false
                 files: ./coverage.xml
-                flags: unittests
                 name: ${{ matrix.os }}-${{ matrix.python }}-${{ matrix.slepc }}
-                env_vars: OS,PYTHON
-                fail_ci_if_error: false
+                token: ${{ secrets.CODECOV_TOKEN }}
                 verbose: true

.github/workflows/lint.yml

@@ -16,14 +16,14 @@ jobs:
     lint:
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v3
+        -   uses: actions/checkout@v4
         -   name: Set up Python 3.10
-            uses: actions/setup-python@v4
+            uses: actions/setup-python@v5
             with:
                 python-version: '3.10'
 
         -   name: Cache pre-commit
-            uses: actions/cache@v3
+            uses: actions/cache@v4
             with:
                 path: ~/.cache/pre-commit
                 key: pre-commit-${{ env.pythonLocation }}-${{ hashFiles('**/.pre-commit-config.yaml') }}

.github/workflows/publish.yml

@@ -8,9 +8,9 @@ jobs:
     deploy:
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v3
+        -   uses: actions/checkout@v4
         -   name: Set up Python
-            uses: actions/setup-python@v4
+            uses: actions/setup-python@v5
             with:
                 python-version: '3.10'
 

.pre-commit-config.yaml

@@ -4,42 +4,41 @@ default_language_version:
 default_stages:
 -   commit
 -   push
-minimum_pre_commit_version: 2.9.0
+minimum_pre_commit_version: 3.0.0
 repos:
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+    rev: v1.13.0
     hooks:
     -   id: mypy
         additional_dependencies: [numpy>=1.20.0, scipy>=1.6.0]
 -   repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.10.0
     hooks:
     -   id: black
         additional_dependencies: [toml]
 -   repo: https://github.com/timothycrosley/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
     -   id: isort
         additional_dependencies: [toml]
         args: [--order-by-type]
 -   repo: https://github.com/asottile/yesqa
-    rev: v1.4.0
+    rev: v1.5.0
     hooks:
     -   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: v2.9.0
+    rev: v2.14.0
     hooks:
     -   id: pretty-format-yaml
         args: [--autofix, --indent, '4', --preserve-quotes]
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
     -   id: detect-private-key
     -   id: check-merge-conflict
     -   id: check-ast
     -   id: check-symlinks
-    -   id: check-added-large-files
     -   id: check-executables-have-shebangs
     -   id: fix-encoding-pragma
         args: [--remove]
@@ -56,12 +55,12 @@ repos:
     -   id: check-toml
     -   id: requirements-txt-fixer
 -   repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+    rev: 7.1.1
     hooks:
     -   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: v2.1.1
+    rev: v2.3.1
     hooks:
     -   id: autoflake
         args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
@@ -72,12 +71,12 @@ repos:
         name: Check executable files use .sh extension
         types: [shell, executable]
 -   repo: https://github.com/asottile/blacken-docs
-    rev: 1.13.0
+    rev: 1.19.1
     hooks:
     -   id: blacken-docs
         additional_dependencies: [black==23.1.0]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.4.0
+    rev: v3.19.0
     hooks:
     -   id: pyupgrade
         args: [--py3-plus, --py37-plus]
@@ -91,6 +90,6 @@ repos:
     -   id: rst-directive-colons
     -   id: rst-inline-touching-normal
 -   repo: https://github.com/PyCQA/doc8
-    rev: v1.1.1
+    rev: v1.1.2
     hooks:
     -   id: doc8

docs/requirements.txt

@@ -1,9 +1,7 @@
 -r ../requirements.txt
-nbsphinx>=0.8
-sphinx>=5
-sphinx-autodoc-annotation
-sphinx-autodoc-typehints>=1.10.3
+myst-nb
+sphinx>=8
 sphinx-copybutton
-sphinx_last_updated_by_git
+sphinx_autodoc_typehints
 sphinx_rtd_theme
 sphinxcontrib-spelling

docs/source/_templates/autosummary/class.rst

@@ -1,33 +1,31 @@
 :github_url: {{ fullname }}
 
-{{ fullname | escape | underline}}
+{{ fullname | escape | underline }}
 
 .. currentmodule:: {{ module }}
 
 .. autoclass:: {{ objname }}
+    {% block methods %}
+    {%- if methods %}
+    .. rubric:: {{ _('Methods') }}
 
-   {% block methods %}
-   {% if methods %}
-   .. rubric:: Methods
+    .. autosummary::
+        :toctree: .
+    {% for item in methods %}
+    {%- if item not in ['__init__', 'tree_flatten', 'tree_unflatten', 'bind', 'tabulate', 'module_paths'] %}
+        ~{{ name }}.{{ item }}
+    {%- endif %}
+    {%- endfor %}
+    {%- endif %}
+    {%- endblock %}
+    {% block attributes %}
+    {%- if attributes %}
+    .. rubric:: {{ _('Attributes') }}
 
-   .. autosummary::
-      :toctree: .
-   {% for item in methods %}
-      {%- if item != '__init__' %}
-      ~{{ fullname }}.{{ item }}
-      {%- endif -%}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-
-   {% block attributes %}
-   {% if attributes %}
-   .. rubric:: Attributes
-
-   .. autosummary::
-      :toctree: .
-   {% for item in attributes %}
-      ~{{ fullname }}.{{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
+    .. autosummary::
+        :toctree: .
+    {% for item in attributes %}
+        ~{{ name }}.{{ item }}
+    {%- endfor %}
+    {%- endif %}
+    {% endblock %}

docs/source/conf.py

@@ -47,7 +47,7 @@
     "sphinx_autodoc_typehints",
     "sphinx_copybutton",
     "typed_returns",
-    "nbsphinx",
+    "myst_nb",
 ]
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
@@ -63,7 +63,7 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ["build", "**.ipynb_checkpoints"]
 
-source_suffix = ".rst"
+source_suffix = {".rst": "restructuredtext", ".ipynb": "myst-nb"}
 add_function_parentheses = True
 
 # -- Options for HTML output -------------------------------------------------
@@ -86,29 +86,21 @@
 napoleon_use_admonition_for_references = False
 todo_include_todos = False
 
-# binder
-nbsphinx_highlight_language = "python3"
-nbsphinx_execute_arguments = [
-    "--InlineBackend.figure_formats={'png', 'pdf'}",  # correct figure resize
-    "--InlineBackend.rc={'figure.dpi': 96}",
+# myst-nb
+myst_heading_anchors = 2
+nb_execution_mode = "off"
+nb_mime_priority_overrides = [("spelling", "text/plain", 0)]
+myst_enable_extensions = [
+    "colon_fence",
+    "amsmath",
+    "dollarmath",
 ]
-nbsphinx_prolog = r"""
-{% set docname = 'docs/source/' + env.doc2path(env.docname, base=None) %}
-.. raw:: html
-
-    <div class="note">
-      Interactive version
-      <a href="https://mybinder.org/v2/gh/msmdev/pygpcca/{{ env.config.release|e }}?filepath={{ docname|e }}"><img alt="Binder badge" src="https://mybinder.org/badge_logo.svg" style="vertical-align:text-bottom">
-      </a>
-    </div>
-"""  # noqa: E501
 
 # spelling
 spelling_lang = "en_US"
 spelling_warning = True
 spelling_word_list_filename = "spelling_wordlist.txt"
 spelling_add_pypi_package_names = True
-spelling_show_suggestions = True
 # see: https://pyenchant.github.io/pyenchant/api/enchant.tokenize.html
 spelling_filters = ["enchant.tokenize.URLFilter", "enchant.tokenize.EmailFilter"]
 
@@ -119,6 +111,7 @@
     "https://pubs.acs.org/doi/abs/10.1021/acs.jctc.8b00079",
     "https://doi.org/10.1063/1.5064530",
 ]
+linkcheck_report_timeouts_as_broken = False
 
 # 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,

environment.yml

@@ -1,6 +1,8 @@
 [build-system]
-requires = ['setuptools', 'setuptools_scm', 'wheel']
-build-backend = 'setuptools.build_meta'
+requires = ["setuptools>=61", "setuptools-scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
 
 [tool.black]
 line-length = 120

pyproject.toml

@@ -42,7 +42,7 @@
             "slepc4py>=3.18.0",
         ],
         dev=["pre-commit>=2.9.0", "bump2version"],
-        test=["tox>=3.20.1"],
+        test=["pytest", "pytest-cov", "pytest-mock", "codecov"],
         docs=[
             line.strip()
             for line in (Path("docs") / "requirements.txt").read_text("utf-8").splitlines()