Misc/tooling (#485)

* Update `pre-commit.yml`

* Remove `.prettierignore`

* Move `.rstcheck.cfg`, remove old templates

* Move `.mypy.ini` to `pyproject.toml`

* Remove `.bump2version.cfg`

* Remove unused pre-commits

* Update MANIFEST.in

* Move `doc8`

* Update `pytest`

* Remove `tox.ini`

* Add `lint-docs` command

* Enable `ruff`

* Fix `mypy`

* Fix flake8

* More CI tests

* Fix TODOs in test

* Remove download tests, fix some warnings

* Fix more warnings

* Auto-close figures in tests

* Don't pass views in tests

* Remove flaky saving in tests

* Update `tests.yml`

* Test on 3.11 as well, fix parallel coverage

* Fix typo in `test.yml`

* Don't test on 3.11 yet because of `matplotlib`

* Don't test on 3.11 yet because of `numba`

* Update `pyproject.toml`

* Fix coverage path, update `codecov.yml`

* Don't use `develop` in `testenv`

.github/workflows/lint.yml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # TODO(michalk8): in the future, lint the docs
+        # TODO(michalk8): enable in the future
         lint-kind: [code] # , docs]
 
     steps:

.github/workflows/test.yml

@@ -19,22 +19,28 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python: [3.8]
+        python: ["3.8", "3.10"]
+        include:
+          - os: macos-latest
+            python: "3.9"
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
 
       - name: Install pip dependencies
-        # TODO(michalk8): remove tox-gh dependency, update tox.ini
         run: |
           python -m pip install --upgrade pip
-          pip install tox tox-gh-actions
+          pip install tox
+
       - name: Test
         run: |
-          tox -vv
+          tox -e py-${{ matrix.python }}
+        env:
+          PYTEST_ADDOPTS: -vv -n 2
 
       - name: Upload coverage
         uses: codecov/codecov-action@v3

.pre-commit-config.yaml

@@ -4,20 +4,21 @@ default_language_version:
 default_stages:
   - commit
   - push
-minimum_pre_commit_version: 2.14.0
+minimum_pre_commit_version: 3.0.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.991
+    rev: v1.1.1
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.21.0, jax]
+        files: ^src
   - repo: https://github.com/psf/black
     rev: 23.1.0
     hooks:
       - id: black
         additional_dependencies: [toml]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.4
+    rev: v3.0.0-alpha.6
     hooks:
       - id: prettier
         language_version: system
@@ -27,95 +28,42 @@ repos:
       - id: isort
         additional_dependencies: [toml]
         args: [--order-by-type]
-  - repo: https://github.com/asottile/yesqa
-    rev: v1.4.0
-    hooks:
-      - id: yesqa
-        additional_dependencies:
-          [
-            flake8-tidy-imports,
-            flake8-docstrings,
-            flake8-rst-docstrings,
-            flake8-comprehensions,
-            flake8-bugbear,
-            flake8-blind-except,
-            flake8-builtins,
-            flake8-pytest-style,
-            flake8-string-format,
-          ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     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]
       - id: end-of-file-fixer
       - id: mixed-line-ending
         args: [--fix=lf]
       - id: trailing-whitespace
-        exclude: ^.bumpversion.cfg$
-      - id: check-case-conflict
       - id: check-docstring-first
       - id: check-yaml
       - id: check-toml
-      - id: requirements-txt-fixer
-  - repo: https://github.com/myint/autoflake
-    rev: v2.0.1
-    hooks:
-      - id: autoflake
-        args:
-          [
-            --in-place,
-            --remove-all-unused-imports,
-            --remove-unused-variable,
-            --ignore-init-module-imports,
-          ]
-  - repo: https://github.com/pycqa/flake8.git
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-        additional_dependencies:
-          [
-            flake8-tidy-imports,
-            flake8-docstrings,
-            flake8-rst-docstrings,
-            flake8-comprehensions,
-            flake8-bugbear,
-            flake8-blind-except,
-            flake8-builtins,
-            flake8-pytest-style,
-            flake8-string-format,
-          ]
-  - repo: https://github.com/jumanjihouse/pre-commit-hooks
-    rev: 3.0.0
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.3.1
     hooks:
-      - id: script-must-have-extension
-        name: Check executable files use .sh extension
-        types: [shell, executable]
+      - id: pyupgrade
+        args: [--py3-plus, --py38-plus, --keep-runtime-typing]
   - repo: https://github.com/asottile/blacken-docs
     rev: 1.13.0
     hooks:
       - id: blacken-docs
         additional_dependencies: [black==23.1.0]
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+  - repo: https://github.com/rstcheck/rstcheck
+    rev: v6.1.1
     hooks:
-      - id: pyupgrade
-        args: [--py3-plus, --py38-plus, --keep-runtime-typing]
-  - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.10.0
-    hooks:
-      - id: python-no-eval
-      - id: python-check-blanket-noqa
-      - id: rst-backticks
-      - id: rst-directive-colons
-      - id: rst-inline-touching-normal
+      - id: rstcheck
+        additional_dependencies: [tomli]
+        args: [--config=pyproject.toml]
   - repo: https://github.com/PyCQA/doc8
     rev: v1.1.1
     hooks:
       - id: doc8
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.0.252
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]

MANIFEST.in

@@ -2,6 +2,5 @@ include src/moscot/utils/data/allTFs_dmel.txt
 include src/moscot/utils/data/allTFs_hg38.txt
 include src/moscot/utils/data/allTFs_mm.txt
 prune docs
-prune resources
+prune tests
 prune .github
-prune tests/data

README.rst

@@ -11,7 +11,7 @@ single-cell genomics. It can be used for
 - prototyping of new OT models in single-cell genomics
 
 **moscot** is powered by
-`OTT <https://ott-jax.readthedocs.io/en/latest/>`_ which is a JAX-based Optimal
+`OTT <https://ott-jax.readthedocs.io>`_ which is a JAX-based Optimal
 Transport toolkit that supports just-in-time compilation, GPU acceleration, automatic
 differentiation and linear memory complexity for OT problems.
 
@@ -39,7 +39,7 @@ If used with GPU, additionally run::
 Resources
 ---------
 
-Please have a look at our `documentation <https://moscot.readthedocs.io/en/latest/index.html/>`_
+Please have a look at our `documentation <https://moscot.readthedocs.io>`_
 
 Reference
 ---------

.github/.codecov.yml → codecov.yml

@@ -1,18 +1,18 @@
 codecov:
-  require_ci_to_pass: false
+  require_ci_to_pass: true
   strict_yaml_branch: main
 
 coverage:
-  range: 90..100
+  range: "80...100"
   status:
     project:
       default:
-        target: 1
+        target: 75%
+        threshold: 1%
     patch: off
 
 comment:
-  layout: reach, diff, files
+  layout: "reach, diff, files"
   behavior: default
   require_changes: true
-  branches:
-    - main
+  branches: [main]

docs/Makefile

@@ -6,7 +6,7 @@
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
-BUILDDIR      = build
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/_templates/autosummary/class.rst

@@ -1,33 +1,29 @@
-:github_url: {{ fullname }}
-
-{{ fullname | escape | underline}}
+{{ fullname | escape | underline }}
 
 .. currentmodule:: {{ module }}
 
 .. autoclass:: {{ objname }}
+    {% block methods %}
+    {%- if methods %}
+    .. rubric:: {{ _('Methods') }}
 
-   {% block attributes %}
-   {% if attributes %}
-   .. rubric:: Attributes
-
-   .. autosummary::
-      :toctree: .
-   {% for item in attributes %}
-      ~{{ fullname }}.{{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-
-   {% block methods %}
-   {% if methods %}
-   .. rubric:: Methods
+    .. autosummary::
+        :toctree: .
+    {% for item in methods %}
+    {%- if item not in ['__init__', 'tree_flatten', 'tree_unflatten', 'bind'] %}
+        ~{{ 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 %}
+    .. autosummary::
+        :toctree: .
+    {% for item in attributes %}
+        ~{{ name }}.{{ item }}
+    {%- endfor %}
+    {%- endif %}
+    {% endblock %}

docs/api/datasets.rst

@@ -1,9 +1,6 @@
 Datasets
 ########
 
-Datasets
-~~~~~~~~
-
 .. currentmodule:: moscot.datasets
 
 .. autosummary::

docs/api/developer.rst

@@ -1,9 +1,8 @@
 Developer
 #########
 
-
 OTT Backend
-~~~~~~~~~~~~
+~~~~~~~~~~~
 
 .. autosummary::
     :toctree: genapi

docs/api/plotting.rst

@@ -1,9 +1,6 @@
 Plotting
 ########
 
-Plotting
-~~~~~~~~
-
 .. currentmodule:: moscot.plotting
 
 .. autosummary::