Update pyproject.toml

.circleci/config.yml

@@ -38,20 +38,18 @@ jobs:
         - run:
             name: Install ffmpeg
             command: |
-              sudo apt update 
+              sudo apt update
               sudo apt install ffmpeg
         - run:
             name: Install latex (for logo)
             command: |
               sudo apt install texlive-latex-base texlive-fonts-recommended texlive-latex-extra cm-super dvipng
-              
+
         - run:
             name: Get Python running
             command: |
               python -m pip install --user --upgrade --progress-bar off pip
-              python -m pip install --user --progress-bar off -r requirements.txt
-              python -m pip install --user --upgrade --progress-bar off -r docs/requirements.txt     
-              python -m pip install --user --upgrade --progress-bar off .
+              python -m pip install --user --upgrade --progress-bar off .[doc]
           # python -m pip install --user --upgrade --progress-bar off ipython "https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master" memory_profiler
         - save_cache:
             key: pip-cache
@@ -176,7 +174,7 @@ workflows:
       - build_docs:
           filters:
             tags:
-              only: /[0-9]+(\.[0-9]+)*$/  
+              only: /[0-9]+(\.[0-9]+)*$/
       - deploy_main:
           requires:
             - build_docs

.github/workflows/testing.yml

@@ -71,18 +71,15 @@ jobs:
       with:
         python-version: "3.10"
     - run: which python
-    - name: Install dependencies
-      run: |
-        python -m pip install --user --upgrade --progress-bar off pip
-        python -m pip install --user -r requirements.txt
-        python -m pip install --user --upgrade pytest pytest-cov codecov
+
     - name: Install 'skada' package
       run: |
-        python -m pip install --user -e .
+        python -m pip install --user --upgrade --progress-bar off pip
+        python -m pip install --user -e .[test]
     # Run Tests
     - name: Run Tests without torch
       run: pytest skada/ --verbose --cov=skada --cov-report term
-    # Codecov 
+    # Codecov
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v3
       env:
@@ -113,18 +110,14 @@ jobs:
       with:
         python-version: "3.10"
     - run: which python
-    - name: Install dependencies
-      run: |
-        python -m pip install --user --upgrade --progress-bar off pip
-        python -m pip install --user -r requirements_full.txt
-        python -m pip install --user --upgrade pytest pytest-cov codecov
     - name: Install 'skada' package
       run: |
-        python -m pip install --user -e .
+        python -m pip install --user --upgrade --progress-bar off pip
+        python -m pip install --user -e .[deep,test]
     # Run Tests
     - name: Run Tests with torch
       run: pytest skada/ --verbose --cov=skada --cov-report term
-    # Codecov 
+    # Codecov
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v3
       env:

.pre-commit-config.yaml

@@ -29,10 +29,6 @@ repos:
           - tomli
         files: ^skada/|^docs/|^examples/
         types_or: [python, bib, rst, inc]
-        args: [
-          "--ignore-words",
-          "ignore-words.txt",
-        ]
 
   # yamllint
   - repo: https://github.com/adrienverge/yamllint.git

CONTRIBUTING.md

@@ -2,7 +2,7 @@ Contributing to SKADA
 =====================
 
 
-First off, thank you for considering contributing to SKADA. 
+First off, thank you for considering contributing to SKADA.
 
 How to contribute
 -----------------
@@ -32,6 +32,13 @@ GitHub, clone, and develop on a branch. Steps:
 
    This will install the pre-commit hooks that will run on every commit. If the hooks fail, the commit will be aborted.
 
+3. Install the dependencies:
+
+   ```bash
+   $ pip install -e .
+   ```
+To install an optional dependency (see pyproject.toml), swap the previous command with ```pip install -e .[dependency_name]```.
+
 3. Create a ``feature`` branch to hold your development changes:
 
    ```bash
@@ -95,7 +102,7 @@ following rules before you submit a pull request:
    to other methods available in SKADA.
 
 -  Documentation and high-coverage tests are necessary for enhancements to be
-   accepted. Bug-fixes or new features should be provided with 
+   accepted. Bug-fixes or new features should be provided with
    [non-regression tests](https://en.wikipedia.org/wiki/Non-regression_testing).
    These tests verify the correct behavior of the fix or feature. In this
    manner, further modifications on the code base are granted to be consistent
@@ -122,7 +129,7 @@ tools:
 
   ```bash
    $ pytest skada
-  ```   
+  ```
 
 Bonus points for contributions that include a performance analysis with
 a benchmark script and profiling output (please report on the mailing

ignore-words.txt

@@ -4,4 +4,4 @@ OT
 repid
 ist
 vor
-fro
+fro

pyproject.toml

@@ -1,10 +1,7 @@
-
-
 [build-system]
 requires = ["setuptools", "setuptools-scm"]
 build-backend = "setuptools.build_meta"
 
-
 [project]
 dynamic = ["version"]
 name = "skada"
@@ -14,13 +11,8 @@ authors = [
         ]
 license = {file = "COPYING"}
 readme = "README.md"
-dependencies = [
-    "numpy >= 1.24",
-    "scipy >= 1.10",
-    "scikit-learn >= 1.5.0",
-    "POT >= 0.9.3",
-]
-keywords = ["domain-adaptation", "scikit-learn", "pytorch", 
+requires-python = ">= 3.9"
+keywords = ["domain-adaptation", "scikit-learn", "pytorch",
             "machine learning", "deep learning"]
 classifiers=[
   "Intended Audience :: Science/Research",
@@ -42,19 +34,126 @@ classifiers=[
   "Programming Language :: Python :: 3.12",
 ]
 
+dependencies = [
+    "numpy >= 1.24",
+    "scipy >= 1.10",
+    "scikit-learn >= 1.5.0",
+    "POT >= 0.9.3",
+    "pandas>=2.3.0",
+]
+
+[project.optional-dependencies]
+subspace = ["torch"]
+
+deep = [
+    "torch",
+    "torchvision",
+    "skorch",
+]
+
+test = [
+    "pytest",
+    "pytest-cov",
+    "codecov"
+]
+
+doc = [
+    "sphinx",
+    "sphinx_gallery",
+    "sphinx_rtd_theme",
+    "numpydoc",
+    "memory_profiler",
+    "myst-parser",
+    "ipython",
+    "matplotlib",
+    "torch",
+    "torchvision",
+    "skorch",
+]
+
 [project.urls]
 homepage = "https://scikit-adaptation.github.io/"
 documentation = "https://scikit-adaptation.github.io/"
 repository = "https://github.com/scikit-adaptation/skada/"
 
-# Optional dependencies
-[project.optional-dependencies]
-all = ["torch", "torchvision", "skorch"]
-deep = ["torch", "torchvision", "skorch"]
-subspace = ["torch"]
-
 [tool.setuptools]
 packages = ["skada"]
 
 [tool.setuptools.dynamic]
-version = {attr = "skada.version.__version__"}
+version = {attr = "skada.version.__version__"}
+
+[tool.pytest.ini_options]
+
+# disable-pytest-warnings should be removed once we rewrite tests
+# using yield with parametrize
+doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS"
+testpaths = "skada"
+addopts = [
+    "--doctest-modules",
+    "--disable-pytest-warnings",
+    "--color=yes",
+    "-rN",
+]
+
+[tool.codespell]
+skip = [
+    "./.git",
+    "./doc/_build",
+    "./doc/auto_examples",
+    "./doc/modules/generated"
+]
+
+ignore-words = "ignore-words.txt"
+
+[tool.rstcheck]
+report_level = "WARNING"
+ignore_roles = [
+    "attr",
+    "class",
+    "doc",
+    "eq",
+    "exc",
+    "file",
+    "footcite",
+    "footcite:t",
+    "func",
+    "gh",
+    "kbd",
+    "meth",
+    "mod",
+    "newcontrib",
+    "py:mod",
+    "ref",
+    "samp",
+    "term"
+]
+
+ignore_directives = [
+    "autoclass",
+    "autofunction",
+    "automodule",
+    "autosummary",
+    "bibliography",
+    "cssclass",
+    "currentmodule",
+    "dropdown",
+    "footbibliography",
+    "glossary",
+    "graphviz",
+    "grid",
+    "highlight",
+    "minigallery",
+    "tabularcolumns",
+    "toctree",
+    "rst-class",
+    "tab-set",
+    "towncrier-draft-entries",
+    "include"
+]
+
+ignore_messages = "^.*(Unknown target name|Undefined substitution referenced)[^`]*$"
+
+
+
+
+