Merge branch 'develop' into experiments

.github/workflows/ci.yml

@@ -0,0 +1,99 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+      - develop
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  FORCE_COLOR: 3
+
+jobs:
+  pre-commit:
+    name: Format
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --hook-stage manual --all-files
+
+  # checks:
+  #   name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+  #   runs-on: ${{ matrix.runs-on }}
+  #   needs: [pre-commit]
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       python-version: ["3.8"]
+  #       runs-on: [ubuntu-latest, macos-latest]
+
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #       with:
+  #         fetch-depth: 0
+
+  #     - uses: actions/setup-python@v4
+  #       with:
+  #         python-version: ${{ matrix.python-version }}
+
+  #     - name: Install torch
+  #       run: pip install torch==1.9.0 torchvision==0.10.0 torchaudio==0.9.0
+
+  #     - name: Debug installed packages
+  #       run: pip list
+
+  #     - name: Debug Python environment
+  #       run: python -V
+
+  #     - name: Install signatory
+  #       run: |
+  #         pip install signatory==1.2.6.1.9.0 --no-cache-dir --force-reinstall
+
+  #     - name: Install package
+  #       run: python -m pip install .[test]
+
+  #     - name: Test package
+  #       run: python -m pytest -ra --cov=nlpsig
+
+  dist:
+    name: Distribution build
+    runs-on: ubuntu-latest
+    needs: [pre-commit]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Build sdist and wheel
+        run: pipx run build
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist
+
+      - name: Check products
+        run: pipx run twine check dist/*
+
+      - uses: pypa/[email protected]
+        if: github.event_name == 'release' && github.event.action == 'published'
+        with:
+          # Remember to generate this and set it in "GitHub Secrets"
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -1,6 +1,167 @@
-*.DS_Store
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# setuptools_scm
+src/*/_version.py
+
+
+# ruff
+.ruff_cache/
+
+# OS specific stuff
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Common editor files
+*~
+*.swp
+
+.vscode/
+
+# Miscellaneous
 *.ipynb_checkpoints/
 **__pycache__
 *.npy
 *.pkl
-paths.py
+paths.py

.pre-commit-config.yaml

@@ -44,12 +44,6 @@ repos:
       - id: blacken-docs
         additional_dependencies: [black==23.1.0]
 
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.260"
-    hooks:
-      - id: ruff
-        args: ["--fix", "--show-fixes"]
-
   - repo: https://github.com/shellcheck-py/shellcheck-py
     rev: "v0.9.0.2"
     hooks:

.readthedocs.yml

@@ -0,0 +1,23 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs