refactor: full scikit-learn compatibility + general refactor (#241)

- Use `scikit-learn` ≥1.4 metadata routing for full API compatibility - Switch from `setup.py` to `pyproject.toml` - Switch to `poetry` for dependency management - Use `tox` for documentation building, unit tests and linting - Add pre-commit hooks - Add coverage checks via `coveralls` - Drop support for Python <3.11 - Support Python 3.11 and 3.12 - Add issue and pull request templates - Add license information to `.py` files - Update repository documentation - Use `cliff` for `CHANGELOG.md` generation - Update Sphinx documenation - Switch to `numpy` docstring format (via `napoleon`) - Move library code from `lib/` to `sequentia/` - Move unit tests from `lib/test` to `tests/` - Add `sequentia.enums` module for configuration values. - Add `sequentia.version` sub-package for versioning information. - Add `sequentia._internal` sub-package for internal logic. - Remove `sequentia.pipeline` module. - Make topologies internal - Remove `pydantic` validation classes for model inputs - Remove `pydantic` validation for `numpy` arrays - Use key-word only arguments more widely (e.g. for `lengths`) - Use `pydantic.validate_call` for validating constructors and other functions - Use type hinting - Use `ABCMeta` metaclass for base classes (e.g. `ClassifierMixin`/`RegressorMixin` and `BaseHMM`) - Use `abc` decorators for abstract methods - Avoid unnecessarily redefining methods on subclasses for only documentation purposes - Add `predict_log_proba` to classifiers - Move majority of validation logic to `sequentia._internal._validation` module - Prefix all HMM parameter setter functions with `set_state` - Rename `set_transitions` to set_state_transition_probs` - Rename `set_state_emissions` to `set_state_emission_probs` - Rename `set_state_covariances` to `set_state_covars` - Use static methods to define default HMM parameters - Handle KNN querying for single training sequences and single query sequences - Update `IndependentFunctionTransformer` to match `FunctionTransformer` from `scikit-learn` ≥1.4 API - Use `Helpers` fixture class for accessing helper methods in unit tests
eonu · Apr 1, 2024 · 2786899 · 2786899
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,46 +1,62 @@
-version: 2
+version: "2.1"
 
-workflows:
-  version: 2
-  test:
-    jobs:
-      - python_3.8
-      - python_3.9
-      - python_3.10
-
-template: &template
-  docker:
-    - image: ubuntu:bionic
-  steps:
-    - checkout
-    - run:
-        name: Set up miniconda
-        command: |
-          apt update
-          apt install -y wget
-          cd $HOME
-          wget "https://repo.anaconda.com/miniconda/Miniconda3-4.7.10-Linux-x86_64.sh" -O miniconda.sh
-          printf '%s' "8a324adcc9eaf1c09e22a992bb6234d91a94146840ee6b11c114ecadafc68121  miniconda.sh" | sha256sum -c
-          bash miniconda.sh -b -p $HOME/miniconda
-    - run:
-        name: Set up environment, dependencies and run tests
-        command: |
-          export PATH="$HOME/miniconda/bin:$PATH"
-          conda create -n sequentia python=$PYTHON_VERSION -y
-          source activate sequentia
-          pip install ".[dev]"
-          pytest lib/test --disable-pytest-warnings
+orbs:
+  python: circleci/python@2.1.1
+  coveralls: coveralls/coveralls@2.2.1
 
 jobs:
-  python_3.8:
-    <<: *template
-    environment:
-      PYTHON_VERSION: "3.8"
-  python_3.9:
-    <<: *template
-    environment:
-      PYTHON_VERSION: "3.9"
-  python_3.10:
-    <<: *template
-    environment:
-      PYTHON_VERSION: "3.10"
+  linting:
+    executor:
+      name: python/default
+      tag: "3.11"
+    steps:
+      - checkout
+      - python/install-packages:
+          pkg-manager: poetry
+          args: --only base
+      - run:
+          name: Linting
+          command: |
+            poetry run tox -e lint
+  tests:
+    parameters:
+      version:
+        type: string
+    executor:
+      name: python/default
+      tag: <<parameters.version>>
+    steps:
+      - checkout
+      - python/install-packages:
+          pkg-manager: poetry
+          args: --only base
+      # - run:
+      #     name: Docstring tests
+      #     command: |
+      #       poetry run tox -e tests.doctest
+      - run:
+          name: Unit tests
+          command: |
+            poetry run -- tox -e tests -- --cov
+      - coveralls/upload:
+          flag_name: <<parameters.version>>
+          parallel: true
+  coverage:
+    executor:
+      name: python/default
+    steps:
+      - coveralls/upload:
+          carryforward: 3.11, 3.12
+          parallel_finished: true
+
+workflows:
+  checks:
+    jobs:
+      - linting
+      - tests:
+          matrix:
+            parameters:
+              version: ["3.11", "3.12"]
+      - coverage:
+          requires:
+            - tests
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -0,0 +1 @@
+*              @eonu
diff --git a/.github/ISSUE_TEMPLATE/bug.yml b/.github/ISSUE_TEMPLATE/bug.yml
@@ -0,0 +1,68 @@
+name: Report unexpected behaviour
+description: If you came across something unexpected, let us know here!
+labels: [bug, pending]
+
+body:
+  - type: checkboxes
+    id: exists
+    attributes:
+      label: Has this already been reported?
+      description: If you haven't already, please look other existing issues to see if this bug has already been reported.
+      options:
+        - label: This is a new bug!
+          required: true
+
+  - type: textarea
+    id: expected-behaviour
+    attributes:
+      label: Expected behaviour
+      description: |
+        Please describe the behaviour that you expected to see.
+
+        If appropriate, provide any links to official Sequentia documentation that indicate this is the behaviour that is expected.
+    validations:
+      required: true
+
+  - type: textarea
+    id: observed-behaviour
+    attributes:
+      label: Observed behaviour
+      description: |
+        Please describe the unexpected behaviour that you observed.
+
+        Make sure to provide as much information as possible, so that we can investigate as thoroughly as we can.
+    validations:
+      required: true
+
+  - type: textarea
+    id: example
+    attributes:
+      label: Code to reproduce
+      description: >
+        Please provide a snippet of code that shows how to reproduce the bug, 
+        making sure that it is [minimal and reproducible](https://stackoverflow.com/help/minimal-reproducible-example).
+
+      placeholder: |
+        import sequentia
+
+        ...
+      render: Python
+
+  - type: textarea
+    id: version
+    attributes:
+      label: Version details
+      description: |
+        To help us get to the root of the problem as fast as possible, please run the following command to display version information about:
+
+        - Python
+        - Sequentia
+        - Operating system
+
+        ```bash
+        python -c "import sequentia; print(sequentia.version.version_info())"
+        ```
+
+      render: Text
+    validations:
+      required: true
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: Got a question?
+    url: "https://github.com/eonu/sequentia/discussions/new?category=questions"
+    about: Start a discussion on GitHub discussions where Sequentia developers and users can respond.
diff --git a/.github/ISSUE_TEMPLATE/feature.yml b/.github/ISSUE_TEMPLATE/feature.yml
@@ -0,0 +1,21 @@
+name: Request a new feature or improvement
+description: If you have a suggestion for something that might improve Sequentia, let us know here!
+labels: [feature, pending]
+
+body:
+  - type: checkboxes
+    id: exists
+    attributes:
+      label: Does this suggestion already exist?
+      description: If you haven't already, please look through the documentation and other existing issues to see if this feature is already implemented.
+      options:
+        - label: This is a new feature!
+          required: true
+
+  - type: textarea
+    id: feature-description
+    attributes:
+      label: Feature description
+      description: Please describe the new feature or improvement that you would like.
+    validations:
+      required: true
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -0,0 +1,13 @@
+## Description
+
+<!-- If your pull request fixes an existing issue (e.g. #xxx), mention "Fixes #xxx" here. -->
+
+<!-- Please describe the purpose of the pull request. -->
+<!-- Provide thorough details about what you changed and why. -->
+
+## Checklist
+
+- [ ] I have added new tests (if necessary).
+- [ ] I have ensured that tests and coverage are passing on CI.
+- [ ] I have updated any relevant documentation (if necessary).
+- [ ] I have used a descriptive pull request title.
diff --git a/.github/workflows/create-github-release.yml b/.github/workflows/create-github-release.yml
@@ -0,0 +1,25 @@
+name: Create GitHub release
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: "Get previous tag"
+        id: latest-tag
+        uses: "WyriHaximus/github-action-get-previous-tag@v1"
+      - uses: ncipollo/release-action@v1
+        with:
+          tag: ${{ steps.latest-tag.outputs.tag }}
+          generateReleaseNotes: true
+          token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/create-pypi-release.yml b/.github/workflows/create-pypi-release.yml
@@ -0,0 +1,19 @@
+name: Create PyPI release
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v4
+      - name: Build and publish to PyPI
+        uses: JRubics/poetry-publish@v1.17
+        with:
+          python_version: "3.11.3"
+          poetry_version: "==1.7.1"
+          pypi_token: ${{ secrets.PYPI_TOKEN }}
diff --git a/.github/workflows/create-release-pr.yml b/.github/workflows/create-release-pr.yml
@@ -0,0 +1,60 @@
+name: Create release PR
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: Version
+        required: true
+
+jobs:
+  create-pull-request:
+    permissions: write-all
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v4
+        with:
+          ref: dev
+          fetch-depth: 0
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11.3
+      - name: Install Poetry
+        uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: 1.7.1
+      - name: Install base dependencies
+        run: poetry install --sync --only base
+      - name: Bump version
+        run: |
+          poetry run -q invoke release.build -- -v ${{ github.event.inputs.version }}
+      - name: Update changelog
+        uses: orhun/git-cliff-action@v2
+        id: cliff-changelog
+        with:
+          config: cliff.toml
+          args: --tag ${{ github.event.inputs.version }}
+        env:
+          OUTPUT: CHANGELOG.md
+      - name: Get changelog entry
+        uses: orhun/git-cliff-action@v2
+        id: cliff-entry
+        with:
+          config: cliff.toml
+          args: --unreleased --strip header
+        env:
+          OUTPUT: ENTRY.md
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@v5.0.2
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "release: v${{ github.event.inputs.version }}"
+          title: "release: v${{ github.event.inputs.version }}"
+          body: "${{ steps.cliff-entry.outputs.content }}"
+          branch: release/${{ github.event.inputs.version }}
+      - uses: rickstaa/action-create-tag@v1
+        with:
+          tag: v${{ github.event.inputs.version }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/semantic-pull-request.yml b/.github/workflows/semantic-pull-request.yml
@@ -0,0 +1,43 @@
+name: Enforce semantic PR title
+
+on:
+  pull_request_target:
+    types:
+      - opened
+      - edited
+      - synchronize
+
+permissions:
+  pull-requests: read
+
+jobs:
+  main:
+    name: validate
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v5
+        with:
+          subjectPattern: ^(?![A-Z]).+$
+          subjectPatternError: |
+            The subject "{subject}" found in the pull request title "{title}"
+            didn't match the configured pattern. Please ensure that the subject
+            doesn't start with an uppercase character.
+          types: |
+            build
+            chore
+            ci
+            docs
+            feat
+            fix
+            perf
+            refactor
+            release
+            revert
+            style
+            tests
+          scopes: |
+            deps
+            git
+            pkg
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -8,7 +8,7 @@ ehthumbs.db
 Thumbs.db
 
 # Byte-compiled / optimized / DLL files
-__pycache__/
+__pycache__
 *.py[cod]
 *$py.class
 
@@ -73,6 +73,7 @@ docs/_build
 #   having no cross-platform support, pipenv may install dependencies that don't work, or not
 #   install all needed dependencies.
 Pipfile.lock
+poetry.lock
 
 # Environments
 .env
@@ -87,3 +88,9 @@ venv.bak/
 .spyderproject
 .spyproject
 .vscode
+
+# Ruff
+.ruff_cache
+
+# Changelog entry
+ENTRY.md