Update pyEnsemblRest

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @gawbul

.github/workflows/pull_request.yaml

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+name: pull_request
+
+on:
+  pull_request:
+    paths:
+      - 'pyensemblrest/**.py'
+
+jobs:
+  test:
+    name: Run Tests
+    runs-on: ubuntu-latest
+    environment: dev
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+    timeout-minutes: 60
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set Poetry Version
+        id: set-poetry-version
+        run: echo "POETRY_VERSION=$(cat .poetry-version)" >> $GITHUB_OUTPUT
+
+      - name: Install Poetry
+        id: install-poetry-version
+        uses: snok/install-poetry@v1
+        with:
+          version: ${{ steps.set-poetry-version.outputs.POETRY_VERSION }}
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          virtualenvs-path: .venv
+          installer-parallel: true
+
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+
+      - name: Install project
+        run: poetry install --no-interaction
+
+      - name: Run pre-commit hooks, excluding unit tests
+        run: SKIP=unit-test poetry run pre-commit run --all-files
+
+      - name: Run unit tests with pytest and code coverage with pytest-cov
+        run: poetry run pytest -v --cov=pyensemblrest --cov-report lcov:./tests/lcov.info
+
+      - name: Upload Coverage Results
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: ./tests/lcov.info

.github/workflows/push_tag.yaml

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+name: push_tag
+
+on:
+  push:
+    tags:
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+
+permissions:
+  contents: read
+
+jobs:
+  release:
+    name: Release to GitHub
+    runs-on: ubuntu-latest
+    environment: dev
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ">=3.10 <3.13"
+
+      - name: Set Poetry Version
+        id: set-poetry-version
+        run: echo "POETRY_VERSION=$(cat .poetry-version)" >> $GITHUB_OUTPUT
+
+      - name: Install Poetry
+        id: install-poetry-version
+        uses: snok/install-poetry@v1
+        with:
+          version: ${{ steps.set-poetry-version.outputs.POETRY_VERSION }}
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          virtualenvs-path: .venv
+          installer-parallel: true
+
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+
+      - name: Install project
+        run: poetry install --no-interaction
+
+      - name: Build project
+        run: poetry build
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Create release
+        uses: softprops/action-gh-release@v2
+        if: startsWith(github.ref, 'refs/tags/')
+        with:
+          files: dist/*
+  publish:
+    needs:
+      - release
+    permissions:
+      id-token: write
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: dev
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish project
+        run: poetry publish
+        env:
+          POETRY_PYPI_TOKEN_PYENSEMBLREST: ${{ secrets.POETRY_PYPI_TOKEN_PYENSEMBLREST }}

.gitignore

@@ -39,6 +39,7 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
+lcov.info
 
 # Translations
 *.mo
@@ -63,3 +64,12 @@ target/
 .spyderproject
 cover/
 .spyproject/
+
+# Ruff
+.ruff_cache/
+
+# Mypy
+.mypy_cache/
+
+# Pytest
+.pytest_cache/

.poetry-version

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+1.8.4

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+    - id: no-commit-to-branch
+    - id: check-added-large-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.4
+    hooks:
+      - id: ruff
+        name: ruff
+        description: "Run 'ruff' for extremely fast Python linting"
+        entry: ruff check --force-exclude
+        language: python
+        types_or: [python, pyi, jupyter]
+        args: []
+        require_serial: true
+        additional_dependencies: []
+        minimum_pre_commit_version: "2.9.2"
+      - id: ruff-format
+        name: ruff-format
+        description: "Run 'ruff format' for extremely fast Python formatting"
+        entry: ruff format --force-exclude
+        language: python
+        types_or: [python, pyi, jupyter]
+        args: []
+        require_serial: true
+        additional_dependencies: []
+        minimum_pre_commit_version: "2.9.2"
+  - repo: local
+    hooks:
+      - id: poetry-check
+        name: poetry-check
+        entry: poetry check --quiet
+        language: system
+        pass_filenames: false
+        files: ^(.*/)?pyproject\.toml$
+      - id: mypy
+        name: mypy
+        entry: poetry run mypy
+        language: system
+        types: [python]
+        require_serial: true
+        exclude: ^(tests/|examples.py)
+      - id: unit-test
+        name: unit-test
+        entry: make unit-test
+        language: system
+        types: [file]
+        pass_filenames: false

CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.3.0] - 2024-11-22
+
+### Added
+
+- Various new endpoints to bring up to Ensembl REST release 15.8
+
+### Fixed
+
+- Fixed existing endpoints and unit tests as well as various bugs
+
+### Changed
+
+- Moved to Python 3.10+
+
+### Removed
+
+- Removed deprecated Ensembl endpoints