fix: ci

.cruft.json

@@ -0,0 +1,21 @@
+{
+  "template": "https://github.com/elixir-cloud-aai/cookiecutter-python",
+  "commit": "82a9aebbdff819758c94e7607c052a3fa5ba3b18",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "author_name": "ELIXIR Cloud AAI",
+      "author_email": "[email protected]",
+      "development_status": "1 - Planning",
+      "short_description": "File handler utilizing TUS and MinIO with DRS-Filer integration.",
+      "project_name": "tus-storagehandler",
+      "project_slug": "tus_storagehandler",
+      "github_username": "elixir-cloud-aai",
+      "python_version": "3.11",
+      "add_script": "n",
+      "year": "2024",
+      "_template": "https://github.com/elixir-cloud-aai/cookiecutter-python"
+    }
+  },
+  "directory": null
+}

.github/ISSUE_TEMPLATE/general-purpose.md

@@ -0,0 +1,45 @@
+Your issue may already be reported! Please search on the
+[issue tracker][issue-tracker] before creating one.
+
+## Expected Behavior
+
+<!--- If you're describing a bug, tell us what should happen -->
+
+<!--- If you're suggesting a change/improvement, tell us how it should work -->
+
+## Current Behavior
+
+<!--- If describing a bug, tell us what happens instead of the expected behavior -->
+
+<!--- If suggesting a change/improvement, explain the difference from current behavior -->
+
+## Possible Solution
+
+<!--- Not obligatory, but suggest a fix/reason for the bug, -->
+
+<!--- or ideas how to implement the addition or change -->
+
+## Steps to Reproduce (for bugs)
+
+<!--- Provide a link to a live example, or an unambiguous set of steps to -->
+
+<!--- reproduce this bug. Include code to reproduce, if relevant -->
+
+1.
+
+## Context
+
+<!--- How has this issue affected you? What are you trying to accomplish? -->
+
+<!--- Providing context helps us come up with a solution that is most useful in the real world -->
+
+## Your Environment
+
+<!--- Include as many relevant details about the environment you experienced the bug in -->
+
+- Version used:
+- Browser Name and version:
+- Operating System and version (desktop or mobile):
+- Link to your project:
+
+[issue-tracker]: https://github.com/elixir-cloud-aai/tus-storagehandler/issues

.github/actions/setup/poetry/action.yaml

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+---
+name: Setup Python and Poetry Action
+description: Configure system, Python, Poetry and deps and cache management.
+
+inputs:
+  os:
+    default: ubuntu-latest
+    description: The operating system to use
+  python-version:
+    default: '3.11'
+    description: The version of Python to use
+  poetry-version:
+    default: '1.8.2'
+    description: The version of Poetry to install
+  poetry-install-options:
+    default: ''
+    description: Additional options to pass to poetry install
+  poetry-export-options:
+    default: ''
+    description: Options to pass to poetry export for hash generation for cache
+                 invalidation
+
+runs:
+  using: composite
+  steps:
+    - uses: 'actions/setup-python@v5'
+      id: setup-python
+      with:
+        python-version: '${{ inputs.python-version }}'
+
+    - name: Setup pipx environment Variables
+      id: pipx-env-setup
+      # pipx default home and bin dir are not writable by the cache action
+      # so override them here and add the bin dir to PATH for later steps.
+      # This also ensures the pipx cache only contains poetry
+      run: |
+        SEP="${{ !startsWith(runner.os, 'windows') && '/' || '\\' }}"
+        PIPX_CACHE="${{ github.workspace }}${SEP}pipx_cache"
+        echo "pipx-cache-path=${PIPX_CACHE}" >> $GITHUB_OUTPUT
+        echo "pipx-version=$(pipx --version)" >> $GITHUB_OUTPUT
+        echo "PIPX_HOME=${PIPX_CACHE}${SEP}home" >> $GITHUB_ENV
+        echo "PIPX_BIN_DIR=${PIPX_CACHE}${SEP}bin" >> $GITHUB_ENV
+        echo "PIPX_MAN_DIR=${PIPX_CACHE}${SEP}man" >> $GITHUB_ENV
+        echo "${PIPX_CACHE}${SEP}bin" >> $GITHUB_PATH
+      shell: bash
+
+    - name: Pipx cache
+      id: pipx-cache
+      uses: actions/cache@v4
+      with:
+        path: ${{ steps.pipx-env-setup.outputs.pipx-cache-path }}
+        key: ${{ runner.os }}-python-
+             ${{ steps.setup-python.outputs.python-version }}-
+             pipx-${{ steps.pipx-env-setup.outputs.pipx-version }}-
+             poetry-${{ inputs.poetry-version }}
+
+    - name: Install poetry
+      if: steps.pipx-cache.outputs.cache-hit != 'true'
+      id: install-poetry
+      shell: bash
+      run: |
+        pipx install poetry \
+        --python "${{ steps.setup-python.outputs.python-path }}"
+
+    - name: Read poetry cache location
+      id: poetry-cache-location
+      shell: bash
+      run: |
+        echo "poetry-venv-location=$(poetry config virtualenvs.path)" \
+        >> $GITHUB_OUTPUT
+
+    - name: Generate hash only for required deps
+      run: |
+        poetry export ${{ inputs.poetry-export-options }} \
+        --format=requirements.txt --output=requirements.txt
+        echo "DEP_HASH=$(sha256sum requirements.txt | cut -d ' ' -f 1)" \
+         >> $GITHUB_ENV
+      shell: bash
+
+    - uses: actions/cache@v4
+      name: Poetry cache
+      with:
+        path: ${{ steps.poetry-cache-location.outputs.poetry-venv-location }}
+        key: ${{ runner.os }}-[python-
+             ${{ steps.setup-python.outputs.python-version }}]-[
+             ${{ env.DEP_HASH }}]-[${{ inputs.poetry-install-options }}]
+
+    - name: 'Poetry install'
+      if: steps.poetry-cache.outputs.cache-hit != 'true'
+      shell: bash
+      run: poetry install ${{ inputs.poetry-install-options }} --no-interaction
+...

.github/workflows/code_quality.yaml

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+---
+name: Code Quality
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  format:
+    name: Format
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up environment
+        uses: ./.github/actions/setup/poetry
+        with:
+          os: ${{ job.os }}
+          python-version: '3.11'
+          poetry-install-options: "--only=code_quality --no-root"
+          poetry-export-options: "--only=code_quality"
+
+      - name: Check code style
+        run: poetry run ruff format --check
+
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up environment
+        uses: ./.github/actions/setup/poetry
+        with:
+          os: ${{ job.os }}
+          python-version: '3.11'
+          poetry-install-options: "--only=code_quality --no-root"
+          poetry-export-options: "--only=code_quality"
+
+      - name: Check code quality
+        run: poetry run ruff check .
+
+  spell-check:
+    name: Spell Check
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up environment
+        uses: ./.github/actions/setup/poetry
+        with:
+          os: ${{ job.os }}
+          python-version: '3.11'
+          poetry-install-options: "--only=code_quality --no-root"
+          poetry-export-options: "--only=code_quality"
+
+      - name: Check spellings
+        run: poetry run typos .
+
+  type-check:
+    name: Type Check
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up environment
+        uses: ./.github/actions/setup/poetry
+        with:
+          os: ${{ job.os }}
+          python-version: '3.11'
+          poetry-install-options: "--with=code_quality --with=types --no-root"
+          poetry-export-options: "--with=code_quality --with=types"
+
+      - name: Check types
+        run: poetry run mypy tus_storagehandler/
+...

.github/workflows/code_test.yaml

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+---
+name: Code Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  integration-test:
+    name: Integration Test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up environment
+        uses: ./.github/actions/setup/poetry
+        with:
+          os: ${{ job.os }}
+          python-version: '3.11'
+          poetry-install-options: "--with=test"
+          poetry-export-options: "--with=test"
+
+      - name: Run tests and generate coverage as test_integration.xml
+        run: |
+          poetry run pytest \
+            --cov-report term \
+            --cov-report xml:test_integration.xml \
+            --cov=tests/test_integration
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          flags: test_integration
+          files: ./test_integration.xml
+          fail_ci_if_error: true
+          verbose: true
+
+  unit-test:
+    name: Unit Test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up environment
+        uses: ./.github/actions/setup/poetry
+        with:
+          os: ${{ job.os }}
+          python-version: '3.11'
+          poetry-install-options: "--with=test"
+          poetry-export-options: "--with=test"
+
+      - name: Run tests and generate coverage as test_unit.xml
+        run: |
+          poetry run pytest \
+            --cov-report term \
+            --cov-report xml:test_unit.xml \
+            --cov=tests/test_unit
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          flags: test_unit
+          files: ./test_unit.xml
+          fail_ci_if_error: true
+          verbose: true
+...

.github/workflows/docs.yaml

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+---
+name: Documentation Check
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  check-api-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up environment
+        uses: ./.github/actions/setup/poetry
+        with:
+          os: ${{ job.os }}
+          python-version: '3.11'
+          poetry-install-options: "--with=docs --with=types --no-root"
+          poetry-export-options: "--with=docs --with=types"
+
+      - name: Generate API docs
+        run: |
+          poetry run sphinx-apidoc -o /tmp/docs tus_storagehandler/
+
+      - name: Compare docs with main branch
+        id: check_docs_diff
+        run: |
+          shasum /tmp/docs/* > /tmp/docs.sha
+          rm -f docs/pages/.gitkeep # Remove placeholder file
+          shasum docs/pages/* > docs/project_doc.sha
+          diff=$(diff /tmp/docs.sha docs/project_doc.sha) || true
+          if [[ -n "$diff" ]]; then
+            echo "::error::API documentation is out of date."
+            exit 1
+          else
+            echo "API documentation is up to date."
+          fi
+...