From 0516517b893e6712717967f0463a6bbaca7fbf25 Mon Sep 17 00:00:00 2001 From: Javed Habib <100477031+JaeAeich@users.noreply.github.com> Date: Tue, 6 Aug 2024 13:49:07 +0530 Subject: [PATCH] chore(init): init from template (#10) Signed-off-by: Prati28 Co-authored-by: Prati28 --- .cruft.json | 22 + .github/ISSUE_TEMPLATE/general-purpose.md | 49 + .github/actions/setup/poetry/action.yaml | 92 + .github/workflows/code_quality.yaml | 84 + .github/workflows/code_test.yaml | 74 + .github/workflows/docs.yaml | 48 + .github/workflows/pr_validation.yaml | 76 + .github/workflows/release_pypi.yaml | 26 + .github/workflows/update.yaml | 55 + .github/workflows/vulnerability.yaml | 48 + .gitignore | 181 ++ .markdownlint.yaml | 74 + .pre-commit-config.yaml | 43 + .readthedocs.yaml | 16 + .safety-policy.yml | 43 + .yamllint.yaml | 13 + LICENSE | 201 +++ Makefile | 137 ++ PULL_REQUEST_TEMPLATE.md | 72 + README.md | 240 ++- docs/Makefile | 20 + docs/make.bat | 35 + docs/source/conf.py | 102 ++ docs/source/index.rst | 15 + docs/source/pages/modules.rst | 7 + docs/source/pages/tus_storagehandler.rst | 21 + images/logo-elixir-cloud-aai.svg | 112 ++ images/logo-elixir.svg | 82 + poetry.lock | 1889 +++++++++++++++++++++ pyproject.toml | 100 ++ tests/__init__.py | 1 + tests/test_integration/__init__.py | 1 + tests/test_integration/test_init.py | 9 + tests/test_unit/__init__.py | 1 + tests/test_unit/test_init.py | 9 + tus_storagehandler/__init__.py | 1 + tus_storagehandler/main.py | 10 + 37 files changed, 3985 insertions(+), 24 deletions(-) create mode 100644 .cruft.json create mode 100644 .github/ISSUE_TEMPLATE/general-purpose.md create mode 100644 .github/actions/setup/poetry/action.yaml create mode 100644 .github/workflows/code_quality.yaml create mode 100644 .github/workflows/code_test.yaml create mode 100644 .github/workflows/docs.yaml create mode 100644 .github/workflows/pr_validation.yaml create mode 100644 .github/workflows/release_pypi.yaml create mode 100644 .github/workflows/update.yaml create mode 100644 .github/workflows/vulnerability.yaml create mode 100644 .gitignore create mode 100644 .markdownlint.yaml create mode 100644 .pre-commit-config.yaml create mode 100644 .readthedocs.yaml create mode 100644 .safety-policy.yml create mode 100644 .yamllint.yaml create mode 100644 LICENSE create mode 100644 Makefile create mode 100644 PULL_REQUEST_TEMPLATE.md create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/source/conf.py create mode 100644 docs/source/index.rst create mode 100644 docs/source/pages/modules.rst create mode 100644 docs/source/pages/tus_storagehandler.rst create mode 100644 images/logo-elixir-cloud-aai.svg create mode 100644 images/logo-elixir.svg create mode 100644 poetry.lock create mode 100644 pyproject.toml create mode 100644 tests/__init__.py create mode 100644 tests/test_integration/__init__.py create mode 100644 tests/test_integration/test_init.py create mode 100644 tests/test_unit/__init__.py create mode 100644 tests/test_unit/test_init.py create mode 100644 tus_storagehandler/__init__.py create mode 100644 tus_storagehandler/main.py diff --git a/.cruft.json b/.cruft.json new file mode 100644 index 0000000..a5de21c --- /dev/null +++ b/.cruft.json @@ -0,0 +1,22 @@ +{ + "template": "https://github.com/elixir-cloud-aai/cookiecutter-python.git", + "commit": "74890427a2926b6943577df5f23001a65325f591", + "checkout": null, + "context": { + "cookiecutter": { + "author_name": "ELIXIR Cloud AAI", + "author_email": "cloud-service@elixir-europe.org", + "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": "y", + "year": "2024", + "add_pypi_release_ci": "y", + "_template": "https://github.com/elixir-cloud-aai/cookiecutter-python.git" + } + }, + "directory": null +} diff --git a/.github/ISSUE_TEMPLATE/general-purpose.md b/.github/ISSUE_TEMPLATE/general-purpose.md new file mode 100644 index 0000000..8f6f2cf --- /dev/null +++ b/.github/ISSUE_TEMPLATE/general-purpose.md @@ -0,0 +1,49 @@ +Your issue may already be reported! Please search on the +[issue tracker][issue-tracker] before creating one. + +## Expected behavior + + + + + +## Current behavior + + + + + +## Possible solution + + + + + +## Context + + + + + +## Steps to reproduce (FOR BUGS) + + + + + +1. + +## Your environment (FOR BUGS) + + + +- 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 diff --git a/.github/actions/setup/poetry/action.yaml b/.github/actions/setup/poetry/action.yaml new file mode 100644 index 0000000..92154b2 --- /dev/null +++ b/.github/actions/setup/poetry/action.yaml @@ -0,0 +1,92 @@ +--- +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 +... diff --git a/.github/workflows/code_quality.yaml b/.github/workflows/code_quality.yaml new file mode 100644 index 0000000..135cd7a --- /dev/null +++ b/.github/workflows/code_quality.yaml @@ -0,0 +1,84 @@ +--- +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/ +... diff --git a/.github/workflows/code_test.yaml b/.github/workflows/code_test.yaml new file mode 100644 index 0000000..8c8f682 --- /dev/null +++ b/.github/workflows/code_test.yaml @@ -0,0 +1,74 @@ +--- +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 +... diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml new file mode 100644 index 0000000..7b528f2 --- /dev/null +++ b/.github/workflows/docs.yaml @@ -0,0 +1,48 @@ +--- +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/source/pages \ + tus_storagehandler/ + + - name: Compare current docs with latest docs + id: check_docs_diff + run: | + shasum /tmp/docs/source/pages/* > /tmp/docs.sha + shasum docs/source/pages/* > docs/project_doc.sha + awk '{print $1}' /tmp/docs.sha > /tmp/docs_hashes.sha + awk '{print $1}' docs/project_doc.sha > docs/project_doc_hashes.sha + diff=$(diff /tmp/docs_hashes.sha docs/project_doc_hashes.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 +... diff --git a/.github/workflows/pr_validation.yaml b/.github/workflows/pr_validation.yaml new file mode 100644 index 0000000..0798f13 --- /dev/null +++ b/.github/workflows/pr_validation.yaml @@ -0,0 +1,76 @@ +--- +name: PR evaluation + +on: + pull_request: + types: [opened, synchronize, reopened, ready_for_review, edited] + branches: ['main'] + +jobs: + detect-unresolved-conflicts: + name: Detect unresolved merge conflicts + runs-on: ubuntu-latest + needs: semantic_pr + steps: + - uses: actions/checkout@v3 + - name: List files with merge conflict markers + run: git --no-pager grep "<<<<<<<" ":(exclude).github/" || true + - name: Fail or succeed job if any files with merge conflict markers + run: exit $(git grep "<<<<<<<" ":(exclude).github/" | wc --lines) + + pre-commit: + name: Pre-commit checks + 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=misc --no-root" + poetry-export-options: "--only=misc" + + - name: Check all the pre-commit hooks passed + run: pre-commit run --all-files + + semantic-pr: + name: Semantic PR title + runs-on: ubuntu-latest + if: ${{ github.event.action != 'edited' || + github.event.changes.title != null }} + steps: + - name: Check if the PR title is semantic + uses: amannn/action-semantic-pull-request@v5 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + types: | + fix + feat + docs + style + refactor + perf + test + build + ci + chore + revert + subjectPattern: ^(?![A-Z])(?=.{1,50}$).+$ + 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 & not have more than 50 + characters. + + - name: Check length of PR title + run: | + PR_TITLE="${{ github.event.pull_request.title }}" + if [ ${#PR_TITLE} -gt 50 ]; then + echo "The PR title is too long. Please keep it under 50 characters." + exit 1 + fi +... diff --git a/.github/workflows/release_pypi.yaml b/.github/workflows/release_pypi.yaml new file mode 100644 index 0000000..e03080f --- /dev/null +++ b/.github/workflows/release_pypi.yaml @@ -0,0 +1,26 @@ +--- +name: Release package + +on: + release: + types: [released] + +jobs: + pypi: + name: Publish to PyPI + runs-on: ubuntu-latest + steps: + - name: Checkout code + 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=main" + poetry-export-options: "--only=main" + + - name: Publish package to PyPI + run: poetry publish --build -u __token__ -p ${{ secrets.PYPI_TOKEN }} +... diff --git a/.github/workflows/update.yaml b/.github/workflows/update.yaml new file mode 100644 index 0000000..d6986cc --- /dev/null +++ b/.github/workflows/update.yaml @@ -0,0 +1,55 @@ +--- +name: Update project structure + +on: + schedule: + - cron: "0 2 * * 1" # Every Monday at 2am + +jobs: + update-template: + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - name: Set up environment + uses: ./.github/actions/setup/poetry + with: + os: ${{ job.os }} + python-version: '3.11' + poetry-install-options: "--only=misc --no-root" + poetry-export-options: "--only=misc" + + - name: Update project structure + run: | + cruft update -y + + - name: Check if there are changes + id: changes + uses: UnicornGlobal/has-changes-action@v1.0.11 + + - name: Apply additional changes and fixes + if: steps.changes.outputs.changed == 1 + run: | + poetry lock --no-update + poetry install + pre-commit run --all-files + + - name: Get new template version + if: steps.changes.outputs.changed == 1 + run: | + COMMIT_HASH=$(cat .cruft.json | jello -r "_['commit'][:8]") + echo "TEMPLATE_COMMIT=${COMMIT_HASH}" >> $GITHUB_ENV + + - name: Create Pull Request + if: steps.changes.outputs.changed == 1 + uses: peter-evans/create-pull-request@v6 + with: + token: ${{ secrets.AUTO_UPDATE_GITHUB_TOKEN }} + commit-message: >- + chore: update project structure to ${{ env.TEMPLATE_COMMIT }} + title: "chore: auto-sync cookiecutter template" + body: "" + branch: chore/cookiecutter-pypackage + delete-branch: true +... diff --git a/.github/workflows/vulnerability.yaml b/.github/workflows/vulnerability.yaml new file mode 100644 index 0000000..ff4db16 --- /dev/null +++ b/.github/workflows/vulnerability.yaml @@ -0,0 +1,48 @@ +--- +name: Vulnerability test + +on: + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + code-vulnerabilities: + name: Code + 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=vulnerability --no-root" + poetry-export-options: "--only=vulnerability" + + - name: Check code vulnerabilities with bandit + run: poetry run bandit -c pyproject.toml -r tus_storagehandler/ + + dependency-vulnerabilities: + name: Dependencies + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - name: Set up environment + uses: ./.github/actions/setup/poetry + with: + os: ${{ job.os }} + python-version: '3.11' + poetry-install-options: "--only=vulnerability --no-root" + poetry-export-options: "--only=vulnerability" + + - name: Check dependency vulnerabilities with safety + run: poetry run safety check --full-report +... diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..7d1a0f5 --- /dev/null +++ b/.gitignore @@ -0,0 +1,181 @@ +######### User-defined project-specific ignore patterns. ######### +######### Add your custom ignore patterns HERE. ######### + +######### End of user-defined project-specific ignore patterns. ######### + +######## This section contains auto-generated ignore patterns for ######### +######## Python projects. ######### + +# Created by https://www.toptal.com/developers/gitignore/api/python +# Edit at https://www.toptal.com/developers/gitignore?templates=python + +### Python ### +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$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 + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__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/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +.idea/ + +### Python Patch ### +# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration +poetry.toml + +# ruff +.ruff_cache/ + +# LSP config files +pyrightconfig.json + +# End of https://www.toptal.com/developers/gitignore/api/python +SquareX Safe File Viewer +✕ + +######### End of auto-generated ignore patterns for Python projects. ######### diff --git a/.markdownlint.yaml b/.markdownlint.yaml new file mode 100644 index 0000000..a051501 --- /dev/null +++ b/.markdownlint.yaml @@ -0,0 +1,74 @@ +--- +default: true + +# Headings +MD001: + level: 1 # Require headings to increment by one level at a time +MD002: + level: 2 # Require that the first heading in a document is a level 2 heading +MD003: + style: atx # Enforce a consistent style for headings (e.g., atx style) + +# Unordered Lists +MD004: + style: dash # Enforce consistent marker style (e.g., - for list items) +MD005: true # Ensure list indentation is consistent +MD006: true # Require proper indentation for list items +MD007: + indent: 2 # Enforce a consistent indentation level for nested list items + +# Line Length +MD013: + line_length: 80 # Limit line length to 80 characters + code_blocks: false # Exclude code blocks from line length rule + tables: false # Exclude tables from line length rule + +# Trailing Spaces +MD009: + strict: true # Ensure no trailing spaces at the end of lines + +# Punctuation +MD026: + punctuation: ".,;:!" # Ensure proper punctuation in headings + +# Horizontal Rules +MD035: + style: "***" # Enforce a consistent style for horizontal rules + +# Links and Images +MD042: true # Require proper use of URLs in links +MD045: true # Ensure alt text is provided for images + +# General Formatting +MD010: true # No hard tabs +MD012: + maximum: 1 # No multiple consecutive blank lines +MD014: true # Dollar signs used before commands without showing output +MD018: true # No space after hash on atx style heading +MD019: true # Multiple spaces after hash on atx style heading +MD020: true # No space inside hashes on closed atx style heading +MD021: true # No multiple spaces inside hashes on closed atx style heading +MD022: true # Headings should be surrounded by blank lines +MD023: true # Headings must start at the beginning of the line +MD024: true # Multiple headings with the same content +MD025: true # Multiple top-level headings in the same document +MD027: true # Multiple spaces after blockquote symbol +MD028: true # Blank line inside blockquote +MD029: true # Ordered list item prefix +MD030: true # Spaces after list markers +MD031: true # Fenced code blocks should be surrounded by blank lines +MD032: true # Lists should be surrounded by blank lines +MD033: true # Inline HTML +MD034: true # Bare URL used +MD036: true # Emphasis used instead of a header +MD037: true # Spaces inside emphasis markers +MD038: true # Spaces inside code span elements +MD039: true # Spaces inside link elements +MD040: true # Fenced code blocks should have a language specified +MD041: false # First line need not be h1 +MD046: true # Code block style +MD047: true # Files should end with a single newline character +MD048: true # Code fence style +MD049: true # Required heading structure +MD050: true # Strong style should be consistent +... diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..2d0f66d --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,43 @@ +--- +# See https://pre-commit.com for more information +# See https://pre-commit.com/hooks.html for more hooks +# Common commands: +# pre-commit install +# pre-commit autoupdate +# pre-commit run --all-files --hook-stage commit +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 + hooks: + - id: check-added-large-files + - id: destroyed-symlinks + - id: detect-private-key + - id: end-of-file-fixer + - id: mixed-line-ending + args: [--fix=auto] + - id: trailing-whitespace + - repo: https://github.com/igorshubovych/markdownlint-cli + rev: v0.41.0 + hooks: + - id: markdownlint + args: ["--fix"] + - repo: https://github.com/executablebooks/mdformat + rev: 0.7.17 + hooks: + - id: mdformat + additional_dependencies: + - mdformat-config + - mdformat-black + - mdformat-frontmatter + args: [--wrap=80] + - repo: https://github.com/adrienverge/yamllint.git + rev: v1.35.1 + hooks: + - id: yamllint + - repo: https://github.com/pappasam/toml-sort + rev: v0.23.1 + hooks: + - id: toml-sort-fix + args: [--in-place, --all, --trailing-comma-inline-array] + exclude: poetry.lock +... diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..ec7defb --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,16 @@ +--- +version: 2 + +build: + os: ubuntu-22.04 + tools: + python: '3.11' + jobs: + post_create_environment: + - python -m pip install poetry + post_install: + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs + +sphinx: + configuration: docs/source/conf.py +... diff --git a/.safety-policy.yml b/.safety-policy.yml new file mode 100644 index 0000000..7089764 --- /dev/null +++ b/.safety-policy.yml @@ -0,0 +1,43 @@ +--- +version: '3.0' + +scanning-settings: + max-depth: 6 + exclude: [] + include-files: [] + system: + targets: [] + +security: + ignore-vulnerabilities: + 70612: + reason: "Won't use untrusted templates without sandboxing." + expires: '2025-5-27' + +report: + dependency-vulnerabilities: + enabled: true + auto-ignore-in-report: + python: + environment-results: true + unpinned-requirements: true + cvss-severity: [] + +fail-scan-with-exit-code: + dependency-vulnerabilities: + enabled: true + fail-on-any-of: + cvss-severity: + - critical + - high + - medium + exploitability: + - critical + - high + - medium + +security-updates: + dependency-vulnerabilities: + auto-security-updates-limit: + - patch +... diff --git a/.yamllint.yaml b/.yamllint.yaml new file mode 100644 index 0000000..ad3171a --- /dev/null +++ b/.yamllint.yaml @@ -0,0 +1,13 @@ +--- +# https://yamllint.readthedocs.io/en/stable/configuration.html#default-configuration +extends: default + +rules: + truthy: + ignore: + .github/**/*.yaml + document-start: + level: error + document-end: + level: error +... diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..35c9d67 --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright 2024 ELIXIR Cloud AAI + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..428044c --- /dev/null +++ b/Makefile @@ -0,0 +1,137 @@ +# NOTE: This Makefile assumes that dependencies are installed and, if a virtual +# environment is used, it is activated. + +## Variables ################################################################## +# NOTE: Define any variables here if needed in the future + +## Documentation ############################################################## +# NOTE: Keep all the targets in alphabetical order for better readability. + +default: help + +.PHONY: help +help: + @echo "\nUsage: make [target] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n" + @echo "Available targets:\n" + + @echo "Code Quality ------------------------------------------------------------------" + @echo " \033[1m\033[35mformat-lint\033[0m \033[37m(fl)\033[0m: \033[36mRun linter, formatter, spellcheck.\033[0m" + @echo " \033[1m\033[35mprecommit-check\033[0m \033[37m(pc)\033[0m: \033[36mRun all pre-commit checks.\033[0m" + @echo " \033[1m\033[35msecurity\033[0m \033[37m(s)\033[0m: \033[36mRun security scans.\033[0m" + @echo " \033[1m\033[35mtype-check\033[0m \033[37m(tc)\033[0m: \033[36mPerform type checking.\033[0m\n" + + @echo "Documentation -----------------------------------------------------------------" + @echo " \033[1m\033[35mdocs\033[0m \033[37m(d)\033[0m: \033[36mGenerate project documentation.\033[0m\n" + + @echo "Environment Management --------------------------------------------------------" + @echo " \033[1m\033[35mclean-venv\033[0m \033[37m(cv)\033[0m: \033[36mRemove virtual environment.\033[0m" + @echo " \033[1m\033[35minstall\033[0m \033[37m(i)\033[0m: \033[36mInstall dependencies and tus_storagehandler.\033[0m" + @echo " \033[1m\033[35mvenv\033[0m \033[37m(v)\033[0m: \033[36mCreate virtual environment.\033[0m\n" + + @echo "Miscellaneous -----------------------------------------------------------------" + @echo " \033[1m\033[35mupdate\033[0m \033[37m(u)\033[0m: \033[36mUpdate the template.\033[0m\n" + + @echo "Testing -----------------------------------------------------------------------" + @echo " \033[1m\033[35mtest\033[0m \033[37m(t)\033[0m: \033[36mRun all tests.\033[0m\n" + +## Autogenerated Targets ###################################################### +# NOTE: Keep all the targets in alphabetical order for better readability. +# NOTE: Do not modify the autogenerated targets, unless necessary, write custom +# targets in the custom section below.. + +.PHONY: clean-venv +clean-venv: + @echo "\nRemoving the virtual environment ++++++++++++++++++++++++++++++++++++++++++++++\n" + @rm -rf .venv + +.PHONY: cv +cv: clean-venv + +.PHONY: docs +docs: + @echo "\nGenerating project documentation ++++++++++++++++++++++++++++++++++++++++++++++\n" + @poetry run sphinx-apidoc -f -o docs/source/pages tus_storagehandler + @cd docs && make html + @echo "\nSummary ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n" + @echo "Documentation generated successfully." + @echo "Open docs/build/html/index.html in your browser." + @echo "Or serve it locally using:" + @echo "python -m http.server -d docs/build/html/" + +.PHONY: d +d: docs + +.PHONY: format-lint +format-lint: + @echo "\nRunning linter and formatter using ruff and typos +++++++++++++++++++++++++++++\n" + @poetry run ruff format && poetry run ruff check --fix + @typos . + +.PHONY: fl +fl: format-lint + +.PHONY: install +install: + @echo "\nInstalling dependencies and with this package +++++++++++++++++++++++++++++++++\n" + @poetry install --with=code_quality,docs,misc,test,types,vulnerability + +.PHONY: i +i: install + +.PHONY: precommit-check +precommit-check: + @echo "\nRunning pre-commit checks +++++++++++++++++++++++++++++++++++++++++++++++++++++\n" + @poetry run pre-commit run --all-files + +.PHONY: pc +pc: precommit-check + +.PHONY: security +security: + @echo "\nRunning security scans using bandit and safety ++++++++++++++++++++++++++++++++\n" + @poetry run safety check --full-report + @poetry run bandit -c pyproject.toml -r tus_storagehandler + +.PHONY: s +s: security + +.PHONY: test +test: + @echo "\nRunning tests using pytest ++++++++++++++++++++++++++++++++++++++++++++++++++++\n" + @poetry run pytest tests/ + +.PHONY: t +t: test + +.PHONY: type-check +type-check: + @echo "\nPerforming type checking with mypy ++++++++++++++++++++++++++++++++++++++++++++\n" + @poetry run mypy tus_storagehandler + +.PHONY: tc +tc: type-check + +.PHONY: update +update: + @echo "\nUpdating the template +++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n" + @echo "Using latest version from remote: https://github.com/elixir-cloud-aai/cookiecutter-python." + @poetry run cruff update -y + +.PHONY: u +u: update + +.PHONY: venv +venv: + @echo "\nCreating a virtual environment ++++++++++++++++++++++++++++++++++++++++++++++++\n" + @python -m venv .venv + @echo "\nSummary +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n" + @echo "Virtual environment created successfully." + @echo "To activate the environment for this shell session, run:" + @echo "source .venv/bin/activate" + +.PHONY: v +v: venv + +## Custom Targets ############################################################# +# NOTE: Keep all the targets in alphabetical order for better readability. +# NOTE: Add any custom targets here if needed in the future. diff --git a/PULL_REQUEST_TEMPLATE.md b/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..e38c4ab --- /dev/null +++ b/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,72 @@ +#### Description + + + +- Fixes #(issue number) + + + +#### Checklist + + + +- \[ \] My code follows the [contributing guidelines][contributing-guidelines] + of this project, including, in particular, with regard to any style guidelines +- \[ \] The title of my PR complies with the + [Conventional Commits specification][conv-commits]; in particular, it clearly + indicates that a change is a breaking change +- \[ \] I acknowledge that all my commits will be squashed into a single commit, + using the PR title as the commit message +- \[ \] I have performed a self-review of my own code +- \[ \] I have commented my code in hard-to-understand areas +- \[ \] I have updated the user-facing documentation to describe any new or + changed behavior +- \[ \] I have added type annotations for all function/class/method interfaces + or updated existing ones (only for Python, TypeScript, etc.) +- \[ \] I have provided appropriate documentation + ([Google-style Python docstrings][py-doc-google]) for all + packages/modules/functions/classes/methods or updated existing ones +- \[ \] My changes generate no new warnings +- \[ \] I have added tests that prove my fix is effective or that my feature + works +- \[ \] New and existing unit tests pass locally with my changes +- \[ \] I have not reduced the existing code coverage + +#### Comments + + + +[contributing-guidelines]: https://elixir-cloud-aai.github.io/guides/guide-contributor/workflow/ +[conv-commits]: https://www.conventionalcommits.org/en +[py-doc-google]: https://google.github.io/styleguide/pyguide.html diff --git a/README.md b/README.md index 9ce6277..a18000a 100644 --- a/README.md +++ b/README.md @@ -1,24 +1,216 @@ -# TUS Storage Handler - -## Synopsis -This Flask application provides endpoints for uploading, downloading, and listing files in a MinIO bucket, with TUS protocol support for uploads, and CORS enabled for cross-origin requests. - -## Installation - -### Prerequisites -This flask application requires a running instance of [minio](https://min.io/download) - -Run the minio instance by executing the following command in the location where minio is installed - -`minio server /data --console-address ":9001"` - -Download the required dependencies - -1. Navigate to the folder `TusStorageHandler` -2. Create a virtual environment and activate it (optional) -3. `pip install -r requirements.txt` - -### Running the application - -`flask run` -The application will be running on `http://127.0.0.1:5000` by default. +[![Bandit](https://img.shields.io/badge/security-bandit-yellow.svg)](https://bandit.readthedocs.io/en/latest/) +[![codecov](https://codecov.io/gh/elixir-cloud-aai/tus-storagehandler/branch/main/graph/badge.svg)](https://codecov.io/gh/elixir-cloud-aai/tus-storagehandler) +[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)][code-of-conduct] +[![Documentation Status](https://readthedocs.org/projects/tus_storagehandler/badge/?version=latest)](https://tus_storagehandler.readthedocs.io/en/latest/?badge=latest) +[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](./LICENSE) +[![Python 3.11](https://img.shields.io/badge/python-3.11-blue.svg)](https://www.python.org/) +[![GitHub contributors](https://img.shields.io/github/contributors/elixir-cloud-aai/tus-storagehandler)](https://github.com/elixir-cloud-aai/tus-storagehandler/graphs/contributors) +[![Ruff](https://img.shields.io/badge/linter%20&%20formatter-ruff-000000.svg)](https://docs.astral.sh/ruff/) +[![Safety](https://img.shields.io/badge/security-safety-orange.svg)](https://safetycli.com/product/safety-cli) + +# tus-storagehandler + +File handler utilizing TUS and MinIO with DRS-Filer integration. + +## Table of Contents + +- [Synopsis](#synopsis) +- [Basic Usage](#basic-usage) +- [Installation](#installation) +- [Development](#development) +- [Contributing](#contributing) +- [Code of Conduct](#code-of-conduct) +- [Versioning](#versioning) +- [License](#license) +- [Contact](#contact) + +## Synopsis +This application provides endpoints for uploading, downloading, and listing files in a MinIO bucket, with TUS protocol support for uploads, and CORS enabled for cross-origin requests. + +## Basic Usage + +## Installation + +### Prerequisites + +This flask application requires a running instance of [minio](https://min.io/download) + +Run the minio instance by executing the following command in the location where minio is installed + +```sh +minio server /data --console-address ":9001" +``` + +### Install Dependencies using Poetry + +1. **Download the required dependencies** + + Navigate to the folder `tus_storagehandler`. + +2. **Install Poetry** + + If you haven't already, install Poetry by following the instructions on the [Poetry website](https://python-poetry.org/docs/#installation). + +3. **Create and Activate a Virtual Environment (optional)** + + Poetry automatically creates and manages a virtual environment for your project. You can activate it using: + ```sh + poetry shell + ``` + +4. **Install Dependencies** + + Run the following command to install the dependencies defined in the `pyproject.toml` file: + ```sh + poetry install + ``` + +## Development + +For ease of use, certain scripts have been abbreviated in `Makefile`, make sure +that you have installed the dependencies before running the commands. + +> **Note**: `make` commands are only available for Unix-based systems. + +To view the commands available, run: + +```sh +make +``` + +Here are certain commands that you might find useful: + +- Make a virtual environment + +```sh +make v +``` + +- Install all dependencies including optional dependencies + +```sh +make i +``` + +> **Note**: This project uses optional dependency groups such as `types`, +> `code_quality`, `docs`, `vulnerability`, `test`, and `misc`. To install stubs +> or types for the dependencies, you **must** use the following command: +> +> ```sh +> poetry add types-foo --group types +> ``` +> +> Replace `types-foo` with the name of the package for the types. All runtime +> dependencies should be added to the `default` group. For example, to install +> `requests` and its type stubs, run: +> +> ```sh +> poetry add requests +> poetry add types-requests --group types +> ``` +> +> This ensures that the type checker functions correctly. +> +> **Note**: Since the dependencies are segregated into groups, if you add a new +> group make sure to add it in `make install` command in [Makefile](Makefile). + +- Run tests + +```sh +make t +``` + +- Run linter, formatter and spell checker + +```sh +make fl +``` + +- Build the documentation + +```sh +make d +``` + +> **Note**: If you make changes to the code, make sure to generate and push the +> documentation using above command, else the documentation check CI will fail. +> Do NOT edit auto-generated documentation manually. + +- Run type checker + +```sh +make tc +``` + +- Run all pre-commit checks + +```sh +make pc +``` + +- Update the cookiecutter template + +```sh +make u +``` + +> **Note**: This is not the complete list of commands, run `make` to find out if +> more have been added. + +## Contributing + +This project is a community effort and lives off _your_ contributions, be it in +the form of bug reports, feature requests, discussions, fixes or any other form +of contribution! + +Please refer to the guidelines available at [`CONTRIBUTING.md`][contributing] if +you are interested in contributing. + +## Code of Conduct + +We kindly request all contributors to abide by our +[organization's Code of Conduct][code-of-conduct]. Please also refer to this +document if you want to report an incident with respect to conduct in our +community. Thank you for your cooperation. + +## Versioning + +The project adopts the [semantic versioning][semver] scheme for versioning. +Currently the software is in a pre-release stage, so changes to the API, +including breaking changes, may occur at any time without further notice. + +## License + +This project is distributed under the [Apache License 2.0][badge-license-url], a +copy of which is also available in [`LICENSE`][license]. + +## Contact + +The project is maintained by [ELIXIR Cloud & AAI][elixir-cloud-aai], a Driver +Project of the [Global Alliance for Genomics and Health (GA4GH)][ga4gh], under +the umbrella of the [ELIXIR] [Compute Platform][elixir-compute]. + +To get in touch with us, please use one of the following routes: + +- For filing bug reports, feature requests or other code-related issues, please + make use of the project's [issue tracker][issue-tracker]. +- For private/personal issues, more involved communication, or if you would like + to join our team as a regular contributor, you can either join our + [chat board][badge-chat-url] or [email] the community leaders. + +[![logo-elixir]][elixir] [![logo-elixir-cloud-aai]][elixir-cloud-aai] + +[badge-chat-url]: https://join.slack.com/t/elixir-cloud/shared_invite/enQtNzA3NTQ5Mzg2NjQ3LTZjZGI1OGQ5ZTRiOTRkY2ExMGUxNmQyODAxMDdjM2EyZDQ1YWM0ZGFjOTJhNzg5NjE0YmJiZTZhZDVhOWE4MWM +[badge-license-url]: http://www.apache.org/licenses/LICENSE-2.0 +[code-of-conduct]: https://elixir-cloud-aai.github.io/about/code-of-conduct/ +[contributing]: https://elixir-cloud-aai.github.io/guides/guide-contributor/ +[elixir]: https://elixir-europe.org/ +[elixir-cloud-aai]: https://elixir-cloud.dcc.sib.swiss/ +[elixir-compute]: https://elixir-europe.org/platforms/compute +[email]: mailto:cloud-service@elixir-europe.org +[ga4gh]: https://ga4gh.org/ +[issue-tracker]: https://github.com/elixir-cloud-aai/tus-storagehandler/issues +[license]: LICENSE +[logo-elixir]: images/logo-elixir.svg +[logo-elixir-cloud-aai]: images/logo-elixir-cloud-aai.svg +[semver]: https://semver.org/ diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..dc1312a --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..8bb724a --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,102 @@ +"""Configuration file for the Sphinx documentation builder.""" + +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +import datetime +import os +import sys +from pathlib import Path + +import tomli + +sys.path.insert(0, os.path.abspath("../..")) + + +# -- Project information ----------------------------------------------------- +def _get_project_meta(): + _pyproject_path = Path(__file__).parents[2] / "pyproject.toml" + with open(_pyproject_path, mode="rb") as pyproject: + return tomli.load(pyproject)["tool"]["poetry"] + + +pkg_meta = _get_project_meta() +current_year = datetime.datetime.now().year +project = str(pkg_meta["name"]) +project_copyright = f"{current_year}, {str(pkg_meta['authors'][0])}" +author = str(pkg_meta["authors"][0]) + +version = str(pkg_meta["version"]) +release = version + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.doctest", + "sphinx.ext.todo", + "sphinx.ext.coverage", + "sphinx.ext.viewcode", + "sphinx.ext.autosummary", + # Used to write beautiful docstrings: + "sphinx.ext.napoleon", + # Used to include .md files: + "m2r2", + # Used to insert typehints into the final docs: + "sphinx_autodoc_typehints", + # Used to embed values from the source code into the docs: + "added_value", +] +# Set `typing.TYPE_CHECKING` to `True`: +# https://pypi.org/project/sphinx-autodoc-typehints/ +set_type_checking_flag = False +always_document_param_types = False + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: + +source_suffix = [".rst", ".md"] + +# The master toctree document. +master_doc = "index" + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = "en" + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path . +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = "furo" + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ["_static"] + +# -- Extension configuration ------------------------------------------------- +napoleon_numpy_docstring = False + +# -- Options for todo extension ---------------------------------------------- + +# If true, `todo` and `todoList` produce output, else they produce nothing. +todo_include_todos = True diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..f51987b --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,15 @@ +Welcome to tus_storagehandler's documentation! +=========================================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + pages/modules + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/source/pages/modules.rst b/docs/source/pages/modules.rst new file mode 100644 index 0000000..66ab2b8 --- /dev/null +++ b/docs/source/pages/modules.rst @@ -0,0 +1,7 @@ +tus_storagehandler +================== + +.. toctree:: + :maxdepth: 4 + + tus_storagehandler diff --git a/docs/source/pages/tus_storagehandler.rst b/docs/source/pages/tus_storagehandler.rst new file mode 100644 index 0000000..50d75ff --- /dev/null +++ b/docs/source/pages/tus_storagehandler.rst @@ -0,0 +1,21 @@ +tus\_storagehandler package +=========================== + +Submodules +---------- + +tus\_storagehandler.main module +------------------------------- + +.. automodule:: tus_storagehandler.main + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: tus_storagehandler + :members: + :undoc-members: + :show-inheritance: diff --git a/images/logo-elixir-cloud-aai.svg b/images/logo-elixir-cloud-aai.svg new file mode 100644 index 0000000..18ecf21 --- /dev/null +++ b/images/logo-elixir-cloud-aai.svg @@ -0,0 +1,112 @@ + + + + + + + + image/svg+xml + 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b/pyproject.toml @@ -0,0 +1,100 @@ +[build-system] +build-backend = "poetry.core.masonry.api" +requires = ["poetry-core"] + +[tool.mypy] +warn_return_any = true +warn_unused_configs = true + +[tool.poetry] +authors = ["ELIXIR Cloud AAI "] +classifiers = [ + "Development Status :: 1 - Planning", + "License :: OSI Approved :: Apache Software License", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.11", +] +description = "File handler utilizing TUS and MinIO with DRS-Filer integration." +license = "Apache-2.0" +maintainers = ["ELIXIR Cloud AAI "] +name = "tus_storagehandler" +readme = "README.md" +repository = "https://github.com/elixir-cloud-aai/tus-storagehandler" +version = "0.1.0" + +[tool.poetry.dependencies] +python = ">=3.11" + +[tool.poetry.group.code_quality] +optional = true + +[tool.poetry.group.code_quality.dependencies] +mypy = ">=1.10.0" +ruff = ">=0.4.10" +typos = ">=1.22.8" + +[tool.poetry.group.docs] +optional = true + +[tool.poetry.group.docs.dependencies] +added-value = ">=0.24.0" +docutils = ">=0.20.1" +furo = ">=2024.5.6" +m2r2 = ">=0.3.3.post2" +sphinx = ">=7.3.7" +sphinx-autodoc-typehints = ">=2.1.0" +tomli = ">=2.0.1" + +[tool.poetry.group.misc] +optional = true + +[tool.poetry.group.misc.dependencies] +cruft = ">=2.15.0" +jello = ">=1.6.0" +pre-commit = ">=3.7.1" + +[tool.poetry.group.test] +optional = true + +[tool.poetry.group.test.dependencies] +pytest = ">=8.2.2,<9.0.0" +pytest-cov = ">=5.0.0,<=6.0.0" + +[tool.poetry.group.types] +optional = true + +[tool.poetry.group.types.dependencies] + +[tool.poetry.group.vulnerability] +optional = true + +[tool.poetry.group.vulnerability.dependencies] +bandit = ">=1.7.8,<2.0.0" +safety = ">=3.2.0,<4.0.0" + +[tool.poetry.scripts] +tus_storagehandler = "tus_storagehandler.main:main" + +[tool.ruff] +indent-width = 4 + +[tool.ruff.format] +docstring-code-format = true +indent-style = "space" +line-ending = "lf" +quote-style = "double" + +[tool.ruff.lint] +select = [ + "B", # flake8-bugbear + "D", # pydocstyle + "E", # pycodestyle + "F", # Pyflakes + "I", # isort + "PL", # pylint + "SIM", # flake8-simplify + "UP", # pyupgrade +] + +[tool.ruff.lint.pydocstyle] +convention = "google" diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..f1365f8 --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1 @@ +"""This package contains tests.""" diff --git a/tests/test_integration/__init__.py b/tests/test_integration/__init__.py new file mode 100644 index 0000000..9a74cfd --- /dev/null +++ b/tests/test_integration/__init__.py @@ -0,0 +1 @@ +"""This package contains integration tests.""" diff --git a/tests/test_integration/test_init.py b/tests/test_integration/test_init.py new file mode 100644 index 0000000..120ea30 --- /dev/null +++ b/tests/test_integration/test_init.py @@ -0,0 +1,9 @@ +"""Integration tests for the __init__.py file.""" + +from pathlib import Path + + +def test_init_file_exists(): + """Check if the __init__.py file exists.""" + path_to_init_file = Path(__file__).parents[2] / "tus_storagehandler" / "__init__.py" + assert path_to_init_file.exists(), f"File {path_to_init_file} does not exist." diff --git a/tests/test_unit/__init__.py b/tests/test_unit/__init__.py new file mode 100644 index 0000000..2f312a6 --- /dev/null +++ b/tests/test_unit/__init__.py @@ -0,0 +1 @@ +"""This package contains unit tests.""" diff --git a/tests/test_unit/test_init.py b/tests/test_unit/test_init.py new file mode 100644 index 0000000..9698931 --- /dev/null +++ b/tests/test_unit/test_init.py @@ -0,0 +1,9 @@ +"""Unit tests for the __init__.py file.""" + +from pathlib import Path + + +def test_init_file_exists(): + """Check if the __init__.py file exists.""" + path_to_init_file = Path(__file__).parents[2] / "tus_storagehandler" / "__init__.py" + assert path_to_init_file.exists(), f"File {path_to_init_file} does not exist." diff --git a/tus_storagehandler/__init__.py b/tus_storagehandler/__init__.py new file mode 100644 index 0000000..9f8346a --- /dev/null +++ b/tus_storagehandler/__init__.py @@ -0,0 +1 @@ +"""This package contains module for the tus_storagehandler.""" diff --git a/tus_storagehandler/main.py b/tus_storagehandler/main.py new file mode 100644 index 0000000..c1c8f60 --- /dev/null +++ b/tus_storagehandler/main.py @@ -0,0 +1,10 @@ +"""Entry point for tus_storagehandler.""" + + +def main(): + """Main entry point for tus_storagehandler.""" + print("Hello from tus_storagehandler!") + + +if __name__ == "__main__": + main()