From 119c581cce745e139c07cc6dc6ae4d9ce2614216 Mon Sep 17 00:00:00 2001 From: Prati28 Date: Tue, 2 Jul 2024 16:27:15 +0530 Subject: [PATCH 01/11] basic structure based on cookiecutter Signed-off-by: Prati28 --- .cruft.json | 21 +++ .github/ISSUE_TEMPLATE/general-purpose.md | 47 +++++ .github/actions/setup/poetry/action.yaml | 92 ++++++++++ .github/workflows/code_quality.yaml | 84 +++++++++ .github/workflows/code_test.yaml | 74 ++++++++ .github/workflows/docs.yaml | 44 +++++ .github/workflows/pr_validation.yaml | 67 ++++++++ .github/workflows/release.yaml | 26 +++ .github/workflows/update.yaml | 55 ++++++ .github/workflows/vulnerability.yaml | 48 ++++++ .gitignore | 182 ++++++++++++++++++++ .pre-commit-config.yaml | 40 +++++ .readthedocs.yaml | 16 ++ .safety-policy.yml | 43 +++++ .yamllint.yaml | 13 ++ CODE_OF_CONDUCT.md | 75 ++++++++ LICENSE | 201 ++++++++++++++++++++++ Makefile | 125 ++++++++++++++ PULL_REQUEST_TEMPLATE.md | 64 +++++++ README.md | 24 --- docs/Makefile | 20 +++ docs/make.bat | 35 ++++ docs/source/conf.py | 102 +++++++++++ docs/source/index.rst | 15 ++ images/logo-elixir-cloud-aai.svg | 112 ++++++++++++ images/logo-elixir.svg | 82 +++++++++ pyproject.toml | 82 +++++++++ tests/__init__.py | 1 + tests/test_integration/__init__.py | 1 + tests/test_integration/test_dummy.py | 10 ++ tests/test_unit/__init__.py | 1 + tests/test_unit/test_dummy.py | 10 ++ tus_storagehandler/__init__.py | 1 + tus_storagehandler/main.py | 10 ++ 34 files changed, 1799 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.yaml create mode 100644 .github/workflows/update.yaml create mode 100644 .github/workflows/vulnerability.yaml create mode 100644 .gitignore 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 CODE_OF_CONDUCT.md create mode 100644 LICENSE create mode 100644 Makefile create mode 100644 PULL_REQUEST_TEMPLATE.md delete mode 100644 README.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 images/logo-elixir-cloud-aai.svg create mode 100644 images/logo-elixir.svg 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_dummy.py create mode 100644 tests/test_unit/__init__.py create mode 100644 tests/test_unit/test_dummy.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..7b7997a --- /dev/null +++ b/.cruft.json @@ -0,0 +1,21 @@ +{ + "template": "D:\\open-source\\gsoc\\final\\cookiecutter-python", + "commit": "88967f43af9799dfa0ad04b2908d7f40259c02d2", + "checkout": null, + "context": { + "cookiecutter": { + "author_name": "Elixir Cloud AAI", + "author_email": "cloud-service@elixir-europe.org", + "development_status": "Beta", + "short_description": "File Handler Utilizing TUS and Minio (S3 Storage) 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", + "_template": "D:\\open-source\\gsoc\\final\\cookiecutter-python" + } + }, + "directory": null +} diff --git a/.github/ISSUE_TEMPLATE/general-purpose.md b/.github/ISSUE_TEMPLATE/general-purpose.md new file mode 100644 index 0000000..8a11bde --- /dev/null +++ b/.github/ISSUE_TEMPLATE/general-purpose.md @@ -0,0 +1,47 @@ +Your issue may already be reported! Please search on the +[issue tracker](https://github.com/elixir-cloud-aai/tus-storagehandler/issues) before creating +one. + +## Expected Behavior + + + + + +## Current Behavior + + + + + +## Possible Solution + + + + + +## Steps to Reproduce (for bugs) + + + + + +1. +1. +1. +1. + +## Context + + + + + +## Your Environment + + + +- Version used: +- Browser Name and version: +- Operating System and version (desktop or mobile): +- Link to your project: 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..0c252da --- /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=lint --no-root" + poetry-export-options: "--only=lint" + + - 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=lint --no-root" + poetry-export-options: "--only=lint" + + - 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=lint --no-root" + poetry-export-options: "--only=lint" + + - 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: "--only=types --no-root" + poetry-export-options: "--only=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..0266d92 --- /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: 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_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..1b417b5 --- /dev/null +++ b/.github/workflows/docs.yaml @@ -0,0 +1,44 @@ +--- +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: ${{ job.os }} + python-version: '3.11' + poetry-install-options: "--with=docs" + poetry-export-options: "--with=docs" + + - name: Generate API docs + run: | + sphinx-apidoc -o /tmp/docs tus_storagehandler/ + + - name: Compare docs with main branch + id: check_docs_diff + run: | + shasum /tmp/docs/* > /tmp/docs.sha + shasum /docs/pages/* > /docs/project_doc.sha + diff=$(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 +... diff --git a/.github/workflows/pr_validation.yaml b/.github/workflows/pr_validation.yaml new file mode 100644 index 0000000..4e43caa --- /dev/null +++ b/.github/workflows/pr_validation.yaml @@ -0,0 +1,67 @@ +--- +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: + - 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. +... diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml new file mode 100644 index 0000000..1e214ed --- /dev/null +++ b/.github/workflows/release.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_PASSWORD }} +... diff --git a/.github/workflows/update.yaml b/.github/workflows/update.yaml new file mode 100644 index 0000000..4edade9 --- /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: ${{ job.os }} + python-version: '3.11' + poetry-install-options: "--with=misc --no-root" + poetry-export-options: "--with=misc" + + - name: Update project structure + run: | + cruft update -y + + - name: Check if there are changes + id: changes + uses: UnicornGlobal/has-changes-action@v1.0.11 + + - name: Apply additional changes and fixes + if: steps.changes.outputs.changed == 1 + run: | + poetry lock --no-update + poetry install + pre-commit run --all-files + + - name: Get new template version + if: steps.changes.outputs.changed == 1 + run: | + COMMIT_HASH=$(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..5bb93b5 --- /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=security --no-root" + poetry-export-options: "--only=security" + + - 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: ${{ job.os }} + python-version: '3.11' + poetry-install-options: "--only=security --no-root" + poetry-export-options: "--only=security" + + - name: Check dependency vulnerabilities with safety + run: poetry run safety check --full-report +... diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..0a558c9 --- /dev/null +++ b/.gitignore @@ -0,0 +1,182 @@ +######## This section contains auto-generated .gitignore patterns for ######### +######## Python projects. Write project level gitignore below this ######### +######## section. ######### + +# Created by https://www.toptal.com/developers/gitignore/api/python +# Edit at https://www.toptal.com/developers/gitignore?templates=python + +### Python ### +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$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 .gitignore file for Python projects. ######### +######### Project level .gitignore. ######### + +# Keep pre-commit hooks and .yamllint file +!.pre-commit-config.yaml +!.yamllint.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..8a34822 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,40 @@ +--- +# 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/executablebooks/mdformat + rev: 0.7.17 + hooks: + - id: mdformat + additional_dependencies: + - mdformat-config + - mdformat-black + - mdformat-frontmatter + args: [--wrap=80] + exclude: _.+\.md|CHANGELOG\.md + - repo: https://github.com/adrienverge/yamllint.git + rev: v1.35.1 + hooks: + - id: yamllint + exclude: ^deployment/charts + - 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/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..bc09eb3 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,75 @@ +# ELIXIR Cloud & AAI Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to making participation in our project and +our community a harassment-free experience for everyone, regardless of age, body +size, disability, ethnicity, sex characteristics, gender identity and expression, +level of experience, education, socio-economic status, nationality, personal +appearance, race, religion, or sexual identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment +include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or + advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic + address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to this Code of Conduct, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces +when an individual is representing the project or its community. Examples of +representing a project or community include using an official project e-mail +address, posting via an official social media account, or acting as an appointed +representative at an online or offline event. Representation of a project may be +further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by contacting [cloud-service@elixir-europe.org][elixir-cloud-aai-email]. All complaints +will be reviewed and investigated and will result in a response that is deemed +necessary and appropriate to the circumstances. The project team is obligated +to maintain confidentiality with regard to the reporter of an incident. Further +details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor +Covenant][contributor-covenant], version 1.4, available at + + +[contributor-covenant]: https://contributor-covenant.org/ +[elixir-cloud-aai-email]: mailto:cloud-service@elixir-europe.org diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..975b5b9 --- /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..27caedf --- /dev/null +++ b/Makefile @@ -0,0 +1,125 @@ +# 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 "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 "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 "Testing -----------------------------------------------------------------------" + @echo " \033[1m\033[35mtest\033[0m \033[37m(t)\033[0m: \033[36mRun all tests.\033[0m\n" + + @echo "Documentation -----------------------------------------------------------------" + @echo " \033[1m\033[35mdocs\033[0m \033[37m(d)\033[0m: \033[36mGenerate project documentation.\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" + @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" + @ruff format && ruff check --fix + @typos . + +.PHONY: fl +fl: format-lint + +.PHONY: install +install: + @echo "\nInstalling dependencies and with this package +++++++++++++++++++++++++++++++++\n" + @poetry install + +.PHONY: i +i: install + +.PHONY: precommit-check +precommit-check: + @echo "\nRunning pre-commit checks +++++++++++++++++++++++++++++++++++++++++++++++++++++\n" + @pre-commit run --all-files + +.PHONY: pc +pc: precommit-check + +.PHONY: security +security: + @echo "\nRunning security scans using bandit and safety ++++++++++++++++++++++++++++++++\n" + @safety check --full-report + @bandit -c pyproject.toml -r tus_storagehandler + +.PHONY: s +s: security + +.PHONY: test +test: + @echo "\nRunning tests using pytest ++++++++++++++++++++++++++++++++++++++++++++++++++++\n" + @pytest tests/ + +.PHONY: t +t: test + +.PHONY: type-check +type-check: + @echo "\nPerforming type checking with mypy ++++++++++++++++++++++++++++++++++++++++++++\n" + @mypy tus_storagehandler + +.PHONY: tc +tc: type-check + +.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..b5dd732 --- /dev/null +++ b/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,64 @@ +#### 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 deleted file mode 100644 index 9ce6277..0000000 --- a/README.md +++ /dev/null @@ -1,24 +0,0 @@ -# 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. 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..747ffb7 --- /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..cfe671f --- /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/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 + + + + + + + + + + + + + + + + + + diff --git a/images/logo-elixir.svg b/images/logo-elixir.svg new file mode 100644 index 0000000..af9d4b9 --- /dev/null +++ b/images/logo-elixir.svg @@ -0,0 +1,82 @@ + + + + + + + + + + + + + diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..6dcc85e --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,82 @@ +[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 :: 4 - Beta", + "License :: OSI Approved :: Apache Software License", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.11", +] +description = "File Handler Utilizing TUS and Minio (S3 Storage) 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.docs.dependencies] +added-value = ">=0.24.0,<1.0.0" +docutils = "0.20.1" +furo = ">=2024.5.6,<2025.0.0" +m2r2 = "^0.3.3.post2" +sphinx = "^7.3.7" +sphinx-autodoc-typehints = "^2.1.0" +tomli = ">=2.0.1,<3.0.0" + +[tool.poetry.group.lint.dependencies] +ruff = ">=0.4.10,<1.0.0" +typos = ">=1.22.8,<2.0.0" + +[tool.poetry.group.misc.dependencies] +cruft = ">=2.15.0,<3.0.0" +jello = ">=1.6.0,<2.0.0" +pre-commit = ">=3.7.1,<4.0.0" + +[tool.poetry.group.security.dependencies] +bandit = ">=1.7.8,<2.0.0" +safety = ">=3.2.0,<4.0.0" + +[tool.poetry.group.test.dependencies] +pytest = ">=8.2.2,<9.0.0" +pytest-cov = ">=5.0.0,<=6.0.0" + +[tool.poetry.group.types.dependencies] +mypy = ">=1.10.0,<2.0.0" + +[tool.poetry.scripts] +tus_storagehandler = "tus_storagehandler.main:main" + +[tool.ruff] +indent-width = 2 + +[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_dummy.py b/tests/test_integration/test_dummy.py new file mode 100644 index 0000000..1491684 --- /dev/null +++ b/tests/test_integration/test_dummy.py @@ -0,0 +1,10 @@ +"""Dummy test file to avoid the error.""" + + +# TODO: Remove this file when adding real tests. +# This test is a placeholder for the integration tests. It is a workaround +# to avoid the error "Module has no tests" when running the tests with pytest. +# Cf. https://github.com/pytest-dev/pytest/issues/2393 +def test_placeholder(): + """Dummy test to avoid the error.""" + pass 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_dummy.py b/tests/test_unit/test_dummy.py new file mode 100644 index 0000000..4443c40 --- /dev/null +++ b/tests/test_unit/test_dummy.py @@ -0,0 +1,10 @@ +"""Dummy test file to avoid the error.""" + + +# TODO: Remove this file when adding real tests. +# This test is a placeholder for the unit tests. It is a workaround +# to avoid the error "Module has no tests" when running the tests with pytest. +# Cf. https://github.com/pytest-dev/pytest/issues/2393 +def test_placeholder(): + """Dummy test to avoid the error.""" + pass 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..666c8b1 --- /dev/null +++ b/tus_storagehandler/main.py @@ -0,0 +1,10 @@ +"""Entry point for python_cookiecutter.""" + + +def main(): + """Main entry point for tus_storagehandler.""" + print("Hello from tus_storagehandler!") + + +if __name__ == "__main__": + main() From af322966351a5bbe3bb82d015b7859a9bdcb8929 Mon Sep 17 00:00:00 2001 From: Prati28 Date: Wed, 3 Jul 2024 14:22:28 +0530 Subject: [PATCH 02/11] basic changes Signed-off-by: Prati28 --- .cruft.json | 12 +- .github/workflows/code_test.yaml | 2 +- .pre-commit-config.yaml | 4 - CODE_OF_CONDUCT.md | 20 +-- LICENSE | 2 +- PULL_REQUEST_TEMPLATE.md | 43 +++---- README.md | 212 +++++++++++++++++++++++++++++++ pyproject.toml | 164 ++++++++++++------------ 8 files changed, 333 insertions(+), 126 deletions(-) create mode 100644 README.md diff --git a/.cruft.json b/.cruft.json index 7b7997a..d0a549f 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,20 +1,20 @@ { - "template": "D:\\open-source\\gsoc\\final\\cookiecutter-python", - "commit": "88967f43af9799dfa0ad04b2908d7f40259c02d2", + "template": "https://github.com/elixir-cloud-aai/cookiecutter-python", + "commit": "43f9bd92eaf21557e87d3932524fe5ffb6fd7ef4", "checkout": null, "context": { "cookiecutter": { - "author_name": "Elixir Cloud AAI", + "author_name": "ELIXIR Cloud AAI", "author_email": "cloud-service@elixir-europe.org", - "development_status": "Beta", - "short_description": "File Handler Utilizing TUS and Minio (S3 Storage) with DRS Filer Integration", + "development_status": "Alpha", + "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", - "_template": "D:\\open-source\\gsoc\\final\\cookiecutter-python" + "_template": "https://github.com/elixir-cloud-aai/cookiecutter-python" } }, "directory": null diff --git a/.github/workflows/code_test.yaml b/.github/workflows/code_test.yaml index 0266d92..07b9309 100644 --- a/.github/workflows/code_test.yaml +++ b/.github/workflows/code_test.yaml @@ -11,7 +11,7 @@ on: jobs: integration-test: - name: Unit Test + name: Integration Test runs-on: ubuntu-latest steps: - name: Check out repository diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8a34822..89a3a17 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -22,10 +22,6 @@ repos: - id: mdformat additional_dependencies: - mdformat-config - - mdformat-black - - mdformat-frontmatter - args: [--wrap=80] - exclude: _.+\.md|CHANGELOG\.md - repo: https://github.com/adrienverge/yamllint.git rev: v1.35.1 hooks: diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index bc09eb3..2b6f9f4 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -14,21 +14,21 @@ appearance, race, religion, or sexual identity and orientation. Examples of behavior that contributes to creating a positive environment include: -* Using welcoming and inclusive language -* Being respectful of differing viewpoints and experiences -* Gracefully accepting constructive criticism -* Focusing on what is best for the community -* Showing empathy towards other community members +- Using welcoming and inclusive language +- Being respectful of differing viewpoints and experiences +- Gracefully accepting constructive criticism +- Focusing on what is best for the community +- Showing empathy towards other community members Examples of unacceptable behavior by participants include: -* The use of sexualized language or imagery and unwelcome sexual attention or +- The use of sexualized language or imagery and unwelcome sexual attention or advances -* Trolling, insulting/derogatory comments, and personal or political attacks -* Public or private harassment -* Publishing others' private information, such as a physical or electronic +- Trolling, insulting/derogatory comments, and personal or political attacks +- Public or private harassment +- Publishing others' private information, such as a physical or electronic address, without explicit permission -* Other conduct which could reasonably be considered inappropriate in a +- Other conduct which could reasonably be considered inappropriate in a professional setting ## Our Responsibilities diff --git a/LICENSE b/LICENSE index 975b5b9..35c9d67 100644 --- a/LICENSE +++ b/LICENSE @@ -186,7 +186,7 @@ same "printed page" as the copyright notice for easier identification within third-party archives. - Copyright 2024 Elixir Cloud AAI + 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. diff --git a/PULL_REQUEST_TEMPLATE.md b/PULL_REQUEST_TEMPLATE.md index b5dd732..150e36a 100644 --- a/PULL_REQUEST_TEMPLATE.md +++ b/PULL_REQUEST_TEMPLATE.md @@ -26,28 +26,27 @@ Generally, **PRs are only reviewed when all boxes are ticked off and all automated checks pass** (use the comment section below if you believe that your PR is ready to be merged even though not all boxes were ticked off). --> -- [ ] 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 - +- \[ \] 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 diff --git a/README.md b/README.md new file mode 100644 index 0000000..5755916 --- /dev/null +++ b/README.md @@ -0,0 +1,212 @@ +# Python Cookiecutter Template + +This is a Cookiecutter template for creating a Python project with Poetry, +including configurations for various project settings. + +## Table of Contents + +- [Introduction](#introduction) +- [Installation](#installation) +- [Usage](#usage) +- [Configurations](#configurations) + - [Package manager - Poetry](#package-manager---poetry) + - [Linters and formatters - Ruff](#linters-and-formatters---ruff) + - [Spell checker - Typos](#spell-checker---typos) + - [Static type checker - Mypy](#static-type-checker---mypy) + - [Documentation - Sphinx](#documentation---sphinx) + - [Testing - pytest and pytest-cov](#testing---pytest-and-pytest-cov) +- [CI/CD - GitHub Actions](#cicd---github-actions) +- [Disclaimer](#disclaimer) +- [Contributing](#contributing) +- [Code of Conduct](#code-of-conduct) +- [Versioning](#versioning) +- [License](#license) +- [Contact](#contact) + +## Usage + +1. **Install cruft** (if you haven't already): + +```sh +pip install cruft +``` + +2. **Generate a New Project**: + +```sh +cruft create https://github.com/elixir-cloud-aai/cookiecutter-python.git +``` + +### Don't wanna use cruft? + +You can also use the `cookiecutter` command directly: + +1. **Install cookiecutter** (if you haven't already): + +```sh +pip install cookiecutter +``` + +2. **Generate a New Project**: + +```sh +cookiecutter gh:elixir-cloud-aai/cookiecutter-python +``` + +> **Note**: If you're using just `cookiecutter`, manually remove + `update-template` job from `update.yaml` github action workflow file as + `cookiecutter` doesn't support autosync like cruft. + +## Configurations + +### Package manager - Poetry + +This project uses [Poetry][poetry-org] as a package manager. Check out the +commands at the [official documentation][poetry-docs]. + +### Linters and formatters - Ruff + +To lint and format `Python` code files, it uses [Ruff][ruff], the default +configuration is set in the `pyproject.toml` file. + +```toml +select = [ + "B", # flake8-bugbear + "E", # pycodestyle + "F", # Pyflakes + "I", # isort + "PL", # pylint + "SIM", # flake8-simplify + "UP", # pyupgrade +] +``` + +To configure it to your needs, refer to the [rules documentation][rudff-linter] +, and for formatter configuration, refer to the +[configuration documentation][ruff-formatter]. + +### Spell checker - Typos + +If you want to ignore certain words, add them to the `pyproject.toml` file, +under the `tool.typos.default.extend-words` key. + +```toml +[tool.typos.default.extend-words] +mke = 'mke' +``` + +For further configuration, refer to the [typos docs][typos-docs]. + +### Static type checker - Mypy + +Change the configuration in `pyproject.toml` file, for further information refer to +the [documentation][mypy-config]. + +### Documentation - Sphinx + +Configuration for Sphinx is in the `docs/source/conf.py` file, for further info refer +to the [Sphinx documentation][sphinx-docs]. The default configuration uses +[furo theme][furo] and [ReadTheDocs][rtd] to host the documentation, you can +change the configuration using `/docs/source/conf.py` and `.readthedocs.yml` +file. + +> **Note**: Make sure to setup the `ReadTheDocs` account and add the project to + the account to host the documentation. + +### Testing - pytest and pytest-cov + +Generate a coverage report using `pytest-cov` and uploads it to codecov.io. + +> **Note**: Make sure to setup the `Codecov` account and add the project to the + account to host the coverage report and add github [token](#cicd---github-actions). + +## CI/CD - GitHub Actions + +Here are the GitHub Actions Secrets that need to be included in the repository +settings: + +- `PYPI_PASSWORD`: PyPI account password. +- `CODECOV_TOKEN`: Codecov token. +- `AUTO_UPDATE_GITHUB_TOKEN`: GitHub token with permissions to write to the repository. + +## Disclaimer + +Some of the links and images have been hardcoded with `ELIXIR Cloud & AAI`'s +assets in the documentation, please update them manually if needed. These +assets **MUST** be included for projects owned by ELIXIR Cloud & AAI, but +**MUST NOT** be included for projects that are not (personal projects, projects +owned by other orgs). + +**Only`markdown` files and `images/` directory need to be changed.** + +## 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 + +Please mind the code of conduct described in +[`CODE_OF_CONDUCT.md`][code-of-conduct] for all interactions with the community. +Please be nice to one another! :) + +If you experience any unacceptable behavior by any member of the community, +please refer to the contact method specified in +[`CODE_OF_CONDUCT.md`][code-of-conduct] to report the incident to the community +leaders. + +## Versioning + +The project adopts the [semantic versioning][semver] scheme for versioning. +Currently the service 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][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](https://github.com/elixir-cloud-aai/cookiecutter-python/issues). +- 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]: CODE_OF_CONDUCT.md +[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/ +[license]: LICENSE +[logo-elixir]: images/logo-elixir.svg +[logo-elixir-cloud-aai]: images/logo-elixir-cloud-aai.svg +[poetry-org]: https://python-poetry.org/ +[poetry-docs]: https://python-poetry.org/docs/cli/ +[ruff]: https://docs.astral.sh/ruff +[ruff-linter]: https://docs.astral.sh/ruff/rules/ +[ruff-formatter]: https://docs.astral.sh/ruff/formatter +[typos-docs]: https://pypi.org/project/typos/ +[mypy-config]: https://mypy.readthedocs.io/en/stable/config_file.html +[sphinx-docs]: https://www.sphinx-doc.org/en/master/usage/configuration.html +[furo]: https://pradyunsg.me/furo/quickstart/ +[rtd]: https://readthedocs.org/ +[semver]:https://semver.org/ diff --git a/pyproject.toml b/pyproject.toml index 6dcc85e..0215c21 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,82 +1,82 @@ -[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 :: 4 - Beta", - "License :: OSI Approved :: Apache Software License", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.11", -] -description = "File Handler Utilizing TUS and Minio (S3 Storage) 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.docs.dependencies] -added-value = ">=0.24.0,<1.0.0" -docutils = "0.20.1" -furo = ">=2024.5.6,<2025.0.0" -m2r2 = "^0.3.3.post2" -sphinx = "^7.3.7" -sphinx-autodoc-typehints = "^2.1.0" -tomli = ">=2.0.1,<3.0.0" - -[tool.poetry.group.lint.dependencies] -ruff = ">=0.4.10,<1.0.0" -typos = ">=1.22.8,<2.0.0" - -[tool.poetry.group.misc.dependencies] -cruft = ">=2.15.0,<3.0.0" -jello = ">=1.6.0,<2.0.0" -pre-commit = ">=3.7.1,<4.0.0" - -[tool.poetry.group.security.dependencies] -bandit = ">=1.7.8,<2.0.0" -safety = ">=3.2.0,<4.0.0" - -[tool.poetry.group.test.dependencies] -pytest = ">=8.2.2,<9.0.0" -pytest-cov = ">=5.0.0,<=6.0.0" - -[tool.poetry.group.types.dependencies] -mypy = ">=1.10.0,<2.0.0" - -[tool.poetry.scripts] -tus_storagehandler = "tus_storagehandler.main:main" - -[tool.ruff] -indent-width = 2 - -[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" +[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 :: 4 - Beta", + "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.docs.dependencies] +added-value = ">=0.24.0,<1.0.0" +docutils = "0.20.1" +furo = ">=2024.5.6,<2025.0.0" +m2r2 = "^0.3.3.post2" +sphinx = "^7.3.7" +sphinx-autodoc-typehints = "^2.1.0" +tomli = ">=2.0.1,<3.0.0" + +[tool.poetry.group.lint.dependencies] +ruff = ">=0.4.10,<1.0.0" +typos = ">=1.22.8,<2.0.0" + +[tool.poetry.group.misc.dependencies] +cruft = ">=2.15.0,<3.0.0" +jello = ">=1.6.0,<2.0.0" +pre-commit = ">=3.7.1,<4.0.0" + +[tool.poetry.group.security.dependencies] +bandit = ">=1.7.8,<2.0.0" +safety = ">=3.2.0,<4.0.0" + +[tool.poetry.group.test.dependencies] +pytest = ">=8.2.2,<9.0.0" +pytest-cov = ">=5.0.0,<=6.0.0" + +[tool.poetry.group.types.dependencies] +mypy = ">=1.10.0,<2.0.0" + +[tool.poetry.scripts] +tus_storagehandler = "tus_storagehandler.main:main" + +[tool.ruff] +indent-width = 2 + +[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" From f114f2c9bd637637f94b0aaa4247f5d4568055fb Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Thu, 4 Jul 2024 00:15:40 +0530 Subject: [PATCH 03/11] minor --- .cruft.json | 8 +- CODE_OF_CONDUCT.md | 29 +- PULL_REQUEST_TEMPLATE.md | 16 +- README.md | 169 +-- docs/source/conf.py | 34 +- poetry.lock | 1891 ++++++++++++++++++++++++++ pyproject.toml | 161 ++- tests/test_integration/test_dummy.py | 4 +- tests/test_unit/test_dummy.py | 4 +- tus_storagehandler/main.py | 6 +- 10 files changed, 2074 insertions(+), 248 deletions(-) create mode 100644 poetry.lock diff --git a/.cruft.json b/.cruft.json index d0a549f..5a3980e 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,18 +1,18 @@ { "template": "https://github.com/elixir-cloud-aai/cookiecutter-python", - "commit": "43f9bd92eaf21557e87d3932524fe5ffb6fd7ef4", + "commit": "fe9787042053d7cae1ccd7ff8d6fef4611f41b2a", "checkout": null, "context": { "cookiecutter": { "author_name": "ELIXIR Cloud AAI", "author_email": "cloud-service@elixir-europe.org", - "development_status": "Alpha", - "short_description": "File handler utilizing TUS and MinIO with DRS-Filer integration", + "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", + "add_script": "n", "year": "2024", "_template": "https://github.com/elixir-cloud-aai/cookiecutter-python" } diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 2b6f9f4..97985fe 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -5,9 +5,9 @@ In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body -size, disability, ethnicity, sex characteristics, gender identity and expression, -level of experience, education, socio-economic status, nationality, personal -appearance, race, religion, or sexual identity and orientation. +size, disability, ethnicity, sex characteristics, gender identity and +expression, level of experience, education, socio-economic status, nationality, +personal appearance, race, religion, or sexual identity and orientation. ## Our Standards @@ -37,11 +37,11 @@ Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. -Project maintainers have the right and responsibility to remove, edit, or -reject comments, commits, code, wiki edits, issues, and other contributions -that are not aligned to this Code of Conduct, or to ban temporarily or -permanently any contributor for other behaviors that they deem inappropriate, -threatening, offensive, or harmful. +Project maintainers have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, or to ban temporarily or permanently any +contributor for other behaviors that they deem inappropriate, threatening, +offensive, or harmful. ## Scope @@ -55,10 +55,11 @@ further defined and clarified by project maintainers. ## Enforcement Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported by contacting [cloud-service@elixir-europe.org][elixir-cloud-aai-email]. All complaints -will be reviewed and investigated and will result in a response that is deemed -necessary and appropriate to the circumstances. The project team is obligated -to maintain confidentiality with regard to the reporter of an incident. Further +reported by contacting +[cloud-service@elixir-europe.org][elixir-cloud-aai-email]. All complaints will +be reviewed and investigated and will result in a response that is deemed +necessary and appropriate to the circumstances. The project team is obligated to +maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. Project maintainers who do not follow or enforce the Code of Conduct in good @@ -67,8 +68,8 @@ members of the project's leadership. ## Attribution -This Code of Conduct is adapted from the [Contributor -Covenant][contributor-covenant], version 1.4, available at +This Code of Conduct is adapted from the +[Contributor Covenant][contributor-covenant], version 1.4, available at [contributor-covenant]: https://contributor-covenant.org/ diff --git a/PULL_REQUEST_TEMPLATE.md b/PULL_REQUEST_TEMPLATE.md index 150e36a..1cf1d22 100644 --- a/PULL_REQUEST_TEMPLATE.md +++ b/PULL_REQUEST_TEMPLATE.md @@ -26,11 +26,11 @@ Generally, **PRs are only reviewed when all boxes are ticked off and all automated checks pass** (use the comment section below if you believe that your PR is ready to be merged even though not all boxes were ticked off). --> -- \[ \] 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 +- \[ \] 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 @@ -39,9 +39,9 @@ your PR is ready to be merged even though not all boxes were ticked off). --> 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 +- \[ \] 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 diff --git a/README.md b/README.md index 5755916..a5fa631 100644 --- a/README.md +++ b/README.md @@ -1,143 +1,90 @@ -# Python Cookiecutter Template +[![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) +[![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) -This is a Cookiecutter template for creating a Python project with Poetry, -including configurations for various project settings. +# tus-storagehandler + +File handler utilizing TUS and MinIO with DRS-Filer integration. ## Table of Contents -- [Introduction](#introduction) +- [Basic Usage](#basic-usage) - [Installation](#installation) -- [Usage](#usage) -- [Configurations](#configurations) - - [Package manager - Poetry](#package-manager---poetry) - - [Linters and formatters - Ruff](#linters-and-formatters---ruff) - - [Spell checker - Typos](#spell-checker---typos) - - [Static type checker - Mypy](#static-type-checker---mypy) - - [Documentation - Sphinx](#documentation---sphinx) - - [Testing - pytest and pytest-cov](#testing---pytest-and-pytest-cov) -- [CI/CD - GitHub Actions](#cicd---github-actions) -- [Disclaimer](#disclaimer) +- [Development](#development) - [Contributing](#contributing) - [Code of Conduct](#code-of-conduct) - [Versioning](#versioning) - [License](#license) - [Contact](#contact) -## Usage +## Basic Usage -1. **Install cruft** (if you haven't already): +## Installation -```sh -pip install cruft -``` +## Development + +For ease, certain scripts have been abbreviated in `Makefile`, make sure that +have installed the dependencies before running the commands. -2. **Generate a New Project**: +> **Note**: `make` commands are only available for Unix-based systems. + +To view the commdands available, run: ```sh -cruft create https://github.com/elixir-cloud-aai/cookiecutter-python.git +make ``` -### Don't wanna use cruft? - -You can also use the `cookiecutter` command directly: +Here are certain commands that you might find useful: -1. **Install cookiecutter** (if you haven't already): +- Making a virtual environment ```sh -pip install cookiecutter +make v ``` -2. **Generate a New Project**: +- Installing dependencies ```sh -cookiecutter gh:elixir-cloud-aai/cookiecutter-python +make i ``` -> **Note**: If you're using just `cookiecutter`, manually remove - `update-template` job from `update.yaml` github action workflow file as - `cookiecutter` doesn't support autosync like cruft. - -## Configurations - -### Package manager - Poetry +- Running tests -This project uses [Poetry][poetry-org] as a package manager. Check out the -commands at the [official documentation][poetry-docs]. - -### Linters and formatters - Ruff - -To lint and format `Python` code files, it uses [Ruff][ruff], the default -configuration is set in the `pyproject.toml` file. - -```toml -select = [ - "B", # flake8-bugbear - "E", # pycodestyle - "F", # Pyflakes - "I", # isort - "PL", # pylint - "SIM", # flake8-simplify - "UP", # pyupgrade -] +```sh +make t ``` -To configure it to your needs, refer to the [rules documentation][rudff-linter] -, and for formatter configuration, refer to the -[configuration documentation][ruff-formatter]. +- Running linter, formatter and spell checker -### Spell checker - Typos - -If you want to ignore certain words, add them to the `pyproject.toml` file, -under the `tool.typos.default.extend-words` key. - -```toml -[tool.typos.default.extend-words] -mke = 'mke' +```sh +make fl ``` -For further configuration, refer to the [typos docs][typos-docs]. +- Building the documentation -### Static type checker - Mypy - -Change the configuration in `pyproject.toml` file, for further information refer to -the [documentation][mypy-config]. - -### Documentation - Sphinx - -Configuration for Sphinx is in the `docs/source/conf.py` file, for further info refer -to the [Sphinx documentation][sphinx-docs]. The default configuration uses -[furo theme][furo] and [ReadTheDocs][rtd] to host the documentation, you can -change the configuration using `/docs/source/conf.py` and `.readthedocs.yml` -file. - -> **Note**: Make sure to setup the `ReadTheDocs` account and add the project to - the account to host the documentation. - -### Testing - pytest and pytest-cov - -Generate a coverage report using `pytest-cov` and uploads it to codecov.io. - -> **Note**: Make sure to setup the `Codecov` account and add the project to the - account to host the coverage report and add github [token](#cicd---github-actions). - -## CI/CD - GitHub Actions +```sh +make d +``` -Here are the GitHub Actions Secrets that need to be included in the repository -settings: +- Running type checker -- `PYPI_PASSWORD`: PyPI account password. -- `CODECOV_TOKEN`: Codecov token. -- `AUTO_UPDATE_GITHUB_TOKEN`: GitHub token with permissions to write to the repository. +```sh +make tc +``` -## Disclaimer +- Running all pre-commit checks -Some of the links and images have been hardcoded with `ELIXIR Cloud & AAI`'s -assets in the documentation, please update them manually if needed. These -assets **MUST** be included for projects owned by ELIXIR Cloud & AAI, but -**MUST NOT** be included for projects that are not (personal projects, projects -owned by other orgs). +```sh +make pc +``` -**Only`markdown` files and `images/` directory need to be changed.** +> **Note**: This is not the complete list of commands, run `make` to find if +> more have been added. ## Contributing @@ -162,7 +109,7 @@ leaders. ## Versioning The project adopts the [semantic versioning][semver] scheme for versioning. -Currently the service is in a pre-release stage, so changes to the API, +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 @@ -174,13 +121,12 @@ copy of which is also available in [`LICENSE`][license]. 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][elixir] [Compute Platform][elixir-compute]. +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](https://github.com/elixir-cloud-aai/cookiecutter-python/issues). + 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. @@ -196,17 +142,8 @@ To get in touch with us, please use one of the following routes: [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 -[poetry-org]: https://python-poetry.org/ -[poetry-docs]: https://python-poetry.org/docs/cli/ -[ruff]: https://docs.astral.sh/ruff -[ruff-linter]: https://docs.astral.sh/ruff/rules/ -[ruff-formatter]: https://docs.astral.sh/ruff/formatter -[typos-docs]: https://pypi.org/project/typos/ -[mypy-config]: https://mypy.readthedocs.io/en/stable/config_file.html -[sphinx-docs]: https://www.sphinx-doc.org/en/master/usage/configuration.html -[furo]: https://pradyunsg.me/furo/quickstart/ -[rtd]: https://readthedocs.org/ -[semver]:https://semver.org/ +[semver]: https://semver.org/ diff --git a/docs/source/conf.py b/docs/source/conf.py index cfe671f..8bb724a 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -20,9 +20,9 @@ # -- 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"] + _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() @@ -38,20 +38,20 @@ def _get_project_meta(): # 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", + "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/ diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..b5fbb83 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1891 @@ +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. + +[[package]] +name = "added-value" +version = "0.24.0" +description = "Sphinx extension for embedding values extracted from Python modules" +optional = false +python-versions = "*" +files = [ + {file = "added-value-0.24.0.tar.gz", hash = "sha256:4c71f756db1589b596a0f2a35c8a35ddd86dd70b9335504c9ee29e2b95d40440"}, + {file = "added_value-0.24.0-py2.py3-none-any.whl", hash = "sha256:637464409e84759cfae1d3809a944ac000d0655bffd46bed958ffb5b8569c1f8"}, +] + +[package.dependencies] +docutils = "*" +les-iterables = ">=0.6.0" 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-1,82 +1,79 @@ -[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 :: 4 - Beta", - "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.docs.dependencies] -added-value = ">=0.24.0,<1.0.0" -docutils = "0.20.1" -furo = ">=2024.5.6,<2025.0.0" -m2r2 = "^0.3.3.post2" -sphinx = "^7.3.7" -sphinx-autodoc-typehints = "^2.1.0" -tomli = ">=2.0.1,<3.0.0" - 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"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.docs.dependencies] +added-value = ">=0.24.0,<1.0.0" +docutils = "0.20.1" +furo = ">=2024.5.6,<2025.0.0" +m2r2 = "^0.3.3.post2" +sphinx = "^7.3.7" +sphinx-autodoc-typehints = "^2.1.0" +tomli = ">=2.0.1,<3.0.0" + +[tool.poetry.group.lint.dependencies] +ruff = ">=0.4.10,<1.0.0" +typos = ">=1.22.8,<2.0.0" + +[tool.poetry.group.misc.dependencies] +cruft = ">=2.15.0,<3.0.0" +jello = ">=1.6.0,<2.0.0" +pre-commit = ">=3.7.1,<4.0.0" + +[tool.poetry.group.security.dependencies] +bandit = ">=1.7.8,<2.0.0" +safety = ">=3.2.0,<4.0.0" + +[tool.poetry.group.test.dependencies] +pytest = ">=8.2.2,<9.0.0" +pytest-cov = ">=5.0.0,<=6.0.0" + +[tool.poetry.group.types.dependencies] +mypy = ">=1.10.0,<2.0.0" + +[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/test_integration/test_dummy.py b/tests/test_integration/test_dummy.py index 1491684..6b28c1b 100644 --- a/tests/test_integration/test_dummy.py +++ b/tests/test_integration/test_dummy.py @@ -6,5 +6,5 @@ # to avoid the error "Module has no tests" when running the tests with pytest. # Cf. https://github.com/pytest-dev/pytest/issues/2393 def test_placeholder(): - """Dummy test to avoid the error.""" - pass + """Dummy test to avoid the error.""" + pass diff --git a/tests/test_unit/test_dummy.py b/tests/test_unit/test_dummy.py index 4443c40..b69c7ca 100644 --- a/tests/test_unit/test_dummy.py +++ b/tests/test_unit/test_dummy.py @@ -6,5 +6,5 @@ # to avoid the error "Module has no tests" when running the tests with pytest. # Cf. https://github.com/pytest-dev/pytest/issues/2393 def test_placeholder(): - """Dummy test to avoid the error.""" - pass + """Dummy test to avoid the error.""" + pass diff --git a/tus_storagehandler/main.py b/tus_storagehandler/main.py index 666c8b1..24de557 100644 --- a/tus_storagehandler/main.py +++ b/tus_storagehandler/main.py @@ -2,9 +2,9 @@ def main(): - """Main entry point for tus_storagehandler.""" - print("Hello from tus_storagehandler!") + """Main entry point for tus_storagehandler.""" + print("Hello from tus_storagehandler!") if __name__ == "__main__": - main() + main() From 94461e79dd9801518f095fb4908e3e5d28cfc992 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Mon, 8 Jul 2024 20:50:57 +0530 Subject: [PATCH 04/11] update latest --- .cruft.json | 2 +- .github/ISSUE_TEMPLATE/general-purpose.md | 8 +++----- .github/workflows/code_quality.yaml | 4 ++-- .github/workflows/release.yaml | 2 +- .gitignore | 1 + .pre-commit-config.yaml | 3 +++ 6 files changed, 11 insertions(+), 9 deletions(-) diff --git a/.cruft.json b/.cruft.json index 5a3980e..5f0d9ec 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,6 +1,6 @@ { "template": "https://github.com/elixir-cloud-aai/cookiecutter-python", - "commit": "fe9787042053d7cae1ccd7ff8d6fef4611f41b2a", + "commit": "0df5d9e910f48d3ab16c22be309c27157d65abf5", "checkout": null, "context": { "cookiecutter": { diff --git a/.github/ISSUE_TEMPLATE/general-purpose.md b/.github/ISSUE_TEMPLATE/general-purpose.md index 8a11bde..9130566 100644 --- a/.github/ISSUE_TEMPLATE/general-purpose.md +++ b/.github/ISSUE_TEMPLATE/general-purpose.md @@ -1,6 +1,5 @@ Your issue may already be reported! Please search on the -[issue tracker](https://github.com/elixir-cloud-aai/tus-storagehandler/issues) before creating -one. +[issue tracker][issue-tracker] before creating one. ## Expected Behavior @@ -26,9 +25,6 @@ one. -1. -1. -1. 1. ## Context @@ -45,3 +41,5 @@ one. - 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/workflows/code_quality.yaml b/.github/workflows/code_quality.yaml index 0c252da..a13fb2b 100644 --- a/.github/workflows/code_quality.yaml +++ b/.github/workflows/code_quality.yaml @@ -76,8 +76,8 @@ jobs: with: os: ${{ job.os }} python-version: '3.11' - poetry-install-options: "--only=types --no-root" - poetry-export-options: "--only=types" + poetry-install-options: "--with=types --no-root" + poetry-export-options: "--with=types" - name: Check types run: poetry run mypy tus_storagehandler/ diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index 1e214ed..e03080f 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -22,5 +22,5 @@ jobs: poetry-export-options: "--only=main" - name: Publish package to PyPI - run: poetry publish --build -u __token__ -p ${{ secrets.PYPI_PASSWORD }} + run: poetry publish --build -u __token__ -p ${{ secrets.PYPI_TOKEN }} ... diff --git a/.gitignore b/.gitignore index 0a558c9..14505df 100644 --- a/.gitignore +++ b/.gitignore @@ -175,6 +175,7 @@ SquareX Safe File Viewer ✕ ######### End of auto generated .gitignore file for Python projects. ######### + ######### Project level .gitignore. ######### # Keep pre-commit hooks and .yamllint file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 89a3a17..1e8f56f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -22,6 +22,9 @@ repos: - 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: From bd21c35398a4db24fbbc347e1f55615b87056ab2 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Mon, 8 Jul 2024 21:09:13 +0530 Subject: [PATCH 05/11] typoes --- .cruft.json | 2 +- PULL_REQUEST_TEMPLATE.md | 2 +- README.md | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.cruft.json b/.cruft.json index 5f0d9ec..6822a87 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,6 +1,6 @@ { "template": "https://github.com/elixir-cloud-aai/cookiecutter-python", - "commit": "0df5d9e910f48d3ab16c22be309c27157d65abf5", + "commit": "dc0f027857b60851e3cb40663f662add4343ef5a", "checkout": null, "context": { "cookiecutter": { diff --git a/PULL_REQUEST_TEMPLATE.md b/PULL_REQUEST_TEMPLATE.md index 1cf1d22..fb6b561 100644 --- a/PULL_REQUEST_TEMPLATE.md +++ b/PULL_REQUEST_TEMPLATE.md @@ -41,7 +41,7 @@ your PR is ready to be merged even though not all boxes were ticked off). --> 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 + 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 diff --git a/README.md b/README.md index a5fa631..ea5c123 100644 --- a/README.md +++ b/README.md @@ -33,7 +33,7 @@ have installed the dependencies before running the commands. > **Note**: `make` commands are only available for Unix-based systems. -To view the commdands available, run: +To view the commands available, run: ```sh make @@ -83,7 +83,7 @@ make tc make pc ``` -> **Note**: This is not the complete list of commands, run `make` to find if +> **Note**: This is not the complete list of commands, run `make` to find out if > more have been added. ## Contributing From 6a674a9553e46d8b1f656afbb6ad5e4283fcafbe Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Mon, 8 Jul 2024 23:03:21 +0530 Subject: [PATCH 06/11] more consistent --- .cruft.json | 2 +- .github/workflows/code_quality.yaml | 16 +- .github/workflows/docs.yaml | 4 +- .github/workflows/update.yaml | 4 +- .github/workflows/vulnerability.yaml | 8 +- README.md | 21 ++- poetry.lock | 261 ++++++++++++++------------- pyproject.toml | 32 +++- 8 files changed, 193 insertions(+), 155 deletions(-) diff --git a/.cruft.json b/.cruft.json index 6822a87..1c488ff 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,6 +1,6 @@ { "template": "https://github.com/elixir-cloud-aai/cookiecutter-python", - "commit": "dc0f027857b60851e3cb40663f662add4343ef5a", + "commit": "82a9aebbdff819758c94e7607c052a3fa5ba3b18", "checkout": null, "context": { "cookiecutter": { diff --git a/.github/workflows/code_quality.yaml b/.github/workflows/code_quality.yaml index a13fb2b..16cd729 100644 --- a/.github/workflows/code_quality.yaml +++ b/.github/workflows/code_quality.yaml @@ -22,8 +22,8 @@ jobs: with: os: ${{ job.os }} python-version: '3.11' - poetry-install-options: "--only=lint --no-root" - poetry-export-options: "--only=lint" + poetry-install-options: "--only=code_quality --no-root" + poetry-export-options: "--only=code_quality" - name: Check code style run: poetry run ruff format --check @@ -40,8 +40,8 @@ jobs: with: os: ${{ job.os }} python-version: '3.11' - poetry-install-options: "--only=lint --no-root" - poetry-export-options: "--only=lint" + poetry-install-options: "--only=code_quality --no-root" + poetry-export-options: "--only=code_quality" - name: Check code quality run: poetry run ruff check . @@ -58,8 +58,8 @@ jobs: with: os: ${{ job.os }} python-version: '3.11' - poetry-install-options: "--only=lint --no-root" - poetry-export-options: "--only=lint" + poetry-install-options: "--only=code_quality --no-root" + poetry-export-options: "--only=code_quality" - name: Check spellings run: poetry run typos . @@ -76,8 +76,8 @@ jobs: with: os: ${{ job.os }} python-version: '3.11' - poetry-install-options: "--with=types --no-root" - poetry-export-options: "--with=types" + poetry-install-options: "--with=code_quality,types --no-root" + poetry-export-options: "--with=code_quality,types" - name: Check types run: poetry run mypy tus_storagehandler/ diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 1b417b5..2c6799b 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -22,8 +22,8 @@ jobs: with: os: ${{ job.os }} python-version: '3.11' - poetry-install-options: "--with=docs" - poetry-export-options: "--with=docs" + poetry-install-options: "--with=docs,types --no-root" + poetry-export-options: "--with=docs,types" - name: Generate API docs run: | diff --git a/.github/workflows/update.yaml b/.github/workflows/update.yaml index 4edade9..10030bb 100644 --- a/.github/workflows/update.yaml +++ b/.github/workflows/update.yaml @@ -17,8 +17,8 @@ jobs: with: os: ${{ job.os }} python-version: '3.11' - poetry-install-options: "--with=misc --no-root" - poetry-export-options: "--with=misc" + poetry-install-options: "--only=misc --no-root" + poetry-export-options: "--only=misc" - name: Update project structure run: | diff --git a/.github/workflows/vulnerability.yaml b/.github/workflows/vulnerability.yaml index 5bb93b5..270104c 100644 --- a/.github/workflows/vulnerability.yaml +++ b/.github/workflows/vulnerability.yaml @@ -22,8 +22,8 @@ jobs: with: os: ${{ job.os }} python-version: '3.11' - poetry-install-options: "--only=security --no-root" - poetry-export-options: "--only=security" + 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/ @@ -40,8 +40,8 @@ jobs: with: os: ${{ job.os }} python-version: '3.11' - poetry-install-options: "--only=security --no-root" - poetry-export-options: "--only=security" + 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/README.md b/README.md index ea5c123..a41b9ff 100644 --- a/README.md +++ b/README.md @@ -47,12 +47,31 @@ Here are certain commands that you might find useful: make v ``` -- Installing dependencies +- Installing 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. + - Running tests ```sh diff --git a/poetry.lock b/poetry.lock index b5fbb83..7084211 100644 --- a/poetry.lock +++ b/poetry.lock @@ -154,13 +154,13 @@ chardet = ">=3.0.2" [[package]] name = "certifi" -version = "2024.6.2" +version = "2024.7.4" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"}, - {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"}, + {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"}, + {file = "certifi-2024.7.4.tar.gz", hash = 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+[tool.poetry.group.code_quality.dependencies] +mypy = ">=1.10.0,<2.0.0" +ruff = ">=0.4.10,<1.0.0" +typos = ">=1.22.8,<2.0.0" + +[tool.poetry.group.docs] +optional = true + [tool.poetry.group.docs.dependencies] added-value = ">=0.24.0,<1.0.0" docutils = "0.20.1" @@ -34,25 +45,32 @@ sphinx = "^7.3.7" sphinx-autodoc-typehints = "^2.1.0" tomli = ">=2.0.1,<3.0.0" -[tool.poetry.group.lint.dependencies] -ruff = ">=0.4.10,<1.0.0" -typos = ">=1.22.8,<2.0.0" +[tool.poetry.group.misc] +optional = true [tool.poetry.group.misc.dependencies] cruft = ">=2.15.0,<3.0.0" jello = ">=1.6.0,<2.0.0" pre-commit = ">=3.7.1,<4.0.0" -[tool.poetry.group.security.dependencies] -bandit = ">=1.7.8,<2.0.0" -safety = ">=3.2.0,<4.0.0" +[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] -mypy = ">=1.10.0,<2.0.0" + +[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.ruff] indent-width = 4 From 48787212379faad09d91e05b005eba952c516c07 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Mon, 8 Jul 2024 23:17:38 +0530 Subject: [PATCH 07/11] remove comma --- .github/workflows/code_quality.yaml | 4 ++-- .github/workflows/docs.yaml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/code_quality.yaml b/.github/workflows/code_quality.yaml index 16cd729..8b64d3b 100644 --- a/.github/workflows/code_quality.yaml +++ b/.github/workflows/code_quality.yaml @@ -76,8 +76,8 @@ jobs: with: os: ${{ job.os }} python-version: '3.11' - poetry-install-options: "--with=code_quality,types --no-root" - poetry-export-options: "--with=code_quality,types" + 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/docs.yaml b/.github/workflows/docs.yaml index 2c6799b..032768d 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -22,8 +22,8 @@ jobs: with: os: ${{ job.os }} python-version: '3.11' - poetry-install-options: "--with=docs,types --no-root" - poetry-export-options: "--with=docs,types" + poetry-install-options: "--with=docs --with=types --no-root" + poetry-export-options: "--with=docs --with=types" - name: Generate API docs run: | From e1270a16e93091fcc46bc786d8a9ca93e8bc9e5b Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Mon, 8 Jul 2024 23:29:43 +0530 Subject: [PATCH 08/11] DEBUG --- .github/workflows/docs.yaml | 7 ++++--- Makefile | 4 ++-- docs/pages/modules.rst | 7 +++++++ 3 files changed, 13 insertions(+), 5 deletions(-) create mode 100644 docs/pages/modules.rst diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 032768d..9481c13 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -27,14 +27,15 @@ jobs: - name: Generate API docs run: | - sphinx-apidoc -o /tmp/docs tus_storagehandler/ + poetry run sphinx-apidoc -o /tmp/docs tus_storagehandler/ - name: Compare docs with main branch id: check_docs_diff run: | shasum /tmp/docs/* > /tmp/docs.sha - shasum /docs/pages/* > /docs/project_doc.sha - diff=$(diff /tmp/docs.sha /docs/project_doc.sha) || true + 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 diff --git a/Makefile b/Makefile index 27caedf..bb3d0e5 100644 --- a/Makefile +++ b/Makefile @@ -69,8 +69,8 @@ fl: format-lint .PHONY: install install: - @echo "\nInstalling dependencies and with this package +++++++++++++++++++++++++++++++++\n" - @poetry install + @echo "\nInstalling all dependencies and with this package +++++++++++++++++++++++++++++++++\n" + @poetry install --with=code_quality,docs,misc,test,types,vulnerability .PHONY: i i: install diff --git a/docs/pages/modules.rst b/docs/pages/modules.rst new file mode 100644 index 0000000..cb090d8 --- /dev/null +++ b/docs/pages/modules.rst @@ -0,0 +1,7 @@ +tus_storagehandler +=================== + +.. toctree:: + :maxdepth: 4 + + tus_storagehandler From e4859217cb768abed39b772446749801cb7387fa Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Tue, 9 Jul 2024 17:57:17 +0530 Subject: [PATCH 09/11] fix docs --- .cruft.json | 2 +- .github/workflows/docs.yaml | 11 +++--- Makefile | 44 +++++++++++++++--------- README.md | 12 +++++++ docs/{ => source}/pages/modules.rst | 2 +- docs/source/pages/tus_storagehandler.rst | 21 +++++++++++ pyproject.toml | 3 ++ 7 files changed, 72 insertions(+), 23 deletions(-) rename docs/{ => source}/pages/modules.rst (78%) create mode 100644 docs/source/pages/tus_storagehandler.rst diff --git a/.cruft.json b/.cruft.json index 1c488ff..e179cc3 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,6 +1,6 @@ { "template": "https://github.com/elixir-cloud-aai/cookiecutter-python", - "commit": "82a9aebbdff819758c94e7607c052a3fa5ba3b18", + "commit": "c9d14eea5af812f12c3e19e1bbdc8affe8759eda", "checkout": null, "context": { "cookiecutter": { diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 9481c13..a0f28a1 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -27,15 +27,16 @@ jobs: - name: Generate API docs run: | - poetry run sphinx-apidoc -o /tmp/docs tus_storagehandler/ + poetry run sphinx-apidoc -o /tmp/docs/source/pages 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 + 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 diff --git a/Makefile b/Makefile index bb3d0e5..428044c 100644 --- a/Makefile +++ b/Makefile @@ -14,23 +14,26 @@ help: @echo "\nUsage: make [target] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n" @echo "Available targets:\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 "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 "Testing -----------------------------------------------------------------------" - @echo " \033[1m\033[35mtest\033[0m \033[37m(t)\033[0m: \033[36mRun all tests.\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 @@ -47,7 +50,7 @@ cv: clean-venv .PHONY: docs docs: @echo "\nGenerating project documentation ++++++++++++++++++++++++++++++++++++++++++++++\n" - @sphinx-apidoc -f -o docs/source/pages tus_storagehandler + @poetry run sphinx-apidoc -f -o docs/source/pages tus_storagehandler @cd docs && make html @echo "\nSummary ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n" @echo "Documentation generated successfully." @@ -61,7 +64,7 @@ d: docs .PHONY: format-lint format-lint: @echo "\nRunning linter and formatter using ruff and typos +++++++++++++++++++++++++++++\n" - @ruff format && ruff check --fix + @poetry run ruff format && poetry run ruff check --fix @typos . .PHONY: fl @@ -69,7 +72,7 @@ fl: format-lint .PHONY: install install: - @echo "\nInstalling all dependencies and with this package +++++++++++++++++++++++++++++++++\n" + @echo "\nInstalling dependencies and with this package +++++++++++++++++++++++++++++++++\n" @poetry install --with=code_quality,docs,misc,test,types,vulnerability .PHONY: i @@ -78,7 +81,7 @@ i: install .PHONY: precommit-check precommit-check: @echo "\nRunning pre-commit checks +++++++++++++++++++++++++++++++++++++++++++++++++++++\n" - @pre-commit run --all-files + @poetry run pre-commit run --all-files .PHONY: pc pc: precommit-check @@ -86,8 +89,8 @@ pc: precommit-check .PHONY: security security: @echo "\nRunning security scans using bandit and safety ++++++++++++++++++++++++++++++++\n" - @safety check --full-report - @bandit -c pyproject.toml -r tus_storagehandler + @poetry run safety check --full-report + @poetry run bandit -c pyproject.toml -r tus_storagehandler .PHONY: s s: security @@ -95,7 +98,7 @@ s: security .PHONY: test test: @echo "\nRunning tests using pytest ++++++++++++++++++++++++++++++++++++++++++++++++++++\n" - @pytest tests/ + @poetry run pytest tests/ .PHONY: t t: test @@ -103,11 +106,20 @@ t: test .PHONY: type-check type-check: @echo "\nPerforming type checking with mypy ++++++++++++++++++++++++++++++++++++++++++++\n" - @mypy tus_storagehandler + @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" diff --git a/README.md b/README.md index a41b9ff..1a3d15c 100644 --- a/README.md +++ b/README.md @@ -72,6 +72,9 @@ make i > > 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). + - Running tests ```sh @@ -90,6 +93,9 @@ make fl 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. + - Running type checker ```sh @@ -102,6 +108,12 @@ make tc 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. diff --git a/docs/pages/modules.rst b/docs/source/pages/modules.rst similarity index 78% rename from docs/pages/modules.rst rename to docs/source/pages/modules.rst index cb090d8..66ab2b8 100644 --- a/docs/pages/modules.rst +++ b/docs/source/pages/modules.rst @@ -1,5 +1,5 @@ tus_storagehandler -=================== +================== .. toctree:: :maxdepth: 4 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/pyproject.toml b/pyproject.toml index b167ac0..f85f11e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -72,6 +72,9 @@ optional = true 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 From 0df873910447c589165ad41d170a151a1db227ff Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Tue, 9 Jul 2024 18:39:58 +0530 Subject: [PATCH 10/11] typo --- .cruft.json | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.cruft.json b/.cruft.json index e179cc3..25bc38e 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,6 +1,6 @@ { "template": "https://github.com/elixir-cloud-aai/cookiecutter-python", - "commit": "c9d14eea5af812f12c3e19e1bbdc8affe8759eda", + "commit": "07cdc94c402c48f05311658d871795c1bd688ddf", "checkout": null, "context": { "cookiecutter": { diff --git a/README.md b/README.md index 1a3d15c..eaa40ed 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ File handler utilizing TUS and MinIO with DRS-Filer integration. ## Development For ease, certain scripts have been abbreviated in `Makefile`, make sure that -have installed the dependencies before running the commands. +you have installed the dependencies before running the commands. > **Note**: `make` commands are only available for Unix-based systems. From ec8fc4db342e5532fc60abc379dbcf13de18bd52 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 24 Jul 2024 13:56:38 +0530 Subject: [PATCH 11/11] chore add COC 2.1 and badge --- .cruft.json | 2 +- CODE_OF_CONDUCT.md | 76 ---------------------------------------------- README.md | 15 ++++----- 3 files changed, 7 insertions(+), 86 deletions(-) delete mode 100644 CODE_OF_CONDUCT.md diff --git a/.cruft.json b/.cruft.json index 25bc38e..d30a3ab 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,6 +1,6 @@ { "template": "https://github.com/elixir-cloud-aai/cookiecutter-python", - "commit": "07cdc94c402c48f05311658d871795c1bd688ddf", + "commit": "ea72128ea94f0693d2a940f3f1657554178b6b66", "checkout": null, "context": { "cookiecutter": { diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md deleted file mode 100644 index 97985fe..0000000 --- a/CODE_OF_CONDUCT.md +++ /dev/null @@ -1,76 +0,0 @@ -# ELIXIR Cloud & AAI Code of Conduct - -## Our Pledge - -In the interest of fostering an open and welcoming environment, we as -contributors and maintainers pledge to making participation in our project and -our community a harassment-free experience for everyone, regardless of age, body -size, disability, ethnicity, sex characteristics, gender identity and -expression, level of experience, education, socio-economic status, nationality, -personal appearance, race, religion, or sexual identity and orientation. - -## Our Standards - -Examples of behavior that contributes to creating a positive environment -include: - -- Using welcoming and inclusive language -- Being respectful of differing viewpoints and experiences -- Gracefully accepting constructive criticism -- Focusing on what is best for the community -- Showing empathy towards other community members - -Examples of unacceptable behavior by participants include: - -- The use of sexualized language or imagery and unwelcome sexual attention or - advances -- Trolling, insulting/derogatory comments, and personal or political attacks -- Public or private harassment -- Publishing others' private information, such as a physical or electronic - address, without explicit permission -- Other conduct which could reasonably be considered inappropriate in a - professional setting - -## Our Responsibilities - -Project maintainers are responsible for clarifying the standards of acceptable -behavior and are expected to take appropriate and fair corrective action in -response to any instances of unacceptable behavior. - -Project maintainers have the right and responsibility to remove, edit, or reject -comments, commits, code, wiki edits, issues, and other contributions that are -not aligned to this Code of Conduct, or to ban temporarily or permanently any -contributor for other behaviors that they deem inappropriate, threatening, -offensive, or harmful. - -## Scope - -This Code of Conduct applies both within project spaces and in public spaces -when an individual is representing the project or its community. Examples of -representing a project or community include using an official project e-mail -address, posting via an official social media account, or acting as an appointed -representative at an online or offline event. Representation of a project may be -further defined and clarified by project maintainers. - -## Enforcement - -Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported by contacting -[cloud-service@elixir-europe.org][elixir-cloud-aai-email]. All complaints will -be reviewed and investigated and will result in a response that is deemed -necessary and appropriate to the circumstances. The project team is obligated to -maintain confidentiality with regard to the reporter of an incident. Further -details of specific enforcement policies may be posted separately. - -Project maintainers who do not follow or enforce the Code of Conduct in good -faith may face temporary or permanent repercussions as determined by other -members of the project's leadership. - -## Attribution - -This Code of Conduct is adapted from the -[Contributor Covenant][contributor-covenant], version 1.4, available at - - -[contributor-covenant]: https://contributor-covenant.org/ -[elixir-cloud-aai-email]: mailto:cloud-service@elixir-europe.org diff --git a/README.md b/README.md index eaa40ed..937e18f 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ [![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.md) [![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/) @@ -128,14 +129,10 @@ you are interested in contributing. ## Code of Conduct -Please mind the code of conduct described in -[`CODE_OF_CONDUCT.md`][code-of-conduct] for all interactions with the community. -Please be nice to one another! :) - -If you experience any unacceptable behavior by any member of the community, -please refer to the contact method specified in -[`CODE_OF_CONDUCT.md`][code-of-conduct] to report the incident to the community -leaders. +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 @@ -166,7 +163,7 @@ To get in touch with us, please use one of the following routes: [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]: CODE_OF_CONDUCT.md +[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/