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| @@ -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": "[email protected]", | ||
| "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" | ||
| } | ||
|
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| 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. | ||
|
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| ## Our Standards | ||
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@@ -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. | ||
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| 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. | ||
|
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| ## Scope | ||
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@@ -55,10 +55,11 @@ further defined and clarified by project maintainers. | |
| ## Enforcement | ||
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| Instances of abusive, harassing, or otherwise unacceptable behavior may be | ||
| reported by contacting [[email protected]][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 | ||
| [[email protected]][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. | ||
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| Project maintainers who do not follow or enforce the Code of Conduct in good | ||
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| ## Attribution | ||
|
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| 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 | ||
| <https://www.contributor-covenant.org/version/1/4/code-of-conduct.html> | ||
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| [contributor-covenant]: https://contributor-covenant.org/ | ||
|
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,143 +1,90 @@ | ||
| # Python Cookiecutter Template | ||
| [](https://bandit.readthedocs.io/en/latest/) | ||
| [](https://codecov.io/gh/elixir-cloud-aai/tus-storagehandler) | ||
| [](https://tus_storagehandler.readthedocs.io/en/latest/?badge=latest) | ||
| [](./LICENSE) | ||
| [](https://www.python.org/) | ||
| [](https://github.com/elixir-cloud-aai/tus-storagehandler/graphs/contributors) | ||
| [](https://docs.astral.sh/ruff/) | ||
| [](https://safetycli.com/product/safety-cli) | ||
|
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| This is a Cookiecutter template for creating a Python project with Poetry, | ||
| including configurations for various project settings. | ||
| # tus-storagehandler | ||
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| File handler utilizing TUS and MinIO with DRS-Filer integration. | ||
|
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| ## Table of Contents | ||
|
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| - [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) | ||
|
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| ## Usage | ||
| ## Basic Usage | ||
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| 1. **Install cruft** (if you haven't already): | ||
| ## Installation | ||
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| ```sh | ||
| pip install cruft | ||
| ``` | ||
| ## Development | ||
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| For ease, certain scripts have been abbreviated in `Makefile`, make sure that | ||
| have installed the dependencies before running the commands. | ||
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| 2. **Generate a New Project**: | ||
| > **Note**: `make` commands are only available for Unix-based systems. | ||
| To view the commdands available, run: | ||
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| ```sh | ||
| cruft create https://github.com/elixir-cloud-aai/cookiecutter-python.git | ||
| make | ||
| ``` | ||
|
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| ### Don't wanna use cruft? | ||
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| You can also use the `cookiecutter` command directly: | ||
| Here are certain commands that you might find useful: | ||
|
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| 1. **Install cookiecutter** (if you haven't already): | ||
| - Making a virtual environment | ||
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| ```sh | ||
| pip install cookiecutter | ||
| make v | ||
| ``` | ||
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| 2. **Generate a New Project**: | ||
| - Installing dependencies | ||
|
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| ```sh | ||
| cookiecutter gh:elixir-cloud-aai/cookiecutter-python | ||
| make i | ||
| ``` | ||
|
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| > **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. | ||
|
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| ## Configurations | ||
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| ### Package manager - Poetry | ||
| - Running tests | ||
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| This project uses [Poetry][poetry-org] as a package manager. Check out the | ||
| commands at the [official documentation][poetry-docs]. | ||
|
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| ### Linters and formatters - Ruff | ||
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| To lint and format `Python` code files, it uses [Ruff][ruff], the default | ||
| configuration is set in the `pyproject.toml` file. | ||
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| ```toml | ||
| select = [ | ||
| "B", # flake8-bugbear | ||
| "E", # pycodestyle | ||
| "F", # Pyflakes | ||
| "I", # isort | ||
| "PL", # pylint | ||
| "SIM", # flake8-simplify | ||
| "UP", # pyupgrade | ||
| ] | ||
| ```sh | ||
| make t | ||
| ``` | ||
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| 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 | ||
|
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| ### Spell checker - Typos | ||
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| If you want to ignore certain words, add them to the `pyproject.toml` file, | ||
| under the `tool.typos.default.extend-words` key. | ||
|
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| ```toml | ||
| [tool.typos.default.extend-words] | ||
| mke = 'mke' | ||
| ```sh | ||
| make fl | ||
| ``` | ||
|
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| For further configuration, refer to the [typos docs][typos-docs]. | ||
| - Building the documentation | ||
|
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| ### Static type checker - Mypy | ||
|
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| Change the configuration in `pyproject.toml` file, for further information refer to | ||
| the [documentation][mypy-config]. | ||
|
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| ### Documentation - Sphinx | ||
|
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| 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. | ||
|
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| > **Note**: Make sure to setup the `ReadTheDocs` account and add the project to | ||
| the account to host the documentation. | ||
|
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| ### Testing - pytest and pytest-cov | ||
|
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| Generate a coverage report using `pytest-cov` and uploads it to codecov.io. | ||
|
|
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| > **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). | ||
|
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| ## CI/CD - GitHub Actions | ||
| ```sh | ||
| make d | ||
| ``` | ||
|
|
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| Here are the GitHub Actions Secrets that need to be included in the repository | ||
| settings: | ||
| - Running type checker | ||
|
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| - `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 | ||
| ``` | ||
|
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| ## Disclaimer | ||
| - Running all pre-commit checks | ||
|
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| 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 | ||
| ``` | ||
|
|
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| **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 | ||
|
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|
|
@@ -162,7 +109,7 @@ leaders. | |
| ## Versioning | ||
|
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| 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. | ||
|
|
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| ## License | ||
|
|
@@ -174,13 +121,12 @@ copy of which is also available in [`LICENSE`][license]. | |
|
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| 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]. | ||
|
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| 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:[email protected] | ||
| [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/ | ||
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