# aind-mri-utils
[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
![Code Style](https://img.shields.io/badge/code%20style-black-black)
[![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
![Interrogate](https://img.shields.io/badge/interrogate-94.5%25-brightgreen)
![Coverage](https://img.shields.io/badge/coverage-52%25-red?logo=codecov)
![Python](https://img.shields.io/badge/python->=3.7-blue?logo=python)
Library for aind mri utilities.
## Installation
To use the software, in the root directory, run
```bash
pip install -e .
```
To develop the code, run
```bash
pip install -e .[dev]
```
## Contributing
### Linters and testing
There are several libraries used to run linters, check documentation, and run tests.
- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
```bash
coverage run -m unittest discover && coverage report
```
- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
```bash
interrogate .
```
- Use **flake8** to check that code is up to standards (no unused imports, etc.):
```bash
flake8 .
```
- Use **black** to automatically format the code into PEP standards:
```bash
black .
```
- Use **isort** to automatically sort import statements:
```bash
isort .
```
### Pull requests
For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
```text
<type>(<scope>): <short summary>
```
where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
- **docs**: Documentation only changes
- **feat**: A new feature
- **fix**: A bugfix
- **perf**: A code change that improves performance
- **refactor**: A code change that neither fixes a bug nor adds a feature
- **test**: Adding missing tests or correcting existing tests
### Documentation
To generate the rst files source files for documentation, run
```bash
sphinx-apidoc -o doc_template/source/ src
```
Then to create the documentation HTML files, run
```bash
sphinx-build -b html doc_template/source/ doc_template/build/html
```
More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
Raw data
{
"_id": null,
"home_page": null,
"name": "aind-mri-utils",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.7",
"maintainer_email": null,
"keywords": null,
"author": "Allen Institute for Neural Dynamics",
"author_email": "Galen Lynch <galen@galenlynch.com>, Yoni Browning <yoni.browning@alleninstitute.org>",
"download_url": "https://files.pythonhosted.org/packages/39/c2/8657e98a86c82ee9e390c3ea6b459985e3c6e02ee11261c9079e7a129a85/aind_mri_utils-0.0.45.tar.gz",
"platform": null,
"description": "# aind-mri-utils\n\n[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)\n![Code Style](https://img.shields.io/badge/code%20style-black-black)\n[![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)\n![Interrogate](https://img.shields.io/badge/interrogate-94.5%25-brightgreen)\n![Coverage](https://img.shields.io/badge/coverage-52%25-red?logo=codecov)\n![Python](https://img.shields.io/badge/python->=3.7-blue?logo=python)\n\nLibrary for aind mri utilities.\n\n## Installation\nTo use the software, in the root directory, run\n```bash\npip install -e .\n```\n\nTo develop the code, run\n```bash\npip install -e .[dev]\n```\n\n## Contributing\n\n### Linters and testing\n\nThere are several libraries used to run linters, check documentation, and run tests.\n\n- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:\n\n```bash\ncoverage run -m unittest discover && coverage report\n```\n\n- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:\n\n```bash\ninterrogate .\n```\n\n- Use **flake8** to check that code is up to standards (no unused imports, etc.):\n```bash\nflake8 .\n```\n\n- Use **black** to automatically format the code into PEP standards:\n```bash\nblack .\n```\n\n- Use **isort** to automatically sort import statements:\n```bash\nisort .\n```\n\n### Pull requests\n\nFor internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:\n```text\n<type>(<scope>): <short summary>\n```\n\nwhere scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:\n\n- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)\n- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)\n- **docs**: Documentation only changes\n- **feat**: A new feature\n- **fix**: A bugfix\n- **perf**: A code change that improves performance\n- **refactor**: A code change that neither fixes a bug nor adds a feature\n- **test**: Adding missing tests or correcting existing tests\n\n### Documentation\nTo generate the rst files source files for documentation, run\n```bash\nsphinx-apidoc -o doc_template/source/ src\n```\nThen to create the documentation HTML files, run\n```bash\nsphinx-build -b html doc_template/source/ doc_template/build/html\n```\nMore info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "MRI utilities library for aind teams.",
"version": "0.0.45",
"project_urls": null,
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "c7c7bc38a04204b71886cac42eda22a0b676c4cc295eff37cec964063c44f72b",
"md5": "a1c82a969cce0b3879f2727357eb8c75",
"sha256": "0b38e0511ed329d5dbcbf1d2fefa55ffe4698596de637b251e099c771b8b7b19"
},
"downloads": -1,
"filename": "aind_mri_utils-0.0.45-py3-none-any.whl",
"has_sig": false,
"md5_digest": "a1c82a969cce0b3879f2727357eb8c75",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.7",
"size": 47411,
"upload_time": "2024-10-03T22:08:47",
"upload_time_iso_8601": "2024-10-03T22:08:47.074486Z",
"url": "https://files.pythonhosted.org/packages/c7/c7/bc38a04204b71886cac42eda22a0b676c4cc295eff37cec964063c44f72b/aind_mri_utils-0.0.45-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "39c28657e98a86c82ee9e390c3ea6b459985e3c6e02ee11261c9079e7a129a85",
"md5": "f55112a64a43a52af590bc83aea56a6a",
"sha256": "33b65dacb9cc5846d2a9a2e1ed8e373d37fd11cadc1ff6f053f04f30e16e0fb9"
},
"downloads": -1,
"filename": "aind_mri_utils-0.0.45.tar.gz",
"has_sig": false,
"md5_digest": "f55112a64a43a52af590bc83aea56a6a",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.7",
"size": 79325,
"upload_time": "2024-10-03T22:08:48",
"upload_time_iso_8601": "2024-10-03T22:08:48.289733Z",
"url": "https://files.pythonhosted.org/packages/39/c2/8657e98a86c82ee9e390c3ea6b459985e3c6e02ee11261c9079e7a129a85/aind_mri_utils-0.0.45.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-10-03 22:08:48",
"github": false,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"lcname": "aind-mri-utils"
}