# aind-large-scale-prediction
This package allows the iteration of a zarr dataset in chunks. It provides the global coordinate of each pulled chunk and also allows overlapping areas.
[![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-100.0%25-brightgreen)
![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
![Python](https://img.shields.io/badge/python->=3.9-blue?logo=python)
## Usage
- To use this template, click the green `Use this template` button and `Create new repository`.
- After github initially creates the new repository, please wait an extra minute for the initialization scripts to finish organizing the repo.
- To enable the automatic semantic version increments: in the repository go to `Settings` and `Collaborators and teams`. Click the green `Add people` button. Add `svc-aindscicomp` as an admin. Modify the file in `.github/workflows/tag_and_publish.yml` and remove the if statement in line 10. The semantic version will now be incremented every time a code is committed into the main branch.
- To publish to PyPI, enable semantic versioning and uncomment the publish block in `.github/workflows/tag_and_publish.yml`. The code will now be published to PyPI every time the code is committed into the main branch.
- The `.github/workflows/test_and_lint.yml` file will run automated tests and style checks every time a Pull Request is opened. If the checks are undesired, the `test_and_lint.yml` can be deleted. The strictness of the code coverage level, etc., can be modified by altering the configurations in the `pyproject.toml` file and the `.flake8` file.
## 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
### Semantic Release
The table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):
| Commit message | Release type |
| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
| `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |
| `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |
| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |
### 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).
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It provides the global coordinate of each pulled chunk and also allows overlapping areas.\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-100.0%25-brightgreen)\n![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)\n![Python](https://img.shields.io/badge/python->=3.9-blue?logo=python)\n\n\n\n## Usage\n - To use this template, click the green `Use this template` button and `Create new repository`.\n - After github initially creates the new repository, please wait an extra minute for the initialization scripts to finish organizing the repo.\n - To enable the automatic semantic version increments: in the repository go to `Settings` and `Collaborators and teams`. Click the green `Add people` button. Add `svc-aindscicomp` as an admin. Modify the file in `.github/workflows/tag_and_publish.yml` and remove the if statement in line 10. The semantic version will now be incremented every time a code is committed into the main branch.\n - To publish to PyPI, enable semantic versioning and uncomment the publish block in `.github/workflows/tag_and_publish.yml`. The code will now be published to PyPI every time the code is committed into the main branch.\n - The `.github/workflows/test_and_lint.yml` file will run automated tests and style checks every time a Pull Request is opened. If the checks are undesired, the `test_and_lint.yml` can be deleted. 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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### Semantic Release\n\nThe table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):\n\n| Commit message | Release type |\n| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |\n| `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |\n| `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |\n| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |\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",
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