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Merge pull request #613 from mehta-lab/doc/update_contributing
Update Contributing.md with documentation on tests
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| We welcome your contributions! Please see the provided steps below and never hesitate to contact us. | ||
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| If you are a new user, we recommend checking out the detailed [Github Guides](https://guides.github.com). | ||
| If you are a new user, we recommend checking out the detailed [Github Docs](https://docs.github.com/). | ||
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| ## Setting up a development installation | ||
| ## Issues | ||
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| In order to make changes to `pycro-manager`, you will need to [fork](https://guides.github.com/activities/forking/#fork) the | ||
| [repository](https://github.com/pycro-manager/pycro-manager). | ||
| We use [issues](https://github.com/micro-manager/pycro-manager/issues) to track bug reports, feature requests, and user questions. Please use the suggested template when creating a new issue to receive the most relevant feedback. | ||
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| If you are not familiar with `git`, we recommend reading up on [this guide](https://guides.github.com/introduction/git-handbook/#basic-git). | ||
| ## Making changes | ||
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| Clone the forked repository to your local machine and change directories: | ||
| ```sh | ||
| git clone https://github.com/your-username/pycro-manager.git | ||
| cd pycro-manager | ||
| ``` | ||
| Changes to `pycro-manager` need to be proposed in a [pull request](https://github.com/micro-manager/pycro-manager/pulls) (PR) to the `main` branch. Please follow the GitHub documentation on [Contributing to projects](https://docs.github.com/en/get-started/quickstart/contributing-to-projects?tool=webui) for instructions on how to fork the repository, make changes, and create a pull request to contribute to the repo. | ||
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| Set the `upstream` remote to the base `pycro-manager` repository: | ||
| ```sh | ||
| git remote add upstream https://github.com/micro-manager/pycro-manager.git | ||
| ``` | ||
| Please reference open issues that can be addressed by your PR. Please include a description of the bug fix or new feature implemented in the PR. | ||
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| Install the package in editable mode, along with all of the developer tools | ||
| ```sh | ||
| pip install -r requirements.txt | ||
| pip install -e .[test] | ||
| ``` | ||
| ## Setting up a development installation | ||
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| `pycro-manager` can be installed in editable mode to allow you to test the changes you have made. We recommend using an environment management tool such as [Conda](https://github.com/conda/conda). | ||
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| ## Making changes | ||
| Create a new conda environment with | ||
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| Create a new feature branch: | ||
| ```sh | ||
| git checkout master -b your-branch-name | ||
| conda create -n pycro-manager | ||
| conda activate pycro-manager | ||
| ``` | ||
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| `git` will automatically detect changes to a repository. | ||
| You can view them with: | ||
| ```sh | ||
| git status | ||
| ``` | ||
| Navigate to the repo directory and install the package in editable mode, along with all of the developer tools | ||
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| Add and commit your changed files: | ||
| ```sh | ||
| git add my-file-or-directory | ||
| git commit -m "my message" | ||
| pip install -e ".[dev]" | ||
| ``` | ||
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| ### Help us make sure it's you | ||
| ## Help us make sure it's you | ||
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| Each commit you make must have a [GitHub-registered email](https://github.com/settings/emails) | ||
| as the `author`. You can read more [here](https://help.github.com/en/github/setting-up-and-managing-your-github-user-account/setting-your-commit-email-address). | ||
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| To set it, use `git config --global user.email [email protected]`. | ||
| To set it, use | ||
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| ## Keeping your branches up-to-date | ||
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| Switch to the `master` branch: | ||
| ```sh | ||
| git checkout master | ||
| git config --global user.email [email protected] | ||
| ``` | ||
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| Fetch changes and update `master`: | ||
| ```sh | ||
| git pull upstream master --tags | ||
| ``` | ||
| ## Keeping your fork up-to-date | ||
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| This is shorthand for: | ||
| ```sh | ||
| git fetch upstream master --tags | ||
| git merge upstream/master | ||
| ``` | ||
| Make sure your fork stays up-to-date with the latest changes in the main repo by [syncing your fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork). | ||
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| Update your other branches: | ||
| ```sh | ||
| git checkout your-branch-name | ||
| git merge master | ||
| ``` | ||
| ## Testing the code | ||
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| ## Sharing your changes | ||
| We use the [pytest](https://docs.pytest.org/) framework to test the code. During development, you can run the tests locally using | ||
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| Update your remote branch: | ||
| ```sh | ||
| git push -u origin your-branch-name | ||
| # in the project root directory | ||
| pytest -v | ||
| ``` | ||
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| You can then make a [pull-request](https://guides.github.com/activities/forking/#making-a-pull-request) to `pycro-manager`'s `master` branch. | ||
| The suite of [tests](https://github.com/micro-manager/pycro-manager/tree/main/pycromanager/test) also runs automatically using [GitHub Actions](https://github.com/micro-manager/pycro-manager/actions) for every PR. All tests must pass before a PR is merged. Please contribute new tests as you fix bugs and develop new features. | ||
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| Execution of the `pycro-manager` tests depends on [Micro-manager](https://micro-manager.org/) and several Java libraries ([AcqEngJ](https://github.com/micro-manager/AcqEngJ), [NDTiffStorage](https://github.com/micro-manager/NDTiffStorage), [NDViewer](https://github.com/micro-manager/NDViewer)). | ||
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| During setup, `pytest` will download the latest [nightly build](https://micro-manager.org/Micro-Manager_Nightly_Builds) of `Micro-manager` and install it in `~/Micro-Manager-nightly`; this step will be skipped if that folder exists. Currently installation of the latest `Micro-manager` nightly build through `pytest` is only supported on Windows platforms. For other platforms, please manually install a working version of `Micro-manager` in `~/Micro-Manager-nightly`. | ||
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| During setup, `pytest` will also look for pre-compiled `.jar` files in the `../../{java_lib_name}/target` directory (e.g. `../../{AcqEngJ}/target`) and replace the ones that are packaged with the `Micro-manager` nightly build if they are older version. This is helpful when co-developing these libraries. The user does need to pre-compile the Java libraries first. When the tests run in GitHub Actions they always use with the `.jar` files that are packaged with `Micro-manager`. | ||
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| Tests of the `pycro-manager` NDViewer and `napari` viewer only execute locally and are skipped by GitHub Actions. When making changes that may affect these viewer, please make sure to always run the tests locally. | ||
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| ## Building the docs | ||
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