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Fixes #{issue-id-number}. | ||
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## Description | ||
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Please provide here a summary of the changes introduced by this PR. | ||
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## How to test? | ||
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Please provide here instructions on how to test the changes introduced by this PR. | ||
(if some changes cannot be tested by automated tests) | ||
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## Checklist | ||
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- [ ] This PR refers to an issue from the [issue tracker](https://github.com/BlueBrain/morphoclass/issues). | ||
(if it is not the case, please create an issue first). | ||
- [ ] Unit tests added. | ||
(if needed) | ||
- [ ] `setup.cfg`, `requirements.txt`, and `constraints.txt` updated with new dependencies. | ||
(if needed) | ||
- [ ] Type annotations added. | ||
(if a function is added or modified) | ||
- [ ] All CI tests pass. |
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version: 2 | ||
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formats: [] | ||
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sphinx: | ||
builder: html | ||
configuration: docs/source/conf.py | ||
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build: | ||
image: latest | ||
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python: | ||
version: "3.8" | ||
install: | ||
- method: pip | ||
path: . | ||
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# inspired by: https://github.com/pyg-team/pytorch_geometric/blob/master/docs/requirements.txt | ||
- requirements: docs/requirements.txt | ||
system_packages: true |
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- [Jelena Banjac](https://github.com/JelenaBanjac) @ Blue Brain Project, EPFL | ||
- [Francesco Casalegno](https://github.com/FrancescoCasalegno) @ Blue Brain Project, EPFL | ||
- [Stanislav Schmidt](https://github.com/Stannislav) @ Blue Brain Project, EPFL |
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# Contributing | ||
Thank you for your interest in contributing to MorphoClass! | ||
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Before you open an issue or start working on a pull request, please make sure | ||
to read the following guidelines. | ||
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1. [Creating Issues](#creating-issues) | ||
1. [Working on the Code](#working-on-the-code) | ||
1. [Creating Pull Requests](#creating-pull-requests) | ||
1. [Refer to an issue](#refer-to-an-issue) | ||
1. [Add unit test](#add-unit-tests) | ||
1. [Add type annotations](#add-type-annotations) | ||
1. [Update dependencies](#update-dependencies) | ||
1. [Ensure all CI tests pass](#ensure-all-ci-tests-pass) | ||
1. [Get reviews and approval](#get-reviews-and-approval) | ||
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## Creating Issues | ||
Before you submit an issue, please search our [issue | ||
tracker](https://github.com/BlueBrain/morphoclass/issues) to verify if any | ||
similar issue was raised in the past. Even if you cannot find a direct answer | ||
to your question, this can allow you to collect a list of related issues that | ||
you can link in your new issue. | ||
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Once you have verified that no similar issues exist yet, feel free to open a | ||
new issue. | ||
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## Working on the Code | ||
Our extended documentation on https://morphoclass.readthedocs.io has a | ||
dedicated installation section that will guide you through a development | ||
installation of MorphoClass. Please follow it to prepare your environment. | ||
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When working on the code please keep the following points in mind: | ||
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* enable pre-commit (`pre-commit install`) | ||
* use `black` and `isort` to auto-format | ||
* `pre-commit` should normally do that for you automatically | ||
* check via `tox -e lint` (also runs `flake8`) | ||
* trigger formatting for all files via `tox -e format` | ||
* apply PEP8, check via `tox -e lint` | ||
* adding type annotations is preferred, use `tox -e type` for checking | ||
* re-generate the API docs for new modules via `tox -e apidoc`, check using `tox -e apidoc-check` | ||
* write unit tests, test by running `pytest tests` in the project root | ||
* add docstrings (NumPy style) | ||
* work on branches, don't push to `main`. | ||
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## Creating Pull Requests | ||
If you wish to contribute to the code base, opening a pull request on GitHub is | ||
the right thing to do! | ||
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Please read the following paragraphs to make sure that your work can be | ||
considered for a potential integration in our source code. | ||
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### Refer to an issue | ||
In general, every pull request should refer to a specific issue. If you would | ||
like to provide your contribution to an untracked issue, please create first an | ||
issue as explained [here](#creating-issues) so that we can discuss the value of | ||
the proposed contribution and its implementation. | ||
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### Add unit tests | ||
Concerning CI tests, we are running various checks on linting, unit tests, | ||
docs, and packaging. If you are adding or modifying a functionality in the | ||
code, you are also expected to provide a unit test demonstrating and checking | ||
the new behavior. | ||
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### Add type annotations | ||
We are gradually introducing type annotations to our code, and our CI performs | ||
type checking with [mypy](https://mypy.readthedocs.io/en/stable/index.html). If | ||
your PR introduces a new function or heavily modifies an existing function, you | ||
should also add type annotations for such function. | ||
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### Update dependencies | ||
If your PR introduces a dependency on a new python package, this should be | ||
added to both the `setup.py` and the `requirements.txt` files. | ||
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### Ensure all CI tests pass | ||
We use GitHub Actions to run [our CI | ||
tests](https://github.com/BlueBrain/morphoclass/actions?query=workflow%3A%22ci+testing%22). | ||
Once you open a PR, the workflow that runs all CI tests is automatically | ||
triggered. This workflow is also triggered every time a new commit is pushed to | ||
that PR branch. If you want to push a commit without triggering the CI tests | ||
(e.g. if a feature is still work in progress, and you want to save time), your | ||
commit message should include an appropriate label like `[skip ci]`, `[ci | ||
skip]`, `[no ci]` etc. (see | ||
[here](https://github.blog/changelog/2021-02-08-github-actions-skip-pull-request-and-push-workflows-with-skip-ci/) | ||
for the complete list). | ||
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All CI tests must pass before the pull request can be considered for review. | ||
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### Get reviews and approval | ||
Once you have satisfied all the previous points, feel free to open your pull | ||
request! | ||
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We will get back to you as soon as possible with comments and feedback in the | ||
format of pull request reviews. A positive review from one of the maintainers | ||
is required for the pull request to be merged into the master. |
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