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Merged
rxu17 merged 7 commits into from
Nov 13, 2025
Merged

[GEN-2380] Update docs #623

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2f1e0c5
update to match current workflows
rxu17 Nov 5, 2025
43a868e
test dynamically getting feature branch image
rxu17 Nov 6, 2025
f08fc7f
add docker env setup, standardize commands and remove dedundancy
rxu17 Nov 6, 2025
c8aa7f0
add docker section
rxu17 Nov 7, 2025
1d07796
Merge branch 'develop' into gen-2380-update-docs
rxu17 Nov 7, 2025
5c92f05
shift docker development and make it sage vs external specific betwee…
rxu17 Nov 7, 2025
e3df613
Merge branch 'gen-2380-update-docs' of https://github.com/Sage-Bionet…
rxu17 Nov 7, 2025
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6 changes: 0 additions & 6 deletions .devcontainer/devcontainer.json
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60 changes: 22 additions & 38 deletions CONTRIBUTING.md
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@rxu17 rxu17 Nov 7, 2025

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I realize this CONTRIBUTING doc has a mix of development guidelines for external and specific to sage developers, e.g: only sage bionetworks developers can utilize the run_integration_tests functionality. I might just migrate all of the sage specific to README under Sage Bionetworks only and keep this section just for the forking and adding changes for external developers.
They can still pull the public images and build images via Dockerfile to do testing. But they won't be able to run any of our pipeline steps etc etc

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@thomasyu888 thomasyu888 Nov 7, 2025

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May be helpful to get xindis feedback on this

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@rxu17 rxu17 Nov 7, 2025 •
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Sounds good, I added that as AC for the relevant onboarding tickets - to review and approve the documentation

Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,22 @@

We welcome all contributions! Please head to [issues](https://github.com/Sage-Bionetworks/Genie/issues) to either file any bugs/feature requests or find a task you want to assist with. Make sure to assign yourself the task if you decide to work on it.

## Table of Contents

- [Coding Style](#coding-style)
- [The Development Life Cycle](#the-development-life-cycle)
- [Fork and clone this repository](#fork-and-clone-this-repository)
- [Install development dependencies](#install-development-dependencies)
- [Developing](#developing)
- [Testing](#testing)
- [Running tests](#running-tests)
- [Tests in Python](#tests-in-python)
- [Tests in R](#tests-in-r)
- [Test Development](#test-development)
- [Mock Testing](#mock-testing)
- [Release Procedure (For Package Maintainers)](#release-procedure-for-package-maintainers)
- [Contributing to the docs](#contributing-to-the-docs)

## Coding Style

This package uses `flake8` - it's settings are described in [setup.cfg](setup.cfg). The code in this package is also automatically formatted by `black` for consistency.
Expand All @@ -23,22 +39,7 @@ This package uses `flake8` - it's settings are described in [setup.cfg](setup.cf

### Install development dependencies

This will install all the dependencies of the package including the active branch of `Genie`. We highly recommend that you leverage some form of python version management like [pyenv](https://github.com/pyenv/pyenv) or [anaconda](https://www.anaconda.com/products/individual). There are two ways you can install the dependencies for this package.

#### pip
This is the more traditional way of installing dependencies. Follow instructions [here](https://pip.pypa.io/en/stable/installation/) to learn how to install pip.

```
pip install -r requirements-dev.txt
pip install -r requirements.txt
```

#### pipenv
`pipenv` is a Python package manager. Learn more about [pipenv](https://pipenv.pypa.io/en/latest/) and how to install it.

```
# Coming soon
```
This will install all the dependencies of the package including the active branch of `Genie`. We highly recommend that you leverage some form of python version management like [pyenv](https://github.com/pyenv/pyenv) or [anaconda](https://www.anaconda.com/products/individual). Follow [dependencies installation instruction here](./README.md#running-locally)

### Developing

Expand All @@ -54,17 +55,17 @@ The GENIE project follows the standard [git flow](https://www.atlassian.com/git/
git pull upstream develop
```

1. Create a feature branch which off the `develop` branch. If there is a GitHub/JIRA issue that you are addressing, name the branch after the issue with some more detail (like `{GH|JIRA}-123-add-some-new-feature`).
1. Create a feature branch which off the `develop` branch. If there is a GitHub/JIRA issue that you are addressing, name the branch after the issue with some more detail (like `{GH|GEN}-123-add-some-new-feature`).

```
git checkout develop
git checkout -b JIRA-123-new-feature
git checkout -b GEN-123-new-feature
```

1. At this point, you have only created the branch locally, you need to push this to your fork on GitHub.
1. At this point, you have only created the branch locally, you need to push this remotely to Github.

```
git push --set-upstream origin JIRA-123-new-feature
git push
```

You should now be able to see the branch on GitHub. Make commits as you deem necessary. It helps to provide useful commit messages - a commit message saying 'Update' is a lot less helpful than saying 'Remove X parameter because it was unused'.
Expand Down Expand Up @@ -92,11 +93,8 @@ The GENIE project follows the standard [git flow](https://www.atlassian.com/git/

This package uses [semantic versioning](https://semver.org/) for releasing new versions. The version should be updated on the `develop` branch as changes are reviewed and merged in by a code maintainer. The version for the package is maintained in the [genie/__init__.py](genie/__init__.py) file. A github release should also occur every time `develop` is pushed into `main` and it should match the version for the package.

### Testing

#### Running test pipeline

Make sure to run each of the [pipeline steps here](README.md#developing-locally) on the test pipeline and verify that your pipeline runs as expected. This is __not__ automatically run by Github Actions and have to be manually run.
### Testing

#### Running tests

Expand All @@ -110,8 +108,6 @@ Here's how to run the test suite:
pytest -vs tests/
```

Tests in Python are also run automatically by Github Actions on any pull request and are required to pass before merging.

##### Tests in R

This package uses [`testthat`](https://testthat.r-lib.org/) to run tests in R. The test code is located in the [testthat](./R/tests/testthat) subdirectory.
Expand Down Expand Up @@ -166,18 +162,6 @@ Follow gitflow best practices as linked above.
12. Push changes in `develop`.
13. Wait for the CI/CD to finish.

### Modifying Docker

Follow this section when modifying the [Dockerfile](https://github.com/Sage-Bionetworks/Genie/blob/main/Dockerfile):

1. Have your synapse authentication token handy
1. ```docker build -f Dockerfile -t <some_docker_image_name> .```
1. ```docker run --rm -it -e SYNAPSE_AUTH_TOKEN=$YOUR_SYNAPSE_TOKEN <some_docker_image_name>```
1. Run [test code](README.md#developing-locally) relevant to the dockerfile changes to make sure changes are present and working
1. Once changes are tested, follow [genie contributing guidelines](#developing) for adding it to the repo
1. Once deployed to main, make sure the CI/CD build successfully completed (our docker image gets automatically deployed via Github Actions CI/CD) [here](https://github.com/Sage-Bionetworks/Genie/actions/workflows/ci.yml)
1. Check that your docker image got successfully deployed [here](https://github.com/Sage-Bionetworks/Genie/pkgs/container/genie)

### Contributing to the docs

This [documentation](https://sagebionetworks.jira.com/wiki/spaces/APGD/pages/3369631808/Contributing+to+Main+GENIE+repository+docs) is internal to Sage employees.
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