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Co-authored-by: Ally Hawkins <[email protected]>
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sjspielman and allyhawkins authored Jun 27, 2024
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4 changes: 2 additions & 2 deletions docs/ensuring-repro/docker/updating-images.md
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Over the course of module development, new dependencies and packages may get added or removed, thereby changing the [module's software environment](../managing-software/index.md).
For example, your environment will change if you add a new R or Python package to perform additional analyses.
Changing the software environment means that module-specific Docker image also needs to be updated to incorporate those changes.
Changing the software environment means that the module-specific Docker image also needs to be updated to incorporate those changes.

!!! note
These instructions assume that the Data Lab has already activated both of the [GitHub Action (GHA) workflows](../../contributing-to-analyses/analysis-modules/creating-a-module.md#module-workflows) that were created when the module was established, including the [module-testing GHA](../workflows/run-module-gha.md) and the [Docker-building GHA](#STUB_LINK../workflows/docker-build-gha.md).
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Whenever you add or remove a new package or dependency to your module's software environment, you will generally need to take a two-step process to add new code that uses those new dependencies:

1. First, file a PR that _only contains_ your updated environment files, e.g. `renv.lock` and/or `conda-lock.yml`.
_This PR should not any additional code changes that need this updated environment._
_This PR should not include any additional code changes that require this updated environment._
- Once this PR is merged, the module's Docker image will be [rebuilt and pushed to the OpenScPCA Docker Registry](#STUB_LINK../workflows/docker-build-gha.md)
1. Then, you can file one or more PRs with code changes that use the update software environment.
- By ensuring the updated Docker image was pushed to the registry _before_ filing this PR, the [module testing GHA](../workflows/run-module-gha.md) will be able to use the most up-to-date Docker image and avoid dependency errors
2 changes: 1 addition & 1 deletion docs/ensuring-repro/managing-software/index.md
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## Updating software environments

As analysis modules mature, the Data Lab will activate several [GitHub Action workflows](../workflows/index.md) that ensure module reproducibility.
Once these workflows are activated, you will need to file _two PRs_ every time you wish to update your software environment:
Once these workflows are activated, you will need to file _two PRs_ every time you wish to update your software environment, including adding or updating a package used in R or Python:

1. First, file a PR that updates your software environment, e.g. `renv.lock`, `conda.lock`, or `Dockerfile` files
1. After that first PR is been merged, you can then file a second PR that contains your code changes that use the updated environment
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