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Merge pull request #702 from sjspielman/700-spacing
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Fix some bullet spacing
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sjspielman authored Aug 8, 2024
2 parents 559d739 + e77a10b commit 4d2cbd5
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Expand Up @@ -9,8 +9,8 @@ You should fill out the template for your analysis module and provide the follow
- Description of module goals
- Usage (How to [run the analysis](running-a-module.md))
- Input files and their sources. These may include:
- ScPCA data files and/or result files from other modules. ([See access instructions.](../../getting-started/accessing-resources/getting-access-to-data.md))
- External data including links to their origins.
- ScPCA data files and/or result files from other modules. ([See access instructions.](../../getting-started/accessing-resources/getting-access-to-data.md))
- External data including links to their origins.
- Output files
- [Software and package dependencies](./module-dependencies.md)
- [Computational resources](./compute-requirements.md)
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4 changes: 2 additions & 2 deletions docs/contributing-to-analyses/index.md
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Expand Up @@ -34,8 +34,8 @@ The below steps outline the process for getting started with a new analysis modu
1. [Create a feature branch](working-with-git/working-with-branches.md) in your fork to begin your analysis (but see the [helpful tips](#helpful-tips) below!)
2. [Create a new analysis module](analysis-modules/creating-a-module.md) (unless you are working on an existing module)
3. Perform your analysis using Git:
- [Commit](working-with-git/making-commits.md) small units of work, [pushing](working-with-git/push-to-origin.md) your commits to your fork on GitHub along the way
- Be sure to [document](analysis-modules/documenting-analysis.md) your analysis module as you build it up
- [Commit](working-with-git/making-commits.md) small units of work, [pushing](working-with-git/push-to-origin.md) your commits to your fork on GitHub along the way
- Be sure to [document](analysis-modules/documenting-analysis.md) your analysis module as you build it up
4. When you've [completed enough work for a pull request (PR)](creating-pull-requests/scoping-pull-requests.md), you'll [file a PR](creating-pull-requests/index.md) to the upstream repository, `AlexsLemonade/OpenScPCA-analysis`
5. The Data Lab will then [review your PR](pr-review-and-merge/index.md)
6. Once we approve your PR, we will merge your feature branch into the upstream `AlexsLemonade/OpenScPCA-analysis` repository
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4 changes: 2 additions & 2 deletions docs/ensuring-repro/managing-software/index.md
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Expand Up @@ -11,7 +11,7 @@ Analysis modules will have files specifying the specific software dependencies a
We specifically recommend these two package managers to specify module-specific software environments:

- The R package manager [`renv`](https://rstudio.github.io/renv/) for modules containing R code.
- Before working with `renv`, we encourage you to read [the excellent introduction](https://rstudio.github.io/renv/articles/renv.html) for more information.
- Before working with `renv`, we encourage you to read [the excellent introduction](https://rstudio.github.io/renv/articles/renv.html) for more information.
- The package manager [conda](https://docs.conda.io/en/latest/), along with [`conda-lock`](https://conda.github.io/conda-lock/), for modules containing Python code.
Conda can also be used to manage standalone software packages that do not depend on a specific language.

Expand All @@ -20,7 +20,7 @@ When you [create a module with `create-analysis-module.py`](../../contributing-t
## 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, including adding or updating a package used in R or Python:
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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2 changes: 1 addition & 1 deletion docs/ensuring-repro/workflows/run-module-gha.md
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Expand Up @@ -10,7 +10,7 @@ Module testing GHAs are automatically run in two circumstances:
- When a pull request is filed with changes to any module files
- This GHA will need to pass without errors for [pull requests](../../contributing-to-analyses/pr-review-and-merge/index.md) to be approved
- On a periodic schedule
- This ensures that changes in data or other code do not break tests within each module
- This ensures that changes in data or other code do not break tests within each module

For examples of existing analysis module GHAs, see the example Python and R module GHAs, [`run_hello-python.yml`](https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/main/.github/workflows/run_hello-python.yml) and [`run_hello-R.yml`](https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/main/.github/workflows/run_hello-R.yml), respectively.

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10 changes: 5 additions & 5 deletions docs/technical-setup/index.md
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Expand Up @@ -17,15 +17,15 @@ To prepare to contribute to OpenScPCA, please do the following in order:
1. [Clone your fork](./clone-the-repo.md) to your computer
2. Set up additional dependencies that you'll need to contribute to OpenScPCA:
- [Download, install, and set up conda](./environment-setup/setup-conda.md)
- OpenScPCA uses conda to manage your software environment and dependencies.
- Installing conda also provides you with Python and other tools you need to write or contribute to Python-based modules
- OpenScPCA uses conda to manage your software environment and dependencies.
- Installing conda also provides you with Python and other tools you need to write or contribute to Python-based modules
- [Set up `pre-commit`](./environment-setup/setup-precommit.md)
- This will allow you to make contributions in Git
- This will allow you to make contributions in Git
- [Configure the AWS command line interface (CLI)](./environment-setup/configure-aws-cli.md)
- You can only complete this step if the Data Lab has [created an Amazon Web Services account for you](../getting-started/accessing-resources/index.md)
- You can only complete this step if the Data Lab has [created an Amazon Web Services account for you](../getting-started/accessing-resources/index.md)
- [Optional] If you plan on writing or contributing to R-based modules, you should also [download and install R and RStudio, along with a few handy R packages](./environment-setup/install-r-rstudio.md)
- [Optional] [Install Docker](../ensuring-repro/docker/index.md#how-to-install-docker)
- This allows you to run your analysis modules inside a Docker container, ensuring reproducibility across machines
- This allows you to run your analysis modules inside a Docker container, ensuring reproducibility across machines

## Special considerations for Windows users

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