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Adds agents #310
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feat: adds agents
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Merge branch 'main' into AGENTS
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pr: comments from @llrs-roche
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Merge branch 'main' into AGENTS
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| # teal.gallery Development Guide | ||
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| `teal.gallery` is a set of `teal` applications that provide examples of ready to use apps exploring clinical trial data. | ||
| It requires extensive knowledge of the teal framework from the app developer perspective and GitHub workflows. | ||
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| The automated workflows allow for the apps' dependencies to be updated and deployed. | ||
| It deploys a stable and development apps to [shinyapps.io](https://shinyapps.io) that contain essentially the same application, but with different dependencies. | ||
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| The application code is written in a simple form to allow users to understand how an app is developed and use it as a base for their own work. | ||
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| ### Direct dependencies | ||
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| - **teal** - Provides the framework and helpers to operate with teal | ||
| modules. | ||
| - **teal.code** - Bare code generation and evaluation ensuring | ||
| reproducibility. | ||
| - **teal.data** - Data management and relationships between datasets via | ||
| join_keys. (contains sample data for ADaM datasets and default keys to | ||
| merge ADaM datasets). | ||
| - **teal.picks** - Helpers to select, transform and manipulate them. | ||
| - **teal.modules.clinical** - Modules to explore ADaM clinical trial datasets | ||
| - **teal.modules.general** - Modules to explore generic datasets | ||
| - **teal.modules.hermes** - Modules to explore RNA-seq analysis | ||
| - **teal.modules.goshawk** - Modules to explore longitudinal clinical trial data | ||
| - **teal.modules.osprey** - Modules to explore community TLGs from the analysis of clinical trials data | ||
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| ## Folder structure | ||
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| Each application has its own folder which should contain: | ||
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| - `app.R` file that creates a `shiny::shinyApp` object. | ||
| - `renv.lock` file with up-to-date versions of the dependencies necessary to run the application | ||
| - `renv` boilerplate folder generated when running `renv::init()` with custom settings if required (such as Bioconductor version) | ||
| - `tests` folder with end-to-end tests | ||
| - `.Rprofile` generated when running `renv::init()` | ||
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llrs-roche marked this conversation as resolved.
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| ## Deployment practices | ||
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| The app deployment should be automated and allow for the update of dependencies in the teal framework to be kept up to date. | ||
| It also updates other dependencies to the latest version from CRAN. | ||
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| The teal packages used differ from `stable` and `dev` deployment channels on the contents of `renv.lock` and `app.R` file. | ||
| The `app.R` file changes should follow the lastest changes and good practices from `teal`, which should be merge to `main` branch once they are released. | ||
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| - `stable`: Using latest packages releases from CRAN and in cases that the package is not released on CRAN, use latest release channel | ||
| - in GitHub it should use `<organization>/<repository>@*release` tag to install from latest GitHub release | ||
| - The git branch for `stable` channel is `main` | ||
| - `dev`: Using latest development versions from `teal` framework and relevant packages (such as `rtables`, `mmrm`, `tern`, ...) | ||
| - The relevant packages should be added especially when there is active development that is closely associated with `teal` | ||
| - The git branch for `dev` channel is `dev` | ||
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| When the update process or any of the end-to-end test fail, it should not re-deploy the app. | ||
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| The CI/CD should be able to run in each Pull Request on GitHub to test every step with the exceptions of deployment and commiting. | ||
| If the pull request targets `main` it should run as if it was the `stable` channel. | ||
| When targeting `dev` branch it should run as the `dev` channel. | ||
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| ## Testing | ||
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| There should be end-to-end tests testing the different applications using cypress.io. | ||
| It should cover: | ||
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| - teal application starts without errors. | ||
| - teal application has X number of tabs. | ||
| - teal application can change to all tabs without errors. | ||
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| ## Quality Assurance | ||
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| - **Use `tidyverse` style**: Write clear, readable code using `dplyr`, `ggplot2` patterns | ||
| - **Use `magrittr` pipes in reproducible execution**: For code executed for `teal_data`/`qenv` data objects with `eval_code()` and `within()` | ||
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| ## Code Review Process | ||
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| - **Pull Request Reviews**: All changes require human review and approval | ||
| - **Automated Checks**: CI must pass before merging | ||
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| # teal.gallery Development Guide | ||
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| The content is on @AGENTS.md |
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