Add r-phylopath
#50994
Add r-phylopath
#50994
Conversation
📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces two new files for the Changes
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/r-phylopath/build.sh (1)
2-2: LGTM: Environment variable set correctly. Consider adding a comment.The environment variable
DISABLE_AUTOBREWis set correctly to prevent the use of Homebrew during the build process, which is consistent with Bioconda's approach.Consider adding a comment to explain the purpose of this variable, for example:
+# Disable automatic brewing of dependencies to ensure a controlled build environment export DISABLE_AUTOBREW=1recipes/r-phylopath/meta.yaml (2)
20-44: LGTM: Requirements section is well-defined with a minor optimization possible.The build, host, and run requirements are correctly specified with appropriate version constraints. The use of 'cross-r-base' for build requirements is correct for cross-compilation.
Consider using YAML anchors and aliases to reduce duplication between host and run requirements. This can make the file more maintainable. For example:
requirements: build: - cross-r-base {{ r_base }} host: &r_requirements - r-ape >=4.1 - r-base # ... other dependencies ... run: *r_requirementsThis change would make future updates easier and reduce the chance of inconsistencies between host and run requirements.
46-48: LGTM: Basic test is present, but consider expanding test coverage.The current test verifies that the package can be loaded, which is a good basic check.
Consider adding more comprehensive tests to ensure the package functions correctly. For example:
test: commands: - $R -e "library('phylopath')" - $R -e "if (!requireNamespace('testthat', quietly = TRUE)) install.packages('testthat'); testthat::test_package('phylopath')"This addition would run the package's built-in tests (if available) and provide more confidence in its functionality.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/r-phylopath/build.sh (1 hunks)
- recipes/r-phylopath/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/r-phylopath/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (7)
recipes/r-phylopath/build.sh (3)
1-1: LGTM: Correct shebang for bash script.The shebang
#!/bin/bashis correct and follows the standard practice for shell scripts.
1-3: Overall: Well-structured build script for r-phylopath package.The
build.shscript is concise and follows Bioconda's best practices for building R packages. It correctly sets up the build environment and uses the standard R installation command. The script should work as intended for building the r-phylopath package.
3-3: LGTM: R package installation command is correct.The R command for package installation is correctly structured and follows the standard approach for building R packages in Bioconda.
To ensure the ${R} variable is properly set in the build environment, we can run the following verification script:
This script will help ensure that the ${R} variable is properly set in the build environment.
recipes/r-phylopath/meta.yaml (4)
1-7: LGTM: Package and version section is well-defined.The package name and version are correctly specified. The use of Jinja2 templating for cross-platform compatibility is appropriate.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source section is correctly configured.The source URL is properly formatted and points to CRAN. The inclusion of a SHA256 checksum ensures package integrity.
13-18: LGTM: Build section is properly configured.The build number, 'noarch: generic' flag, and R library paths are all correctly specified for this R package.
50-59: LGTM: About section provides comprehensive metadata.The about section includes all necessary information: home page URL, package summary, and correct license details. The use of an environment variable for the license file path is a good practice.
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/r-phylopath/meta.yaml (1)
47-49: LGTM with suggestion: Consider adding more comprehensive tests.The current test command verifies that the 'phylopath' library can be loaded, which is a good basic check. However, to ensure the package functions correctly, consider adding more comprehensive tests, such as:
- Running a simple analysis using the package.
- Checking if key functions are available.
- Verifying the package version.
Example:
test: commands: - $R -e "library(phylopath); stopifnot(packageVersion('phylopath') == '{{ version }}'); res <- phylopath::define_model_set(list(m1 = x ~ y)); print(res)"
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/r-phylopath/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/r-phylopath/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/r-phylopath/meta.yaml (5)
1-7: LGTM: Package and version information looks good.The package name and version are correctly defined. The use of Jinja2 templating for platform-specific variables is appropriate for ensuring cross-platform compatibility.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source information is correctly specified.The source URL correctly points to CRAN and uses the version variable. The inclusion of the SHA256 checksum is good practice for ensuring package integrity.
13-19: LGTM: Build configuration is well-defined.The build section is correctly configured:
- Build number is appropriately set to 0 for a new package.
- The
noarch: genericflag is correctly used for R packages.- The
run_exportssection ensures proper version pinning, which aligns with the PR objectives.- R library paths are correctly specified.
21-45: LGTM: Dependencies are well-defined and consistent.The requirements section is correctly structured:
- Build and host requirements are appropriately separated.
- Run requirements match the host requirements, ensuring consistency.
- Version constraints are properly used where necessary for compatibility.
- The use of
cross-r-basein the build section is correct for cross-compilation scenarios.
51-60: LGTM: Metadata is comprehensive and well-formatted.The about section provides all necessary metadata:
- The home page URL is correct and uses HTTPS.
- The summary clearly describes the package's purpose and cites the relevant paper.
- License information is correctly specified as GPL-3.0-or-later.
- The license file path is appropriately set using an environment variable.
This PR adds the
r-phylopathR library.Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.Summary by CodeRabbit
New Features
r-phylopath, version1.3.0, detailing dependencies and integrity verification.Documentation