Add gene-trajectory-python recipe #51476
Conversation
📝 Walkthrough📝 WalkthroughWalkthroughThe changes in this pull request introduce a new Possibly related PRs
Suggested labels
Suggested reviewers
📜 Recent review detailsConfiguration used: CodeRabbit UI 📒 Files selected for processing (1)
🧰 Additional context used🪛 yamllint
🔇 Additional comments (7)
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 (2)
recipes/gene-trajectory-python/meta.yaml (2)
17-34: Requirements are well-defined, but consider addingrun_exports.The host and run requirements are comprehensive and include appropriate version constraints. However, as mentioned in the PR objectives, consider adding a
run_exportssection to prevent API, ABI, and CLI breakage issues.Example:
build: ... run_exports: - {{ pin_subpackage('gene-trajectory-python', max_pin='x.x') }}This ensures that packages depending on gene-trajectory-python will use a compatible version.
44-50: LGTM: About section is comprehensive.The about section includes all required fields and provides valuable information about the package. Consider adding a more detailed description of the package functionality if available.
Suggestion:
about: ... description: | Gene Trajectory is a Python package that computes and analyzes gene trajectories in single-cell data. It provides tools for trajectory inference, gene expression analysis along trajectories, and visualization of results.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/gene-trajectory-python/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/gene-trajectory-python/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/gene-trajectory-python/meta.yaml (6)
1-6: LGTM: Package section is well-defined.The package name and version are correctly specified using Jinja2 variables. The lowercase filter on the package name is a good practice to ensure consistency.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-15: LGTM: Build section follows Bioconda best practices.The build section is well-configured:
noarch: pythonis appropriate for a pure Python package.- The installation command uses
--no-depsand--no-build-isolation, which aligns with Bioconda guidelines.- The build number is correctly set to 0 for a new package.
36-42: LGTM: Test section is well-configured.The test section includes appropriate checks:
- Import check for
gene_trajectoryverifies the package can be imported.pip checkensures all dependencies are satisfied.
These tests align with Bioconda best practices for package verification.
53-55: LGTM: Extra section correctly specifies the recipe maintainer.The recipe maintainer is properly listed, which is essential for package maintenance and updates.
1-1: Note on static analysis warningThe yamllint tool reported a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' is part of the Jinja2 template syntax, which is correctly used in Conda recipe meta.yaml files. No action is required to address this warning.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: LGTM: Source section is correctly defined.The source URL is properly structured for PyPI packages, and the use of Jinja2 variables ensures consistency. The inclusion of the SHA256 checksum is crucial for package integrity.
Let's verify the checksum:
There was a problem hiding this comment.
Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (4)
recipes/gene-trajectory-python/meta.yaml (4)
8-10: LGTM: Source section is correctly defined.The source URL and SHA256 checksum are properly specified. The use of Jinja2 variables in the URL construction is a good practice.
Consider adding a comment above the
sha256line to indicate the version of the package this checksum corresponds to. This can be helpful when updating the recipe in the future.# sha256 for version 1.0.4 sha256: 133e22dd167cbc83b8d4ecffa98bfc623f98584b91d2ecf31b915aeb11072b73
12-17: LGTM: Build section is well-configured.The build configuration is correct for a pure Python package. The use of
run_exportsis good for managing dependency versions across the Conda ecosystem.Consider adding a comment explaining the purpose of the
run_exportssection, as it's not immediately obvious to all contributors. For example:run_exports: # This ensures that other packages depending on gene-trajectory-python # will use a compatible version when it's updated - {{ pin_subpackage(name|lower, max_pin="x") }}
38-44: LGTM: Test section is adequate.The test section includes basic checks to ensure the package can be imported and that all dependencies are satisfied.
Consider adding a simple functional test to verify that the package works as expected. For example:
test: imports: - gene_trajectory commands: - pip check - python -c "import gene_trajectory; print(gene_trajectory.__version__)" requires: - pipThis additional test will verify that the package's version can be accessed, which is a common way to ensure the package is installed correctly.
59-61: LGTM: Extra section includes a maintainer.The inclusion of a recipe maintainer is crucial for the Bioconda ecosystem.
Consider adding more maintainers to ensure continued support and maintenance of the package. It's a good practice to have at least two maintainers. You could reach out to other contributors of the gene-trajectory-python project or Bioconda community members who might be interested in helping maintain this recipe.
Example:
extra: recipe-maintainers: - fra-pcmgf # Consider adding additional maintainers here
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/gene-trajectory-python/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/gene-trajectory-python/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/gene-trajectory-python/meta.yaml (3)
1-6: LGTM: Package section is well-defined.The package name and version are correctly specified using Jinja2 variables, which is a best practice in Conda recipes.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-61: Overall, the gene-trajectory-python recipe is well-structured and follows Bioconda guidelines.Great job on creating this recipe! It covers all the necessary sections and provides comprehensive information about the package. Here's a summary of the suggestions for improvement:
- Add a version comment for the SHA256 checksum.
- Include a comment explaining the purpose of the
run_exportssection.- Verify the build system (Flit) by checking the
pyproject.tomlfile.- Add a simple functional test to verify the package version.
- Include the LICENSE file in the recipe directory.
- Consider adding more maintainers to the recipe.
These minor enhancements will improve the recipe's maintainability and completeness. Once these suggestions are addressed, the recipe will be in excellent shape for inclusion in the Bioconda repository.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
19-36: LGTM: Requirements are well-defined.The host and run requirements are comprehensive and include appropriate version constraints. The use of flit-core in the host requirements suggests this package uses the Flit build system.
To ensure the build system is correctly specified, let's verify the presence of a
pyproject.tomlfile in the source distribution:This script will help confirm that the package indeed uses Flit as its build system.
| about: | ||
| home: https://github.com/KlugerLab/GeneTrajectory-python | ||
| summary: Compute gene trajectories | ||
| description: | | ||
| Gene Trajectory is a Python package that computes and analyzes gene trajectories in single-cell data. | ||
| It provides tools for trajectory inference, gene expression analysis along trajectories, and visualization of results. | ||
|
|
||
| license: MIT | ||
| license_file: LICENSE | ||
| doc_url: https://github.com/KlugerLab/GeneTrajectory-python | ||
| dev_url: https://github.com/KlugerLab/GeneTrajectory-python |
There was a problem hiding this comment.
LGTM: About section is comprehensive.
The about section provides all necessary information about the package, including its purpose, license, and relevant URLs.
The license_file is specified, but it's not included in the recipe. To ensure compliance with Conda packaging guidelines, you should include the LICENSE file in the recipe directory. Please add the following steps:
- Download the LICENSE file from the GitHub repository.
- Add it to the recipe directory (next to meta.yaml).
- Update the meta.yaml to reference the local LICENSE file:
about:
...
license_file: LICENSE
...This ensures that the license is properly packaged with the Conda package.
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/gene-trajectory-python/meta.yaml (2)
19-36: LGTM: Requirements are well-defined, with a minor suggestion.The host and run requirements are comprehensive and include appropriate version constraints. The use of
matplotlib-baseinstead ofmatplotlibis a good practice for conda-forge recipes.For consistency with other packages, consider adding upper bounds to the Python requirement in both host and run sections:
- python >=3.9,<4.0a0This helps prevent potential issues with future major Python versions while still allowing for minor version updates.
38-45: LGTM: Test section is good, with a suggestion for improvement.The test section includes appropriate checks:
- Verifying that the package can be imported.
- Using
pip checkto ensure all dependencies are satisfied.To enhance the test coverage, consider adding a command to run the package's test suite if one is available. For example:
commands: - pip check - python -m pytest --pyargs gene_trajectoryThis would provide more comprehensive testing of the package functionality.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/gene-trajectory-python/LICENSE (1 hunks)
- recipes/gene-trajectory-python/meta.yaml (1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/gene-trajectory-python/LICENSE
🧰 Additional context used
🪛 yamllint
recipes/gene-trajectory-python/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/gene-trajectory-python/meta.yaml (5)
1-10: LGTM: Package and source information are well-defined.The package name, version, and source URL are correctly specified using Jinja2 templating. The SHA256 checksum is provided, ensuring integrity of the downloaded package.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-18: LGTM: Build section is well-configured.The build section is correctly set up:
noarch: pythonis appropriate for a pure Python package.- The installation script uses the correct flags to prevent dependency resolution during build.
- The use of
run_exportswithpin_subpackageis excellent. This ensures that when other packages depend on gene-trajectory-python, they will automatically get the correct version constraints.This configuration helps maintain consistency and prevents potential compatibility issues in the Conda ecosystem.
59-61: LGTM: Maintainer information is correct.The extra section correctly lists the recipe maintainer as fra-pcmgf, which matches the PR submitter mentioned in the PR objectives.
1-61: Overall, the recipe is well-constructed and ready for inclusion.This meta.yaml file follows Bioconda guidelines and provides all necessary information for building and distributing the gene-trajectory-python package. Here's a summary of the key points and action items:
- The package, source, build, and requirements sections are well-defined.
- Test and about sections provide good coverage, with minor suggestions for improvement.
- The use of
run_exportsis excellent for maintaining consistency in the Conda ecosystem.Action items:
- Verify the presence of the LICENSE file in the recipe directory and add it if missing.
- Consider adding upper bounds to the Python requirement for consistency.
- If available, add a command to run the package's test suite in the test section.
These minor improvements will further enhance the quality of the recipe, but the current version is already in good shape for inclusion in the Bioconda repository.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
46-56: Verify the LICENSE file inclusion.The about section is comprehensive and provides all necessary information. However, there's an important step to complete:
- Ensure that the LICENSE file is present in the recipe directory (next to meta.yaml).
- If it's not there, download it from the GitHub repository and add it to the recipe directory.
This step is crucial for compliance with Conda packaging guidelines and ensures that the license is properly packaged with the Conda package.
To verify the presence of the LICENSE file, you can run the following command:
✅ Verification successful
LICENSE file is correctly included in the recipe directory.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if the LICENSE file exists in the recipe directory if [ -f "recipes/gene-trajectory-python/LICENSE" ]; then echo "LICENSE file is present in the recipe directory." else echo "LICENSE file is missing from the recipe directory." echo "Please download it from the GitHub repository and add it to the recipe directory." fiLength of output: 158
There was a problem hiding this comment.
Actionable comments posted: 2
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/gene-trajectory-python/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/gene-trajectory-python/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/gene-trajectory-python/meta.yaml (5)
1-10: LGTM: Package and source sections are well-defined.The package name, version, and source URL are correctly specified. The inclusion of the SHA256 checksum is a good practice for ensuring package integrity.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
38-46: LGTM: Comprehensive test section.The test section is well-defined and includes:
- Import checks for the main package.
- Dependency verification using
pip check.- Running package tests with pytest.
This approach ensures thorough testing of the package installation and functionality.
60-62: LGTM: Maintainer information is correctly specified.The extra section properly identifies the recipe maintainer.
1-1: Note: Ignore the YAML syntax error for Jinja2 templating.The static analysis tool (yamllint) reports a syntax error for the '%' character. This is a false positive due to the use of Jinja2 templating in Conda recipes. The syntax is correct for this context and can be safely ignored.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
47-57:⚠️ Potential issueAddress the LICENSE file issue.
The about section is comprehensive and provides all necessary information. However, there's an outstanding issue regarding the LICENSE file.
To resolve this issue:
- Download the LICENSE file from the GitHub repository.
- Add it to the recipe directory (next to meta.yaml).
- Ensure the meta.yaml references the local LICENSE file:
about: ... license_file: LICENSE ...This ensures that the license is properly packaged with the Conda package and complies with Conda packaging guidelines.
| build: | ||
| noarch: python | ||
| script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation | ||
| number: 0 | ||
| run_exports: | ||
| - {{ pin_subpackage(name|lower, max_pin="x") }} |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider a more flexible pinning strategy.
The build section is well-defined, but the run_exports pinning strategy might be too strict. For most Python packages, it's recommended to use a more flexible pinning strategy to allow for minor version updates.
Consider updating the run_exports section as follows:
run_exports:
- {{ pin_subpackage(name|lower, max_pin='x.x') }}This allows for minor version updates while still maintaining compatibility.
| requirements: | ||
| host: | ||
| - python >=3.9,<4.0a0 | ||
| - flit-core >=3.2,<4 | ||
| - pip | ||
| run: | ||
| - python >=3.9 | ||
| - igraph >=0.10 | ||
| - matplotlib-base >=3.6 | ||
| - numpy >=1.25 | ||
| - pandas >=1.5 | ||
| - pot >=0.8.2 | ||
| - scanpy >=1.9.3 | ||
| - scikit-misc >=0.1.3 | ||
| - scikit-learn >=0.24 | ||
| - scipy >=1.8 | ||
| - seaborn >=0.13 | ||
| - tqdm >=4.64.1 |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider relaxing version constraints for some dependencies.
The requirements section is comprehensive, but some version constraints might be unnecessarily strict. This could lead to potential conflicts with other packages in the Conda environment.
Consider relaxing the version constraints for some dependencies, especially those that are unlikely to introduce breaking changes in minor versions. For example:
requirements:
run:
- python >=3.9
- igraph >=0.10,<0.11
- matplotlib-base >=3.6,<4
- numpy >=1.25,<2
- pandas >=1.5,<2
- pot >=0.8.2,<0.9
- scanpy >=1.9.3,<2
- scikit-misc >=0.1.3,<0.2
- scikit-learn >=0.24,<2
- scipy >=1.8,<2
- seaborn >=0.13,<0.14
- tqdm >=4.64.1,<5This approach allows for minor version updates while still maintaining compatibility.
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/gene-trajectory-python/meta.yaml (1)
38-44: LGTM: Test section is well-defined. Consider adding a simple functionality test.The test section includes appropriate import checks and a pip check command, which are good practices. To further improve the testing, consider adding a simple functionality test if possible. For example:
test: imports: - gene_trajectory commands: - pip check - python -c "import gene_trajectory; assert gene_trajectory.__version__ == '1.0.4'" requires: - pipThis additional test ensures that the imported package has the correct version.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/gene-trajectory-python/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/gene-trajectory-python/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/gene-trajectory-python/meta.yaml (6)
1-10: LGTM: Package and source sections are well-defined.The package name, version, source URL, and SHA256 checksum are correctly specified. This ensures proper identification and integrity of the package source.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
59-61: LGTM: Extra section is correctly defined.The extra section properly specifies the recipe maintainer, which is important for package management and communication.
1-1: Note: Ignore yamllint syntax error for '%' character.The static analysis tool yamllint reports a syntax error for the '%' character at the beginning of the file. This is a false positive. The '%' character is correctly used here for Jinja2 templating in Conda recipes and is valid in this context. No action is required to address this warning.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-17: 🛠️ Refactor suggestionConsider a more flexible pinning strategy.
The build section is well-defined, but the
run_exportspinning strategy might be too strict. For most Python packages, it's recommended to use a more flexible pinning strategy to allow for minor version updates.Consider updating the
run_exportssection as follows:run_exports: - {{ pin_subpackage(name|lower, max_pin='x.x') }}This allows for minor version updates while still maintaining compatibility.
19-36: 🛠️ Refactor suggestionConsider relaxing version constraints for some dependencies.
The requirements section is comprehensive, but some version constraints might be unnecessarily strict. This could lead to potential conflicts with other packages in the Conda environment.
Consider relaxing the version constraints for some dependencies, especially those that are unlikely to introduce breaking changes in minor versions. For example:
requirements: run: - python >=3.9 - python-igraph >=0.10,<0.11 - matplotlib-base >=3.6,<4 - numpy >=1.25,<2 - pandas >=1.5,<2 - pot >=0.8.2,<0.9 - scanpy >=1.9.3,<2 - scikit-misc >=0.1.3,<0.2 - scikit-learn >=0.24,<2 - scipy >=1.8,<2 - seaborn >=0.13,<0.14 - tqdm >=4.64.1,<5This approach allows for minor version updates while still maintaining compatibility.
46-56:⚠️ Potential issueInclude the LICENSE file in the recipe directory.
The about section provides comprehensive information about the package. However, the
license_fileis specified, but it's not included in the recipe directory. To ensure compliance with Conda packaging guidelines, please follow these steps:
- Download the LICENSE file from the GitHub repository.
- Add it to the recipe directory (next to meta.yaml).
- Ensure that the meta.yaml references the local LICENSE file:
about: ... license_file: LICENSE ...This ensures that the license is properly packaged with the Conda package.
|
@BiocondaBot please add label |
Add the Python version of Gene-Trajectory (https://github.com/KlugerLab/GeneTrajectory-python) to bioconda.
The method is described in detail in the article Gene trajectory inference for single-cell data by optimal transport metrics, Documentation and tutorials are available at https://genetrajectory-python.readthedocs.io/.
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>.