install_rotate_1.0 #51801
install_rotate_1.0 #51801
Conversation
📝 Walkthrough📝 WalkthroughWalkthroughThe changes introduced in the pull request involve the addition of a new metadata file named The requirements section lists the build dependencies, which are A new Bash script named Possibly related PRs
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: 1
🧹 Outside diff range and nitpick comments (2)
recipes/rotate/meta.yaml (2)
14-15: Consider removing run_exports
The run_exports section is typically used for shared libraries to ensure ABI compatibility. Since this appears to be a standalone command-line tool without a library component, this section might not be necessary.
build:
number: 0
- run_exports:
- - {{ pin_subpackage("rotate", max_pin="x") }}17-22: Consider specifying minimum compiler version
For C++ programs, it's recommended to specify minimum compiler versions to ensure compatibility. Also, empty sections can be removed.
requirements:
build:
- make
- - {{ compiler('cxx') }}
+ - {{ compiler('cxx') }} >=5.4 # or appropriate minimum version
- host:
- run:📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/rotate/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/rotate/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/rotate/meta.yaml (2)
28-33: Verify LICENSE file existence
The license metadata looks correct, but let's verify the LICENSE file exists in the source repository.
9-10: Verify source tarball integrity
The source URL and checksum format are correct. Let's verify the checksum matches the actual tarball.
There was a problem hiding this comment.
Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/rotate/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/rotate/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/rotate/meta.yaml (5)
1-6: LGTM!
Package metadata follows conda naming conventions and best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
25-27: Existing comment is still valid.
The previous review comment about improving test reliability remains applicable.
8-10: Verify source URL and checksum.
Let's ensure the source URL is accessible and the checksum matches.
#!/bin/bash
# Description: Verify source URL accessibility and checksum
URL="https://github.com/richarddurbin/rotate/archive/refs/tags/v1.0.tar.gz"
EXPECTED_SHA="da8a3c848cc05d59b579c375824008dd2d533c28d8a436a6e4761312d2152906"
# Test 1: Check if URL is accessible
if curl --output /dev/null --silent --head --fail "$URL"; then
echo "URL is accessible"
else
echo "Error: URL is not accessible"
exit 1
fi
# Test 2: Download and verify checksum
if curl -L -s "$URL" | sha256sum | grep -q "^$EXPECTED_SHA"; then
echo "Checksum verified successfully"
else
echo "Error: Checksum mismatch"
exit 1
fi12-16: Verify Makefile requirements.
The build script assumes the presence of a Makefile with an install target that respects the PREFIX variable. Please ensure:
- The upstream repository contains a Makefile
- The Makefile has an
installtarget - The install target properly uses the
PREFIXvariable
#!/bin/bash
# Description: Check Makefile configuration
URL="https://raw.githubusercontent.com/richarddurbin/rotate/v1.0/Makefile"
# Test: Download and analyze Makefile
curl -L -s "$URL" | grep -A 5 "^install:"
curl -L -s "$URL" | grep -i "prefix"29-34: Verify license information.
Let's confirm the LICENSE file exists and contains MIT license text.
✅ Verification successful
License information verified successfully
The upstream repository contains a valid MIT license file that matches the license information specified in the meta.yaml file. The LICENSE file exists in the repository root and contains the standard MIT license text with copyright by Richard Durbin.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify license file and content
URL="https://raw.githubusercontent.com/richarddurbin/rotate/v1.0/LICENSE"
# Test: Download and check license content
curl -L -s "$URL" | grep -i "MIT"
Length of output: 1002
Script:
#!/bin/bash
# Let's verify the license information directly from the repository
# First, check if LICENSE file exists in the repository
fd LICENSE --type f --hidden --no-ignore
# Then, display its content
cat LICENSE 2>/dev/null || echo "LICENSE file not found"
Length of output: 8743
Script:
#!/bin/bash
# Let's check the specific recipe's directory for any LICENSE file
cd recipes/rotate 2>/dev/null && ls -la LICENSE* 2>/dev/null || echo "No LICENSE file in recipes/rotate/"
# Let's also check the upstream repository directly
curl -sI "https://raw.githubusercontent.com/richarddurbin/rotate/main/LICENSE" | head -n 1
curl -sI "https://raw.githubusercontent.com/richarddurbin/rotate/master/LICENSE" | head -n 1
Length of output: 327
Script:
#!/bin/bash
# Let's fetch and check the content of the LICENSE file from the upstream repository
curl -sL "https://raw.githubusercontent.com/richarddurbin/rotate/main/LICENSE"
# Also check if there's any license information in the README
curl -sL "https://raw.githubusercontent.com/richarddurbin/rotate/main/README.md" | grep -i "licen"
Length of output: 1246
recipes/rotate/meta.yaml
Outdated
| requirements: | ||
| build: | ||
| - make | ||
| - {{ compiler('cxx') }} | ||
| host: | ||
| run: |
There was a problem hiding this comment.
Consider adding C++ runtime dependency.
The recipe is missing runtime dependencies. For C++ programs, you typically need to specify the C++ runtime in the run section.
Add the following to the run section:
run:
+ - {{ pin_compatible('libstdcxx-ng') }}Committable suggestion was skipped due to low confidence.
There was a problem hiding this comment.
Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/rotate/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/rotate/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/rotate/meta.yaml (3)
1-6: LGTM!
The package metadata section follows conda packaging best practices with proper use of Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: Consider using GitHub release asset URL instead of archive URL.
While the current source URL is functional, using GitHub's release asset URL (if available) would be more reliable as it's explicitly published by the maintainer.
Let's check if a release asset exists:
#!/bin/bash
# Check if v1.0 release has any assets
gh release view v1.0 --repo richarddurbin/rotate --json assets29-34: Verify LICENSE file and enhance package description.
Please verify:
- The existence of the LICENSE file in the source repository
- Consider adding a more detailed description of the package functionality
Let's verify the LICENSE file:
✅ Verification successful
LICENSE file exists, but description could be enhanced
The LICENSE file exists in the repository as verified, which validates the license_file entry in the meta.yaml. However, I recommend enhancing the package description to provide more context about the tool's functionality and use cases. Consider expanding the summary to include:
- Input/output format details
- Common use cases
- Key features or capabilities
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if LICENSE file exists in the repository
gh api repos/richarddurbin/rotate/contents/LICENSE --jq '.name'
Length of output: 71
Script:
#!/bin/bash
# Let's check the content of the LICENSE file to verify it's a valid MIT license
gh api repos/richarddurbin/rotate/contents/LICENSE --jq '.content' | base64 -d
# Also check README for potential description enhancements
gh api repos/richarddurbin/rotate/contents/README.md --jq '.content' | base64 -d
Length of output: 307
Script:
#!/bin/bash
# Let's try a different approach to check the LICENSE and README contents
gh api repos/richarddurbin/rotate/contents/LICENSE --raw
echo "---"
gh api repos/richarddurbin/rotate/contents/README.md --raw
Length of output: 2862
recipes/rotate/meta.yaml
Outdated
| build: | ||
| number: 0 | ||
| script: make PREFIX=${PREFIX} | ||
| run_exports: | ||
| - {{ pin_subpackage("rotate", max_pin="x") }} |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Improve build configuration robustness.
Several improvements can be made to the build configuration:
- Add parallel build support
- Quote the PREFIX variable
- The run_exports section might be unnecessary unless this package provides a shared library
Consider this improvement:
build:
number: 0
- script: make PREFIX=${PREFIX}
+ script: make -j${CPU_COUNT} PREFIX="${PREFIX}"
- run_exports:
- - {{ pin_subpackage("rotate", max_pin="x") }}📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| build: | |
| number: 0 | |
| script: make PREFIX=${PREFIX} | |
| run_exports: | |
| - {{ pin_subpackage("rotate", max_pin="x") }} | |
| build: | |
| number: 0 | |
| script: make -j${CPU_COUNT} PREFIX="${PREFIX}" |
jayramr
force-pushed
the
install_rotate_1.0
branch
from
812f059 to
24a4f57
Compare
|
@BiocondaBot please update |
|
@BiocondaBot please add label |
|
I encountered an error updating your PR branch. You can report this to bioconda/core if you'd like. |
|
@BiocondaBot please fetch artifacts |
|
Package(s) built are ready for inspection:
|
There was a problem hiding this comment.
Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/rotate/build.sh (1 hunks)
- recipes/rotate/meta.yaml (1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/rotate/build.sh
🧰 Additional context used
🪛 yamllint
recipes/rotate/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/rotate/meta.yaml (6)
1-6: LGTM!
Package metadata follows conda-forge/bioconda best practices using Jinja2 variables.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-15: LGTM with previous suggestions.
The build configuration has been previously reviewed with suggestions for improvement.
28-30: LGTM with previous suggestions.
The test configuration has been previously reviewed with detailed suggestions for improvement.
8-10: Verify source tarball integrity.
The source configuration looks good, but let's verify the checksum.
32-37: Verify license information.
The about section looks good, but let's verify the license information matches the source repository.
1-37: Verify package relevance to bioconda.
Since bioconda is specifically for bioinformatics tools, let's verify this package's relevance.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
remove make from the run field.
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/rotate/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/rotate/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (1)
recipes/rotate/meta.yaml (1)
31-36: Verify package relevance to bioconda.
The summary suggests this is a general-purpose sequence rotation tool. Please verify that this tool is specifically designed for biological sequences. If it's a general-purpose tool without specific biological applications, it might be more appropriate for conda-forge.
|
@BiocondaBot please add label |
recipes/rotate/meta.yaml
Outdated
|
|
||
| test: | ||
| commands: | ||
| - rotate 2>&1 | grep can |
There was a problem hiding this comment.
hi @bgruening for this package, the help menu shows the whole output. To simply the output, i just did a grep. If this is not a recommended practice then , we can keep below as it as. Please advise
rotate
rotate [options] <input fasta filename>
-x <pos> position to become new start [0]
-rc reverse complement after rotating [false]
-s <string> rotate to start of search string
-m <n_mismatch> maximum number of mismatches allowed in search [0]
-o <outfilename> output file [standard output]
use either -x and optionally -rc, or -s
use filename '-' for standard input
can read .fa.gz files as well as .fa files
Yes for running zlib not required. Hence proceeding with this commit Co-authored-by: Björn Grüning <[email protected]>
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/rotate/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/rotate/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/rotate/meta.yaml (4)
1-6: LGTM! Package metadata is well-structured.
The package name and version are properly templated using Jinja2 variables, following conda packaging best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: LGTM! Source configuration is secure and follows best practices.
The source URL is properly templated and includes a SHA256 checksum for security verification.
14-15: Remove unnecessary run_exports section.
This issue was previously identified. Since this is a command-line tool and not a shared library, the run_exports section should be removed as suggested in the previous review.
29-34: LGTM! About section is complete and well-documented.
All required metadata fields are present and properly formatted.
| requirements: | ||
| build: | ||
| - make | ||
| - {{ compiler('c') }} | ||
| host: | ||
| - zlib | ||
|
|
There was a problem hiding this comment.
Add runtime dependencies section.
The recipe is missing the run section with necessary runtime dependencies.
Add the following section after the host requirements:
host:
- zlib
+ run:
+ - {{ pin_compatible('libgcc-ng') }}
+ - {{ pin_compatible('libstdcxx-ng') }}
+ - zlib📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| requirements: | |
| build: | |
| - make | |
| - {{ compiler('c') }} | |
| host: | |
| - zlib | |
| requirements: | |
| build: | |
| - make | |
| - {{ compiler('c') }} | |
| host: | |
| - zlib | |
| run: | |
| - {{ pin_compatible('libgcc-ng') }} | |
| - {{ pin_compatible('libstdcxx-ng') }} | |
| - zlib | |
recipes/rotate/meta.yaml
Outdated
| test: | ||
| commands: | ||
| - rotate 2>&1 | grep can |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Improve test command robustness.
The current test command using grep can is fragile and may not effectively verify the program's functionality. Based on the previous discussion, it would be better to verify the full help output.
Replace the test command with:
test:
commands:
- - rotate 2>&1 | grep can
+ - rotate --help 2>&1 # Verify help menu is accessible
+ - rotate 2>&1 # Verify program runs without arguments and shows usage📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| test: | |
| commands: | |
| - rotate 2>&1 | grep can | |
| test: | |
| commands: | |
| - rotate --help 2>&1 # Verify help menu is accessible | |
| - rotate 2>&1 # Verify program runs without arguments and shows usage |
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/rotate/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/rotate/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/rotate/meta.yaml (2)
14-15: Remove unnecessary run_exports section.
Since this is a command-line tool that doesn't provide shared libraries for linking, the run_exports section is not needed.
17-23: Add runtime dependencies section.
The recipe needs runtime dependencies for the C runtime library and zlib.
| test: | ||
| commands: | ||
| - rotate |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Improve test command coverage.
The current test command only verifies that the program runs. Add more comprehensive tests to verify functionality.
test:
commands:
- - rotate
+ - rotate --help 2>&1 # Verify help menu is accessible
+ - rotate 2>&1 # Verify program runs without arguments and shows usage
+ - rotate -h 2>&1 | grep "position to become new start" # Verify specific functionality📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| test: | |
| commands: | |
| - rotate | |
| test: | |
| commands: | |
| - rotate --help 2>&1 # Verify help menu is accessible | |
| - rotate 2>&1 # Verify program runs without arguments and shows usage | |
| - rotate -h 2>&1 | grep "position to become new start" # Verify specific functionality |
| {% set name = "rotate" %} | ||
| {% set version = "1.0" %} | ||
|
|
||
| package: | ||
| name: "{{ name|lower }}" | ||
| version: "{{ version }}" | ||
|
|
||
| source: | ||
| url: "https://github.com/richarddurbin/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" | ||
| sha256: "da8a3c848cc05d59b579c375824008dd2d533c28d8a436a6e4761312d2152906" | ||
|
|
||
| build: | ||
| number: 0 | ||
| run_exports: | ||
| - {{ pin_subpackage("rotate", max_pin="x") }} | ||
|
|
||
| requirements: | ||
| build: | ||
| - make | ||
| - {{ compiler('c') }} | ||
| host: | ||
| - zlib | ||
|
|
||
|
|
||
| test: | ||
| commands: | ||
| - rotate | ||
|
|
||
| about: | ||
| home: "https://github.com/richarddurbin/rotate" | ||
| license: MIT | ||
| license_family: MIT | ||
| license_file: LICENSE | ||
| summary: "Simple program to rotate a circular sequence to start at a given position or string." |
There was a problem hiding this comment.
💡 Codebase verification
Build script includes undocumented executable 'composition'
The build script installs two executables (rotate and composition), but only rotate is documented and tested in meta.yaml. This needs to be addressed:
- Add test command for the
compositionexecutable in meta.yaml - Add description of the
compositiontool in the package summary
🔗 Analysis chain
Verify package build artifacts.
Let's ensure the package builds correctly and includes all necessary files.
Let me gather more specific information about the package's source files.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify package contents and build artifacts
# Check if LICENSE file exists in the source
fd -t f "LICENSE$"
# Check if Makefile exists and contains expected targets
fd -t f "Makefile$" -x cat {} \; | grep -E "install|PREFIX"
# Look for main source file
fd -t f -e "c" -x head -n 1 {}
Length of output: 5758
Script:
#!/bin/bash
# Check for source files in the rotate package directory
fd -t f . recipes/rotate
# Check contents of the rotate source directory for build-related files
fd -t f . recipes/rotate -x cat {}
Length of output: 1023
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
Describe your pull request here
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>.