Update atlas to 2.0.0-rc.6 #52030
Update atlas to 2.0.0-rc.6 #52030
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces significant modifications to the In the Possibly related PRs
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (3)
recipes/atlas/build.sh (1)
14-16: Consider using install command for better error handling.While the current implementation works, using the
installcommand would provide better error handling and permission setting in one step.Consider this alternative:
mkdir -p ${PREFIX}/bin -cp atlas ${PREFIX}/bin || exit 1 -chmod +x ${PREFIX}/bin/atlas +install -m 755 atlas ${PREFIX}/bin || exit 1recipes/atlas/meta.yaml (2)
17-44: Consider using Jinja2 variable for repeated sysroot version.The sysroot version "2.17" is repeated in multiple sections. Consider using a Jinja2 variable to improve maintainability:
+{% set sysroot_version = "2.17" %} requirements: build: - {{ compiler('cxx') }} - cmake - git - ninja - - sysroot_linux-64 =2.17 # [linux] + - sysroot_linux-64 ={{ sysroot_version }} # [linux] host: ... - - sysroot_linux-64 =2.17 # [linux] + - sysroot_linux-64 ={{ sysroot_version }} # [linux] run: ... - - sysroot_linux-64 =2.17 # [linux] + - sysroot_linux-64 ={{ sysroot_version }} # [linux]
47-54: Consider improving test command reliability.A few suggestions for the test commands:
- The
grep "successfully"test is fragile. Consider usingatlas --versionor a more specific check.- The cleanup command's
|| exit 1is redundant as any non-zero exit in the test section will fail the build.test: commands: - - atlas | grep "successfully" + - atlas --version - atlas simulate - atlas HKY85 --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta - atlas GLF --bam ATLAS_simulations.bam - atlas saf --glf ATLAS_simulations.glf.gz --fasta ATLAS_simulations.fasta - atlas majorMinor --glf ATLAS_simulations.glf.gz - - rm ATLAS_* *.parameters saf.saf.* || exit 1 + - rm ATLAS_* *.parameters saf.saf.*
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
recipes/atlas/build.sh(1 hunks)recipes/atlas/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/atlas/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/atlas/build.sh (1)
12-12: LGTM!
Good practice to include error handling with the ninja build command.
recipes/atlas/meta.yaml (2)
12-14: LGTM! Proper version pinning implemented.
The run_exports section with pin_subpackage correctly implements the PR guidelines for avoiding ABI breakage.
57-64: Verify license change from GPLv3 to MPL-2.0.
Please confirm that this license change is intentional and properly documented in the upstream repository.
The addition of ARM platform support is a welcome improvement for broader compatibility.
recipes/atlas/build.sh
Outdated
| cmake . -GNinja \ | ||
| -DCONDA=ON \ | ||
| -DCMAKE_BUILD_TYPE=Release \ | ||
| -DCMAKE_CXX_COMPILER=${CXX} \ | ||
| -DCMAKE_CXX_FLAGS="-D_LIBCPP_DISABLE_AVAILABILITY" \ | ||
| -DCMAKE_LIBRARY_PATH=${CONDA_PREFIX}/lib \ | ||
| -DCMAKE_INCLUDE_PATH=${CONDA_PREFIX}/include \ | ||
| -DCMAKE_INSTALL_PREFIX=$PREFIX |
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🛠️ Refactor suggestion
Add error handling for cmake configuration.
While the cmake configuration looks correct, it's missing error handling. Also, it would be good to verify the required environment variables.
Consider applying this improvement:
+# Verify required environment variables
+if [ -z "${CXX}" ]; then
+ echo "Error: CXX environment variable is not set"
+ exit 1
+fi
+if [ -z "${CONDA_PREFIX}" ]; then
+ echo "Error: CONDA_PREFIX environment variable is not set"
+ exit 1
+fi
+
cmake . -GNinja \
-DCONDA=ON \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_CXX_COMPILER=${CXX} \
-DCMAKE_CXX_FLAGS="-D_LIBCPP_DISABLE_AVAILABILITY" \
-DCMAKE_LIBRARY_PATH=${CONDA_PREFIX}/lib \
-DCMAKE_INCLUDE_PATH=${CONDA_PREFIX}/include \
- -DCMAKE_INSTALL_PREFIX=$PREFIX
+ -DCMAKE_INSTALL_PREFIX=$PREFIX || exit 1📝 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.
| cmake . -GNinja \ | |
| -DCONDA=ON \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -DCMAKE_CXX_COMPILER=${CXX} \ | |
| -DCMAKE_CXX_FLAGS="-D_LIBCPP_DISABLE_AVAILABILITY" \ | |
| -DCMAKE_LIBRARY_PATH=${CONDA_PREFIX}/lib \ | |
| -DCMAKE_INCLUDE_PATH=${CONDA_PREFIX}/include \ | |
| -DCMAKE_INSTALL_PREFIX=$PREFIX | |
| # Verify required environment variables | |
| if [ -z "${CXX}" ]; then | |
| echo "Error: CXX environment variable is not set" | |
| exit 1 | |
| fi | |
| if [ -z "${CONDA_PREFIX}" ]; then | |
| echo "Error: CONDA_PREFIX environment variable is not set" | |
| exit 1 | |
| fi | |
| cmake . -GNinja \ | |
| -DCONDA=ON \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -DCMAKE_CXX_COMPILER=${CXX} \ | |
| -DCMAKE_CXX_FLAGS="-D_LIBCPP_DISABLE_AVAILABILITY" \ | |
| -DCMAKE_LIBRARY_PATH=${CONDA_PREFIX}/lib \ | |
| -DCMAKE_INCLUDE_PATH=${CONDA_PREFIX}/include \ | |
| -DCMAKE_INSTALL_PREFIX=$PREFIX || exit 1 |
| {% set version = "2.0.0" %} | ||
|
|
||
| package: | ||
| package: | ||
| name: atlas | ||
| version: {{ version }} | ||
|
|
||
| source: | ||
| url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}.tar.gz | ||
| sha256: 7b65eae5ab7ff439accd53febf8caa15ad9d8230278eee31fd5c2e95bf021990 | ||
| url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}-rc.6.tar.gz | ||
| sha256: 017235049dddfac88fedf16bfc444cf38aed25ac84df084dc555736b5d48d6a3 |
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Version string should include release candidate suffix.
The package version is set to "2.0.0" but the source URL downloads "2.0.0-rc.6". This mismatch could cause issues with version tracking and dependencies. Consider updating the version to match exactly:
-{% set version = "2.0.0" %}
+{% set version = "2.0.0-rc.6" %}📝 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.
| {% set version = "2.0.0" %} | |
| package: | |
| package: | |
| name: atlas | |
| version: {{ version }} | |
| source: | |
| url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}.tar.gz | |
| sha256: 7b65eae5ab7ff439accd53febf8caa15ad9d8230278eee31fd5c2e95bf021990 | |
| url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}-rc.6.tar.gz | |
| sha256: 017235049dddfac88fedf16bfc444cf38aed25ac84df084dc555736b5d48d6a3 | |
| {% set version = "2.0.0-rc.6" %} | |
| package: | |
| name: atlas | |
| version: {{ version }} | |
| source: | |
| url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}.tar.gz | |
| sha256: 017235049dddfac88fedf16bfc444cf38aed25ac84df084dc555736b5d48d6a3 |
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
|
Should we maybe wait until the final release? |
Actually, it is the other way around. We plan to drop the "release candidate" as soon as installation through conda works. v2.0.0-rc.6 is already much more stable than v0.9.9, which is on conda. |
|
@BiocondaBot please add label |
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/atlas/meta.yaml (1)
48-55: Consider improving test command error handling.While the test commands cover various functionalities, they might benefit from better error handling. Consider adding
set -eor|| exit 1to each command to ensure failures are caught.test: commands: - - atlas | grep "successfully" - - atlas simulate - - atlas HKY85 --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta - - atlas GLF --bam ATLAS_simulations.bam - - atlas saf --glf ATLAS_simulations.glf.gz --fasta ATLAS_simulations.fasta - - atlas majorMinor --glf ATLAS_simulations.glf.gz + - atlas | grep "successfully" || exit 1 + - atlas simulate || exit 1 + - atlas HKY85 --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta || exit 1 + - atlas GLF --bam ATLAS_simulations.bam || exit 1 + - atlas saf --glf ATLAS_simulations.glf.gz --fasta ATLAS_simulations.fasta || exit 1 + - atlas majorMinor --glf ATLAS_simulations.glf.gz || exit 1 - rm ATLAS_* *.parameters saf.saf.* || exit 1
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Review profile: CHILL
📒 Files selected for processing (2)
recipes/atlas/build.sh(1 hunks)recipes/atlas/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/atlas/build.sh
🧰 Additional context used
🪛 yamllint
recipes/atlas/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (1)
recipes/atlas/meta.yaml (1)
12-14: LGTM! Good practice using run_exports.
The addition of run_exports with appropriate pinning will help prevent ABI breakage, which is crucial for a major version upgrade.
| - cmake | ||
| - git | ||
| - ninja | ||
| - sysroot_linux-64 =2.17 # [linux] |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Remove duplicate sysroot_linux-64 dependency.
The sysroot_linux-64 package appears in both build and host sections. It should typically only be in the build section.
requirements:
build:
- {{ compiler('cxx') }}
- cmake
- git
- ninja
- sysroot_linux-64 =2.17 # [linux]
host:
- armadillo
- fmt
- htslib
- lapack
- libgomp # [linux]
- llvm-openmp # [osx]
- nlohmann_json
- openblas
- - sysroot_linux-64 =2.17 # [linux]
- jsoncpp
- zlibAlso applies to: 32-32
| license: GPLv3 | ||
| summary: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" | ||
| home: https://atlaswiki.netlify.app | ||
| license: MPL-2.0 |
There was a problem hiding this comment.
💡 Codebase verification
License change was not verified successfully.
- License file does not contain Mozilla license text.
🔗 Analysis chain
Verify license change from GPLv3 to MPL-2.0.
The license has been changed from GPLv3 to MPL-2.0. This is a significant change that should be verified against the source repository.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the license in the source repository
# Expected: Should find MPL-2.0 license file or header
# Download and check the source
curl -sL https://bitbucket.org/wegmannlab/atlas/get/2.0.0-rc.6.tar.gz | \
tar xz --to-stdout "*/LICENSE" "*/license*" "*/COPYING" 2>/dev/null | \
grep -i "mozilla" || echo "License file not found or doesn't contain Mozilla license text"
# Check source files for license headers
curl -sL https://bitbucket.org/wegmannlab/atlas/get/2.0.0-rc.6.tar.gz | \
tar xz --to-stdout "*/src/*.cpp" "*/src/*.hpp" 2>/dev/null | \
grep -i "mozilla" || echo "Source files don't contain Mozilla license headers"
Length of output: 538
Update atlas to 2.0.0-rc.6:
https://atlaswiki.netlify.app/
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