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longreadsum: add aarch64/arm64 builds #51121

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merged 3 commits into from
Oct 3, 2024

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@martin-g martin-g commented Oct 3, 2024

Describe your pull request here


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Summary by CodeRabbit

  • New Features
    • Updated meta.yaml to include new requirements (zlib, setuptools) and support for additional platforms (linux-aarch64, osx-arm64).
  • Bug Fixes
    • Corrected indentation issues in the meta.yaml file for better clarity.
  • Chores
    • Removed outdated build failure metadata files for both Linux and OSX platforms to streamline the repository.

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
@martin-g martin-g added aarch64 Related to adding linux-aarch64 support osx-arm64 Related to adding osx-arm64 support labels Oct 3, 2024
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coderabbitai bot commented Oct 3, 2024

📝 Walkthrough

Walkthrough

This pull request involves the deletion of two YAML files related to failed builds for the LongReadSum recipe on Linux and OSX platforms, respectively. Additionally, the meta.yaml file for the LongReadSum package has been modified to increment the build number, remove the skip attribute, and add new host requirements for zlib and setuptools. The file structure has been refined, including corrections to indentation and the addition of extra platforms.

Changes

File Path Change Summary
recipes/longreadsum/build_failure.linux-64.yaml Deleted file containing metadata of a failed Linux build, including logs and error details related to a missing header file (zlib.h).
recipes/longreadsum/build_failure.osx-64.yaml Deleted file containing metadata of a failed OSX build, documenting a ModuleNotFoundError for setuptools and other build process details.
recipes/longreadsum/meta.yaml Updated build number from 1 to 2, removed the skip attribute, added zlib and setuptools to host requirements, corrected indentation for swig and hdf5, and added extra platforms.

Possibly related PRs

  • Add recipe for consensify #50969: The meta.yaml file for the consensify package includes zlib as a host requirement, which is relevant to the changes in the main PR where zlib was added to the meta.yaml of the longreadsum package.
  • trnascan-se: add aarch64/arm64 build #50996: The meta.yaml for tRNAscan-SE also includes zlib in its additional-platforms section, similar to the changes made in the longreadsum package.
  • pgrc: add linux-aarch64 build #51009: The meta.yaml for pgrc includes linux-aarch64 and osx-arm64 under additional-platforms, which aligns with the changes made in the longreadsum package regarding platform support.
  • bambamc: add aarch64/arm64 builds #51067: The meta.yaml for bambamc introduces support for linux-aarch64 and osx-arm64, similar to the platform updates in the longreadsum package.
  • metacache: add linux-aarch64 build #51106: The meta.yaml for metacache adds linux-aarch64 as an additional platform, which is consistent with the changes made in the longreadsum package regarding platform support.

Suggested reviewers

  • mencian

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 73b7059 and 364146b.

📒 Files selected for processing (3)
  • recipes/longreadsum/build_failure.linux-64.yaml (0 hunks)
  • recipes/longreadsum/build_failure.osx-64.yaml (0 hunks)
  • recipes/longreadsum/meta.yaml (3 hunks)
💤 Files with no reviewable changes (2)
  • recipes/longreadsum/build_failure.linux-64.yaml
  • recipes/longreadsum/build_failure.osx-64.yaml
🔇 Additional comments (4)
recipes/longreadsum/meta.yaml (4)

13-13: LGTM: Build number increment is correct.

Incrementing the build number is appropriate when making changes to the package without changing the version. This aligns with the PR objective of adding aarch64/arm64 builds.


28-29: LGTM: Correct implementation of suggested dependencies.

The addition of zlib and setuptools to the host requirements is correct and follows the suggestions from past reviews. These dependencies are commonly needed for building Python packages, especially those with C extensions.


Line range hint 1-53: Overall changes look good, suggest final verification.

The changes made to the meta.yaml file align well with the PR objectives:

  1. The build number has been correctly incremented.
  2. New dependencies (zlib and setuptools) have been added as suggested.
  3. Support for aarch64/arm64 architectures has been added.

Additionally, the AI summary mentions some formatting improvements that enhance the overall quality of the file:

  • Removal of the skip attribute (if no longer needed).
  • Corrected indentation for swig and hdf5 in the host section.
  • Adjusted formatting in the run requirements section.

These changes collectively improve the readability and correctness of the yaml file.

To ensure all changes are correct and no unintended modifications were made, please run a final diff check:

This will display all changes made to the file, allowing for a final verification that all modifications are intentional and correct.

✅ Verification successful

Verification Successful: All changes align with PR objectives.

The git diff confirms that the following adjustments have been correctly implemented:

  • Build Section:

    • Incremented number from 1 to 2.
    • Removed skip: true, allowing builds across all platforms.
  • Requirements:

    • Added zlib and setuptools under host requirements.
  • Extra Platforms:

    • Included linux-aarch64 and osx-arm64 support.

All modifications enhance the meta.yaml file's accuracy and compatibility without introducing unintended changes.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Perform a final diff check on the meta.yaml file

# Test: Show the full diff of the meta.yaml file
git diff origin/master -- recipes/longreadsum/meta.yaml

Length of output: 823


50-53: LGTM: Addition of aarch64/arm64 platforms is correct.

The addition of the extra section with additional-platforms for linux-aarch64 and osx-arm64 aligns perfectly with the PR objective of adding aarch64/arm64 builds. This change is crucial for enabling builds for these architectures.

To ensure the new architectures are properly recognized, let's verify the conda-build output:

This command will show the output file names that would be generated, which should include the new architectures.


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```
 $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c++ -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longreadsum-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -Iinclude -I$PREFIX/include/python3.9 -Iinclude -I$PREFIX/include/python3.9 -c src/fasta_module.cpp -o build/temp.linux-aarch64-cpython-39/src/fasta_module.o -std=c++11
07:14:01 BIOCONDA INFO (OUT) src/fasta_module.cpp:7:10: fatal error: zlib.h: No such file or directory
07:14:01 BIOCONDA INFO (OUT)     7 | #include <zlib.h>
07:14:01 BIOCONDA INFO (OUT)       |          ^~~~~~~~
```

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Should fix the following error on osx-arm64
```
Traceback (most recent call last):�[0m
07:41:23 �[32mBIOCONDA INFO�[0m (ERR)   File "setup.py", line 8, in <module>�[0m
07:41:23 �[32mBIOCONDA INFO�[0m (ERR)     import setuptools�[0m
07:41:23 �[32mBIOCONDA INFO�[0m (ERR) ModuleNotFoundError: No module named 'setuptools'�[0m
07:41:24 �[32mBIOCONDA INFO�[0m (OUT) Extracting download�[0m
```
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martin-g commented Oct 3, 2024

@BiocondaBot please fetch artifacts

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martin-g commented Oct 3, 2024

@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 longreadsum-1.3.1-py310h16889fc_2.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 longreadsum-1.3.1-py311he0c9dd2_2.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 longreadsum-1.3.1-py312hd42163c_2.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 longreadsum-1.3.1-py38haa35054_2.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 longreadsum-1.3.1-py39h5b2e93f_2.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
osx-64 longreadsum-1.3.1-py310h47e40e8_2.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-64 longreadsum-1.3.1-py311h0c228fd_2.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-64 longreadsum-1.3.1-py312hbfe41f6_2.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-64 longreadsum-1.3.1-py38h62cd0f6_2.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-64 longreadsum-1.3.1-py39h2849e56_2.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-arm64 longreadsum-1.3.1-py310hb4898bc_2.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/a7f1d142-2f93-4c08-b43e-995b923f8edf/artifacts/0/tmp/artifacts/packages <package name>
osx-arm64 longreadsum-1.3.1-py311h5ba83ed_2.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/a7f1d142-2f93-4c08-b43e-995b923f8edf/artifacts/0/tmp/artifacts/packages <package name>
osx-arm64 longreadsum-1.3.1-py312h07c10ab_2.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/a7f1d142-2f93-4c08-b43e-995b923f8edf/artifacts/0/tmp/artifacts/packages <package name>
osx-arm64 longreadsum-1.3.1-py38hb8b35ae_2.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/a7f1d142-2f93-4c08-b43e-995b923f8edf/artifacts/0/tmp/artifacts/packages <package name>
osx-arm64 longreadsum-1.3.1-py39h4fb785a_2.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/a7f1d142-2f93-4c08-b43e-995b923f8edf/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 longreadsum-1.3.1-py310h712c43f_2.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/ffa88dbc-08e5-4cc4-9e72-203c1c607baa/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 longreadsum-1.3.1-py311h1d5a9a6_2.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/ffa88dbc-08e5-4cc4-9e72-203c1c607baa/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 longreadsum-1.3.1-py312h6e7c6f3_2.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/ffa88dbc-08e5-4cc4-9e72-203c1c607baa/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 longreadsum-1.3.1-py38h0393dec_2.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/ffa88dbc-08e5-4cc4-9e72-203c1c607baa/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 longreadsum-1.3.1-py39hdd53528_2.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/ffa88dbc-08e5-4cc4-9e72-203c1c607baa/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
longreadsum 1.3.1--py310h16889fc_2 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/longreadsum:1.3.1--py310h16889fc_2.tar.gz | docker load
longreadsum 1.3.1--py311he0c9dd2_2 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/longreadsum:1.3.1--py311he0c9dd2_2.tar.gz | docker load
longreadsum 1.3.1--py312hd42163c_2 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/longreadsum:1.3.1--py312hd42163c_2.tar.gz | docker load
longreadsum 1.3.1--py38haa35054_2 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/longreadsum:1.3.1--py38haa35054_2.tar.gz | docker load
longreadsum 1.3.1--py39h5b2e93f_2 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/longreadsum:1.3.1--py39h5b2e93f_2.tar.gz | docker load

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martin-g commented Oct 3, 2024

mgrigorov in 🌐 euler-arm-22 in /tmp/longreadsum via 🅒 test123 took 5s 
❯ tar xvf longreadsum-1.3.1-py310h712c43f_2.tar.bz2                                                                                                                                                        (test123) 
info/test/run_test.sh
info/run_exports.json
info/hash_input.json
info/files
info/has_prefix
info/index.json
info/recipe/build.sh
info/recipe/meta.yaml.template
info/paths.json
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/git
bin/entry_point.py
bin/generate_html.py
bin/cli.py
lib/lrst.py
bin/plot_utils.py
lib/__init__.py
bin/__init__.py
lib/__pycache__/__init__.cpython-310.pyc
lib/__pycache__/lrst.cpython-310.pyc
bin/longreadsum
lib/_lrst.cpython-310-aarch64-linux-gnu.so

mgrigorov in 🌐 euler-arm-22 in /tmp/longreadsum via 🅒 test123 
❯ file bin/* lib/_lrst.cpython-310-aarch64-linux-gnu.so                                                                                                                                                    (test123) 
bin/__init__.py:                            empty
bin/cli.py:                                 Python script, ASCII text executable
bin/entry_point.py:                         Python script, ASCII text executable
bin/generate_html.py:                       Python script, ASCII text executable
bin/longreadsum:                            a /opt/conda/conda-bld/longreadsum_1727942247136/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla script, ASCII text executable
bin/plot_utils.py:                          Python script, ASCII text executable
lib/_lrst.cpython-310-aarch64-linux-gnu.so: ELF 64-bit LSB shared object, ARM aarch64, version 1 (GNU/Linux), dynamically linked, not stripped

LGTM!

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martin-g commented Oct 3, 2024

@BiocondaBot please add label

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