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phables: add aarch64/arm64 builds #51124

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Oct 4, 2024
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@martin-g martin-g commented Oct 3, 2024

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Summary by CodeRabbit

  • New Features
    • Updated version to 1.4.1, introducing support for additional platforms: Linux (aarch64) and macOS (arm64).
  • Bug Fixes
    • Corrected formatting in the dev_url entry for consistency.
  • Chores
    • Incremented build number and updated source URL and checksum for the new version.

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
@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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📝 Walkthrough

Walkthrough

The pull request modifies the meta.yaml file of the phables package. It updates the version to 1.4.1 and increments the build number from 0 to 1. The source URL is revised, and a sha256 checksum is added. Two new platforms, linux-aarch64 and osx-arm64, are introduced in the extra section, while the dev_url entry is corrected. The requirements section remains unchanged, and a test command is added to verify the help output of the phables command.

Changes

File Path Change Summary
recipes/phables/meta.yaml - Version updated to 1.4.1
- Build number incremented to 1
- Source URL adjusted
- Added sha256 checksum
- Added platforms: linux-aarch64, osx-arm64
- Corrected dev_url formatting
- Test section includes help output command

Possibly related PRs

  • Update phables to 1.4.1 #51043: This PR updates the phables package to version 1.4.1, which is directly related to the main PR that also updates the version of phables to 1.4.1.
  • pyslow5: add aarch64/arm64 builds #51105: This PR adds support for linux-aarch64 and osx-arm64 platforms in the pyslow5 package, similar to the main PR which also adds these platforms in the phables package.
  • metacache: add linux-aarch64 build #51106: This PR introduces support for the linux-aarch64 platform in the metacache package, aligning with the main PR's addition of the same platform in the phables package.
  • longreadsum: add aarch64/arm64 builds #51121: This PR adds support for linux-aarch64 and osx-arm64 platforms in the longreadsum package, which is consistent with the platform additions in the main PR for phables.

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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 phables-1.4.1-py310h9ee0642_1.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 phables-1.4.1-py310h527b516_1.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 phables-1.4.1-py310h4f1019d_1.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/6204b526-fc4d-4574-a7ad-02a3cefc5235/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 phables-1.4.1-py310h23ed54d_1.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/c6af5546-7eda-4591-b5a8-c8c7a98ded23/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
phables 1.4.1--py310h9ee0642_1 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/phables:1.4.1--py310h9ee0642_1.tar.gz | docker load

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martin-g commented Oct 3, 2024

mgrigorov in 🌐 euler-arm-22 in /tmp/phables via 🅒 test123 took 5s 
❯ tar xvf phables-1.4.1-py310h23ed54d_1.tar.bz2                                                                                                                                                            (test123) 
info/test/run_test.sh
info/run_exports.json
info/hash_input.json
info/has_prefix
info/index.json
info/licenses/LICENSE
info/recipe/meta.yaml.template
info/recipe/meta.yaml
info/files
info/recipe/conda_build_config.yaml
info/about.json
info/paths.json
info/git
LICENSE
lib/python3.10/site-packages/phables/workflow/envs/curl.yaml
lib/python3.10/site-packages/phables/workflow/envs/mmseqs.yaml
lib/python3.10/site-packages/phables/workflow/envs/smg.yaml
lib/python3.10/site-packages/phables/workflow/envs/mapping.yaml
lib/python3.10/site-packages/phables/workflow/envs/koverage.yaml
lib/python3.10/site-packages/phables/workflow/envs/phables.yaml
lib/python3.10/site-packages/phables/config/config.yaml
lib/python3.10/site-packages/phables/config/databases.yaml
lib/python3.10/site-packages/phables-1.4.1.dist-info/top_level.txt
lib/python3.10/site-packages/phables-1.4.1.dist-info/entry_points.txt
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/genome_utils.py
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/flow_utils.py
lib/python3.10/site-packages/phables/workflow/scripts/combine_cov.py
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/gene_utils.py
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/component_utils.py
lib/python3.10/site-packages/phables/workflow/scripts/gfa2fasta.py
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/coverage_utils.py
lib/python3.10/site-packages/phables/workflow/scripts/format_koverage_results.py
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/output_utils.py
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/edge_graph_utils.py
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/FD_Inexact.py
lib/python3.10/site-packages/phables/__main__.py
lib/python3.10/site-packages/phables/workflow/scripts/phables.py
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/short_utils.py
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/long_utils.py
lib/python3.10/site-packages/phables/__init__.py
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__init__.py
lib/python3.10/site-packages/phables/test_data/junction_pe_coverage.pickle
lib/python3.10/site-packages/phables-1.4.1.dist-info/direct_url.json
lib/python3.10/site-packages/phables/phables.VERSION
lib/python3.10/site-packages/phables/__pycache__/__init__.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__pycache__/__init__.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__pycache__/component_utils.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__pycache__/genome_utils.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__pycache__/gene_utils.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/__pycache__/combine_cov.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__pycache__/flow_utils.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/__pycache__/gfa2fasta.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/__pycache__/format_koverage_results.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__pycache__/coverage_utils.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__pycache__/output_utils.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__pycache__/edge_graph_utils.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/__pycache__/phables.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__pycache__/FD_Inexact.cpython-310.pyc
lib/python3.10/site-packages/phables/__pycache__/__main__.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__pycache__/short_utils.cpython-310.pyc
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/__pycache__/long_utils.cpython-310.pyc
lib/python3.10/site-packages/phables/test_data/edge_coverages.tsv
lib/python3.10/site-packages/phables/test_data/phrogs_annotations.tsv
lib/python3.10/site-packages/phables/workflow/scripts/phables_utils/phrogs/phrog_annot.tsv
lib/python3.10/site-packages/phables/phables.LICENSE
lib/python3.10/site-packages/phables/test_data/assembly_graph.gfa
README.md
lib/python3.10/site-packages/phables/workflow/rules/03_test_targets.smk
lib/python3.10/site-packages/phables/workflow/rules/gfa2fasta.smk
lib/python3.10/site-packages/phables/workflow/rules/00_database_preflight.smk
lib/python3.10/site-packages/phables/workflow/rules/03_test_preflight.smk
lib/python3.10/site-packages/phables/workflow/rules/phables.smk
lib/python3.10/site-packages/phables/workflow/rules/02_phables_targets.smk
lib/python3.10/site-packages/phables/workflow/install.smk
lib/python3.10/site-packages/phables/workflow/phables.smk
lib/python3.10/site-packages/phables/workflow/rules/02_phables_preflight.smk
lib/python3.10/site-packages/phables/workflow/rules/coverage.smk
lib/python3.10/site-packages/phables/workflow/rules/genes.smk
lib/python3.10/site-packages/phables/workflow/rules/postprocess.smk
lib/python3.10/site-packages/phables/workflow/test_phables.smk
lib/python3.10/site-packages/phables/phables.CITATION
lib/python3.10/site-packages/phables/test_data/edges.fasta.hmmout
lib/python3.10/site-packages/phables-1.4.1.dist-info/INSTALLER
lib/python3.10/site-packages/phables-1.4.1.dist-info/WHEEL
lib/python3.10/site-packages/phables-1.4.1.dist-info/LICENSE
lib/python3.10/site-packages/phables-1.4.1.dist-info/RECORD
lib/python3.10/site-packages/phables-1.4.1.dist-info/METADATA
lib/python3.10/site-packages/phables-1.4.1.dist-info/REQUESTED
bin/phables

mgrigorov in 🌐 euler-arm-22 in /tmp/phables via 🅒 test123 
❯ file bin/*                                                                                                                                                                                               (test123) 
bin/phables: a /opt/conda/conda-bld/phables_1727940340633/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho script, ASCII text executable

There are no arch specific binaries!

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martin-g commented Oct 4, 2024

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Oct 4, 2024
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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
recipes/phables/meta.yaml (1)

Line range hint 13-19: LGTM: Build section changes are appropriate.

The build number increment and noarch: false setting are correct for this update. The addition of run_exports is a good practice for maintaining compatibility with dependent packages.

Consider adding a comment explaining why noarch: false is set, as it's not immediately obvious without the context of the PR objectives.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 73b7059 and 33742fb.

📒 Files selected for processing (1)
  • recipes/phables/meta.yaml (2 hunks)
🔇 Additional comments (3)
recipes/phables/meta.yaml (3)

Line range hint 2-11: LGTM: Version update and source changes look good.

The version has been correctly updated to 1.4.1, and the source URL has been adjusted accordingly. The inclusion of a new SHA256 checksum is a good practice for ensuring the integrity of the downloaded source.


Line range hint 1-57: Overall, the changes look good and achieve the PR objectives.

The updates to version, build number, and additional platforms are consistent with the goal of adding aarch64/arm64 builds for the phables package. The run_exports addition is a good practice for maintaining compatibility.

A few minor suggestions:

  1. Consider adding a comment explaining the noarch: false setting.
  2. Verify the successful creation of build artifacts for the new platforms.

These changes should be ready for merging once the suggested verifications are complete.


51-53: LGTM: Additional platforms added as intended.

The addition of linux-aarch64 and osx-arm64 to the additional-platforms list is consistent with the PR objective of adding aarch64/arm64 builds.

To ensure these changes are reflected in the build process, let's verify the build artifacts:

This script will search for mentions of the new platforms in the PR comments, which should include information about the build artifacts if they were successfully created.

✅ Verification successful

Verification Successful: Builds for added platforms are present.

The build artifacts for linux-aarch64 and osx-arm64 have been successfully generated, confirming the changes.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify that builds for the new platforms exist

# Test: Check if build artifacts for the new platforms are present
gh pr view 51124 --json comments -q '.comments[].body' | grep -E 'linux-aarch64|osx-arm64'

Length of output: 1356

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