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genodsp: add linux-aarch64 build #51597

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merged 1 commit into from
Oct 23, 2024
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Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
@martin-g martin-g added the aarch64 Related to adding linux-aarch64 support label Oct 23, 2024
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coderabbitai bot commented Oct 23, 2024

📝 Walkthrough

Walkthrough

The pull request modifies the meta.yaml file for the genodsp package. The version number remains 0.0.3, but the build number is incremented from 0 to 1. The condition for skipping the build process is updated to allow broader platform compatibility, changing from not linux or not x86_64 to not linux. A new section labeled extra is introduced, which specifies additional-platforms, including linux-aarch64 as a supported platform. Other elements, such as the source URL, SHA256 checksum, build requirements, and test commands, remain unchanged.

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please review & merge

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  • rpetit3

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Actionable comments posted: 0

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

40-40: Add newline at end of file

Add a newline character at the end of the file to comply with YAML best practices.

     - linux-aarch64
+
🧰 Tools
🪛 yamllint

[error] 40-40: no new line character at the end of file

(new-line-at-end-of-file)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 9b88759 and bbf1741.

📒 Files selected for processing (1)
  • recipes/genodsp/meta.yaml (2 hunks)
🧰 Additional context used
🪛 yamllint
recipes/genodsp/meta.yaml

[error] 40-40: no new line character at the end of file

(new-line-at-end-of-file)

🔇 Additional comments (3)
recipes/genodsp/meta.yaml (3)

20-21: LGTM: Build configuration changes are appropriate

The build number increment and modified skip condition are correct for adding aarch64 support. The existing run_exports configuration with max_pin="x.x" properly handles ABI compatibility.


38-40: LGTM: Platform configuration is correct

The addition of linux-aarch64 as an additional platform aligns with the PR objective.

🧰 Tools
🪛 yamllint

[error] 40-40: no new line character at the end of file

(new-line-at-end-of-file)


Line range hint 11-13: Verify patch compatibility with aarch64

The package includes a stringop-truncation.patch. Please ensure this patch is compatible with the aarch64 architecture.

✅ Verification successful

Let me gather more information about the patch file to better understand its contents and purpose.


Patch is architecture-independent and safe to use

The patch is focused on fixing string truncation warnings by replacing strncpy calls with a safer safe_strncpy implementation. The changes are:

  1. Removing hardcoded gcc compiler in Makefile
  2. Adding a new safe_strncpy function that properly handles null-termination
  3. Replacing all strncpy calls with safe_strncpy

The modifications are purely C standard library related and don't contain any architecture-specific code or assembly. The patch will work correctly on aarch64 and all other architectures.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if the patch contains any architecture-specific code

# Test: Look for architecture-specific patterns in the patch
rg -i "x86|amd64|arm|aarch" recipes/genodsp/stringop-truncation.patch

Length of output: 71


Script:

#!/bin/bash
# Check the contents of the patch file
cat recipes/genodsp/stringop-truncation.patch

# Also check if the patch file exists
ls -l recipes/genodsp/stringop-truncation.patch

Length of output: 5755

@martin-g
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@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 genodsp-0.0.3-h031d066_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>
linux-aarch64 genodsp-0.0.3-h8a409c4_1.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/4752f9ff-5013-48f7-a262-2cb17084a32f/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
genodsp 0.0.3--h031d066_1 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/genodsp:0.0.3--h031d066_1.tar.gz | docker load

@martin-g
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mgrigorov in 🌐 euler-arm-22 in genodsp on  master [✘?] via 🅒 test123 took 3s 
❯ tar xvf genodsp-0.0.3-h8a409c4_1.tar.bz2                                                                                                                                                                 (test123) 
info/files
info/run_exports.json
info/test/run_test.sh
info/hash_input.json
info/recipe/build.sh
info/paths.json
info/index.json
info/recipe/meta.yaml.template
info/recipe/meta.yaml
info/recipe/stringop-truncation.patch
info/recipe/conda_build_config.yaml
info/about.json
info/licenses/LICENSE
info/git
bin/genodsp

mgrigorov in 🌐 euler-arm-22 in genodsp on  master [✘?] via 🅒 test123 
❯ file bin/*                                                                                                                                                                                               (test123) 
bin/genodsp: ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, not stripped

mgrigorov in 🌐 euler-arm-22 in genodsp on  master [✘?] via 🅒 test123 
❯ ./bin/genodsp                                                                                                                                                                                            (test123) 
usage: [cat <file>] | genodsp --chromosomes=<filename> [options] [operations]

  --chromosomes=<filename>  (required) read chromosome names and lengths from
                            a file
  --value=<col>             input intervals contain a value in the specified
                            column;  by default we assume this is in column 4
  --novalue                 input intervals have no value (value given is 1)
  --nooutputvalue           don't write value with output intervals
  --precision=<number>      number of digits to round output values to
                            (by default, output is rounded to integers)
  --nocollapse              in output, don't collapse runs of identical values
                            to intervals
  --uncovered:hide          don't output intervals that have no coverage
                            (this is the default)
  --uncovered:show          in output, include intervals that have no coverage
  --uncovered:NA            in output, mark uncovered intervals as NA
  --cliptochromosome        clip interals to chromosome length
                            (default is to report such intervals as errors)
  --origin=one              input/output intervals are origin-one, closed
  --origin=zero             input/output intervals are origin-zero, half-open
                            (this is the default)
  --nooutput                don't output the resulting intervals/values
                            (by default these are written to stdout)
  --window=<length>         (W=) size of window
                            (for operators that have a window size)
  --help[=<operator>]       get detail about a particular operator
  ?                         list available operators with brief descriptions
  ?<operator>               same as --help=<operator>
  --progress=operations     report each operation as it begins
  --version                 report the program version and quit

Note that if input intervals overlap, their values are summed.

Input is usually piped in on stdin. However, if the first operator is "input"
stdin is ignored.

For a list of available operations, do "genodsp ?".
For more detailed descriptions of the operations, do "genodsp --help".

LGTM!

@martin-g
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@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 genodsp-0.0.3-h031d066_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>
linux-aarch64 genodsp-0.0.3-h8a409c4_1.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/4752f9ff-5013-48f7-a262-2cb17084a32f/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
genodsp 0.0.3--h031d066_1 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/genodsp:0.0.3--h031d066_1.tar.gz | docker load

@rpetit3 rpetit3 merged commit bdd6769 into bioconda:master Oct 23, 2024
7 checks passed
@martin-g martin-g deleted the aarch64-genodsp branch October 25, 2024 11:10
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