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Add M1 builds for PopPUNK #50011

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merged 14 commits into from
Nov 7, 2024
Merged

Add M1 builds for PopPUNK #50011

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2cb8f49
Add M1 builds for PopPUNK
johnlees Aug 13, 2024
298a36b
Merge branch 'master' into poppunk-arm64
johnlees Aug 14, 2024
2940735
Merge branch 'master' into poppunk-arm64
johnlees Aug 14, 2024
589fe61
Merge branch 'master' into poppunk-arm64
johnlees Aug 15, 2024
aec9386
Merge branch 'master' into poppunk-arm64
johnlees Aug 19, 2024
7c314a1
clean up recipe
mencian Aug 21, 2024
4a817b8
Merge branch 'master' into poppunk-arm64
mencian Aug 21, 2024
c06b1ce
clean up recipe
mencian Aug 21, 2024
3977f05
Merge branch 'master' into poppunk-arm64
johnlees Sep 20, 2024
cb67ba0
Merge branch 'master' into poppunk-arm64
johnlees Nov 7, 2024
5930f8c
Update poppunk to v2.7.1
johnlees Nov 7, 2024
cbc69b1
Reset build to zero
johnlees Nov 7, 2024
d929ce9
Add libfortran dep
johnlees Nov 7, 2024
e69d567
Add fortran compiler
johnlees Nov 7, 2024
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30 changes: 14 additions & 16 deletions recipes/poppunk/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
{% set version = "2.7.0" %}
{% set version = "2.7.1" %}
{% set name = "PopPUNK" %}

package:
Expand All @@ -7,12 +7,12 @@ package:

source:
url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz
sha256: bba7cb9fad5027abc78fd6761755169ae999d3d86a96bdfbfe577a360f907067
sha256: 7e6f7242b8c2150c7963fc5f4a95cfd7f2656b8a80317ff87bf97dc75f753788

build:
number: 0
skip: true # [py < 38]
script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
skip: True # [py < 38]
script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
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💡 Codebase verification

🛠️ Refactor suggestion

Based on the search results, I can see that --no-build-isolation is widely used across numerous bioconda recipes (200+ packages). This is a strong indication that it's a standard practice in the bioconda ecosystem to ensure reproducible builds by preventing pip from downloading or building dependencies during installation.

Keep the --no-build-isolation flag to maintain build reproducibility

The --no-build-isolation flag is a crucial part of conda's build process, preventing pip from downloading or building dependencies during installation. Removing it could lead to inconsistent builds.

🔗 Analysis chain

Consider keeping the build isolation flag.

The removal of --no-build-isolation might affect build reproducibility. This flag prevents pip from downloading or building dependencies during installation, ensuring consistent builds.

Consider restoring the flag:

-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if other bioconda recipes use build isolation
rg --type yaml "no-build-isolation" -A 2 -B 2

Length of output: 415

Script:

#!/bin/bash
# Let's check for build isolation patterns in conda-forge and bioconda recipes
fd -e yaml -e yml meta.yaml$ | xargs rg "pip install.*--no-build-isolation" -l

Length of output: 16423

Script:

#!/bin/bash
# Let's also check for any pip install commands in meta.yaml files to understand the common patterns
fd -e yaml -e yml meta.yaml$ | xargs rg "pip install\." -A 1 -B 1

Length of output: 69

entry_points:
- poppunk = PopPUNK.__main__:main
- poppunk_assign = PopPUNK.assign:main
Expand All @@ -27,13 +27,12 @@ build:

requirements:
build:
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- {{ compiler('fortran') }}
- llvm-openmp # [osx]
- libgomp # [linux64]
- cmake >=3.18
- make
- llvm-openmp # [osx]
- libgomp # [linux]
host:
# python
- python
Expand Down Expand Up @@ -64,7 +63,6 @@ requirements:
- treeswift
- requests
# C++ extension
- zlib
# The xorg-* requirements are only used for gtk3 which is pulled in via graph-tool.
- xorg-libxi
- xorg-libxcursor
Expand All @@ -80,7 +78,6 @@ test:
imports:
- PopPUNK
- poppunk_refine

commands:
- poppunk --help
- poppunk_assign --help
Expand All @@ -92,16 +89,17 @@ test:
- poppunk_lineages_from_strains --help

about:
home: https://poppunk.bacpop.org/
license: Apache-2.0
home: "https://poppunk.bacpop.org"
license: "Apache-2.0"
license_family: APACHE
license_file: LICENSE
summary: 'PopPUNK (POPulation Partitioning Using Nucleotide Kmers)'
dev_url: "https://github.com/bacpop/PopPUNK"
doc_url: "https://poppunk.bacpop.org/index.html"

extra:
identifiers:
- doi:10.1101/gr.241455.118
# enabling this would require arm64 packages for: mandrake, pp-sketchlib,
# rapidnj
# additional-platforms:
# - linux-aarch64
# - osx-arm64
- biotools:poppunk
additional-platforms:
- osx-arm64