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Update kmer-db #49740

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merged 20 commits into from
Oct 9, 2024
Merged

Update kmer-db #49740

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9a74a34
Update kmer-db
agudys Aug 1, 2024
e885a28
build number reset
agudys Aug 1, 2024
7fd9746
fixed tag name
agudys Aug 1, 2024
43dbfea
fix
agudys Aug 1, 2024
73edda5
custom build steps
agudys Aug 2, 2024
671bf6d
fix
agudys Aug 2, 2024
f2e29db
fix
agudys Oct 3, 2024
0d20f19
fix
agudys Oct 3, 2024
4699e19
script fix
agudys Oct 3, 2024
38799bc
Kmer-db downloads precompiled binaries.
agudys Oct 4, 2024
2036432
fix
agudys Oct 4, 2024
edef118
another one
agudys Oct 4, 2024
0eb8b13
fix
agudys Oct 4, 2024
bb4eeb4
noarch fix
agudys Oct 4, 2024
ba2639c
version fix
agudys Oct 4, 2024
a6be9b2
better verbosity
agudys Oct 4, 2024
f890212
fix
agudys Oct 4, 2024
11c9fac
sha fix
agudys Oct 4, 2024
21f20c5
lowercase sha
agudys Oct 4, 2024
06b940d
Update meta.yaml
agudys Oct 9, 2024
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9 changes: 0 additions & 9 deletions recipes/kmer-db/build.sh
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This file was deleted.

43 changes: 29 additions & 14 deletions recipes/kmer-db/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,28 +1,33 @@
{% set version = "1.11.1" %}
{% set sha256 = "63886057a752a890f492bf4ca7ec97435eceebb4ac5ecb5664c69ae2736eaa80" %}
{% set version = "2.2.2" %}

{% set system = "x64_linux" %} # [linux and x86_64]
{% set system = "x64_mac" %} # [osx and x86_64]
{% set system = "arm64_linux" %} # [linux and aarch64]
{% set system = "arm64_mac" %} # [osx and arm64]

{% set sha256 = "e4bccee6380b7c0bfb4746285d36af52a9874b1cf66d62a8862e8579097b5e77" %} # [linux and x86_64]
{% set sha256 = "bfb22576eef88293af4695d297b0b6d3cddc726a882e09ef29bd4684a705977f" %} # [osx and x86_64]
{% set sha256 = "62055ecaf81fac76cfc05a8cd64eba958d2c45350312556777dc4db7355a802a" %} # [linux and aarch64]
{% set sha256 = "6ba58753b1141a005e8a97bf581c1eada5cec6713a1f516518167f1da71b820b" %} # [osx and arm64]


package:
name: kmer-db
version: {{ version }}

build:
number: 2
number: 0
run_exports:
- {{ pin_subpackage('kmer-db', max_pin='x.x.x') }}
script: |
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mkdir -p "${PREFIX}/bin"
cp -v kmer-db "${PREFIX}/bin/" || { echo "Error: Failed to copy kmer-db binary"; exit 1; }


source:
url: https://github.com/refresh-bio/kmer-db/archive/v{{ version }}.tar.gz
url: https://github.com/refresh-bio/kmer-db/releases/download/v{{ version }}/kmer-db-v{{ version }}-{{ system }}.tar.gz
sha256: {{ sha256 }}

requirements:
build:
- make
- {{ compiler('cxx') }}
- make
host:
- zlib
run:
- zlib

about:
home: https://github.com/refresh-bio/kmer-db
summary: "Kmer-db is a fast and memory-efficient tool for estimating evolutionary distances."
Expand All @@ -33,3 +38,13 @@ about:
test:
commands:
- kmer-db > /dev/null
- kmer-db -help

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
skip-lints:
- should_be_noarch_generic
- should_not_be_noarch_source

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⚠️ Potential issue

Good addition of platform support, but skip-lints need review.

The addition of support for linux-aarch64 and osx-arm64 is excellent for broader compatibility. However, the skip-lints for 'should_be_noarch_generic' and 'should_not_be_noarch_source' seem unnecessary and potentially contradictory given the nature of the package (architecture-specific binaries).

Consider removing the skip-lints section:

 extra:
   additional-platforms:
     - linux-aarch64
     - osx-arm64
-  skip-lints:
-    - should_be_noarch_generic
-    - should_not_be_noarch_source

These lints are typically used for packages that should be architecture-independent, which doesn't apply to kmer-db as it provides architecture-specific binaries.

📝 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.

Suggested change
extra:
additional-platforms:
- linux-aarch64
- osx-arm64
skip-lints:
- should_be_noarch_generic
- should_not_be_noarch_source
extra:
additional-platforms:
- linux-aarch64
- osx-arm64

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