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Patch repodata to relax HTSlib dependency upper bounds #42895

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Sep 12, 2023
Merged

Patch repodata to relax HTSlib dependency upper bounds #42895

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adc7d34
Patch repodata to relax HTSlib dependency upper bounds
jmarshall Aug 30, 2023
9274255
¯\_(ツ)_/¯
jmarshall Sep 7, 2023
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6 changes: 6 additions & 0 deletions recipes/bioconda-repodata-patches/gen_patch_json.py
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Original file line number Diff line number Diff line change
Expand Up @@ -165,6 +165,12 @@ def _gen_new_index(repodata, subdir):
if record_name.startswith('samtools') and record['subdir']=='linux-64' and not has_dep(record, "openssl") and not has_dep(record, "htslib"):
deps.append('openssl >=1.1.0,<=1.1.1')

# future HTSlib versions are binary compatible until they bump their soversion
if has_dep(record, 'htslib'):
# skip deps prior to 1.10, which was the first with soversion 3
# TODO adjust replacement (exclusive) upper bound with each new compatible HTSlib
_pin_looser(fn, record, 'htslib', min_lower_bound='1.10', upper_bound='1.19')

# future libdeflate versions are compatible until they bump their soversion; relax dependencies accordingly
if record_name in ['htslib', 'staden_io_lib', 'fastp'] and has_dep(record, 'libdeflate'):
# skip deps that allow anything <1.3, which contained an incompatible library filename
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6 changes: 4 additions & 2 deletions recipes/bioconda-repodata-patches/meta.yaml
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@@ -1,13 +1,15 @@
package:
name: bioconda-repodata-patches
version: 20230506 # ensure that this is the "current" date, and always higher than the latest version in master
version: 20230907 # ensure that this is the "current" date, and always higher than the latest version in master

source:
path: .

build:
noarch: generic
number: 1
number: 0
run_exports:
- {{ pin_subpackage("bioconda-repodata-patches", max_pin=None) }}

requirements:
build:
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