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Update pkg_archiver.py

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general bug fixes
This commit is contained in:
sukanka 2022-11-04 09:46:40 +08:00 • committed by GitHub
parent 5ec97da3c8
commit c5b59a20f8
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1 changed files with 21 additions and 13 deletions
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34
pkg_archiver.py
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@ -27,9 +27,10 @@ def archive_pkg_by_file_list(file, bioarch_path="BioArchLinux", biconductor_vers
pkgname = 'r-'+pkgname.lower()
os.chdir(f"{bioarch_path}/{pkgname}")
bump_pkgrel(step)
archive_pkg_yaml(biconductor_version)
archive_pkg_pkgbuild(biconductor_version)
changed = archive_pkg_pkgbuild(biconductor_version)
if changed:
bump_pkgrel(step)
os.chdir(current_dir)
@ -40,17 +41,14 @@ def bump_pkgrel(step=1):
new_pkgrel = int(line.split("=")[1])+step
line = re.sub(
r'pkgrel=\d+', f'pkgrel={new_pkgrel}', line)
break
print(line.rstrip())
def archive_pkg_yaml(bioconductor_version=3.15, yaml_file="lilac.yaml"):
'''
archive pkg in CRAN and bioconductor (the latest bioconductor_version that contains the pkg needed)
'''
'''
archive pkg in CRAN and bioconductor (the latest bioconductor_version that contains the pkg needed)
'''
with open(yaml_file, "r") as f:
docs = yaml.load(f, Loader=yaml.FullLoader)
print(docs)
url_idx = -1
for i in range(len(docs['update_on'])):
if "url" in docs['update_on'][i].keys():
@ -78,36 +76,46 @@ def archive_pkg_pkgbuild(bioconductor_version=3.15, _pkgname="_pkgname"):
with open("PKGBUILD", "r") as f:
lines = f.readlines()
changed = False
flag = False
for i in range(len(lines)):
if lines[i].startswith("source="):
flag = True
if flag:
new_line = lines[i]
if 'cran.r-project.org' in lines[i] and "src/contrib/Archive" not in lines[i]:
# https://cran.r-project.org/src/contrib/${_pkgname}_${pkgver}.tar.gz
# to
# https://cran.r-project.org/src/contrib/Archive/${_pkgname}/${_pkgname}_${pkgver}.tar.gz
lines[i] = lines[i].replace(
new_line = lines[i].replace(
"src/contrib", r"src/contrib/Archive/${" + _pkgname + '}')
elif '//bioconductor.org' in lines[i]:
# https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz
# to
# https://bioconductor.org/packages/3.14/bioc/src/contrib/ABAEnrichment_1.24.0.tar.gz
lines[i] = lines[i].replace(
new_line = lines[i].replace(
"packages/release/bioc", f"packages/{bioconductor_version}/bioc")
else:
NotImplemented
if new_line != lines[i]:
changed = True
lines[i] = new_line
with open("PKGBUILD", "w") as f:
f.writelines(lines)
return changed
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument(
'--file', help='The file that contains the pkgname to be archived, one pkgname per line')
parser.add_argument('--bioarch_path', help='The path of BioArchLinux repo')
parser.add_argument(
'--bico_ver', help='The Bioconductor version to be used in archived url, default 3.15')
'--bioarch_path', help='The path of BioArchLinux repo', default="BioArchLinux")
parser.add_argument(
'--bioc_ver', help="The Bioconductor version to be used in archived url", default="3.15")
args = parser.parse_args()
if args.file:
archive_pkg_by_file_list(args.file, args.bioarch_path, args.bico_ver)
archive_pkg_by_file_list(args.file, args.bioarch_path, args.bioc_ver)
else:
parser.print_help()