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https://github.com/BioArchLinux/bioarchlinux-tools.git
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write newly added depends to file
This commit is contained in:
sukanka
parent
923ba04cc3
commit
86f882d45c
1 changed files with 28 additions and 34 deletions
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@ -2,8 +2,6 @@
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'''
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Update the `depends` and `optdepends` part of an R package PKGBUILD listed in `pkgname.txt`
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'''
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import requests
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from re import findall
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from packaging import version
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import configparser
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import logging
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@ -13,6 +11,7 @@ import os
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import yaml
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from typing import Optional
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import sqlite3
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from dbmanager import get_bioc_versions
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EXCLUDED_PKGS = {
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"base",
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@ -50,14 +49,14 @@ EXCLUDED_PKGS = {
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class PkgInfo:
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def __init__(self, pkgname=None, depends=None, optdepends=None,
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bioc_meta_mirror="https://bio.askk.cc",
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bioc_meta_mirror="https://bioconductor.org",
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bioc_versions=[],
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bioc_min_version="3.0",):
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'''
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pkgname: name of the package, style in CRAN and Bioconductor, e.g. "Rcpp",
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depends: depends of the package, style in PKGBUILD, e.g. "r-base". Updated automatically if not provided.
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optdepends: optdepends of the package, style in PKGBUILD, e.g. "r-rmarkdown: for vignettes". Updated automatically if not provided.
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bioc_meta_mirror: remote mirror of Bioconductor versions numbers, default to "https://bio.askk.cc"
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bioc_mirror: remote mirror of Bioconductor, default to "https://bioconductor.org"
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bioc_versions: list of Bioconductor versions to be supported, default to empty list. Updated automatically if not provided.
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bioc_min_version: minimum version of Bioconductor we want to support, default to "3.0".
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'''
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@ -68,6 +67,8 @@ class PkgInfo:
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self.pkgver = None
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self.new_depends = []
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self.new_optdepends = []
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# newly introduced depends, may be missing in BioArchLinux, need to be added
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self.added_depends = [] # named in CRAN style
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self.bioc_versions = bioc_versions
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self.bioc_meta_mirror = bioc_meta_mirror
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@ -77,7 +78,7 @@ class PkgInfo:
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self.optdepends_changed = False
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if self.bioc_versions == []:
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self.set_bioc_versions()
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self.bioc_versions = get_bioc_versions(self.bioc_meta_mirror)
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def build_body(self, conn_cursor):
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self.parse_pkgbuild()
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@ -85,19 +86,6 @@ class PkgInfo:
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self.update_info(desc)
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self.merge_depends()
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def set_bioc_versions(self) -> None:
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'''
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get all Bioconductor versions
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'''
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version_page = requests.get(
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f"{self.bioc_meta_mirror}/bioc_version")
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if version_page.status_code != requests.codes.ok:
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raise RuntimeError(
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f"Failed to get Bioconductor versions due to: {version_page.status_code}: {version_page.reason}")
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z = version_page.text.split(',')
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self.bioc_versions = list(map(lambda x: version.parse(x), z))
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def __str__(self) -> str:
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return f"""
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Pkgname: {self.pkgname}
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@ -162,6 +150,9 @@ class PkgInfo:
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if '' in r_deps:
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r_deps.remove('')
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# now r_deps contains all depends in named CRAN style
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self.added_depends = [
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x for x in r_deps if f"r-{x.lower()}" not in self.depends]
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self.new_depends += [f"r-{_.lower()}" for _ in r_deps]
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self.new_depends.sort()
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@ -219,9 +210,10 @@ class PkgInfo:
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if sorted(self.new_optdepends) != sorted(self.optdepends):
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self.optdepends_changed = True
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def update_pkgbuild(self):
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def update_pkgbuild(self) -> list[str]:
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'''
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write new depends to PKGBUILD if depends change
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return the newly added depends which may not be in BioArchLinux Repo.
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'''
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if not self.depends_changed and not self.optdepends_changed:
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return
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@ -277,6 +269,7 @@ class PkgInfo:
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logging.info(f"Writing new PKGBUILD for {self.pkgname}")
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with open("PKGBUILD", "w") as f:
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f.writelines(lines)
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return self.added_depends
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def update_yaml(self, yaml_file='lilac.yaml'):
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'''
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@ -298,7 +291,7 @@ class PkgInfo:
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yaml.dump(docs, f, sort_keys=False)
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def update_depends_by_file(file, bioarch_path="BioArchLinux", db="sqlite.db", bioc_min_ver="3.0", bioc_meta_mirror='https://bio.askk.cc'):
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def update_depends_by_file(file, bioarch_path="BioArchLinux", db="sqlite.db", bioc_min_ver="3.0", bioc_meta_mirror="https://bioconductor.org", output_file="added_depends.txt"):
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'''
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Update depends of packages listed in `file`, one package name per line, CRAN style(e.g. `Rcpp`) and pkgname style (`r-rcpp`) are both supported.
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@ -307,33 +300,32 @@ def update_depends_by_file(file, bioarch_path="BioArchLinux", db="sqlite.db", bi
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db: path to the database to be read
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bioc_min_ver: minimum version of Bioconductor to be supported.
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bioc_meta_mirror: The server used to get all version numbers of BIOC
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output_file: file to write the added depends to.
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'''
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bioc_versions = get_bioc_versions(bioc_meta_mirror)
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current_dir = os.getcwd()
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# where the name are _pkgname (May have upper letters) or pkgname (r-xxx)
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case = "_pkgname"
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with open(file, "r") as f:
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for pkgname in f:
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pkgname = pkgname.strip()
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if pkgname.startswith("r-"):
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case = "pkgname"
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break
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conn = sqlite3.connect(db)
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cursor = conn.cursor()
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added_deps = []
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with open(file, "r") as f:
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for pkgname in f:
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logging.info(f"Updating {pkgname}")
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pkgname = pkgname.strip()
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if case == '_pkgname':
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pkgname = 'r-'+pkgname.lower()
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if not pkgname.strip().startswith("r-"):
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pkgname = "r-"+pkgname.lower()
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logging.info(f"Updating {pkgname}")
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os.chdir(f"{bioarch_path}/{pkgname}")
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pkginfo = PkgInfo(bioc_min_version=bioc_min_ver,
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bioc_meta_mirror=bioc_meta_mirror)
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bioc_meta_mirror=bioc_meta_mirror, bioc_versions=bioc_versions)
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pkginfo.build_body(cursor)
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pkginfo.update_pkgbuild()
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pkginfo.update_yaml()
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if pkginfo.added_depends:
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added_deps += pkginfo.added_depends
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os.chdir(current_dir)
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conn.close()
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with open(output_file, "w") as f:
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f.write('\n'.join(set(added_deps)))
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if __name__ == '__main__':
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@ -351,12 +343,14 @@ if __name__ == '__main__':
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parser.add_argument(
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'--bioc_min_ver', help="The minimum version of Bioconductor supported, must be greater than 3.0", default="3.0")
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parser.add_argument(
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'--bioc_meta_mirror', help="The server used to get all version numbers of BIOC", default="https://bio.askk.cc")
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'--bioc_meta_mirror', help="The server used to get all version numbers of BIOC", default="https://bioconductor.org")
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parser.add_argument(
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'-o', '--output', help='The file to save newly added depends name', default="added_depends.txt")
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args = parser.parse_args()
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if args.file:
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update_depends_by_file(args.file, args.bioarch_path, args.db,
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args.bioc_min_ver, bioc_meta_mirror=args.bioc_meta_mirror)
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args.bioc_min_ver, bioc_meta_mirror=args.bioc_meta_mirror, output_file=args.output)
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else:
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parser.print_help()
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