mirror of
https://github.com/BioArchLinux/bioarchlinux-tools.git
synced 2025-03-09 22:53:31 +00:00
361 lines
14 KiB
Python
Executable file
361 lines
14 KiB
Python
Executable file
#!/usr/bin/python
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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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from lilac2 import api as lilac
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import argparse
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import os
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import yaml
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from typing import Optional
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EXCLUDED_PKGS = {
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"base",
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"boot",
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"class",
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"cluster",
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"codetools",
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"compiler",
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"datasets",
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"foreign",
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"graphics",
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"grDevices",
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"grid",
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"KernSmooth",
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"lattice",
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"MASS",
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"Matrix",
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"methods",
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"mgcv",
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"nlme",
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"nnet",
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"parallel",
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"rpart",
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"spatial",
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"splines",
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"stats",
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"stats4",
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"survival",
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"tcltk",
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"tools",
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"utils",
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"R"
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}
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class PkgInfo:
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def __init__(self, pkgname=None, depends=None, optdepends=None,
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cran_meta_mirror="https://cran.r-project.org",
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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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cran_meta_mirror: remote mirror of CRAN use to download PACKAGES file, default to "https://cran.r-project.org"
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bioc_meta_mirror: remote mirror of Bioconductor use to download PACKAGES file, 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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self.pkgname = pkgname
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self.depends = depends
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self.optdepends = optdepends
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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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self.bioc_versions = bioc_versions
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self.cran_meta_mirror = cran_meta_mirror
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self.bioc_meta_mirror = bioc_meta_mirror
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self.bioc_min_version = bioc_min_version
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self.depends_changed = False
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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.parse_pkgbuild()
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desc = self.get_desc()
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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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Pkgver: {self.pkgver}
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Depends: {self.depends}
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Optdepends: {self.optdepends}
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new_depends: {self.new_depends}
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new_optdepends: {self.new_optdepends}
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"""
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def parse_pkgbuild(self) -> None:
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'''
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use lilac to get _pkgname and depends and optdepends of PKGBUILD, set the value to self
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'''
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with open('PKGBUILD', 'r') as f:
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lines = f.readlines()
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for line in lines:
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if line.startswith('_pkgname'):
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self.pkgname = line.split(
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'=')[-1].strip().strip("'").strip('"')
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break
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depends = lilac.obtain_depends()
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optdepends = lilac.obtain_optdepends(parse_dict=False)
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self.depends = depends
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self.optdepends = optdepends
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def get_desc(self) -> Optional[str]:
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'''
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get new depends from CRAN or Bioconductor
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'''
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pkgname = self.pkgname
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CRAN_URL = f"{self.cran_meta_mirror}/src/contrib/PACKAGES"
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# try cran first
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r_cran = requests.get(CRAN_URL)
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if r_cran.status_code == requests.codes.ok:
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self.cran_descs = r_cran.text.split('\n\n')
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for desc in self.cran_descs:
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if desc.startswith(f'Package: {pkgname}'):
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logging.info(f"Found {pkgname} in CRAN")
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return desc
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else:
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raise RuntimeError(
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f"Failed to get CRAN descriptions due to: {r_cran.status_code}: {r_cran.reason}")
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# try bioconductor
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for ver in self.bioc_versions:
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if ver < version.parse(self.bioc_min_version):
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continue
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for p in ['bioc', 'data/annotation', 'data/experiment']:
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url = f"{self.bioc_meta_mirror}/packages/{ver}/{p}/src/contrib/PACKAGES"
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bioconductor_descs = requests.get(url)
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if bioconductor_descs.status_code == requests.codes.ok:
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bioconductor_descs = bioconductor_descs.text.split('\n\n')
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for desc in bioconductor_descs:
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if desc.startswith(f'Package: {pkgname}'):
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logging.info(
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f"Found {pkgname} in Bioconductor {ver}: {p}")
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return desc
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else:
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logging.error(
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f'Failed to get Bioconductor descriptions for version: {ver}, {p}, due to: {bioconductor_descs.status_code}: {bioconductor_descs.reason}')
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continue
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def update_info(self, desc) -> None:
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'''
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obtain new depends and optdepends from `desc`, and write them to `self`
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'''
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config = configparser.ConfigParser()
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config.read_string('[pkg]\n'+desc)
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self.pkgver = config['pkg'].get('version')
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r_deps = []
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r_optdeps = []
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# depends
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dep_depends = config['pkg'].get('depends')
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if dep_depends:
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r_deps.extend(dep_depends.split(','))
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dep_imports = config['pkg'].get('imports')
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if dep_imports:
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r_deps.extend(dep_imports.split(','))
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dep_linkingto = config['pkg'].get('linkingto')
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if dep_linkingto:
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r_deps.extend(dep_linkingto.split(','))
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r_deps = [_.split('(')[0].strip() for _ in r_deps]
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r_deps = list(set(r_deps) - EXCLUDED_PKGS)
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if '' in r_deps:
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r_deps.remove('')
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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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if 'r' in self.new_depends:
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self.new_depends.remove('r')
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# opt depends
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dep_optdepends = config['pkg'].get('suggests')
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if dep_optdepends:
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r_optdeps.extend(dep_optdepends.split(','))
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dep_enhances = config['pkg'].get('enhances')
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if dep_enhances:
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r_optdeps.extend(dep_enhances.split(','))
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r_optdeps = [_.split('(')[0].strip() for _ in r_optdeps]
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if '' in r_optdeps:
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r_optdeps.remove('')
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self.new_optdepends += [f"r-{_.lower()}" for _ in r_optdeps]
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self.new_optdepends.sort()
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def merge_depends(self):
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'''
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Merge old `depends` and `optdepends` in to the new ones
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'''
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system_reqs = [x for x in self.depends if not x.startswith('r-')]
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system_reqs.sort()
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self.new_depends = system_reqs+self.new_depends
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if sorted(self.new_depends) != sorted(self.depends):
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self.depends_changed = True
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# keep explanation of optdepends
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if any(map(lambda x: ':' in x, self.optdepends)):
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self.new_optdepends = [
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x+': ' for x in self.new_optdepends if ':' not in x]
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opt_dict = {pkg.strip(): desc.strip() for (pkg, desc) in
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(item.split(':', 1) for item in self.optdepends)}
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if sorted(self.new_optdepends) != sorted(opt_dict.keys()):
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self.optdepends_changed = True
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for i in range(len(self.new_optdepends)):
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val = opt_dict.get(self.optdepends[i])
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if val:
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self.new_optdepends[i] += ': '+val
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else:
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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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'''
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write new depends to PKGBUILD if depends change
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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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with open("PKGBUILD", "r") as f:
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lines = f.readlines()
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depends_interval = [-1, -1]
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optdepends_interval = [-1, -1]
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for i, line in enumerate(lines):
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if line.strip().startswith("depends"):
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depends_interval[0] = i
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elif line.strip().startswith("optdepends"):
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optdepends_interval[0] = i
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if depends_interval[0] > -1 and depends_interval[1] == -1:
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if ')' in line:
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# end depends
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depends_interval[1] = i
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if optdepends_interval[0] > -1 and optdepends_interval[1] == -1:
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if ')' in line:
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# end optdepends
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optdepends_interval[1] = i
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if not (depends_interval[1] < optdepends_interval[0] or optdepends_interval[1] < depends_interval[0]):
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logging.error(
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"depends and optdepends overlap, please fix it manually")
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return
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if self.depends_changed:
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for i in range(depends_interval[0], depends_interval[1]):
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lines[i] = ''
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lines[depends_interval[1]] = '\n'.join(
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['depends=(', '\n'.join([' ' + _ for _ in self.new_depends]), ')\n'])
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if self.optdepends_changed:
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for i in range(optdepends_interval[0], optdepends_interval[1]):
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lines[i] = ''
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if self.new_optdepends:
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lines[optdepends_interval[1]] = '\n'.join(
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['optdepends=(', '\n'.join([' ' + _ for _ in self.new_optdepends]), ')\n'])
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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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def update_yaml(self, yaml_file='lilac.yaml'):
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'''
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update the `repo_depends` part of pkg
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'''
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with open(yaml_file, "r") as f:
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docs = yaml.load(f, Loader=yaml.FullLoader)
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old_depends = docs.get('repo_depends', [])
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non_r_depends = [x for x in old_depends if not x.startswith('r-')]
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# only keep non-r depends also in new_depends
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non_r_depends = [x for x in non_r_depends if x in self.new_depends]
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non_r_depends.sort()
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r_new_depends = [x for x in self.new_depends if x.startswith('r-')]
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r_new_depends.sort()
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new_deps = non_r_depends+r_new_depends
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if new_deps:
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docs['repo_depends'] = new_deps
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with open(yaml_file, 'w') as f:
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yaml.dump(docs, f, sort_keys=False)
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def update_depends_by_file(file, bioarch_path="BioArchLinux", bioc_min_ver="3.0", cran_meta_mirror="https://cran.r-project.org",
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bioc_meta_mirror="https://bioconductor.org",):
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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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file: file containing package names
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bioarch_path: path to BioArchLinux
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bioc_min_ver: minimum version of Bioconductor to be supported, generally not needed to be changed
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cran_meta_mirror: mirror of CRAN metadata, recommended to be changed to a local https mirror.
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bioc_meta_mirror: mirror of Bioconductor metadata, recommended to be changed to a local https mirror.
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'''
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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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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 case == '_pkgname':
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pkgname = 'r-'+pkgname.lower()
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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, cran_meta_mirror=cran_meta_mirror)
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pkginfo.update_pkgbuild()
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pkginfo.update_yaml()
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os.chdir(current_dir)
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(
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description='update the depends of R packages from CRAN and Bioconductor automatically',
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formatter_class=argparse.ArgumentDefaultsHelpFormatter
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)
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parser.add_argument(
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'--file', help='The file that contains the pkgname to be archived, one pkgname per line')
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parser.add_argument(
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'--bioarch_path', help='The path of BioArchLinux repo', default="BioArchLinux")
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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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'--cran_meta_mirror', help="The mirror of CRAN metadata, recommended to be changed to a local https mirror. Only http(s) is supported", default="https://cran.r-project.org")
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parser.add_argument(
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'--bioc_meta_mirror', help="The mirror of Bioconductor metadata, recommended to be changed to a local https mirror. Only http(s) is supported", default="https://bioconductor.org")
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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.bioc_min_ver,
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cran_meta_mirror=args.cran_meta_mirror, bioc_meta_mirror=args.bioc_meta_mirror)
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else:
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parser.print_help()
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