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mkubuntu.py
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#!/usr/bin/env python3
# vi: set sw=4 et:
"""
How to take a ChimeraX.app on Linux and turn it into a debian package
for Ubuntu
References:
https://wiki.debian.org/FilesystemHierarchyStandard
https://www.debian.org/doc/debian-policy/
https://www.freedesktop.org/wiki/Specifications/desktop-entry-spec/
#
Designed for Ubuntu, would mostly work on Debian except that ffmpeg
not available in Debian
Steps:
1. build ChimeraX without Debian supplied prerequisites
2. create Debian binary package layout
3. build Deiban package
"""
import os
import subprocess
import sys
import tempfile
import textwrap
# app_author and app_name are the same as ChimeraX_main.py
app_author = "UCSF"
app_name = "ChimeraX"
CHIMERAX_INSTALL = f"{app_name}.app"
CHIMERAX_BIN = f"{CHIMERAX_INSTALL}/bin/{app_name}"
# lintian(1) complains about files /opt
# INST_DIR = "opt"
INST_DIR = "usr/lib"
UBUNTU_DEPENDENCIES = {
"16.04": {
"libasound2": "1.1.0",
"libatk1.0-0": "2.18.0",
"libbz2-1.0": "1.0.6",
"libc6": "2.23",
"libcairo-gobject2": "1.14.6",
"libcairo2": "1.14.6",
"libcups2": "2.1.3",
"libdbus-1-3": "1.10.6",
"libdrm2": "2.4.83",
"libegl1-mesa": "17.2.8",
"libexpat1": "2.1.0",
"libfftw3-single3": "3.3.4",
"libfontconfig1": "2.11.94",
"libfreetype6": "2.6.1",
"libgcc1": "6.0.1",
"libgdk-pixbuf2.0-0": "2.32.2",
"libgfortran3": "5.4.0",
"libgl1-mesa-glx": "17.2.8",
"libglib2.0-0": "2.48.2",
"libglu1-mesa": "9.0.0",
"libgstreamer-plugins-base1.0-0": "1.8.3",
"libgstreamer1.0-0": "1.8.3",
"libgtk-3-0": "3.18.9",
"libllvm3.8": "3.8",
"liblzma5": "5.1.1alpha+20120614",
"libnspr4": "4.13.1",
"libnss3": "3.28.4",
"libpango-1.0-0": "1.38.1",
"libpangocairo-1.0-0": "1.38.1",
"libpulse-mainloop-glib0": "8.0",
"libpulse0": "8.0",
"libsqlite3-0": "3.11.0",
"libssl1.0.0": "1.0.2g",
"libstdc++6": "5.4.0",
"libx11-6": "1.6.3",
"libx11-xcb1": "1.6.3",
"libxcb-glx0": "1.11.1",
"libxcb-util1": "0.4.0",
"libxcb-xfixes0": "1.11.1",
"libxcb-xinerama0": "1.11.1",
"libxcb1": "1.11.1",
"libxcomposite1": "0.4.4",
"libxcursor1": "1.1.14",
"libxdamage1": "1.1.4",
"libxext6": "1.3.3",
"libxfixes3": "5.0.1",
"libxi6": "1.7.6",
"libxrandr2": "1.5.0",
"libxrender1": "0.9.9",
"libxtst6": "1.2.2",
"zlib1g": "1.2.8.dfsg",
"xdg-utils": "1.0", # TODO: get right version
},
"18.04": {
"libasound2": "1.1.3",
"libatk1.0-0": "2.28.1",
"libbz2-1.0": "1.0.6",
"libc6": "2.27",
"libcairo-gobject2": "1.15.10",
"libcairo2": "1.15.10",
"libcups2": "2.2.7",
"libdbus-1-3": "1.12.2",
"libdrm2": "2.4.91",
"libegl1": "1.0.0",
"libexpat1": "2.2.5",
"libffi6": "3.2.1",
"libfftw3-single3": "3.3.7",
"libfontconfig1": "2.12.6",
"libfreetype6": "2.8.1",
"libgcc1": "8-20180414",
"libgdk-pixbuf2.0-0": "2.36.11",
"libgfortran4": "7.5.0",
"libgl1": "1.0.0",
"libglib2.0-0": "2.56.1",
"libglu1-mesa": "9.0.0",
"libgstreamer-plugins-base1.0-0": "1.14.1",
"libgstreamer1.0-0": "1.14.1",
"libgtk-3-0": "3.22.30",
"liblzma5": "5.2.2",
"libnspr4": "4.18",
"libnss3": "3.35",
"libosmesa6": "18.0.0",
"libpango-1.0-0": "1.40.14",
"libpangocairo-1.0-0": "1.40.14",
"libpulse-mainloop-glib0": "11.1",
"libpulse0": "11.1",
"libsqlite3-0": "3.22.0",
"libssl1.1": "1.1.0g",
"libstdc++6": "8-20180414",
"libx11-6": "1.6.4",
"libx11-xcb1": "1.6.4",
"libxcb-glx0": "1.13",
"libxcb-util1": "0.4.0",
"libxcb-xfixes0": "1.13",
"libxcb-xinerama0": "1.13",
"libxcb1": "1.13",
"libxcomposite1": "0.4.4",
"libxcursor1": "1.1.15",
"libxdamage1": "1.1.4",
"libxext6": "1.3.3",
"libxfixes3": "5.0.3",
"libxi6": "1.7.9",
"libxrandr2": "1.5.1",
"libxrender1": "0.9.10",
"libxtst6": "1.2.3",
"xdg-utils": "1.1.2",
"zlib1g": "1.2.11.dfsg",
},
"20.04": {
"libasound2": "1.2.2",
"libatk1.0-0": "2.35.1",
"libbz2-1.0": "1.0.8",
"libc6": "2.31",
"libcairo-gobject2": "1.16.0",
"libcairo2": "1.16.0",
"libcrypt1": "4.4.10",
"libcups2": "2.3.1",
"libdbus-1-3": "1.12.16",
"libdrm2": "2.4.101",
"libegl1": "1.3.1",
"libexpat1": "2.2.9",
"libffi7": "3.3",
"libfftw3-single3": "3.3.8",
"libfontconfig1": "2.13.1",
"libfreetype6": "2.10.1",
"libgcc-s1": "10-20200411",
"libgdk-pixbuf2.0-0": "2.40.0+dfsg",
"libgfortran5": "10-20200411",
"libgl1": "1.3.1",
"libglib2.0-0": "2.64.2",
"libglu1-mesa": "9.0.1",
"libgstreamer-plugins-base1.0-0": "1.16.2",
"libgstreamer1.0-0": "1.16.2",
"libgtk-3-0": "3.24.18",
"liblzma5": "5.2.4",
"libncursesw6": "6.2",
"libnspr4": "4.25",
"libnss3": "3.49.1",
"libopenjp2-7": "2.3.1",
"libosmesa6": "20.0.4",
"libpango-1.0-0": "1.44.7",
"libpangocairo-1.0-0": "1.44.7",
"libpulse-mainloop-glib0": "13.99.1",
"libpulse0": "13.99.1",
"libsqlite3-0": "3.31.1",
"libssl1.1": "1.1.1f",
"libstdc++6": "10-20200411",
"libtinfo6": "6.2",
"libuuid1": "2.34",
"libwayland-client0": "1.18.0",
"libwayland-cursor0": "1.18.0",
"libwayland-egl1": "1.18.0",
"libwayland-server0": "1.18.0",
"libx11-6": "1.6.9",
"libx11-xcb1": "1.6.9",
"libxcb-cursor0": "0.1.1",
"libxcb-glx0": "1.14",
"libxcb-icccm4": None,
"libxcb-image0": None,
"libxcb-keysyms1": None,
"libxcb-render-util0": None,
"libxcb-util1": "0.4.0",
"libxcb-xinerama0": "1.14",
"libxcb1": "1.14",
"libxcomposite1": "0.4.5",
"libxcursor1": "1.2.0",
"libxdamage1": "1.1.5",
"libxext6": "1.3.4",
"libxfixes3": "5.0.3",
"libxi6": "1.7.10",
"libxkbcommon0": "0.10.0",
"libxkbcommon-x11-0": None,
"libxrender1": "0.9.10",
"libxtst6": "1.2.3",
"xdg-utils": "1.1.3",
"zlib1g": "1.2.11.dfsg",
},
"22.04": {
# TODO: update versions
"libasound2": "1.2.6.1",
"libatk1.0-0": "2.36.0",
"libbz2-1.0": "1.0.8",
"libc6": "2.35",
"libcairo-gobject2": "1.16.0",
"libcairo2": "1.16.0",
"libcrypt1": "1:4.4.17",
"libcups2": "2.3.1",
"libdbus-1-3": "1.12.16",
"libdrm2": "2.4.101",
"libegl1": "1.3.1",
"libexpat1": "2.2.9",
"libffi7": "3.3",
"libfftw3-single3": "3.3.8",
"libfontconfig1": "2.13.1",
"libfreetype6": "2.10.1",
"libgcc-s1": "10-20200411",
"libgdk-pixbuf2.0-0": "2.40.0+dfsg",
"libgfortran5": "10-20200411",
"libgl1": "1.3.1",
"libglib2.0-0": "2.64.2",
"libglu1-mesa": "9.0.1",
"libgstreamer-plugins-base1.0-0": "1.16.2",
"libgstreamer1.0-0": "1.16.2",
"libgtk-3-0": "3.24.18",
"liblzma5": "5.2.4",
"libncursesw6": "6.2",
"libnspr4": "4.25",
"libnss3": "3.49.1",
"libopenjp2-7": "2.3.1",
"libosmesa6": "20.0.4",
"libpango-1.0-0": "1.44.7",
"libpangocairo-1.0-0": "1.44.7",
"libpulse-mainloop-glib0": "13.99.1",
"libpulse0": "13.99.1",
"libsqlite3-0": "3.31.1",
"libssl3": "3.0.2",
"libstdc++6": "10-20200411",
"libtinfo6": "6.2",
"libuuid1": "2.34",
"libwayland-client0": "1.18.0",
"libwayland-cursor0": "1.18.0",
"libwayland-egl1": "1.18.0",
"libwayland-server0": "1.18.0",
"libx11-6": "1.6.9",
"libx11-xcb1": "1.6.9",
"libxcb-cursor0": "0.1.1",
"libxcb-glx0": "1.14",
"libxcb-icccm4": None,
"libxcb-image0": None,
"libxcb-keysyms1": None,
"libxcb-render-util0": None,
"libxcb-util1": "0.4.0",
"libxcb-xinerama0": "1.14",
"libxcb1": "1.14",
"libxcomposite1": "0.4.5",
"libxcursor1": "1.2.0",
"libxdamage1": "1.1.5",
"libxext6": "1.3.4",
"libxfixes3": "5.0.3",
"libxi6": "1.7.10",
"libxkbcommon0": "0.10.0",
"libxkbcommon-x11-0": None,
"libxrender1": "0.9.10",
"libxtst6": "1.2.3",
"xdg-utils": "1.1.3",
"zlib1g": "1.2.11.dfsg",
},
"24.04": {
# TODO: update versions
"libasound2": "1.2.6.1",
"libatk1.0-0": "2.36.0",
"libbz2-1.0": "1.0.8",
"libc6": "2.35",
"libcairo-gobject2": "1.16.0",
"libcairo2": "1.16.0",
"libcrypt1": "1:4.4.17",
"libcups2": "2.3.1",
"libdbus-1-3": "1.12.16",
"libdrm2": "2.4.101",
"libegl1": "1.3.1",
"libexpat1": "2.2.9",
"libffi8": "3.3",
"libfftw3-single3": "3.3.8",
"libfontconfig1": "2.13.1",
"libfreetype6": "2.10.1",
"libgcc-s1": "10-20200411",
"libgdk-pixbuf2.0-0": "2.40.0+dfsg",
"libgfortran5": "10-20200411",
"libgl1": "1.3.1",
"libglib2.0-0": "2.64.2",
"libglu1-mesa": "9.0.1",
"libgstreamer-plugins-base1.0-0": "1.16.2",
"libgstreamer1.0-0": "1.16.2",
"libgtk-3-0": "3.24.18",
"liblzma5": "5.2.4",
"libncursesw6": "6.2",
"libnspr4": "4.25",
"libnss3": "3.49.1",
"libopenjp2-7": "2.3.1",
"libosmesa6": "20.0.4",
"libpango-1.0-0": "1.44.7",
"libpangocairo-1.0-0": "1.44.7",
"libpulse-mainloop-glib0": "13.99.1",
"libpulse0": "13.99.1",
"libsqlite3-0": "3.31.1",
"libssl3": "3.0.2",
"libstdc++6": "10-20200411",
"libtinfo6": "6.2",
"libuuid1": "2.34",
"libwayland-client0": "1.18.0",
"libwayland-cursor0": "1.18.0",
"libwayland-egl1": "1.18.0",
"libwayland-server0": "1.18.0",
"libx11-6": "1.6.9",
"libx11-xcb1": "1.6.9",
"libxcb-cursor0": "0.1.1",
"libxcb-glx0": "1.14",
"libxcb-icccm4": None,
"libxcb-image0": None,
"libxcb-keysyms1": None,
"libxcb-render-util0": None,
"libxcb-util1": "0.4.0",
"libxcb-xinerama0": "1.14",
"libxcb1": "1.14",
"libxcomposite1": "0.4.5",
"libxcursor1": "1.2.0",
"libxdamage1": "1.1.5",
"libxext6": "1.3.4",
"libxfixes3": "5.0.3",
"libxi6": "1.7.10",
"libxkbcommon0": "0.10.0",
"libxkbcommon-x11-0": None,
"libxrender1": "0.9.10",
"libxtst6": "1.2.3",
"xdg-utils": "1.1.3",
"zlib1g": "1.2.11.dfsg",
},
}
def main():
"""main program"""
# assume ChimeraX.app already has appropriate binaries
error = False
os_version = None
build = 'release'
if len(sys.argv) >= 2:
os_version = sys.argv[1]
else:
error = True
if len(sys.argv) >= 3:
build = sys.argv[2]
if build not in ['release', 'candidate', 'daily', 'techpreview']:
error = True
if error or len(sys.argv) > 3 or os_version not in UBUNTU_DEPENDENCIES:
print(f'Usage: {sys.argv[0]} ubuntu-version [build-type]', file=sys.stderr)
print(' Supported Ubuntu versions are:', ', '.join(UBUNTU_DEPENDENCIES.keys()),
file=sys.stderr)
print(' Build-type is one of "release", "candidate", or "daily"', file=sys.stderr)
raise SystemExit(2)
dependencies = UBUNTU_DEPENDENCIES[os_version]
output = subprocess.check_output([
CHIMERAX_BIN, "--nocolor", "--version"], stderr=subprocess.DEVNULL).decode()
full_version = [line for line in output.split('\n') if 'version:' in line]
if not full_version:
print("Not able to determine version number")
raise SystemExit(1)
full_version = full_version[0].split(':', maxsplit=1)[1].strip()
version_number, version_date = full_version.split(maxsplit=1)
from packaging.version import Version
version = Version(version_number)
version_date = version_date[1:-1].replace('-', '.')
pkg_name = f"{app_author.lower()}-{app_name.lower()}"
bin_name = app_name.lower() # name of command in /usr/bin
if build == 'daily':
# daily build, version is date
version = version_date
pkg_name += "-daily"
bin_name += "-daily"
elif build == 'techpreview':
# like daily build, version is date
version = version_date
pkg_name += "-techpreview"
bin_name += "-techpreview"
elif build == 'release':
# release build
version = version.base_version
else:
# candidate build
version = f"{version.base_version}+rc{version_date}"
version = f"{version}ubuntu{os_version}"
deb_name = f"{pkg_name}-{version}" # name of .deb file
# print('full_version:', repr(full_version))
# print('version_number:', version_number)
# print('version_date:', version_date)
# print('deb_name:', deb_name)
# print('pkg_name:', pkg_name)
# print('bin_name:', bin_name)
os.umask(0o22) # turn off group and other writability
pkg_root = f"{deb_name}"
os.mkdir(pkg_root)
debian_dir = f"{pkg_root}/DEBIAN"
os.mkdir(debian_dir)
make_control_file(debian_dir, pkg_name, version, dependencies)
make_postinst(debian_dir, pkg_name, bin_name)
make_prerm(debian_dir, pkg_name, bin_name)
doc_dir = f"{pkg_root}/usr/share/doc/{pkg_name}"
os.makedirs(doc_dir)
make_copyright_file(doc_dir)
make_changelog_file(doc_dir)
# add_readme(doc_dir)
copy_app(pkg_root, pkg_name)
make_bin(pkg_root, pkg_name, bin_name)
src = f'{app_name}.app/share/man/man1/{app_name}.1'
make_man_file(src, pkg_root, bin_name)
subprocess.check_call(['/bin/chmod', '-R', 'a+rX,go-w', pkg_root])
dst_dir = f'./ubuntu-{os_version}'
os.makedirs(dst_dir, exist_ok=True)
# fakeroot environment file
frenv = tempfile.NamedTemporaryFile(prefix='frenv-', suffix='.db')
subprocess.check_call([
'/usr/bin/fakeroot',
'-s', frenv.name,
'--',
'/bin/chown',
'-hRP',
'0:0',
pkg_root
], env={'FAKEROOTDONTTRYCHOWN':'1'})
subprocess.check_call([
'/usr/bin/fakeroot',
'-i', frenv.name,
'--',
'/usr/bin/dpkg-deb',
'--build',
pkg_root,
dst_dir
])
def copy_app(pkg_root, pkg_name):
"""Copy application to correct place in package hierarchy"""
import shutil
src = f'{app_name}.app'
dst_dir = f'{pkg_root}/{INST_DIR}'
dst = f'{pkg_root}/{INST_DIR}/{pkg_name}'
os.makedirs(dst_dir)
shutil.copytree(src, dst, symlinks=True)
# cleanup -- remove __pycache__ directories
cache_dirs = subprocess.check_output([
'/usr/bin/find',
dst,
'-name', '__pycache__'
]).strip().decode().split('\n')
for d in cache_dirs:
shutil.rmtree(d)
# cleanup -- remove python shell scripts
for fn in os.listdir(f'{dst}/bin'):
filename = f'{dst}/bin/{fn}'
if not os.path.isfile(filename):
continue
with open(filename, 'rb') as f:
header = f.read(64)
if header[0:2] != b'#!':
continue
program = header[2:].lstrip()
if program.startswith(b'/bin/') or \
program.startswith(b'/usr/bin/'):
continue
os.remove(filename)
def make_bin(pkg_root, pkg_name, bin_name):
"""Make symbolic link to executable"""
bin_dir = f'{pkg_root}/usr/bin'
os.makedirs(bin_dir, exist_ok=True)
os.symlink(f'../../{INST_DIR}/{pkg_name}/bin/{app_name}', f'{bin_dir}/{bin_name}')
def make_control_file(debian_dir, pkg_name, version, dependencies):
"""Make control file"""
# see "man 1 deb-control"
if dependencies is not None:
deps = list(dependencies)
else:
deps = []
deps.insert(0, 'ffmpeg')
depends = ', '.join(deps)
with open(f"{debian_dir}/control", 'w') as f:
print(textwrap.dedent(f"""\
Package: {pkg_name}
Version: {version}
Architecture: amd64
Depends: {depends}
Maintainer: Chimera Staff <chimera-staff@cgl.ucsf.edu>
Description: molecular visualization
UCSF ChimeraX (or simply ChimeraX) is the next-generation
molecular visualization program from the Resource for Biocomputing
Visualization, and Informatics (RBVI), following UCSF Chimera.
ChimeraX can be downloaded free of charge for academic, government
nonprofit, and personal use. Commercial users, please see licensing.
Homepage: https://www.rbvi.ucsf.edu/chimerax/
Bugs: mailto:chimerax-bugs@cgl.ucsf.edu
Section: contrib/science
Priority: optional
Suggests: opencl-icd
Tag: science::visualisation, science::modelling, field::biology, field::chemistry,
field::biology:structural, field::biology:bioinformatics,
biology::nucleic-acids, biology::peptidic,
use::viewing, use::analysing,
scope::application, x11::application, role::program,
interface::3d, interface::graphical, interface::commandline,
implemented-in::c++, implemented-in::python, uitoolkit::qt,
network::client
"""), file=f)
def make_postinst(debian_dir, pkg_name, bin_name):
# see "man 1 deb-postinst"
with open(f"{debian_dir}/postinst", 'w') as f:
print(textwrap.dedent(f"""\
#!/bin/sh
set -e
case "$1" in
configure)
echo "Install desktop menu and associated mime types"
{bin_name} --exit --nogui --silent --cmd 'linux xdg-install system true'
echo "Precompiling Python packages"
({bin_name} -m compileall /{INST_DIR}/{pkg_name} || exit 0)
;;
esac
"""), file=f)
os.fchmod(f.fileno(), 0o755)
def make_prerm(debian_dir, pkg_name, bin_name):
# see "man 1 deb-prerm"
with open(f"{debian_dir}/prerm", 'w') as f:
print(textwrap.dedent(f"""\
#!/bin/sh
set -e
echo "Deregister desktop menu and associated mime types"
{bin_name} --exit --nogui --silent --cmd 'linux xdg-uninstall system true'
echo "Remove Python cache files"
find /{INST_DIR}/{pkg_name} -name __pycache__ -print0 | xargs -0 /bin/rm -rf
"""), file=f)
os.fchmod(f.fileno(), 0o755)
def make_copyright_file(doc_dir):
"""Copy the copyright file"""
# copyright file
with open("copyright.txt") as f:
our_copyright = f.read()
with open(f"{doc_dir}/copyright", 'w') as f:
print(textwrap.dedent("""\
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: ChimeraX
Upstream-Contact: chimerax@rbvi.ucsf.edu
Source: https://www.rbvi.ucsf.edu/chimerax/
Disclaimer: Package is maintained by the ChimeraX team
Copyrights for embedded code are given in the documentation
in INSTALLDIR/share/docs/embeded.html
Comment:
The computer code and documentation that comprises UCSF ChimeraX is protected
by copyrights held by The Regents of the University of California ("The Regents")
and is licensed for non-commercial use at no cost by The Regents.
COMMERCIAL USE OF UCSF CHIMERAX IS COVERED BY A SEPARATE WRITTEN LICENSE AGREEMENT.
Commercial licensing costs are tier-based, depending on the number of users.
Please email chimerax@cgl.ucsf.edu
if you are interested in using ChimeraX for commercial purposes.
License: free for non-commercial use
"""), file=f)
for line in our_copyright.split('\n'):
if line.startswith("=== UCSF ChimeraX"):
continue
print(' ', line, file=f)
def gzip(filename):
"""Gzip without saving timestamp (nor name) so it is reproducible"""
subprocess.check_call(['gzip', '-n9', filename])
def make_changelog_file(doc_dir):
"""Copy the change log file"""
filename = f"{doc_dir}/changelog"
with open(filename, 'wt') as f:
print("See https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog", file=f)
gzip(filename)
def make_man_file(src_file, pkg_root, bin_name):
base, ext = os.path.splitext(src_file)
if not ext or not os.path.exists(src_file):
return
section = ext[1:]
man_dir = f'{pkg_root}/usr/share/man/man{section}'
man_file = f'{man_dir}/{bin_name}.{section}'
os.makedirs(man_dir, exist_ok=True)
with open(src_file, 'rb') as f:
src = f.read()
with open(man_file, 'wb') as f:
f.write(src)
gzip(man_file)
if __name__ == '__main__':
main()