Nilesh Patra pushed to branch upstream at Debian Med / python-parasail
Commits: 8959e602 by Nilesh Patra at 2020-12-20T17:57:02+05:30 New upstream version 1.2.3 - - - - - 3 changed files: - CHANGELOG.rst - parasail/__init__.py - setup.py Changes: ===================================== CHANGELOG.rst ===================================== @@ -10,6 +10,11 @@ Unreleased_ ----------- The Unreleased section will be empty for tagged releases. Unreleased functionality appears in the develop branch. +------------------- +1.2.3_ - 2020-12-16 +------------------- +- Fix #57 Install error with parasail v1.2.2 + ------------------- 1.2.2_ - 2020-12-01 ------------------- @@ -153,7 +158,8 @@ The Unreleased section will be empty for tagged releases. Unreleased functionali ------------------- First tagged release. The 'master' branch always represents the latest stable code. Tagged releases correspond to pypi releases. -.. _Unreleased: https://github.com/jeffdaily/parasail-python/compare/v1.2.2...master +.. _Unreleased: https://github.com/jeffdaily/parasail-python/compare/v1.2.3...master +.. _1.2.3: https://github.com/jeffdaily/parasail-python/compare/v1.2.2...v1.2.3 .. _1.2.2: https://github.com/jeffdaily/parasail-python/compare/v1.2.1...v1.2.2 .. _1.2.1: https://github.com/jeffdaily/parasail-python/compare/v1.2...v1.2.1 .. _1.2: https://github.com/jeffdaily/parasail-python/compare/v1.1.20...v1.2 ===================================== parasail/__init__.py ===================================== @@ -6,7 +6,7 @@ import sys import numpy -__version__ = "1.2.2" +__version__ = "1.2.3" __title__ = "parasail" __description__ = "pairwise sequence alignment library" __uri__ = "https://github.com/jeffdaily/parasail-python"; ===================================== setup.py ===================================== @@ -186,8 +186,11 @@ def run_autoreconf(root): all_good = False return all_good -def build_autotools(): - print("Building autotools") +def build_autotools(patch_m4=False): + if patch_m4: + print("Building autotools with patched m4") + else: + print("Building autotools") save_cwd = os.getcwd() top = os.path.join(os.getcwd(), 'autotools') if not os.path.exists(top): @@ -218,7 +221,9 @@ def build_autotools(): break else: # we failed all the attempts - deal with the consequences. - raise RuntimeError("All attempts to download {} have failed".format(tarball)) + print("All attempts to download {} have failed".format(tarball)) + os.chdir(save_cwd) + return False if os.path.exists(tdir): print("{} already exists! Using existing sources.".format(tdir)) else: @@ -228,14 +233,31 @@ def build_autotools(): print("{} already exists! Skipping build.".format(binary)) else: os.chdir(os.path.join(top,tdir)) + CPPFLAGS="" + if tool == 'm4' and patch_m4: + CPPFLAGS="CPPFLAGS=-D_IO_IN_BACKUP=0x100" + for filename in ['lib/freading.c', 'lib/fseeko.c', 'lib/fpurge.c', 'lib/freadahead.c', 'lib/fflush.c']: + with open(filename, "r") as source: + lines = source.readlines() + newlines = [line.replace('_IO_ftrylockfile','_IO_EOF_SEEN') for line in lines] + if lines == newlines: + print("{} skipped".format(filename)) + else: + with open(filename, "w") as source: + for line in newlines: + source.write(line) + print("{} patched".format(filename)) print("configuring {}".format(tool)) + print("running ./configure --prefix={} {}".format(top,CPPFLAGS)) proc = subprocess.Popen([ - './configure', '--prefix={}'.format(top) + './configure', '--prefix={}'.format(top), '{}'.format(CPPFLAGS) ], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) stdout,stderr = proc.communicate() if 0 != proc.returncode: print(stdout) - raise RuntimeError("configure of {} failed".format(tool)) + print("configure of {} failed".format(tool)) + os.chdir(save_cwd) + return False print("making and installing {}".format(tool)) proc = subprocess.Popen([ 'make', '-j', str(cpu_count()), 'install' @@ -243,8 +265,11 @@ def build_autotools(): stdout,stderr = proc.communicate() if 0 != proc.returncode: print(stdout) - raise RuntimeError("make of {} failed".format(tool)) + print("make of {} failed".format(tool)) + os.chdir(save_cwd) + return False os.chdir(save_cwd) + return True # Download, unzip, configure, and make parasail C library from github. # Attempt to skip steps that may have already completed. @@ -302,7 +327,9 @@ def build_parasail(libname): if platform.system() == "Darwin" and 'M4' not in os.environ: os.environ['M4'] = '/usr/bin/m4' print("PATH={}".format(os.environ['PATH'])) - build_autotools() + if not build_autotools(): + if not build_autotools(True): + raise RuntimeError("building autotools failed") if not run_autoreconf(root): raise RuntimeError("autoreconf -fi failed") root = find_file('configure', parasail_root) View it on GitLab: https://salsa.debian.org/med-team/python-parasail/-/commit/8959e6027b292ed90c174f8895387e00468d9563 -- View it on GitLab: https://salsa.debian.org/med-team/python-parasail/-/commit/8959e6027b292ed90c174f8895387e00468d9563 You're receiving this email because of your account on salsa.debian.org.
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