[med-svn] [Git][med-team/python-parasail][upstream] New upstream version 1.2.3
Nilesh Patra
gitlab at salsa.debian.org
Sun Dec 20 12:30:11 GMT 2020
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
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