The package rpms/moose.git has added or updated architecture specific content in its
spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s):
https://src.fedoraproject.org/cgit/rpms/moose.git/commit/?id=3690f664ddcd....
Change:
+%ifarch armv7hl
Thanks.
Full change:
============
commit 1f1b72f9407c8f80c2a9327d8b73ed8ece99c2a3
Author: Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur(a)gmail.com>
Date: Mon Aug 31 17:47:24 2020 +0100
undefine cmake macro for f<33
diff --git a/moose.spec b/moose.spec
index 2995c25..c89a433 100644
--- a/moose.spec
+++ b/moose.spec
@@ -1,10 +1,14 @@
+# for F < 33
+# If it isn't defined, undefine doesn't do anything, so no conditional required
+%undefine __cmake_in_source_build
+
#global commit 0e12e41b52deb8ea746bc760cddd6e100ca5cfd8
#global shortcommit %%(c=%{commit}; echo ${c:0:7})
Name: moose
Version: 3.1.5
%global codename chamcham
-Release: 3%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
+Release: 4%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
Summary: Multiscale Neuroscience and Systems Biology Simulator
License: GPLv3
URL:
http://moose.ncbs.res.in/
@@ -144,6 +148,9 @@ PYTHONPATH=%{buildroot}%{python3_sitearch} %{__python3} -c \
%doc README.md
%changelog
+* Mon Aug 31 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.1.5-4
+- Undefine cmake macro for F < 33
+
* Sat Aug 29 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.1.5-3
- Update patch
commit 6de1186f34c0eb1c506c71dce45e6d814b6d57e5
Author: Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur(a)gmail.com>
Date: Mon Aug 31 17:26:59 2020 +0100
Add new upstream patch
diff --git a/665c532745987fb1c7a8fc2a9a57bffa330480b4.patch
b/665c532745987fb1c7a8fc2a9a57bffa330480b4.patch
new file mode 100644
index 0000000..660b90f
--- /dev/null
+++ b/665c532745987fb1c7a8fc2a9a57bffa330480b4.patch
@@ -0,0 +1,36 @@
+From 665c532745987fb1c7a8fc2a9a57bffa330480b4 Mon Sep 17 00:00:00 2001
+From: Dilawar <dilawars(a)ncbs.res.in>
+Date: Sat, 29 Aug 2020 06:44:37 +0000
+Subject: [PATCH] A better fix to #419
+
+dict `locals_` is not Py_XINCREF anywhere that is why Py_XDECREF caused segfault.
+While `globals_` does not have this issue. In the previous fix
https://github.com/BhallaLab/moose-core/pull/420/commits/c570f7c057f9c0ca...,
+I removed the `Py_XINCREF(globals_)` line as well which would cause memory leak.
+---
+ pymoose/PyRun.cpp | 5 +----
+ 1 file changed, 1 insertion(+), 4 deletions(-)
+
+diff --git a/pymoose/PyRun.cpp b/pymoose/PyRun.cpp
+index 765226c453..d7d6a7974a 100644
+--- a/pymoose/PyRun.cpp
++++ b/pymoose/PyRun.cpp
+@@ -188,6 +188,7 @@ PyRun::PyRun():mode_(0), initstr_(""),
runstr_(""),
+ cerr << "Could not initialize locals dict" << endl;
+ return;
+ }
++
+ PyObject * value = PyFloat_FromDouble(0.0);
+ if (!value && PyErr_Occurred()){
+ PyErr_Print();
+@@ -200,11 +201,7 @@ PyRun::PyRun():mode_(0), initstr_(""),
runstr_(""),
+
+ PyRun::~PyRun()
+ {
+-#if 0
+- // Fixes to BhallaLab/moose-core#420
+ Py_XDECREF(globals_);
+- Py_XDECREF(locals_);
+-#endif
+ }
+
+ void PyRun::setRunString(string statement)
diff --git a/moose.spec b/moose.spec
index 346eed0..2995c25 100644
--- a/moose.spec
+++ b/moose.spec
@@ -4,7 +4,7 @@
Name: moose
Version: 3.1.5
%global codename chamcham
-Release: 2%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
+Release: 3%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
Summary: Multiscale Neuroscience and Systems Biology Simulator
License: GPLv3
URL:
http://moose.ncbs.res.in/
@@ -17,8 +17,9 @@ Source0:
https://github.com/BhallaLab/moose-core/archive/v%{version}.tar.
# Fix segfault on py3.9
#
https://github.com/BhallaLab/moose-core/pull/420
Patch0: c570f7c057f9c0ca7360c82a8932bcb0df222da9.patch
+Patch1: 665c532745987fb1c7a8fc2a9a57bffa330480b4.patch
# ppc defines a different suffix which breaks the build
-Patch1: 0001-Use-.so-suffix-for-all-arches.patch
+Patch2: 0001-Use-.so-suffix-for-all-arches.patch
ExcludeArch: s390x
@@ -143,6 +144,9 @@ PYTHONPATH=%{buildroot}%{python3_sitearch} %{__python3} -c \
%doc README.md
%changelog
+* Sat Aug 29 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.1.5-3
+- Update patch
+
* Thu Aug 27 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.1.5-2
- Add patch to fix ppc build
- Disable lto on arm
commit 3690f664ddcd851b95f788db8a06c426e8352a2a
Author: Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur(a)gmail.com>
Date: Thu Aug 27 11:16:43 2020 +0100
Fix builds on arm and ppc
diff --git a/0001-Use-.so-suffix-for-all-arches.patch
b/0001-Use-.so-suffix-for-all-arches.patch
new file mode 100644
index 0000000..ebaa985
--- /dev/null
+++ b/0001-Use-.so-suffix-for-all-arches.patch
@@ -0,0 +1,33 @@
+From bf5527190a3309176282a49f2fc302bfa551866a Mon Sep 17 00:00:00 2001
+From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur(a)gmail.com>
+Date: Thu, 27 Aug 2020 10:43:54 +0100
+Subject: [PATCH] Use .so suffix for all arches
+
+---
+ python/setup.cmake.py | 9 ---------
+ 1 file changed, 9 deletions(-)
+
+diff --git a/python/setup.cmake.py b/python/setup.cmake.py
+index 17665e2cf..39637491c 100644
+--- a/python/setup.cmake.py
++++ b/python/setup.cmake.py
+@@ -30,16 +30,7 @@ with open(os.path.join(script_dir, 'VERSION'), 'r') as
f:
+ version = f.read()
+ print('Got %s from VERSION file' % version)
+
+-# importlib is available only for python3. Since we build wheels, prefer .so
+-# extension. This way a wheel built by any python3.x will work with any python3.
+ suffix = '.so'
+-try:
+- import importlib.machinery
+- suffix = importlib.machinery.EXTENSION_SUFFIXES[-1]
+-except Exception as e:
+- print('[WARN] Failed to determine importlib suffix')
+- suffix = '.so'
+-assert (suffix)
+ print('[INFO] Suffix for python SO: %s' % suffix)
+
+ setup(
+--
+2.26.2
+
diff --git a/moose.spec b/moose.spec
index d3fb92a..346eed0 100644
--- a/moose.spec
+++ b/moose.spec
@@ -4,7 +4,7 @@
Name: moose
Version: 3.1.5
%global codename chamcham
-Release: 1%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
+Release: 2%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
Summary: Multiscale Neuroscience and Systems Biology Simulator
License: GPLv3
URL:
http://moose.ncbs.res.in/
@@ -17,6 +17,8 @@ Source0:
https://github.com/BhallaLab/moose-core/archive/v%{version}.tar.
# Fix segfault on py3.9
#
https://github.com/BhallaLab/moose-core/pull/420
Patch0: c570f7c057f9c0ca7360c82a8932bcb0df222da9.patch
+# ppc defines a different suffix which breaks the build
+Patch1: 0001-Use-.so-suffix-for-all-arches.patch
ExcludeArch: s390x
@@ -76,6 +78,12 @@ sed -i 's/-O3//' CMakeLists.txt
%global py_setup setup.cmake.py
%build
+# On armv7 we get a failure with LTO.
+# Disable LTO for armv7
+%ifarch armv7hl
+%define _lto_cflags %{nil}
+%endif
+
cmake_opts=(
-DBUILD_SHARED_LIBS:BOOL=OFF
-DCMAKE_SKIP_RPATH:BOOL=ON
@@ -135,6 +143,10 @@ PYTHONPATH=%{buildroot}%{python3_sitearch} %{__python3} -c \
%doc README.md
%changelog
+* Thu Aug 27 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.1.5-2
+- Add patch to fix ppc build
+- Disable lto on arm
+
* Wed Aug 26 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.1.5-1
- Update to 3.1.5
- Use new cmake macros
commit 197248d69dcd2c60f4027536dc18b25820062eeb
Author: Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur(a)gmail.com>
Date: Thu Aug 27 09:57:56 2020 +0100
Update to 3.1.5
Also fixes bug with python 3.9
diff --git a/.gitignore b/.gitignore
index e8c81dd..68ab750 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@
/moose-0e12e41.tar.gz
/moose-3.1.3.tar.gz
/moose-core-3.1.4.tar.gz
+/moose-core-3.1.5.tar.gz
diff --git a/0001-Avoid-open-coded-strdup-that-cause-compilation-failu.patch
b/0001-Avoid-open-coded-strdup-that-cause-compilation-failu.patch
deleted file mode 100644
index 0315707..0000000
--- a/0001-Avoid-open-coded-strdup-that-cause-compilation-failu.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-From d30711511cc8ee21c49700c6593a8a18e3164126 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Zbigniew=20J=C4=99drzejewski-Szmek?= <zbyszek(a)in.waw.pl>
-Date: Tue, 14 Aug 2018 14:58:00 +0200
-Subject: [PATCH] Avoid open-coded strdup that cause compilation failure with
- new gcc
-
-/builddir/build/BUILD/moose-3.1.3/moose-core/pymoose/moosemodule.cpp:2724:32: error:
invalid conversion from 'const char*' to 'char*' [-fpermissive]
- strncpy(vec[currIndex].name,
----
- moose-core/pymoose/moosemodule.cpp | 13 ++++---------
- 1 file changed, 4 insertions(+), 9 deletions(-)
-
-diff --git a/moose-core/pymoose/moosemodule.cpp b/moose-core/pymoose/moosemodule.cpp
-index 62a9ea2eb8..7d002abe8e 100644
---- a/pymoose/moosemodule.cpp
-+++ b/pymoose/moosemodule.cpp
-@@ -2720,17 +2720,12 @@ int defineDestFinfos(const Cinfo * cinfo)
- PyGetSetDef destFieldGetSet;
- vec.push_back(destFieldGetSet);
-
-- vec[currIndex].name = (char*)calloc(name.size() + 1, sizeof(char));
-- strncpy(vec[currIndex].name,
-- const_cast<char*>(name.c_str()),
-- name.size());
--
-+ vec[currIndex].name = strdup(name.c_str());
- vec[currIndex].doc = (char*) "Destination field";
- vec[currIndex].get = (getter)moose_ObjId_get_destField_attr;
-- PyObject * args = PyTuple_New(1);
-- if (args == NULL)
-- {
-- cerr << "moosemodule.cpp: defineDestFinfos: Failed to allocate
tuple" << endl;
-+ PyObject *args = PyTuple_New(1);
-+ if (!args || !vec[currIndex].name) {
-+ cerr << "moosemodule.cpp: defineDestFinfos: allocation
failed\n";
- return 0;
- }
- PyTuple_SetItem(args, 0, PyString_FromString(name.c_str()));
diff --git a/0002-Avoid-open-coded-strdup-that-causes-a-warning.patch
b/0002-Avoid-open-coded-strdup-that-causes-a-warning.patch
deleted file mode 100644
index 007292b..0000000
--- a/0002-Avoid-open-coded-strdup-that-causes-a-warning.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-From 7bff444a2b06a4a2ef5eb05f9206d0672f73053a Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Zbigniew=20J=C4=99drzejewski-Szmek?= <zbyszek(a)in.waw.pl>
-Date: Tue, 14 Aug 2018 15:57:54 +0200
-Subject: [PATCH] Avoid open-coded strdup that causes a warning
-
-/home/zbyszek/python/moose/moose-core/pymoose/mfield.cpp: In function 'int
moose_Field_init(_Field*, PyObject*, PyObject*)':
-/home/zbyszek/python/moose/moose-core/pymoose/mfield.cpp:122:12: warning: 'char*
strncpy(char*, const char*, size_t)' output truncated before terminating nul copying
as many bytes from a string as its length [-Wstringop-truncation]
- strncpy(name, fieldName, size);
- ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
-/home/zbyszek/python/moose/moose-core/pymoose/mfield.cpp:120:25: note: length computed
here
- size_t size = strlen(fieldName);
- ~~~~~~^~~~~~~~~~~
-
-Add error handling while at it.
----
- moose-core/pymoose/mfield.cpp | 11 ++++++-----
- 1 file changed, 6 insertions(+), 5 deletions(-)
-
-diff --git a/moose-core/pymoose/mfield.cpp b/moose-core/pymoose/mfield.cpp
-index dd452890f2..e16837c741 100644
---- a/pymoose/mfield.cpp
-+++ b/pymoose/mfield.cpp
-@@ -116,11 +116,12 @@ int moose_Field_init(_Field * self, PyObject * args, PyObject *
kwargs)
- }
- self->owner = ((_ObjId*)owner);
- Py_INCREF(self->owner);
-- ObjId tmp = ((_ObjId*)owner)->oid_;
-- size_t size = strlen(fieldName);
-- char * name = (char*)calloc(size+1, sizeof(char));
-- strncpy(name, fieldName, size);
-- self->name = name;
-+ self->name = strdup(fieldName);
-+ if (!self->name) {
-+ PyErr_NoMemory();
-+ return -1;
-+ }
-+
- // In earlier version I tried to deallocate the existing
- // self->name if it is not NULL. But it turns out that it
- // causes a SIGABRT. In any case it should not be an issue as
diff --git a/0003-Use-sys.executable-to-execute-test.-It-breaks-on-pyt.patch
b/0003-Use-sys.executable-to-execute-test.-It-breaks-on-pyt.patch
deleted file mode 100644
index 36fd1d6..0000000
--- a/0003-Use-sys.executable-to-execute-test.-It-breaks-on-pyt.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-From 46b7e96a9bd8070b12738dd6a710974c5593e334 Mon Sep 17 00:00:00 2001
-From: Dilawar Singh <dilawars(a)ncbs.res.in>
-Date: Tue, 27 Mar 2018 10:45:48 +0530
-Subject: [PATCH] Use sys.executable to execute test. It breaks on python3.
-
----
- python/moose/moose_test.py | 5 ++++-
- 1 file changed, 4 insertions(+), 1 deletion(-)
-
-diff --git a/python/moose/moose_test.py b/python/moose/moose_test.py
-index e5f908bcfd..d295f53b8d 100644
---- a/python/moose/moose_test.py
-+++ b/python/moose/moose_test.py
-@@ -86,6 +86,9 @@ class Command(object):
- self.process.terminate()
- thread.join()
-
-+ if self.process.stderr is not None:
-+ _logger.warn( '%s' % self.process.stderr.read() )
-+
- return self.process.returncode
-
- def init_test_dir( ):
-@@ -115,7 +118,7 @@ def run_test( index, testfile, timeout, **kwargs):
- """
- global test_status_
- global total_
-- pyExec = os.environ.get( 'PYTHON_EXECUTABLE', '/usr/bin/python' )
-+ pyExec = os.environ.get( 'PYTHON_EXECUTABLE', sys.executable )
- cmd = Command( [ pyExec, testfile ] )
-
- ti = time.time( )
diff --git a/0004-Do-not-try-to-access-position-1-in-string.patch
b/0004-Do-not-try-to-access-position-1-in-string.patch
deleted file mode 100644
index e8d9049..0000000
--- a/0004-Do-not-try-to-access-position-1-in-string.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-From dc8dd21a4786a7e1e25c8a58fd2a6a3e330b6a6d Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Zbigniew=20J=C4=99drzejewski-Szmek?= <zbyszek(a)in.waw.pl>
-Date: Tue, 14 Aug 2018 17:59:09 +0200
-Subject: [PATCH] Do not try to access position -1 in string
-
-This ain't python ;(
----
- utility/strutil.cpp | 10 +++-------
- 1 file changed, 3 insertions(+), 7 deletions(-)
-
-diff --git a/utility/strutil.cpp b/utility/strutil.cpp
-index 643e3baf99..da2819d13f 100644
---- a/utility/strutil.cpp
-+++ b/utility/strutil.cpp
-@@ -72,20 +72,16 @@ std::string fix(const std::string userPath, const string&
delimiters)
- string trimmedPath = trim(userPath, delimiters);
-
- string fixedPath;
-+ char prev = 0;
-
- // In this loop, we check if there are more than one '/' together. If yes,
- // then accept only first one and reject other.
- for(unsigned int i = 0; i < trimmedPath.size(); ++i)
- {
- const char c = trimmedPath[i];
-- if('/' == c)
-- {
-- if('/' != fixedPath[fixedPath.size()-1])
-- fixedPath.push_back(c);
-- }
-- else
-+ if(c != '/' || c != prev)
- fixedPath.push_back(c);
--
-+ prev = c;
- }
- return fixedPath;
- }
diff --git a/137e348313436782f8cf5eccc8e707ebbdc07170.patch
b/137e348313436782f8cf5eccc8e707ebbdc07170.patch
deleted file mode 100644
index fea6e04..0000000
--- a/137e348313436782f8cf5eccc8e707ebbdc07170.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-From 137e348313436782f8cf5eccc8e707ebbdc07170 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Zbigniew=20J=C4=99drzejewski-Szmek?= <zbyszek(a)in.waw.pl>
-Date: Fri, 27 Sep 2019 10:53:23 +0200
-Subject: [PATCH] neuroml: do not use "is" with strings
-
-This works, but only because of an implementation detail: short
-strings are interned as part of module code. But the rules are complicated
-and we should not rely on this.
-
-See
http://guilload.com/python-string-interning/ for a nice writeup.
-
-Python3.8 now warns about this.
----
- python/moose/neuroml/MorphML.py | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/python/moose/neuroml/MorphML.py b/python/moose/neuroml/MorphML.py
-index 57b983cf83..42f774db33 100644
---- a/python/moose/neuroml/MorphML.py
-+++ b/python/moose/neuroml/MorphML.py
-@@ -585,7 +585,7 @@ def set_compartment_param(self, compartment, name, value,
mechanismname):
- compartment.refractoryPeriod = value # compartment is a moose.LIF instance
(intfire)
- elif name == 'g_refrac':
- _logger.info("SORRY, current moose.LIF doesn't support
g_refrac.")
-- elif mechanismname is 'synapse': # synapse being added to the
compartment
-+ elif mechanismname == 'synapse': # synapse being added to the
compartment
- ## these are potential locations, we do not actually make synapses,
- ## unless the user has explicitly asked for it
- if self.createPotentialSynapses:
-@@ -595,7 +595,7 @@ def set_compartment_param(self, compartment, name, value,
mechanismname):
- ## I assume below that compartment name has _segid at its end
- segid = compartment.name.split('_')[-1] # get segment id from
compartment name
- self.segDict[segid][5].append(value)
-- elif mechanismname is 'spikegen': # spikegen being added to the
compartment
-+ elif mechanismname == 'spikegen': # spikegen being added to the
compartment
- ## these are potential locations, we do not actually make the spikegens.
- ## spikegens for different synapses can have different thresholds,
- ## hence include synapse_type in its name
diff --git a/c570f7c057f9c0ca7360c82a8932bcb0df222da9.patch
b/c570f7c057f9c0ca7360c82a8932bcb0df222da9.patch
new file mode 100644
index 0000000..bb5bf38
--- /dev/null
+++ b/c570f7c057f9c0ca7360c82a8932bcb0df222da9.patch
@@ -0,0 +1,25 @@
+From c570f7c057f9c0ca7360c82a8932bcb0df222da9 Mon Sep 17 00:00:00 2001
+From: Dilawar Singh <dilawars(a)ncbs.res.in>
+Date: Wed, 26 Aug 2020 22:14:38 +0000
+Subject: [PATCH] Fixes to BhallaLab/moose-core#419
+
+---
+ pymoose/PyRun.cpp | 3 +++
+ 1 file changed, 3 insertions(+)
+
+diff --git a/pymoose/PyRun.cpp b/pymoose/PyRun.cpp
+index 73d88c0cf8..765226c453 100644
+--- a/pymoose/PyRun.cpp
++++ b/pymoose/PyRun.cpp
+@@ -200,8 +200,11 @@ PyRun::PyRun():mode_(0), initstr_(""),
runstr_(""),
+
+ PyRun::~PyRun()
+ {
++#if 0
++ // Fixes to BhallaLab/moose-core#420
+ Py_XDECREF(globals_);
+ Py_XDECREF(locals_);
++#endif
+ }
+
+ void PyRun::setRunString(string statement)
diff --git a/moose.spec b/moose.spec
index 5fe740f..d3fb92a 100644
--- a/moose.spec
+++ b/moose.spec
@@ -1,11 +1,10 @@
-%global __cmake_in_source_build 1
#global commit 0e12e41b52deb8ea746bc760cddd6e100ca5cfd8
#global shortcommit %%(c=%{commit}; echo ${c:0:7})
Name: moose
-Version: 3.1.4
+Version: 3.1.5
%global codename chamcham
-Release: 15%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
+Release: 1%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
Summary: Multiscale Neuroscience and Systems Biology Simulator
License: GPLv3
URL:
http://moose.ncbs.res.in/
@@ -15,18 +14,14 @@ Source0:
https://github.com/BhallaLab/moose-core/archive/%{commit}.tar.gz
Source0:
https://github.com/BhallaLab/moose-core/archive/v%{version}.tar.gz#/moose...
%endif
-#
https://github.com/BhallaLab/moose-core/pull/282
-Patch0001: 0001-Avoid-open-coded-strdup-that-cause-compilation-failu.patch
-Patch0002: 0002-Avoid-open-coded-strdup-that-causes-a-warning.patch
-Patch0003: 0003-Use-sys.executable-to-execute-test.-It-breaks-on-pyt.patch
-Patch0004: 0004-Do-not-try-to-access-position-1-in-string.patch
-
-#
https://github.com/BhallaLab/moose-core/pull/375
-Patch0005:
https://github.com/BhallaLab/moose-core/pull/375/commits/137e348313436782...
+# Fix segfault on py3.9
+#
https://github.com/BhallaLab/moose-core/pull/420
+Patch0: c570f7c057f9c0ca7360c82a8932bcb0df222da9.patch
ExcludeArch: s390x
BuildRequires: gcc-c++
+BuildRequires: git-core
BuildRequires: make
BuildRequires: cmake
BuildRequires: rsync
@@ -73,7 +68,10 @@ Requires: python3-lxml
This package contains the %{summary}.
%prep
-%autosetup -p1 -n moose-core-%{version}
+%autosetup -n moose-core-%{version} -S git
+
+# Remove O3 flag set in CMakeLists
+sed -i 's/-O3//' CMakeLists.txt
%global py_setup setup.cmake.py
@@ -91,20 +89,19 @@ cmake_opts=(
-DPYTHON_EXECUTABLE=%{__python3}
)
-mkdir -p build
-pushd build
CXXFLAGS="%optflags" \
-%cmake .. "${cmake_opts[@]}"
-%make_build VERBOSE=1
-cd python
+%cmake "${cmake_opts[@]}"
+%cmake_build
+
+pushd %{__cmake_builddir}/python
%py3_build
popd
%install
-install -vD build/moose.bin %{buildroot}%{_bindir}/moose
-install -vDt %{buildroot}%{_libdir}/ build/libmoose.so
+install -vD %{__cmake_builddir}/moose.bin %{buildroot}%{_bindir}/moose
+install -vDt %{buildroot}%{_libdir}/ %{__cmake_builddir}/libmoose.so
-pushd build/python
+pushd %{__cmake_builddir}/python
%py3_install \--install-lib=%{python3_sitearch}
# this is necessary for the dependency generator to work
chmod +x %{buildroot}%{python3_sitearch}/moose/_moose*.so
@@ -113,9 +110,10 @@ popd
%check
checksec --file=%{buildroot}%{_bindir}/moose
-pushd build
+pushd %{__cmake_builddir}
# test_streamer fails randomly when quitting moose every once in a while.
-ctest --output-on-failure -V -E test_streamer
+ctest --output-on-failure -V -E 'test_streamer'
+# ctest --output-on-failure -V -E 'test_streamer|test_pyrun'
popd
PYTHONPATH=%{buildroot}%{python3_sitearch} %{__python3} -c \
@@ -137,6 +135,11 @@ PYTHONPATH=%{buildroot}%{python3_sitearch} %{__python3} -c \
%doc README.md
%changelog
+* Wed Aug 26 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.1.5-1
+- Update to 3.1.5
+- Use new cmake macros
+- Include patch to fix on Py3.9
+
* Sat Aug 01 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 3.1.4-15
- Second attempt - Rebuilt for
https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
diff --git a/sources b/sources
index b3f32b6..d55b231 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-SHA512 (moose-core-3.1.4.tar.gz) =
7b98d8bbc89e3ddf26753cf307b5b5ed32946055452c7cec02d7fef3294bb0d70e94f2e31b9631acb44e31cae9873cbdce190339328993966c3453674caa86d0
+SHA512 (moose-core-3.1.5.tar.gz) =
49036145438a81839b52b4342265faaa9bae187ac5770c5db40d63af7fe8c3abb79eb152527d2474d8636da05476d1ad620f49a23a656798c171e989a50537f2
commit 77c3e6dac1ed09235378120dff3c35f577c32443
Author: Fedora Release Engineering <releng(a)fedoraproject.org>
Date: Sat Aug 1 04:33:59 2020 +0000
- Second attempt - Rebuilt for
https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
Signed-off-by: Fedora Release Engineering <releng(a)fedoraproject.org>
diff --git a/moose.spec b/moose.spec
index 6f9f579..5fe740f 100644
--- a/moose.spec
+++ b/moose.spec
@@ -5,7 +5,7 @@
Name: moose
Version: 3.1.4
%global codename chamcham
-Release: 14%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
+Release: 15%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
Summary: Multiscale Neuroscience and Systems Biology Simulator
License: GPLv3
URL:
http://moose.ncbs.res.in/
@@ -137,6 +137,10 @@ PYTHONPATH=%{buildroot}%{python3_sitearch} %{__python3} -c \
%doc README.md
%changelog
+* Sat Aug 01 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 3.1.4-15
+- Second attempt - Rebuilt for
+
https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
* Tue Jul 28 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 3.1.4-14
- Rebuilt for
https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
commit 1b0092cff1f819bf70824d4b91ac8b27a8bceaa7
Author: Fedora Release Engineering <releng(a)fedoraproject.org>
Date: Tue Jul 28 08:25:11 2020 +0000
- Rebuilt for
https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
Signed-off-by: Fedora Release Engineering <releng(a)fedoraproject.org>
diff --git a/moose.spec b/moose.spec
index 21f6ce2..6f9f579 100644
--- a/moose.spec
+++ b/moose.spec
@@ -5,7 +5,7 @@
Name: moose
Version: 3.1.4
%global codename chamcham
-Release: 13%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
+Release: 14%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
Summary: Multiscale Neuroscience and Systems Biology Simulator
License: GPLv3
URL:
http://moose.ncbs.res.in/
@@ -137,6 +137,9 @@ PYTHONPATH=%{buildroot}%{python3_sitearch} %{__python3} -c \
%doc README.md
%changelog
+* Tue Jul 28 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 3.1.4-14
+- Rebuilt for
https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
* Fri Jul 24 2020 Jeff Law <law(a)redhat.com> - 3.1.4-13
- Use __cmake_in_source_build
commit deebe0f7633abcdb7b468f8399086f858ac9faef
Author: Jeff Law <law(a)redhat.com>
Date: Fri Jul 24 09:43:46 2020 -0600
Use __cmake_in_source_build
diff --git a/moose.spec b/moose.spec
index b8232b9..21f6ce2 100644
--- a/moose.spec
+++ b/moose.spec
@@ -1,10 +1,11 @@
+%global __cmake_in_source_build 1
#global commit 0e12e41b52deb8ea746bc760cddd6e100ca5cfd8
#global shortcommit %%(c=%{commit}; echo ${c:0:7})
Name: moose
Version: 3.1.4
%global codename chamcham
-Release: 12%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
+Release: 13%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
Summary: Multiscale Neuroscience and Systems Biology Simulator
License: GPLv3
URL:
http://moose.ncbs.res.in/
@@ -136,6 +137,9 @@ PYTHONPATH=%{buildroot}%{python3_sitearch} %{__python3} -c \
%doc README.md
%changelog
+* Fri Jul 24 2020 Jeff Law <law(a)redhat.com> - 3.1.4-13
+- Use __cmake_in_source_build
+
* Thu Jun 25 2020 Orion Poplawski <orion(a)cora.nwra.com> - 3.1.4-12
- Rebuild for hdf5 1.10.6
commit 816408cce4fad877276f78eca5e56991f0c3a004
Author: Orion Poplawski <orion(a)nwra.com>
Date: Thu Jun 25 14:24:21 2020 -0600
Rebuild for hdf5 1.10.6
diff --git a/moose.spec b/moose.spec
index 443ec9a..b8232b9 100644
--- a/moose.spec
+++ b/moose.spec
@@ -4,7 +4,7 @@
Name: moose
Version: 3.1.4
%global codename chamcham
-Release: 11%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
+Release: 12%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
Summary: Multiscale Neuroscience and Systems Biology Simulator
License: GPLv3
URL:
http://moose.ncbs.res.in/
@@ -136,6 +136,9 @@ PYTHONPATH=%{buildroot}%{python3_sitearch} %{__python3} -c \
%doc README.md
%changelog
+* Thu Jun 25 2020 Orion Poplawski <orion(a)cora.nwra.com> - 3.1.4-12
+- Rebuild for hdf5 1.10.6
+
* Tue May 26 2020 Miro Hrončok <mhroncok(a)redhat.com> - 3.1.4-11
- Rebuilt for Python 3.9
commit 955524aafca30162ee086666324ed7e6d23d9007
Author: Miro Hrončok <miro(a)hroncok.cz>
Date: Tue May 26 02:53:27 2020 +0200
Rebuilt for Python 3.9
diff --git a/moose.spec b/moose.spec
index 883a2ae..443ec9a 100644
--- a/moose.spec
+++ b/moose.spec
@@ -4,7 +4,7 @@
Name: moose
Version: 3.1.4
%global codename chamcham
-Release: 10%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
+Release: 11%{?dist}%{?prerelease:.%{prerelease}}%{?commit:.git%{shortcommit}}
Summary: Multiscale Neuroscience and Systems Biology Simulator
License: GPLv3
URL:
http://moose.ncbs.res.in/
@@ -136,6 +136,9 @@ PYTHONPATH=%{buildroot}%{python3_sitearch} %{__python3} -c \
%doc README.md
%changelog
+* Tue May 26 2020 Miro Hrončok <mhroncok(a)redhat.com> - 3.1.4-11
+- Rebuilt for Python 3.9
+
* Wed Jan 29 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 3.1.4-10
- Rebuilt for
https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild