The package rpms/ProDy.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/ProDy.git/commit/?id=3c5c120b251a....
Change:
-ExcludeArch: ppc64 s390x
Thanks.
Full change:
============
commit a466804f7cdb3dc68b852f56b0e69b457b833d15
Author: sagitter <sagitter(a)fedoraproject.org>
Date: Sat Mar 3 14:42:56 2018 +0100
Pre-release 1.9.4
diff --git a/.gitignore b/.gitignore
index c58bec7..de3302b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,4 @@
/ProDy-1.8.2.tar.gz
/ProDy-1.9.3.tar.gz
/ProDy-1.9.tar.gz
+/ProDy-1.9.4.tar.gz
diff --git a/ProDy.spec b/ProDy.spec
index 25d5d5b..82cd2a8 100644
--- a/ProDy.spec
+++ b/ProDy.spec
@@ -29,12 +29,12 @@ ExcludeArch: ppc64 s390x
Name: ProDy
Summary: Application for protein structure, dynamics and sequence analysis
-Version: 1.9.3
-Release: 5.final%{?dist}
+Version: 1.9.4
+Release: 0.1%{?dist}
License: GPLv3+
Group: Applications/Engineering
URL:
http://www.csb.pitt.edu/ProDy
-Source0:
https://github.com/prody/ProDy/archive/v%{version}.tar.gz/%{name}-1.9.tar.gz
+Source0:
https://files.pythonhosted.org/packages/fe/c8/5c8642fd6630f6fe8d3bbca13c3...
BuildRequires: gcc
@@ -124,14 +124,14 @@ visual analysis.
%prep
%setup -qc
-rm -rf %{name}-1.9/kdtree
+rm -rf %{name}-%{version}/kdtree
%if 0%{?rhel}
-cp -a %{name}-1.9 python2
+cp -a %{name}-%{version} python2
%endif
%if 0%{?with_python3}
-mv %{name}-1.9 python3
+mv %{name}-%{version} python3
%endif # with_python3
%build
@@ -260,6 +260,9 @@ popd
%endif
%changelog
+* Sat Mar 03 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.9.4-0.1
+- Pre-release 1.9.4
+
* Wed Feb 28 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.9.3-5.final
- Release 1.9 final (1.9.3 post-release)
diff --git a/sources b/sources
index 6ffa941..eb8d93c 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-SHA512 (ProDy-1.9.tar.gz) =
2d2f674eea685bf1cb81b199502ac92afbf0c560a973de99f72cd5af9ed7ea5a59581adb11c4ba8e97479f592035c7b44dcd45d28da41a56ba11e4c36a3fbec9
+SHA512 (ProDy-1.9.4.tar.gz) =
146d2321f082f480e01c7276550c94224f8a6f6ba1c719442e0251c905783e8bf581e054f8a13fbf975f70641f5769affe71c8f0d3945bd46458bc962e0d5bb6
commit 3c5c120b251a8b9e97a1a3839e04621cee4d53ff
Author: sagitter <sagitter(a)fedoraproject.org>
Date: Thu Mar 1 18:39:06 2018 +0100
Release 1.9 final (1.9.3 post-release)
diff --git a/.gitignore b/.gitignore
index 0c4b06e..c58bec7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@
/ProDy-1.8.tar.gz
/ProDy-1.8.2.tar.gz
/ProDy-1.9.3.tar.gz
+/ProDy-1.9.tar.gz
diff --git a/ProDy.spec b/ProDy.spec
index 58a9e79..25d5d5b 100644
--- a/ProDy.spec
+++ b/ProDy.spec
@@ -1,8 +1,13 @@
+##
https://github.com/prody/ProDy/issues/266
+ExcludeArch: ppc64 s390x
+
%if 0%{?fedora}
%global with_python3 1
%endif
-%global with_check 1
+# Tests need internet connection;
+# correctly executed in local.
+%global with_check 0
%if 0%{?rhel} && 0%{?rhel} <= 6
%{!?__python2: %global __python2 /usr/bin/python2}
@@ -25,14 +30,13 @@
Name: ProDy
Summary: Application for protein structure, dynamics and sequence analysis
Version: 1.9.3
-Release: 4%{?dist}
+Release: 5.final%{?dist}
License: GPLv3+
Group: Applications/Engineering
URL:
http://www.csb.pitt.edu/ProDy
-Source0:
https://github.com/prody/ProDy/archive/v%{version}.tar.gz/%{name}-%{versi...
+Source0:
https://github.com/prody/ProDy/archive/v%{version}.tar.gz/%{name}-1.9.tar.gz
-##
https://github.com/prody/ProDy/issues/266
-ExcludeArch: ppc64 s390x
+BuildRequires: gcc
%description
ProDy is a free and open-source Python package for protein structure, dynamics,
@@ -59,7 +63,7 @@ BuildRequires: python2-devel
BuildRequires: python-nose
BuildRequires: python-argparse
BuildRequires: scipy
-BuildRequires: python-biopython
+BuildRequires: python2-biopython
BuildRequires: numpy
BuildRequires: python-matplotlib
BuildRequires: python-unittest2
@@ -67,7 +71,7 @@ BuildRequires: pyparsing
Requires: python-argparse
Requires: pyparsing
-Requires: python-biopython
+Requires: python2-biopython
Requires: ipython, pyparsing
Requires: scipy
@@ -87,6 +91,8 @@ visual analysis.
%if 0%{?with_python3}
%package -n python3-%{name}
Summary: Application for protein structure, dynamics and sequence analysis
+%{?python_provide:%python_provide python3-%{name}}
+Provides: ProDy-python3 = 0:%{version}-%{release}
BuildRequires: python3-devel
BuildRequires: python3-nose
@@ -104,7 +110,6 @@ Requires: python3-pyparsing
## Explicit library require for using plotting functions
Requires: python3-matplotlib
-%{?python_provide:%python_provide python3-%{name}}
%description -n python3-%{name}
This is ProDy Python3 package for protein structure, dynamics,
@@ -118,18 +123,15 @@ visual analysis.
%prep
%setup -qc
-mv %{name}-%{version} python2
-pushd python2
-## Removing bundled files
-rm prody/atomic/pyparsing*
-rm -rf prody/KDTree
-rm prody/proteins/pairwise2.py prody/proteins/cpairwise2.c
-rm prody/apps/argparse.py
-popd
+rm -rf %{name}-1.9/kdtree
+
+%if 0%{?rhel}
+cp -a %{name}-1.9 python2
+%endif
%if 0%{?with_python3}
-cp -a python2 python3
+mv %{name}-1.9 python3
%endif # with_python3
%build
@@ -214,21 +216,6 @@ popd
##Some tests skipped for missing internet connections on koji
pushd python2/scripts
PYTHONPATH=$RPM_BUILD_ROOT%{python2_sitearch} nosetests --verbosity=2 \
- -e test_select.py \
-%if 0%{?rhel} && 0%{?rhel} < 7
- -e test_frame.py \
- -e test_dcdfile.py \
- -e test_analysis.py \
- -e test_kdtree.py \
- -e test_ensemble.py \
- -e test_prody_anm.py \
- -e test_prody_gnm.py \
- -e test_prody_catdcd.py \
- -e test_prody_pca.py \
- -e test_prody_examples.py \
- -e test_enms.py \
- -e test_editing.py \
-%endif
-w $RPM_BUILD_ROOT%{python2_sitearch}/prody/tests --tests prody -a '!slow'
popd
%endif
@@ -236,16 +223,6 @@ popd
%if 0%{?with_python3}
pushd python3/scripts
PYTHONPATH=$RPM_BUILD_ROOT%{python3_sitearch} nosetests-%{python3_version} --verbosity=2
\
- -e test_atomic.py \
- -e test_pdbfile.py \
- -e test_measure.py \
- -e test_wwpdb.py \
- -e test_localpdb.py \
- -e test_msafile.py \
- -e test_pathtools.py \
- -e test_select.py \
- -e test_dcdfile.py \
- -e test_enms.py \
-w $RPM_BUILD_ROOT%{python3_sitearch}/prody/tests --tests prody -a '!slow'
popd
%endif
@@ -283,6 +260,9 @@ popd
%endif
%changelog
+* Wed Feb 28 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.9.3-5.final
+- Release 1.9 final (1.9.3 post-release)
+
* Mon Feb 19 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.9.3-4
- Fix python3 shebang
diff --git a/sources b/sources
index 9234da4..6ffa941 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-SHA512 (ProDy-1.9.3.tar.gz) =
a1ef78863116c92e4389435b037480da83187ded9bccb62006eabdec3db29fbbcaeb5eeb626faf4ca6ebded8daee3d55f8f1a72db316ddd8fe4ecd40d795a82d
+SHA512 (ProDy-1.9.tar.gz) =
2d2f674eea685bf1cb81b199502ac92afbf0c560a973de99f72cd5af9ed7ea5a59581adb11c4ba8e97479f592035c7b44dcd45d28da41a56ba11e4c36a3fbec9
commit 545d1f35e41cf43e2d9f8389659c1d7134689f57
Author: sagitter <sagitter(a)fedoraproject.org>
Date: Mon Feb 19 18:36:54 2018 +0100
Fix python3 shebang
diff --git a/ProDy.spec b/ProDy.spec
index 85ec1de..58a9e79 100644
--- a/ProDy.spec
+++ b/ProDy.spec
@@ -25,7 +25,7 @@
Name: ProDy
Summary: Application for protein structure, dynamics and sequence analysis
Version: 1.9.3
-Release: 3%{?dist}
+Release: 4%{?dist}
License: GPLv3+
Group: Applications/Engineering
URL:
http://www.csb.pitt.edu/ProDy
@@ -283,6 +283,9 @@ popd
%endif
%changelog
+* Mon Feb 19 2018 Antonio Trande <sagitterATfedoraproject.org> - 1.9.3-4
+- Fix python3 shebang
+
* Wed Feb 07 2018 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.9.3-3
- Rebuilt for
https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
commit 19ccdcb0e2a898b0688e4e14f91c6fc021536364
Author: Iryna Shcherbina <shcherbina.iryna(a)gmail.com>
Date: Mon Feb 19 13:54:08 2018 +0100
Fix shebangs for Python 3 subpackage
Both executables contain #!/usr/bin/env python shebangs, which are
forbidden by the guidelins and are automatically mangled to
#!/usr/bin/python2 during build, which makes python3-ProDy depend
on Python 2.
diff --git a/ProDy.spec b/ProDy.spec
index e991e72..85ec1de 100644
--- a/ProDy.spec
+++ b/ProDy.spec
@@ -159,6 +159,10 @@ mkdir -p $RPM_BUILD_ROOT%{_bindir}
cd scripts
mv ./prody ./python%{python3_version}-prody
mv ./evol ./python%{python3_version}-evol
+# Fix shebangs
+sed -i '1s=^#!/usr/bin/\(python\|env python\)[0-9.]*=#!%{__python3}=' \
+ ./python%{python3_version}-prody \
+ ./python%{python3_version}-evol
for i in prody-3 prody-%{python3_version}; do
touch -r ./python%{python3_version}-prody $i
commit 2d73c2692412eddc461a57f07fa0439778362814
Author: Fedora Release Engineering <releng(a)fedoraproject.org>
Date: Wed Feb 7 00:56:35 2018 +0000
- Rebuilt for
https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
Signed-off-by: Fedora Release Engineering <releng(a)fedoraproject.org>
diff --git a/ProDy.spec b/ProDy.spec
index 3214641..e991e72 100644
--- a/ProDy.spec
+++ b/ProDy.spec
@@ -25,7 +25,7 @@
Name: ProDy
Summary: Application for protein structure, dynamics and sequence analysis
Version: 1.9.3
-Release: 2%{?dist}
+Release: 3%{?dist}
License: GPLv3+
Group: Applications/Engineering
URL:
http://www.csb.pitt.edu/ProDy
@@ -279,6 +279,9 @@ popd
%endif
%changelog
+* Wed Feb 07 2018 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.9.3-3
+- Rebuilt for
https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
+
* Wed Jan 10 2018 Iryna Shcherbina <ishcherb(a)redhat.com> - 1.9.3-2
- Remove useless Python 2 build-time requirements for Fedora
commit 8f8fa09efad42e978359ddf6bcf0206302f833fb
Author: Iryna Shcherbina <shcherbina.iryna(a)gmail.com>
Date: Wed Jan 10 15:21:15 2018 +0100
Remove useless Python 2 build-time requirements
Since python2-ProDy is no longer built for Fedora, only in EPEL,
it should not pull Python 2 packages as BuildRequires as they are not
used.
This removes all extra build-time requirements, and reorganizes
reuiirements for Python 2 subpackage.
diff --git a/ProDy.spec b/ProDy.spec
index a98f69a..3214641 100644
--- a/ProDy.spec
+++ b/ProDy.spec
@@ -25,7 +25,7 @@
Name: ProDy
Summary: Application for protein structure, dynamics and sequence analysis
Version: 1.9.3
-Release: 1%{?dist}
+Release: 2%{?dist}
License: GPLv3+
Group: Applications/Engineering
URL:
http://www.csb.pitt.edu/ProDy
@@ -34,40 +34,6 @@ Source0:
https://github.com/prody/ProDy/archive/v%{version}.tar.gz/%{name}-%{ver
##
https://github.com/prody/ProDy/issues/266
ExcludeArch: ppc64 s390x
-BuildRequires: python2-devel
-BuildRequires: python-nose
-BuildRequires: scipy
-BuildRequires: python-biopython
-BuildRequires: numpy
-BuildRequires: python-matplotlib
-BuildRequires: python-unittest2
-
-Requires: scipy
-Requires: python-biopython
-
-## Explicit library require for using plotting functions
-Requires: python-matplotlib
-
-### Pyparsing is used to define the atom selection grammar
-### Biopython KDTree package and pairwise2 module are used for distance based
-## atom selections and pairwise sequence alignment, respectively.
-#
-### argparse is used to implement applications and provided for
-## compatibility with Python 2.6.
-%if 0%{?rhel}
-BuildRequires: python-argparse
-BuildRequires: python-unittest2
-BuildRequires: pyparsing
-Requires: python-argparse
-Requires: pyparsing
-Requires: python-biopython
-Requires: ipython, pyparsing
-%else
-Requires: python-biopython
-Requires: python-ipython
-Requires: pyparsing
-%endif
-
%description
ProDy is a free and open-source Python package for protein structure, dynamics,
and sequence analysis. It allows for comparative analysis and modeling of
@@ -82,11 +48,6 @@ visual analysis.
Summary: Application for protein structure, dynamics and sequence analysis
%{?python_provide:%python_provide python2-%{name}}
Provides: ProDy = 0:%{version}-%{release}
-Requires: scipy
-Requires: python-biopython
-
-## Explicit library require for using plotting functions
-Requires: python-matplotlib
### Pyparsing is used to define the atom selection grammar
### Biopython KDTree package and pairwise2 module are used for distance based
@@ -94,19 +55,24 @@ Requires: python-matplotlib
#
### argparse is used to implement applications and provided for
## compatibility with Python 2.6.
-%if 0%{?rhel}
+BuildRequires: python2-devel
+BuildRequires: python-nose
BuildRequires: python-argparse
+BuildRequires: scipy
+BuildRequires: python-biopython
+BuildRequires: numpy
+BuildRequires: python-matplotlib
BuildRequires: python-unittest2
BuildRequires: pyparsing
+
Requires: python-argparse
Requires: pyparsing
Requires: python-biopython
Requires: ipython, pyparsing
-%else
-Requires: python-biopython
-Requires: python-ipython
-Requires: pyparsing
-%endif
+Requires: scipy
+
+## Explicit library require for using plotting functions
+Requires: python-matplotlib
%description -n python2-%{name}
This is ProDy Python2 package for protein structure, dynamics,
@@ -313,6 +279,9 @@ popd
%endif
%changelog
+* Wed Jan 10 2018 Iryna Shcherbina <ishcherb(a)redhat.com> - 1.9.3-2
+- Remove useless Python 2 build-time requirements for Fedora
+
* Sat Nov 04 2017 Antonio Trande <sagitterATfedoraproject.org> - 1.9.3-1
- Update to 1.9.3
- Obsolete old patch