7:16 a.m.
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
Bug ID: 1790882
Summary: Review Request: python-pyscf - Python module for
quantum chemistry
Product: Fedora
Version: rawhide
Hardware: All
OS: Linux
Status: NEW
Component: Package Review
Severity: medium
Priority: medium
Assignee: nobody(a)fedoraproject.org
Reporter: susi.lehtola(a)iki.fi
QA Contact: extras-qa(a)fedoraproject.org
CC: package-review(a)lists.fedoraproject.org
Target Milestone: ---
Classification: Fedora
Spec URL: https://jussilehtola.fedorapeople.org/python-pyscf.spec
SRPM URL:
https://jussilehtola.fedorapeople.org/python-pyscf-1.7.0-1.fc31.src.rpm
Fedora Account System Username: jussilehtola
Description:
Python‐based simulations of chemistry framework (PySCF) is a
general‐purpose electronic structure platform designed from the ground
up to emphasize code simplicity, so as to facilitate new method
development and enable flexible computational workflows. The package
provides a wide range of tools to support simulations of finite‐size
systems, extended systems with periodic boundary conditions,
low‐dimensional periodic systems, and custom Hamiltonians, using
mean‐field and post‐mean‐field methods with standard Gaussian basis
functions. To ensure ease of extensibility, PySCF uses the Python
language to implement almost all of its features, while
computationally critical paths are implemented with heavily optimized
C routines. Using this combined Python/C implementation, the package
is as efficient as the best existing C or Fortran‐based quantum
chemistry programs.
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7:17 a.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
Susi Lehtola <susi.lehtola(a)iki.fi> changed:
What |Removed |Added
----------------------------------------------------------------------------
Depends On| |1790838
Alias| |python-pyscf
Doc Type|--- |If docs needed, set a value
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1790838
[Bug 1790838] Re-Review Request: libcint - General Gaussian-type orbitals
integrals for quantum chemistry
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3:28 p.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
Robert-André Mauchin <zebob.m(a)gmail.com> changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |zebob.m(a)gmail.com
--- Comment #1 from Robert-André Mauchin <zebob.m(a)gmail.com> ---
- Please remove shebangs in prep for all *.py files:
python3-pyscf.x86_64: E: non-executable-script
/usr/lib64/python3.8/site-packages/pyscf/ao2mo/__init__.py 644 /usr/bin/env
python
python3-pyscf.x86_64: E: non-executable-script
/usr/lib64/python3.8/site-packages/pyscf/ao2mo/_ao2mo.py 644 /usr/bin/env
python
python3-pyscf.x86_64: E: non-executable-script
/usr/lib64/python3.8/site-packages/pyscf/ao2mo/addons.py 644 /usr/bin/env
python
python3-pyscf.x86_64: E: non-executable-script
/usr/lib64/python3.8/site-packages/pyscf/ao2mo/incore.py 644 /usr/bin/env
python
python3-pyscf.x86_64: E: non-executable-script
/usr/lib64/python3.8/site-packages/pyscf/ao2mo/outcore.py 644 /usr/bin/env
python
python3-pyscf.x86_64: E: non-executable-script
/usr/lib64/python3.8/site-packages/pyscf/ao2mo/r_outcore.py 644 /usr/bin/env
python
python3-pyscf.x86_64: E: non-executable-script
/usr/lib64/python3.8/site-packages/pyscf/ao2mo/semi_incore.py 644 /usr/bin/env
python
and so on
- Remove rpath:
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libao2mo.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libcc.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libcgto.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libcvhf.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libdft.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libfci.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libhci.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libicmpspt.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libmbd.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libmcscf.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libnp_helper.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libpbc.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libri.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libsemiempirical.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libshciscf.so ['$ORIGIN',
'$ORIGIN/deps/lib']
python3-pyscf.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.8/site-packages/pyscf/lib/libxc_itrf.so ['$ORIGIN',
'$ORIGIN/deps/lib']
Try setting -DCMAKE_SKIP_BUILD_RPATH=1 for that
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4:24 a.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
--- Comment #2 from Susi Lehtola <susi.lehtola(a)iki.fi> ---
Shebangs and rpaths removed.
https://jussilehtola.fedorapeople.org/python-pyscf.spec
https://jussilehtola.fedorapeople.org/python-pyscf-1.7.0-2.fc31.src.rpm
There's still the issue of internal provides and requires. The provides are
easy to remove, but I've been unsuccessful in trying to remove the internal
requires. The problem is that there are both internal and external requires;
the latter should be included but the former should not.
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10:49 a.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
--- Comment #3 from Robert-André Mauchin <zebob.m(a)gmail.com> ---
- This should work:
# Omit internal libraries from dependency generation. This works
%global __provides_exclude_from ^%{python3_sitearch}/pyscf/lib/.*\\.so$
# .. but this doesn't. We still need to pick up the dependencies for libcint,
libxc, etc; only filter out the internal deps
%global __requires_exclude
^(libao2mo\\.so|libcgto\\.so|libcvhf\\.so|libfci\\.so|libnp_helper\\.so).*$
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2:38 a.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
--- Comment #4 from Susi Lehtola <susi.lehtola(a)iki.fi> ---
Thanks, that did the trick.
https://jussilehtola.fedorapeople.org/python-pyscf.spec
https://jussilehtola.fedorapeople.org/python-pyscf-1.7.0-3.fc31.src.rpm
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9:25 a.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
Robert-André Mauchin <zebob.m(a)gmail.com> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |POST
Assignee|nobody(a)fedoraproject.org |zebob.m(a)gmail.com
Flags| |fedora-review+
--- Comment #5 from Robert-André Mauchin <zebob.m(a)gmail.com> ---
Package is approved.
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10:19 a.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
--- Comment #6 from Susi Lehtola <susi.lehtola(a)iki.fi> ---
Thanks for the review!
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11:31 a.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
--- Comment #7 from Gwyn Ciesla <gwync(a)protonmail.com> ---
(fedscm-admin): The Pagure repository was created at
https://src.fedoraproject.org/rpms/python-pyscf
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1:33 p.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
Fedora Update System <updates(a)fedoraproject.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|POST |MODIFIED
--- Comment #8 from Fedora Update System <updates(a)fedoraproject.org> ---
FEDORA-2020-5d3090636b has been submitted as an update to Fedora 30.
https://bodhi.fedoraproject.org/updates/FEDORA-2020-5d3090636b
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1:33 p.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
--- Comment #9 from Fedora Update System <updates(a)fedoraproject.org> ---
FEDORA-2020-75fcd7c6aa has been submitted as an update to Fedora 31.
https://bodhi.fedoraproject.org/updates/FEDORA-2020-75fcd7c6aa
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1:47 p.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
Fedora Update System <updates(a)fedoraproject.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|MODIFIED |ON_QA
--- Comment #10 from Fedora Update System <updates(a)fedoraproject.org> ---
libcint-3.0.19-4.fc30, python-pyscf-1.7.0-4.fc30 has been pushed to the Fedora
30 testing repository. If problems still persist, please make note of it in
this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here:
https://bodhi.fedoraproject.org/updates/FEDORA-2020-5d3090636b
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2:18 a.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
--- Comment #11 from Fedora Update System <updates(a)fedoraproject.org> ---
libcint-3.0.19-4.fc31, python-pyscf-1.7.0-4.fc31 has been pushed to the Fedora
31 testing repository. If problems still persist, please make note of it in
this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here:
https://bodhi.fedoraproject.org/updates/FEDORA-2020-75fcd7c6aa
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7:19 p.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
Bug 1790882 depends on bug 1790838, which changed state.
Bug 1790838 Summary: Re-Review Request: libcint - General Gaussian-type orbitals integrals
for quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790838
What |Removed |Added
----------------------------------------------------------------------------
Status|ON_QA |CLOSED
Resolution|--- |ERRATA
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7:19 p.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
Fedora Update System <updates(a)fedoraproject.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|ON_QA |CLOSED
Resolution|--- |ERRATA
Last Closed| |2020-02-01 01:19:58
--- Comment #12 from Fedora Update System <updates(a)fedoraproject.org> ---
libcint-3.0.19-4.fc30, python-pyscf-1.7.0-4.fc30 has been pushed to the Fedora
30 stable repository. If problems still persist, please make note of it in this
bug report.
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7:34 p.m.
New subject: [Bug 1790882] Review Request: python-pyscf - Python module for
quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1790882
--- Comment #13 from Fedora Update System <updates(a)fedoraproject.org> ---
libcint-3.0.19-4.fc31, python-pyscf-1.7.0-4.fc31 has been pushed to the Fedora
31 stable repository. If problems still persist, please make note of it in this
bug report.
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