[Bug 1150105] Review Request: python-pynn - Simulator-independent specification of neuronal network models

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https://bugzilla.redhat.com/show_bug.cgi?id=1150105



--- Comment #11 from Jerry James <loganjerry@xxxxxxxxx> ---
Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated


Issues:
=======
- Package must not depend on deprecated() packages.
  Note: python3-nose is deprecated, you must not depend on it.
  See: https://docs.fedoraproject.org/en-US/packaging-
  guidelines/deprecating-packages/

- There are 2 BRs for neuron-devel

- These warnings from the compiler should be looked into, as they may indicate
  code that does not behave as expected:

x86_64/quantal_stp.c:324:21: warning: type of 'nrn_random_pick' does not match
original declaration [-Wlto-type-mismatch]
  324 |             value = nrn_random_pick(_p_rng);
      |                     ^
x86_64/gif.c:397:8: note: return value type mismatch
  397 | double nrn_random_pick(void* r);
      |        ^
x86_64/gif.c:397:8: note: type 'double' should match type 'int'
x86_64/gif.c:397:8: note: 'nrn_random_pick' was previously declared here
x86_64/gif.c:397:8: note: code may be misoptimized unless
'-fno-strict-aliasing' is used
x86_64/quantal_stp.c:298:19: warning: type of 'nrn_random_arg' does not match
original declaration [-Wlto-type-mismatch]
  298 |             *pv = nrn_random_arg(1);
      |                   ^
x86_64/gif.c:398:7: note: return value type mismatch
  398 | void* nrn_random_arg(int argpos);
      |       ^
x86_64/gif.c:398:7: note: 'nrn_random_arg' was previously declared here
x86_64/gif.c:398:7: note: code may be misoptimized unless
'-fno-strict-aliasing' is used

- Likewise, this python warning may indicate an issue:

/builddir/build/BUILD/PyNN-0.9.6/pyNN/recording/__init__.py:262: SyntaxWarning:
"is not" with a literal. Did you mean "!="?
  if variables is not 'all':

- Remove the unnecessary rpath from libnrnmech.so, or prevent it from being
  generated in the first place

- Please review the private-shared-object-provides warnings from rpmlint and
  filter Provides if appropriate.

- Something funny is going on in %{python3_sitearch}/pyNN/neuron/nmodl/x86_64.
  That directory contains libnrnmech.so, but also contains a .libs directory
  with another copy of libnrnmech.so, and an empty directory named x86_64.

- The devel subpackage Requires on the main package should include %{?_isa}:

  Requires:       python3-%{lower_name}%{?_isa}


===== MUST items =====

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[!]: Rpath absent or only used for internal libs.
     Note: See rpmlint output
[x]: Development (unversioned) .so files in -devel subpackage, if present.
     Note: Unversioned so-files in private %_libdir subdirectory (see
     attachment). Verify they are not in ld path.
[x]: If your application is a C or C++ application you must list a
     BuildRequires against gcc, gcc-c++ or clang.
[x]: Header files in -devel subpackage, if present.
[x]: Package does not contain any libtool archives (.la)

Generic:
[x]: Package is licensed with an open-source compatible license and meets
     other legal requirements as defined in the legal section of Packaging
     Guidelines.
[x]: License field in the package spec file matches the actual license.
[x]: License file installed when any subpackage combination is installed.
[x]: %build honors applicable compiler flags or justifies otherwise.
[x]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[-]: Package contains desktop file if it is a GUI application.
[x]: Development files must be in a -devel package
[x]: Package uses nothing in %doc for runtime.
[x]: Package consistently uses macros (instead of hard-coded directory
     names).
[x]: Package is named according to the Package Naming Guidelines.
[x]: Package does not generate any conflict.
[x]: Package obeys FHS, except libexecdir and /usr/target.
[-]: If the package is a rename of another package, proper Obsoletes and
     Provides are present.
[x]: Requires correct, justified where necessary.
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[x]: Useful -debuginfo package or justification otherwise.
[x]: Package is not known to require an ExcludeArch tag.
[x]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 51200 bytes in 3 files.
[x]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
[x]: Package installs properly.
[x]: Rpmlint is run on all rpms the build produces.
     Note: There are rpmlint messages (see attachment).
[x]: If (and only if) the source package includes the text of the
     license(s) in its own file, then that file, containing the text of the
     license(s) for the package is included in %license.
[x]: Package requires other packages for directories it uses.
[x]: Package must own all directories that it creates.
[x]: Package does not own files or directories owned by other packages.
[x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT
[x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the
     beginning of %install.
[x]: Macros in Summary, %description expandable at SRPM build time.
[x]: Dist tag is present.
[x]: Package does not contain duplicates in %files.
[x]: Permissions on files are set properly.
[x]: Package use %makeinstall only when make install DESTDIR=... doesn't
     work.
[x]: Package is named using only allowed ASCII characters.
[x]: Package does not use a name that already exists.
[x]: Package is not relocatable.
[x]: Sources used to build the package match the upstream source, as
     provided in the spec URL.
[x]: Spec file name must match the spec package %{name}, in the format
     %{name}.spec.
[x]: File names are valid UTF-8.
[x]: Packages must not store files under /srv, /opt or /usr/local

Python:
[x]: Python eggs must not download any dependencies during the build
     process.
[x]: A package which is used by another package via an egg interface should
     provide egg info.
[x]: Package meets the Packaging Guidelines::Python
[x]: Package contains BR: python2-devel or python3-devel
[x]: Packages MUST NOT have dependencies (either build-time or runtime) on
     packages named with the unversioned python- prefix unless no properly
     versioned package exists. Dependencies on Python packages instead MUST
     use names beginning with python2- or python3- as appropriate.
[x]: Python packages must not contain %{pythonX_site(lib|arch)}/* in %files
[x]: Binary eggs must be removed in %prep

===== SHOULD items =====

Generic:
[-]: If the source package does not include license text(s) as a separate
     file from upstream, the packager SHOULD query upstream to include it.
[x]: Final provides and requires are sane (see attachments).
[x]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in python-
     pynn-devel , python3-pynn
[?]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[x]: Patches link to upstream bugs/comments/lists or are otherwise
     justified.
[-]: Sources are verified with gpgverify first in %prep if upstream
     publishes signatures.
     Note: gpgverify is not used.
[-]: Description and summary sections in the package spec file contains
     translations for supported Non-English languages, if available.
[x]: Package should compile and build into binary rpms on all supported
     architectures.
[x]: %check is present and all tests pass.
[x]: Packages should try to preserve timestamps of original installed
     files.
[x]: Reviewer should test that the package builds in mock.
[x]: Buildroot is not present
[x]: Package has no %clean section with rm -rf %{buildroot} (or
     $RPM_BUILD_ROOT)
[x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin.
[x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
[x]: Sources can be downloaded from URI in Source: tag
[x]: SourceX is a working URL.
[x]: Spec use %global instead of %define unless justified.

===== EXTRA items =====

Generic:
[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).
[x]: Large data in /usr/share should live in a noarch subpackage if package
     is arched.
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Checking: python-pynn-devel-0.9.6-1.fc34.x86_64.rpm
          python3-pynn-0.9.6-1.fc34.x86_64.rpm
          python-pynn-doc-0.9.6-1.fc34.noarch.rpm
          python-pynn-debugsource-0.9.6-1.fc34.x86_64.rpm
          python-pynn-0.9.6-1.fc34.src.rpm
python-pynn-devel.x86_64: W: spelling-error %description -l en_US neuromorphic
-> anthropomorphic
python-pynn-devel.x86_64: W: spelling-error %description -l en_US modelling ->
modeling, model ling, model-ling
python-pynn-devel.x86_64: W: no-documentation
python3-pynn.x86_64: W: spelling-error %description -l en_US neuromorphic ->
anthropomorphic
python3-pynn.x86_64: W: spelling-error %description -l en_US modelling ->
modeling, model ling, model-ling
python3-pynn.x86_64: W: private-shared-object-provides
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/.libs/libnrnmech.so
libnrnmech.so()(64bit)
python3-pynn.x86_64: W: private-shared-object-provides
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/libnrnmech.so
libnrnmech.so()(64bit)
python3-pynn.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/.libs/libnrnmech.so
['/usr/lib']
python3-pynn.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/libnrnmech.so
['/usr/lib']
python3-pynn.x86_64: W: hidden-file-or-dir
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/.libs
python3-pynn.x86_64: W: hidden-file-or-dir
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/.libs
python-pynn-doc.noarch: W: description-shorter-than-summary
python-pynn.src: W: spelling-error %description -l en_US neuromorphic ->
anthropomorphic
python-pynn.src: W: spelling-error %description -l en_US modelling -> modeling,
model ling, model-ling
5 packages and 0 specfiles checked; 2 errors, 12 warnings.




Rpmlint (installed packages)
----------------------------
python3-pynn.x86_64: W: spelling-error %description -l en_US neuromorphic ->
anthropomorphic
python3-pynn.x86_64: W: spelling-error %description -l en_US modelling ->
modeling, model ling, model-ling
python3-pynn.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/.libs/libnrnmech.so
['/usr/lib']
python3-pynn.x86_64: E: binary-or-shlib-defines-rpath
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/libnrnmech.so
['/usr/lib']
python3-pynn.x86_64: W: hidden-file-or-dir
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/.libs
python3-pynn.x86_64: W: hidden-file-or-dir
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/.libs
python-pynn-doc.noarch: W: description-shorter-than-summary
python-pynn-devel.x86_64: W: spelling-error %description -l en_US neuromorphic
-> anthropomorphic
python-pynn-devel.x86_64: W: spelling-error %description -l en_US modelling ->
modeling, model ling, model-ling
python-pynn-devel.x86_64: W: no-documentation
4 packages and 0 specfiles checked; 2 errors, 8 warnings.



Unversioned so-files
--------------------
python3-pynn: /usr/lib64/nest/libpynn_extensions.so
python3-pynn: /usr/lib64/nest/pynn_extensions.so
python3-pynn:
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/.libs/libnrnmech.so
python3-pynn:
/usr/lib64/python3.9/site-packages/pyNN/neuron/nmodl/x86_64/libnrnmech.so

Source checksums
----------------
https://files.pythonhosted.org/packages/source/P/PyNN/PyNN-0.9.6.tar.gz :
  CHECKSUM(SHA256) this package     :
d85226800e30bc1692d3f84485c3fa20b921c2ab55f1201d0a3bf23432e16cd2
  CHECKSUM(SHA256) upstream package :
d85226800e30bc1692d3f84485c3fa20b921c2ab55f1201d0a3bf23432e16cd2


Requires
--------
python-pynn-devel (rpmlib, GLIBC filtered):
    python3-pynn

python3-pynn (rpmlib, GLIBC filtered):
    /usr/bin/sh
    libc.so.6()(64bit)
    libconngen.so()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgcc_s.so.1(GCC_3.3.1)(64bit)
    libgsl.so.25()(64bit)
    libgslcblas.so.0()(64bit)
    libltdl.so.7()(64bit)
    libm.so.6()(64bit)
    libncurses.so.6()(64bit)
    libnest.so()(64bit)
    libnestkernel.so()(64bit)
    libnestutil.so()(64bit)
    libneurosim.so.0()(64bit)
    libnrniv.so.0.0.0()(64bit)
    libpy3neurosim.so.0()(64bit)
    librandom.so()(64bit)
    libreadline.so.8()(64bit)
    libsli.so()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libtinfo.so.6()(64bit)
    libtopology.so()(64bit)
    python(abi)
    python3.9dist(lazyarray)
    python3.9dist(neo)
    python3.9dist(numpy)
    python3.9dist(quantities)
    rtld(GNU_HASH)

python-pynn-doc (rpmlib, GLIBC filtered):

python-pynn-debugsource (rpmlib, GLIBC filtered):



Provides
--------
python-pynn-devel:
    python-pynn-devel
    python-pynn-devel(x86-64)

python3-pynn:
    libnrnmech.so()(64bit)
    libpynn_extensions.so()(64bit)
    python-pynn
    python3-pynn
    python3-pynn(x86-64)
    python3.9-pynn
    python3.9dist(pynn)
    python3dist(pynn)

python-pynn-doc:
    python-pynn-doc

python-pynn-debugsource:
    python-pynn-debugsource
    python-pynn-debugsource(x86-64)



Generated by fedora-review 0.7.6 (b083f91) last change: 2020-11-10
Command line :/usr/bin/fedora-review -b 1150105 -m fedora-rawhide-x86_64
Buildroot used: fedora-rawhide-x86_64
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