[Bug 1672047] Review Request: smoldyn - A particle-based spatial stochastic simulator

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https://bugzilla.redhat.com/show_bug.cgi?id=1672047

Ankur Sinha (FranciscoD) <sanjay.ankur@xxxxxxxxx> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |POST
       Docs Contact|                            |neuro-sig@lists.fedoraproje
                   |                            |ct.org
           Doc Type|If docs needed, set a value |Enhancement
              Flags|fedora-review?              |fedora-review+


--- Doc Text *updated* ---
Feature: 
Smoldyn is now available in NeuroFedora!


--- Comment #10 from Ankur Sinha (FranciscoD) <sanjay.ankur@xxxxxxxxx> ---
Looks good XXX APPROVED XXX

Non blockers:

- I'd think the SFMT bundling needs to be indicated in the spec, please check:
  https://docs.fedoraproject.org/en-US/packaging-guidelines/#bundling
- The package is not providing the -devel subpackage, but that's up to you :)
- Please use the srpm version of the spec, it seems to be newer.

Please remember to update the neurofedora docs when this is in testing etc. :)
Thanks very much!


Package Review
==============

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


Issues:
=======
- Header files in -devel subpackage, if present.
  Note: smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/NextSubVolume/Constants.h
  smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/NextSubVolume/Geometry.h
  smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/NextSubVolume/Kairos.h
  smoldyn-debugsource :
 
/usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/NextSubVolume/NextSubvolumeMethod.h
  smoldyn-debugsource :
 
/usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/NextSubVolume/ReactionEquation.h
  smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/NextSubVolume/Species.h
  smoldyn-debugsource :
 
/usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/NextSubVolume/StructuredGrid.h
  smoldyn-debugsource :
 
/usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/NextSubVolume/StructuredGrid.impl.h
  smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/NextSubVolume/Vector.h
  smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/NextSubVolume/nsvc.h
  smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/Smoldyn/smoldyn.h
  smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/Smoldyn/smoldynfuncs.h
  smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/Geometry.h smoldyn-
  debugsource : /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/List.h
  smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/Rn.h smoldyn-
  debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/RnSort.h smoldyn-
  debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/SFMT/SFMT.h smoldyn-
  debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/SimCommand.h
  smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/Sphere.h smoldyn-
  debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/SurfaceParam.h
  smoldyn-debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/Zn.h smoldyn-
  debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/math2.h smoldyn-
  debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/opengl2.h smoldyn-
  debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/parse.h smoldyn-
  debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/queue.h smoldyn-
  debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/random2.h smoldyn-
  debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/rxnparam.h smoldyn-
  debugsource :
  /usr/src/debug/smoldyn-2.58-1.fc30.x86_64/source/lib/string2.h
  See: http://fedoraproject.org/wiki/Packaging/Guidelines#DevelPackages

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

C/C++:
[x]: Package does not contain kernel modules.
[ ]: Package contains no static executables.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.

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.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "GNU Lesser General Public License (v3 or later)", "Public
     domain", "Unknown or generated", "BSD 3-clause "New" or "Revised"
     License". 2029 files have unknown license. Detailed output of
     licensecheck in /home/asinha/dump/fedora-
     reviews/1672047-smoldyn/licensecheck.txt
[x]: License file installed when any subpackage combination is installed.
[x]: If the package is under multiple licenses, the licensing breakdown
     must be documented in the spec.
[x]: Package does not own files or directories owned by other packages.
[x]: %build honors applicable compiler flags or justifies otherwise.
[?]: Package contains no bundled libraries without FPC exception.
^ It's bundling SFMT, no? That should be specified in the spec as per:
https://docs.fedoraproject.org/en-US/packaging-guidelines/#bundling

[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 10240 bytes in 1 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 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

===== 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).
[?]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in smoldyn-
     doc , smoldyn-debuginfo , smoldyn-debugsource
^ False positive. The doc does not need to require the arch specific package,
does it?

[?]: Package functions as described.
^ Checked? :)

[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[-]: Patches link to upstream bugs/comments/lists or are otherwise
     justified.
[-]: 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.
[-]: %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:
[!]: Spec file according to URL is the same as in SRPM.
     Note: Spec file as given by url is not the same as in SRPM (see
     attached diff).
^ Getting this again. Can you please check the the spec and srpm refer to the
same bits?

[x]: Rpmlint is run on debuginfo package(s).
     Note: No rpmlint messages.
[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.


Rpmlint
-------
Checking: smoldyn-2.58-1.fc30.x86_64.rpm
          smoldyn-doc-2.58-1.fc30.noarch.rpm
          smoldyn-debuginfo-2.58-1.fc30.x86_64.rpm
          smoldyn-debugsource-2.58-1.fc30.x86_64.rpm
          smoldyn-2.58-1.fc30.src.rpm
smoldyn.x86_64: W: spelling-error %description -l en_US stochasticity ->
stochastic, chastity
smoldyn.x86_64: W: spelling-error %description -l en_US nanometer -> manometer,
anemometer, anteroom
smoldyn.x86_64: W: no-manual-page-for-binary smoldyn
smoldyn-doc.noarch: W: summary-not-capitalized C smoldyn PDF documentation
smoldyn.src: W: spelling-error %description -l en_US stochasticity ->
stochastic, chastity
smoldyn.src: W: spelling-error %description -l en_US nanometer -> manometer,
anemometer, anteroom
5 packages and 0 specfiles checked; 0 errors, 6 warnings.




Rpmlint (debuginfo)
-------------------
Checking: smoldyn-debuginfo-2.58-1.fc30.x86_64.rpm
1 packages and 0 specfiles checked; 0 errors, 0 warnings.





Rpmlint (installed packages)
----------------------------
smoldyn.x86_64: W: spelling-error %description -l en_US stochasticity ->
stochastic
smoldyn.x86_64: W: spelling-error %description -l en_US nanometer -> manometer,
anemometer, anteroom
smoldyn.x86_64: W: invalid-url URL: http://www.smoldyn.org <urlopen error
[Errno -2] Name or service not known>
smoldyn.x86_64: W: no-manual-page-for-binary smoldyn
smoldyn-debugsource.x86_64: W: invalid-url URL: http://www.smoldyn.org <urlopen
error [Errno -2] Name or service not known>
smoldyn-doc.noarch: W: summary-not-capitalized C smoldyn PDF documentation
smoldyn-doc.noarch: W: invalid-url URL: http://www.smoldyn.org <urlopen error
[Errno -2] Name or service not known>
smoldyn-debuginfo.x86_64: W: invalid-url URL: http://www.smoldyn.org <urlopen
error [Errno -2] Name or service not known>
4 packages and 0 specfiles checked; 0 errors, 8 warnings.



Diff spec file in url and in SRPM
---------------------------------
--- /home/asinha/dump/fedora-reviews/1672047-smoldyn/srpm/smoldyn.spec 
2019-04-02 13:57:01.629617769 +0100
+++ /home/asinha/dump/fedora-reviews/1672047-smoldyn/srpm-unpacked/smoldyn.spec
2019-03-29 21:06:47.000000000 +0000
@@ -6,5 +6,4 @@

 # VTK support?
-# See https://github.com/ssandrews/Smoldyn-official/issues/3
 %global with_vtk 0


^^ Ah, it's in the srpm, but not in the spec file. Please ensure that you use
the srpm version.

Requires
--------
smoldyn (rpmlib, GLIBC filtered):
    bionetgen-perl
    libGL.so.1()(64bit)
    libGLU.so.1()(64bit)
    libc.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libglut.so.3()(64bit)
    libm.so.6()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.8)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    libtiff.so.5()(64bit)
    libtiff.so.5(LIBTIFF_4.0)(64bit)
    rtld(GNU_HASH)

smoldyn-debugsource (rpmlib, GLIBC filtered):

smoldyn-doc (rpmlib, GLIBC filtered):
    smoldyn

smoldyn-debuginfo (rpmlib, GLIBC filtered):



Provides
--------
smoldyn:
    smoldyn
    smoldyn(x86-64)

smoldyn-debugsource:
    smoldyn-debugsource
    smoldyn-debugsource(x86-64)

smoldyn-doc:
    smoldyn-doc

smoldyn-debuginfo:
    debuginfo(build-id)
    smoldyn-debuginfo
    smoldyn-debuginfo(x86-64)



Source checksums
----------------
http://www.smoldyn.org/smoldyn-2.58.tgz :
  CHECKSUM(SHA256) this package     :
e6b080290079ff53411d06bf32ee7a5f36215d3c9dacc94e3dcb0f31a2b9ed51
  CHECKSUM(SHA256) upstream package :
e6b080290079ff53411d06bf32ee7a5f36215d3c9dacc94e3dcb0f31a2b9ed51


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1672047
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