[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873

gil cattaneo  changed:

   What|Removed |Added

 Blocks|652183 (FE-JAVASIG) |




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=652183
[Bug 652183] Java SIG tracker bug
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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873
Bug 1318873 depends on bug 1323010, which changed state.

Bug 1323010 Summary: add maven depmap
https://bugzilla.redhat.com/show_bug.cgi?id=1323010

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA



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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873

Zbigniew Jędrzejewski-Szmek  changed:

   What|Removed |Added

 Status|ASSIGNED|CLOSED
   Fixed In Version||neurord-3.0.0-7.20160426git
   ||d5b0d94.fc25
 Resolution|--- |RAWHIDE
Last Closed||2016-04-27 09:58:37



--- Comment #26 from Zbigniew Jędrzejewski-Szmek  ---
Thank you for the review.

Package built in rawhide.

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #25 from Kevin Fenzi  ---
Package request has been approved:
https://admin.fedoraproject.org/pkgdb/package/rpms/neurord

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873

gil cattaneo  changed:

   What|Removed |Added

  Flags|fedora-review?  |fedora-review+



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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #24 from Zbigniew Jędrzejewski-Szmek  ---
Please see my comment #21, I believe it addresses your concerns. If I'm wrong,
please point me at the place in the guidelines that requires a license header
in every file.

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873

gil cattaneo  changed:

   What|Removed |Added

  Flags|needinfo?(puntogil@libero.i |
   |t)  |



--- Comment #23 from gil cattaneo  ---
(In reply to Zbigniew Jędrzejewski-Szmek from comment #22)
> Any progress here? I'm waiting for your response.

I'm waiting for stating the problem to upstream and add the references of the
"upstream bugs" to fix this issues

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873

Zbigniew Jędrzejewski-Szmek  changed:

   What|Removed |Added

  Flags||needinfo?(puntogil@libero.i
   ||t)



--- Comment #22 from Zbigniew Jędrzejewski-Szmek  ---
Any progress here? I'm waiting for your response.

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #21 from Zbigniew Jędrzejewski-Szmek  ---
I don't think that there's a requirement to have a license in every file. At
least the guidelines don't say anything like that. The guidelines say that the
license should be unambiguous, and I think in this case it is: there's a
LICENSE file, the README and metadata files all say that the project is
licensed under GPLv2+. Every java source file has a 'package neurord...' header
that identifies it as part of this project. I don't think there's any ambiguity
here.

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #20 from gil cattaneo  ---
(In reply to Zbigniew Jędrzejewski-Szmek from comment #19)
> The license information is now specified in the README, and in the file that
> contains main(), src/main/java/neurord/StochDiff.java. As before the text of
> the license is specified in LICENSE and the license is specified in pom.xml.

You should (read must) ask upstream to add the headers of the license where
they lack and add the references of that "bug" in the spec file

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #19 from Zbigniew Jędrzejewski-Szmek  ---
The license information is now specified in the README, and in the file that
contains main(), src/main/java/neurord/StochDiff.java. As before the text of
the license is specified in LICENSE and the license is specified in pom.xml.


Spec URL: http://in.waw.pl/~zbyszek/fedora/neurord.spec
SRPM URL:
http://in.waw.pl/~zbyszek/fedora/neurord-3.0.0-6.20160412git97a41ab.fc25.src.rpm

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #18 from gil cattaneo  ---
Issues:

[!]: License field in the package spec file matches the actual license.
 Note: Checking patched sources after %prep for licenses. Licenses
 found: "Unknown or generated". 195 files have unknown license.
 Detailed output of licensecheck in
 /home/gil/1318873-neurord/licensecheck.txt

All source files are without license headers. Please, ask to upstream to
confirm the licensing of code and/or content/s (see file attached)
https://fedoraproject.org/wiki/Packaging:LicensingGuidelines?rd=Packaging/LicensingGuidelines#License_Clarification

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #16 from gil cattaneo  ---
Created attachment 1146265
  --> https://bugzilla.redhat.com/attachment.cgi?id=1146265=edit
licensecheck.txt

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873

gil cattaneo  changed:

   What|Removed |Added

 Status|NEW |ASSIGNED



--- Comment #17 from gil cattaneo  ---
Package Review
==

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



= MUST items =

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.
[!]: License field in the package spec file matches the actual license.
 Note: Checking patched sources after %prep for licenses. Licenses
 found: "Unknown or generated". 195 files have unknown license.
 Detailed output of licensecheck in
 /home/gil/1318873-neurord/licensecheck.txt
[x]: License file installed when any subpackage combination is installed.
[?]: Package contains no bundled libraries without FPC exception.
[?]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[-]: Package contains desktop file if it is a GUI application.
[-]: Development files must be in a -devel package
[-]: Package uses nothing in %doc for runtime.
[?]: 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]: Package is not known to require an ExcludeArch tag.
[-]: Large documentation must go in a -doc subpackage. Large could be size
 (~1MB) or number of files.
 Note: Documentation size is 143360 bytes in 6 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]: All build dependencies are listed in BuildRequires, except for any
 that are listed in the exceptions section of Packaging Guidelines.
[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

Java:
[x]: Bundled jar/class files should be removed before build
[x]: Packages have proper BuildRequires/Requires on jpackage-utils
 Note: Maven packages do not need to (Build)Require jpackage-utils. It
 is pulled in by maven-local
[x]: Javadoc documentation files are generated and included in -javadoc
 subpackage
[x]: Javadoc subpackages should not have Requires: jpackage-utils
[x]: Javadocs are placed in %{_javadocdir}/%{name} (no -%{version} symlink)

Maven:
[x]: If package contains pom.xml files install it (including metadata) even
 when building with ant
[x]: POM files have correct Maven mapping
[x]: Maven packages should use new style packaging
[x]: Old add_to_maven_depmap macro is not being used
[x]: Packages DO NOT have Requires(post) and Requires(postun) on jpackage-
 utils for %update_maven_depmap macro
[x]: Package DOES NOT use %update_maven_depmap in %post/%postun
[x]: Packages use .mfiles file list instead of %{_datadir}/maven2/poms

= 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 

[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #15 from Zbigniew Jędrzejewski-Szmek  ---
No reason except my ignorance :)

Spec URL: http://in.waw.pl/~zbyszek/fedora/neurord.spec
SRPM URL:
http://in.waw.pl/~zbyszek/fedora/neurord-3.0.0-5.20160317gitb17d063.fc25.src.rpm

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #14 from gil cattaneo  ---
why do not use 
%jpackage_script neurord.StochDiff "" ""
jhdf5:jhdfobj:log4j/log4j-core:log4j/log4j-api:jblas:commons-cli:neurord
neurord true
?

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #13 from Zbigniew Jędrzejewski-Szmek  ---
Mistyped the URL, sorry.

Spec URL: http://in.waw.pl/~zbyszek/fedora/neurord.spec
SRPM URL:
http://in.waw.pl/~zbyszek/fedora/neurord-3.0.0-4.20160317gitb17d063.fc25.src.rpm

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #12 from gil cattaneo  ---
ERROR: 'Error 404 downloading
http://in.waw.pl/~zbyszek/fedora/neurord-3.0.0-4.20160317gitb17d063.src.rpm'

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #11 from gil cattaneo  ---
(In reply to Zbigniew Jędrzejewski-Szmek from comment #10)
> Patched jdfh5 has been built in rawhide a few days ago, can you continue the
> review?
> 
> (The update of jhdf5 for F24 could also be pushed to stable, but I'd prefer
> to wait and see if any issues are found during this review.)

sure

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #10 from Zbigniew Jędrzejewski-Szmek  ---
Patched jdfh5 has been built in rawhide a few days ago, can you continue the
review?

(The update of jhdf5 for F24 could also be pushed to stable, but I'd prefer to
wait and see if any issues are found during this review.)

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #9 from Zbigniew Jędrzejewski-Szmek  ---
Updated.

Thanks for the review so far, I think the package is in much better shape now
;)

Spec URL: http://in.waw.pl/~zbyszek/fedora/neurord.spec
SRPM URL:
http://in.waw.pl/~zbyszek/fedora/neurord-3.0.0-4.20160317gitb17d063.src.rpm

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #8 from gil cattaneo  ---
(In reply to Zbigniew Jędrzejewski-Szmek from comment #6)
> All changes implemented as requested.
> 
> Spec URL: http://in.waw.pl/~zbyszek/fedora/neurord.spec
> SRPM URL:
> http://in.waw.pl/~zbyszek/fedora/neurord-3.0.0-3.20160317gitb17d063.src.rpm
> koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=13523998

Please, remove also:
Requires:  java-headless
Requires:  jhdf5
Requires:  jhdfobj
Requires:  log4j
Requires:  jblas
Requires:  apache-commons-cli

and change
Summary:   Javadocs for %{name}
with
Summary:   Javadoc for %{name}

Waiting RHBZ#1323010 is resolved
Thanks

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873

Zbigniew Jędrzejewski-Szmek  changed:

   What|Removed |Added

 Attachment|0   |1
#1142397 is||
   obsolete||



--- Comment #7 from Zbigniew Jędrzejewski-Szmek  ---
Comment on attachment 1142397
  --> https://bugzilla.redhat.com/attachment.cgi?id=1142397
jhdf5 maven depmap

Newer patches are in the other bug.

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #6 from Zbigniew Jędrzejewski-Szmek  ---
All changes implemented as requested.

Spec URL: http://in.waw.pl/~zbyszek/fedora/neurord.spec
SRPM URL:
http://in.waw.pl/~zbyszek/fedora/neurord-3.0.0-3.20160317gitb17d063.src.rpm
koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=13523998

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873

gil cattaneo  changed:

   What|Removed |Added

 Depends On||1323010




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1323010
[Bug 1323010] add maven depmap
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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #5 from gil cattaneo  ---
Created attachment 1142397
  --> https://bugzilla.redhat.com/attachment.cgi?id=1142397=edit
jhdf5 maven depmap

This is a proposed spec file for jhdf5
- generate maven depmap and javadoc
- add javadoc sub package
- minor changes to adapt to current guideline
- fix some rpmlint problems
- introduce license macro

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #4 from gil cattaneo  ---
These plugins/BuildRequires are installed by default and should be removed

BuildRequires: java-devel
BuildRequires: maven-compiler-plugin
BuildRequires: maven-install-plugin
BuildRequires: maven-jar-plugin
BuildRequires: maven-javadoc-plugin
BuildRequires: maven-resources-plugin
BuildRequires: maven-surefire-plugin

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #3 from gil cattaneo  ---
Some problem must be solved before continue/strat with the review:

- disable/remove maven-shade-plugin, is not safe bundle system libraries
- scope system and systemPath are not supported instead open a bug for add
  maven poms or simply depmap for the required artifacts
  e.g.
  @ http://pkgs.fedoraproject.org/cgit/rpms/jhdf5.git/tree/jhdf5.spec#n178

  %mvn_file org.hdfgroup:jhdf5 jhdf5
  %mvn_artifact org.hdfgroup:jhdf5:%{version} lib/jhdf5.jar

  @ http://pkgs.fedoraproject.org/cgit/rpms/jhdf5.git/tree/jhdf5.spec#n194
  %mvn_file org.hdfgroup:jhdfobj jhdfobj
  %mvn_artifact org.hdfgroup:jhdfobj:%{version} lib/jhdfobj.jar

- remove
install -Dm0644 target/%{name}-%{version}.jar
%{buildroot}%{_javadir}/%{name}.jar
install -Dm0755 %{SOURCE1} %{buildroot}%{_bindir}/%{name}
install -Dm0644 pom.xml %{buildroot}%{_mavenpomdir}/%{name}.pom
 and use

 %files -f .mfiles
 %{_bindir}/%{name}
 %license LICENSE
 %doc README.rst README.html stim-params{,2}.{svg,png}

 %files javadoc -f .mfiles-javadoc
 %license LICENSE

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873

gil cattaneo  changed:

   What|Removed |Added

 Blocks||652183 (FE-JAVASIG)




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=652183
[Bug 652183] Java SIG tracker bug
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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873

gil cattaneo  changed:

   What|Removed |Added

 CC||punto...@libero.it
   Assignee|nob...@fedoraproject.org|punto...@libero.it
  Flags||fedora-review?



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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873



--- Comment #2 from Zbigniew Jędrzejewski-Szmek  ---
Spec URL: http://in.waw.pl/~zbyszek/fedora/neurord.spec
SRPM URL:
http://in.waw.pl/~zbyszek/fedora/neurord-3.0.0-2.20160317gitb17d063.src.rpm
koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=13382801

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[Bug 1318873] Review Request: neurord - Stochastic reaction-diffusion simulator

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1318873

Zbigniew Jędrzejewski-Szmek  changed:

   What|Removed |Added

 Blocks||1276941 (fedora-neuro)



--- Comment #1 from Zbigniew Jędrzejewski-Szmek  ---
http://koji.fedoraproject.org/koji/taskinfo?taskID=13379782


Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1276941
[Bug 1276941] Fedora NeuroImaging and NeuroScience tracking bug
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