Spec URL: http://in.waw.pl/~zbyszek/fedora/python-pysb.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/python-pysb-0.1.11-1.fc22.src.rpm Description: PySB is a framework for building mathematical models of biochemical systems as Python programs. PySB abstracts the complex process of creating equations describing interactions among multiple proteins or other biomolecules into a simple and intuitive domain specific programming language, which is internally translated into BioNetGen or Kappa rules and from there into systems of equations. PySB makes it straightforward to divide models into modules and to call libraries of reusable elements (macros) that encode standard biochemical actions. These features promote model transparency, reuse and accuracy. PySB also interoperates with standard scientific Python libraries such as NumPy, SciPy and SymPy enabling model simulation and analysis. Fedora Account System Username: zbyszek
Copr build: https://copr-fe.cloud.fedoraproject.org/coprs/zbyszek/neurord/build/61119/
As mentioned in the mailing list, I can review all these three packages. We have break coming up (from Thursday) and I can review it that day. I am assigning the bugs to myself. If someone wants to go review the packages before I get to it, please go ahead.
Hi, here is the initial review. There are non-executable-script issues ... Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed Issues: ======= - 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 %doc. Note: Cannot find LICENSE.txt in rpm(s) See: http://fedoraproject.org/wiki/Packaging/LicensingGuidelines#License_Text --->Bogus warning. License file is installed using %license macro. /usr/share/licenses/python-pysb/LICENSE.txt ===== 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. [x]: License field in the package spec file matches the actual license. Note: Checking patched sources after %prep for licenses. Licenses found: "Unknown or generated". 48 files have unknown license. Detailed output of licensecheck in /home/mukundan/ownCloud/pkg_reviews/1167478-python- pysb/licensecheck.txt [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. [-]: Development files must be in a -devel package [-]: 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]: 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 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]: 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]: 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 do not use a name that already exist [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: [ ]: Python eggs must not download any dependencies during the build process. [ ]: 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]: 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]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [x]: 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. ---> https://koji.fedoraproject.org/koji/taskinfo?taskID=8281518 [x]: %check is present and all tests pass. [x]: Packages should try to preserve timestamps of original installed files. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Sources can be downloaded from URI in Source: tag [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]: Dist tag is present (not strictly required in GL). [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [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]: Spec file according to URL is the same as in SRPM. Rpmlint ------- Checking: python-pysb-0.1.11-1.fc22.noarch.rpm python-pysb-0.1.11-1.fc22.src.rpm python-pysb.noarch: E: explicit-lib-dependency python-matplotlib python-pysb.noarch: W: spelling-error %description -l en_US biomolecules -> bio molecules, bio-molecules, molecules python-pysb.noarch: W: spelling-error %description -l en_US interoperates -> inter operates, inter-operates, interpenetrates python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/examples/run_kinase_cascade.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/examples/run_earm_1_0.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/examples/run_bax_pore.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/tools/render_reactions.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/examples/run_bax_pore_sequential.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/tools/render_species.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/tools/export_hoda.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/examples/run_robertson.py 0644L /usr/bin/env python-pysb.noarch: W: no-manual-page-for-binary pysb_export python-pysb.src: W: spelling-error %description -l en_US biomolecules -> bio molecules, bio-molecules, molecules python-pysb.src: W: spelling-error %description -l en_US interoperates -> inter operates, inter-operates, interpenetrates 2 packages and 0 specfiles checked; 9 errors, 5 warnings. Rpmlint (installed packages) ---------------------------- ]0;<mock-chroot><mock-chroot>[root@imladris /]# rpmlint python-pysb python-pysb.noarch: E: explicit-lib-dependency python-matplotlib ---> I think this is fine- I am not sure why rpmlint is complaining ... :( python-pysb.noarch: W: spelling-error %description -l en_US biomolecules -> bio molecules, bio-molecules, molecules python-pysb.noarch: W: spelling-error %description -l en_US interoperates -> inter operates, inter-operates, interpenetrates python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/examples/run_kinase_cascade.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/examples/run_earm_1_0.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/examples/run_bax_pore.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/tools/render_reactions.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/examples/run_bax_pore_sequential.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/tools/render_species.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/tools/export_hoda.py 0644L /usr/bin/env python-pysb.noarch: E: non-executable-script /usr/lib/python2.7/site-packages/pysb/examples/run_robertson.py 0644L /usr/bin/env ---> This could be fixed by either removing the shebang or changing the permisiond - which do you think is more appropriate? python-pysb.noarch: W: no-manual-page-for-binary pysb_export 1 packages and 0 specfiles checked; 9 errors, 3 warnings. ]0;<mock-chroot><mock-chroot>[root@imladris /]# echo 'rpmlint-done:' Requires -------- python-pysb (rpmlib, GLIBC filtered): /usr/bin/python bionetgen numpy python(abi) python-matplotlib python-pygraphviz scipy sympy Provides -------- python-pysb: python-pysb Source checksums ---------------- https://pypi.python.org/packages/source/p/pysb/pysb-0.1.11.tar.gz : CHECKSUM(SHA256) this package : 3af0a2d37d0dde81b2479c03e3d0cb6c4c0b439559c0ae2552e2507c044dc3fd CHECKSUM(SHA256) upstream package : 3af0a2d37d0dde81b2479c03e3d0cb6c4c0b439559c0ae2552e2507c044dc3fd Generated by fedora-review 0.5.2 (63c24cb) last change: 2014-07-14 Command line :/usr/bin/fedora-review -m fedora-rawhide-x86_64 -b 1167478 Buildroot used: fedora-rawhide-x86_64 Active plugins: Python, Generic, Shell-api Disabled plugins: Java, C/C++, fonts, SugarActivity, Ocaml, Perl, Haskell, R, PHP, Ruby Disabled flags: EXARCH, EPEL5, BATCH, DISTTAG
---> This could be fixed by either removing the shebang or changing the permisiond - which do you think is more appropriate? I fixed the permissions and updated the shebangs to refer to %{__python2}. Some of the files in examples/ are supposed to be directly executed, but other not, so it is nice to mark the ones that are with explicit +x, makes them easy to distinguish at first glance. Spec URL: http://in.waw.pl/~zbyszek/fedora/python-pysb.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/python-pysb-0.1.11-2.fc22.src.rpm koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8290694
Spec URL: http://in.waw.pl/~zbyszek/fedora/python-pysb.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/python-pysb-0.1.11-2.fc22.src.rpm koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8290825
Just noticed that I had left the review incomplete here (copy/paste snafu). (In reply to Mukundan Ragavan from comment #3) > Python: > [ ]: Python eggs must not download any dependencies during the build process. > [ ]: 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]: Binary eggs must be removed in %prep This should be 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]: Binary eggs must be removed in %prep With the updated spec and srpm, I have no further issues. Package APPROVED!
Thank you for the review! New Package SCM Request ======================= Package Name: python-pysb Short Description: Rule-based modeling of biochemical systems as Python programs Upstream URL: http://pysb.org/ Owners: zbyszek Branches: f19 f20 f21 epel7 InitialCC:
Git done (by process-git-requests).
python-pysb-0.1.11-2.fc21 has been submitted as an update for Fedora 21. https://admin.fedoraproject.org/updates/python-pysb-0.1.11-2.fc21
python-pysb-0.1.11-2.fc21 has been pushed to the Fedora 21 testing repository.
python-pysb-0.1.11-2.fc21 has been pushed to the Fedora 21 stable repository.