[Bug 1452644] New: Review Request: python-mmtf - A decoding library for the macromolecular transmission format (MMTF)
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
Bug ID: 1452644 Summary: Review Request: python-mmtf - A decoding library for the macromolecular transmission format (MMTF) Product: Fedora Version: rawhide Component: Package Review Severity: medium Priority: medium Assignee: nobody@fedoraproject.org Reporter: dominik@greysector.net QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org
Spec URL: https://rathann.fedorapeople.org/review/python-mmtf/python-mmtf.spec SRPM URL: https://rathann.fedorapeople.org/review/python-mmtf/python-mmtf-1.0.5-1.fc27... Description: The Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis.
Bradley AR, Rose AS, Pavelka A, Valasatava Y, Duarte JM, Prlić A, Rose PW (2017) MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures. bioRxiv 122689. doi: 10.1101/122689
Valasatava Y, Bradley AR, Rose AS, Duarte JM, Prlić A, Rose PW (2017) Towards an efficient compression of 3D coordinates of macromolecular structures. PLOS ONE 12(3): e0174846. doi: 10.1371/journal.pone.01748464
Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prlić A, Rose PW (2016) Web-based molecular graphics for large complexes. In Proceedings of the 21st International Conference on Web3D Technology (Web3D '16). ACM, New York, NY, USA, 185-186. doi: 10.1145/2945292.2945324
Fedora Account System Username: rathann
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
Dominik 'Rathann' Mierzejewski dominik@greysector.net changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1441007
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1441007 [Bug 1441007] python-MDAnalysis-0.16.0 is available
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
--- Comment #1 from Dominik 'Rathann' Mierzejewski dominik@greysector.net --- Spec URL: https://rathann.fedorapeople.org/review/python-mmtf/python-mmtf.spec SRPM URL: https://rathann.fedorapeople.org/review/python-mmtf/python-mmtf-1.0.6-1.fc27...
* Sat Jun 03 2017 Dominik Mierzejewski dominik@greysector.net 1.0.6-1 - update to 1.0.6 - drop workarounds for issues fixed upstream
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
Björn "besser82" Esser besser82@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED CC| |besser82@fedoraproject.org Assignee|nobody@fedoraproject.org |besser82@fedoraproject.org Flags| |fedora-review?
--- Comment #2 from Björn "besser82" Esser besser82@fedoraproject.org --- Taken.
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
--- Comment #3 from Björn "besser82" Esser besser82@fedoraproject.org --- Some comments from a look on the spec file:
%if 0%{?rhel} && 0%{?rhel} <= 6 %{!?__python2: %global __python2 /usr/bin/python2} %{!?python2_sitelib: %global python2_sitelib %(%{__python2} -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")} %{!?python2_sitearch: %global python2_sitearch %(%{__python2} -c "from distutils.sysconfig import get_python_lib; print(get_python_lib(1))")} %endif
---> Isn't needed anymore; rhel 5+ has been updated to ship all Python2 related macros.
%check nosetests nosetests-3
---> I recommend to use nosetest-%{python(2|3)_version} here. Same goes for picking up the egg-info in %files.
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
Björn "besser82" Esser besser82@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |POST Flags|fedora-review? |fedora-review+
--- Comment #4 from Björn "besser82" Esser besser82@fedoraproject.org --- Package Review ==============
Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
===== 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", "*No copyright* Apache (v2.0)". 34 files have unknown license. Detailed output of licensecheck in /home/besser82/vm_shared/fedora/review/1452644-python- mmtf/licensecheck.txt [x]: License file installed when any subpackage combination is installed. [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 [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]: 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 20480 bytes in 4 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
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
===== 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 python2-mmtf , python3-mmtf
---> Those package are fine to be standalone.
[x]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [-]: 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.
---> Package is noarch.
[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]: Spec file according to URL is the same as in SRPM.
Rpmlint ------- Checking: python2-mmtf-1.0.6-1.fc27.noarch.rpm python3-mmtf-1.0.6-1.fc27.noarch.rpm python-mmtf-1.0.6-1.fc27.src.rpm python2-mmtf.noarch: W: spelling-error Summary(en_US) macromolecular -> macro molecular, macro-molecular, molecular python2-mmtf.noarch: W: spelling-error %description -l en_US biomolecular -> bio molecular, bio-molecular, molecularity python2-mmtf.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular python2-mmtf.noarch: W: spelling-error %description -l en_US bioRxiv -> biorhythm python2-mmtf.noarch: W: spelling-error %description -l en_US doi -> dpi, do, oi python3-mmtf.noarch: W: spelling-error Summary(en_US) macromolecular -> macro molecular, macro-molecular, molecular python3-mmtf.noarch: W: spelling-error %description -l en_US biomolecular -> bio molecular, bio-molecular, molecularity python3-mmtf.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular python3-mmtf.noarch: W: spelling-error %description -l en_US bioRxiv -> biorhythm python3-mmtf.noarch: W: spelling-error %description -l en_US doi -> dpi, do, oi python-mmtf.src: W: spelling-error Summary(en_US) macromolecular -> macro molecular, macro-molecular, molecular python-mmtf.src: W: spelling-error %description -l en_US biomolecular -> bio molecular, bio-molecular, molecularity python-mmtf.src: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular python-mmtf.src: W: spelling-error %description -l en_US bioRxiv -> biorhythm python-mmtf.src: W: spelling-error %description -l en_US doi -> dpi, do, oi python-mmtf.src: E: specfile-error Python runtime initialized with LC_CTYPE=C (a locale with default ASCII encoding), which may cause Unicode compatibility problems. Using C.UTF-8, C.utf8, or UTF-8 (if available) as alternative Unicode-compatible locales is recommended. python-mmtf.src: E: specfile-error Python runtime initialized with LC_CTYPE=C (a locale with default ASCII encoding), which may cause Unicode compatibility problems. Using C.UTF-8, C.utf8, or UTF-8 (if available) as alternative Unicode-compatible locales is recommended. 3 packages and 0 specfiles checked; 2 errors, 15 warnings.
Rpmlint (installed packages) ---------------------------- sh: /usr/bin/python: No such file or directory python2-mmtf.noarch: W: spelling-error Summary(en_US) macromolecular -> macro molecular, macro-molecular, molecular python2-mmtf.noarch: W: spelling-error %description -l en_US biomolecular -> bio molecular, bio-molecular, molecularity python2-mmtf.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular python2-mmtf.noarch: W: spelling-error %description -l en_US bioRxiv -> biorhythm python2-mmtf.noarch: W: spelling-error %description -l en_US doi -> dpi, do, oi python3-mmtf.noarch: W: spelling-error Summary(en_US) macromolecular -> macro molecular, macro-molecular, molecular python3-mmtf.noarch: W: spelling-error %description -l en_US biomolecular -> bio molecular, bio-molecular, molecularity python3-mmtf.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular python3-mmtf.noarch: W: spelling-error %description -l en_US bioRxiv -> biorhythm python3-mmtf.noarch: W: spelling-error %description -l en_US doi -> dpi, do, oi 2 packages and 0 specfiles checked; 0 errors, 10 warnings.
Requires -------- python2-mmtf (rpmlib, GLIBC filtered): python(abi) python2-msgpack
python3-mmtf (rpmlib, GLIBC filtered): python(abi) python3-msgpack
Provides -------- python2-mmtf: python-mmtf python2-mmtf python2.7dist(mmtf-python) python2dist(mmtf-python)
python3-mmtf: python3-mmtf python3.6dist(mmtf-python) python3dist(mmtf-python)
Source checksums ---------------- https://files.pythonhosted.org/packages/source/m/mmtf-python/mmtf-python-1.0... : CHECKSUM(SHA256) this package : 4b92567baf09a1c50244f30f3aba2d006e967e82fe679418ae4c5a7d48e9258f CHECKSUM(SHA256) upstream package : 4b92567baf09a1c50244f30f3aba2d006e967e82fe679418ae4c5a7d48e9258f
Generated by fedora-review 0.6.1 (f03e4e7) last change: 2016-05-02 Command line :/usr/bin/fedora-review -m fedora-rawhide-x86_64 -b 1452644 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, DISTTAG, EPEL5, BATCH, EPEL6
===== Solution =====
Package APPROVED! Please consider my previous comments, when importing to SCM.
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
--- Comment #5 from Dominik 'Rathann' Mierzejewski dominik@greysector.net --- Thanks for the quick review, I'll include your suggestions when importing.
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
--- Comment #6 from Gwyn Ciesla limburgher@gmail.com --- Package request has been approved: https://admin.fedoraproject.org/pkgdb/package/rpms/python-mmtf
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
--- Comment #7 from Fedora Update System updates@fedoraproject.org --- python-mmtf-1.0.6-2.fc26 has been submitted as an update to Fedora 26. https://bodhi.fedoraproject.org/updates/FEDORA-2017-7a5219cbc6
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |MODIFIED
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|MODIFIED |ON_QA
--- Comment #8 from Fedora Update System updates@fedoraproject.org --- python-mmtf-1.0.6-2.fc26 has been pushed to the Fedora 26 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-2017-7a5219cbc6
https://bugzilla.redhat.com/show_bug.cgi?id=1452644
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ON_QA |CLOSED Resolution|--- |ERRATA Last Closed| |2017-06-11 12:17:09
--- Comment #9 from Fedora Update System updates@fedoraproject.org --- python-mmtf-1.0.6-2.fc26 has been pushed to the Fedora 26 stable repository. If problems still persist, please make note of it in this bug report.
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