https://bugzilla.redhat.com/show_bug.cgi?id=2282778
Bug ID: 2282778 Summary: Review Request: python-pybbi - Python bindings to the UCSC source for Big Binary Indexed (bigWig/bigBed) files Product: Fedora Version: rawhide Hardware: All OS: Linux Status: NEW Component: Package Review Severity: medium Priority: medium Assignee: nobody@fedoraproject.org Reporter: gui1ty@penguinpee.nl QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org Target Milestone: --- Classification: Fedora
Spec URL: https://gui1ty.fedorapeople.org/review/python-pybbi.spec SRPM URL: https://gui1ty.fedorapeople.org/review/python-pybbi-0.4.0-1.fc41.src.rpm
Description:
Python interface to Jim Kent's Big Binary Indexed file (BBI) library from the UCSC Genome Browser source tree using Cython.
This provides read-level access to local and remote bigWig and bigBed files but no write capabilitites. The main feature is fast retrieval of range queries into numpy arrays.
Fedora Account System Username: gui1ty
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
Sandro gui1ty@penguinpee.nl changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1276941 | |(fedora-neuro,NeuroFedora), | |2282277 Doc Type|--- |If docs needed, set a value
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1276941 [Bug 1276941] Fedora NeuroImaging and NeuroScience tracking bug https://bugzilla.redhat.com/show_bug.cgi?id=2282277 [Bug 2282277] python-bioframe-0.7.0 is available
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
--- Comment #1 from Fedora Review Service fedora-review-bot@fedoraproject.org --- Copr build: https://copr.fedorainfracloud.org/coprs/build/7478036 (succeeded)
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https://bugzilla.redhat.com/show_bug.cgi?id=2282778
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED Flags| |fedora-review? CC| |sanjay.ankur@gmail.com
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags|fedora-review? |fedora-review+
--- Comment #2 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Looks good XXX APPROVED XXX
Package Review ==============
Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed
Issues: ======= - Dist tag is present.
===== MUST items =====
C/C++: [-]: Package does not contain kernel modules. [-]: 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) [x]: Package contains no static executables. [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: "Unknown or generated", "MIT License", "*No copyright* MIT License", "BSD 4-Clause License". 576 files have unknown license. Detailed output of licensecheck in /home/asinha/dump/fedora- reviews/2282778-python-pybbi/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]: %build honors applicable compiler flags or justifies otherwise. ^ No build, but stuff has already been built correctly in generate_buildrequires
[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 ^ C/header files in Python packages tend to remain in the main 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]: 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). ^
All messages are OK.
[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]: The License field must be a valid SPDX expression. [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]: Package does not contain duplicates in %files. [x]: Permissions on files are set properly. [x]: Package must not depend on deprecated() packages. [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]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 6688 bytes in 2 files. [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). [-]: Fully versioned dependency in subpackages if applicable. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in python3-pybbi [x]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [-]: Sources are verified with gpgverify first in %prep if upstream publishes signatures. Note: gpgverify is not used. [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: [!]: 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). See: (this test has no URL) ^ This is fine, we're using rpmautospec
[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: python3-pybbi-0.4.0-1.fc41.x86_64.rpm python-pybbi-debugsource-0.4.0-1.fc41.x86_64.rpm python-pybbi-0.4.0-1.fc41.src.rpm =================================================================================== rpmlint session starts =================================================================================== rpmlint: 2.5.0 configuration: /usr/lib/python3.12/site-packages/rpmlint/configdefaults.toml /etc/xdg/rpmlint/fedora-legacy-licenses.toml /etc/xdg/rpmlint/fedora-spdx-licenses.toml /etc/xdg/rpmlint/fedora.toml /etc/xdg/rpmlint/scoring.toml /etc/xdg/rpmlint/users-groups.toml /etc/xdg/rpmlint/warn-on-functions.toml rpmlintrc: [PosixPath('/tmp/tmp9z64vknq')] checks: 32, packages: 3
python-pybbi.src: E: spelling-error ('bigWig', 'Summary(en_US) bigWig -> big Wig, bigwig, bigwigs') python-pybbi.src: E: spelling-error ('bigBed', 'Summary(en_US) bigBed -> big Bed, big-bed, bigoted') python-pybbi.src: E: spelling-error ('bigWig', '%description -l en_US bigWig -> big Wig, bigwig, bigwigs') python-pybbi.src: E: spelling-error ('bigBed', '%description -l en_US bigBed -> big Bed, big-bed, bigoted') python-pybbi.src: E: spelling-error ('capabilitites', '%description -l en_US capabilitites -> capabilities, capability, liabilities') python-pybbi.src: E: spelling-error ('numpy', '%description -l en_US numpy -> bumpy, lumpy, dumpy') python3-pybbi.x86_64: E: spelling-error ('bigWig', 'Summary(en_US) bigWig -> big Wig, bigwig, bigwigs') python3-pybbi.x86_64: E: spelling-error ('bigBed', 'Summary(en_US) bigBed -> big Bed, big-bed, bigoted') python3-pybbi.x86_64: E: spelling-error ('bigWig', '%description -l en_US bigWig -> big Wig, bigwig, bigwigs') python3-pybbi.x86_64: E: spelling-error ('bigBed', '%description -l en_US bigBed -> big Bed, big-bed, bigoted') python3-pybbi.x86_64: E: spelling-error ('capabilitites', '%description -l en_US capabilitites -> capabilities, capability, liabilities') python3-pybbi.x86_64: E: spelling-error ('numpy', '%description -l en_US numpy -> bumpy, lumpy, dumpy') python-pybbi.spec: W: no-%build-section python3-pybbi.x86_64: W: devel-file-in-non-devel-package /usr/lib64/python3.13/site-packages/bbi/cbbi.c ============================================ 3 packages and 0 specfiles checked; 12 errors, 2 warnings, 12 filtered, 12 badness; has taken 0.9 s =============================================
Rpmlint (installed packages) ---------------------------- ============================ rpmlint session starts ============================ rpmlint: 2.5.0 configuration: /usr/lib/python3.13/site-packages/rpmlint/configdefaults.toml /etc/xdg/rpmlint/fedora-legacy-licenses.toml /etc/xdg/rpmlint/fedora-spdx-licenses.toml /etc/xdg/rpmlint/fedora.toml /etc/xdg/rpmlint/scoring.toml /etc/xdg/rpmlint/users-groups.toml /etc/xdg/rpmlint/warn-on-functions.toml checks: 32, packages: 2
python3-pybbi.x86_64: E: spelling-error ('bigWig', 'Summary(en_US) bigWig -> big Wig, bigwig, bigwigs') python3-pybbi.x86_64: E: spelling-error ('bigBed', 'Summary(en_US) bigBed -> big Bed, big-bed, bigoted') python3-pybbi.x86_64: E: spelling-error ('bigWig', '%description -l en_US bigWig -> big Wig, bigwig, bigwigs') python3-pybbi.x86_64: E: spelling-error ('bigBed', '%description -l en_US bigBed -> big Bed, big-bed, bigoted') python3-pybbi.x86_64: E: spelling-error ('capabilitites', '%description -l en_US capabilitites -> capabilities, capability, liabilities') python3-pybbi.x86_64: E: spelling-error ('numpy', '%description -l en_US numpy -> bumpy, lumpy, dumpy') python3-pybbi.x86_64: W: devel-file-in-non-devel-package /usr/lib64/python3.13/site-packages/bbi/cbbi.c 2 packages and 0 specfiles checked; 6 errors, 1 warnings, 8 filtered, 6 badness; has taken 0.3 s
Unversioned so-files -------------------- python3-pybbi: /usr/lib64/python3.13/site-packages/bbi/cbbi.cpython-313-x86_64-linux-gnu.so
Source checksums ---------------- https://github.com/nvictus/pybbi/archive/v0.4.0/pybbi-0.4.0.tar.gz : CHECKSUM(SHA256) this package : 369cb96b2bf1534c40ce4d5e8e8b429132e2c1ea429614e71f48d42f534cebdf CHECKSUM(SHA256) upstream package : 369cb96b2bf1534c40ce4d5e8e8b429132e2c1ea429614e71f48d42f534cebdf
Requires -------- python3-pybbi (rpmlib, GLIBC filtered): libc.so.6()(64bit) libcrypto.so.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libssl.so.3()(64bit) libssl.so.3(OPENSSL_3.0.0)(64bit) libz.so.1()(64bit) python(abi) python3.13dist(numpy) rtld(GNU_HASH)
python-pybbi-debugsource (rpmlib, GLIBC filtered):
Provides -------- python3-pybbi: python-pybbi python3-pybbi python3-pybbi(x86-64) python3.13-pybbi python3.13dist(pybbi) python3dist(pybbi)
python-pybbi-debugsource: python-pybbi-debugsource python-pybbi-debugsource(x86-64)
Diff spec file in url and in SRPM --------------------------------- --- /home/asinha/dump/fedora-reviews/2282778-python-pybbi/srpm/python-pybbi.spec 2024-06-18 13:08:28.424325179 +0100 +++ /home/asinha/dump/fedora-reviews/2282778-python-pybbi/srpm-unpacked/python-pybbi.spec 2024-05-22 01:00:00.000000000 +0100 @@ -1,2 +1,12 @@ +## START: Set by rpmautospec +## (rpmautospec version 0.6.3) +## RPMAUTOSPEC: autorelease, autochangelog +%define autorelease(e:s:pb:n) %{?-p:0.}%{lua: + release_number = 1; + base_release_number = tonumber(rpm.expand("%{?-b*}%{!?-b:1}")); + print(release_number + base_release_number - 1); +}%{?-e:.%{-e*}}%{?-s:.%{-s*}}%{!?-n:%{?dist}} +## END: Set by rpmautospec + %global pypi_name pybbi
@@ -74,3 +84,6 @@
%changelog -%autochangelog +## START: Generated by rpmautospec +* Wed May 22 2024 Sandro devel@penguinpee.nl - 0.4.0-1 +- Initial package +## END: Generated by rpmautospec
Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24 Command line :/usr/bin/fedora-review -b 2282778 Buildroot used: fedora-rawhide-x86_64 Active plugins: C/C++, Generic, Shell-api, Python Disabled plugins: Haskell, Perl, SugarActivity, Ocaml, PHP, fonts, R, Java Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
Fedora Admin user for bugzilla script actions fedora-admin-xmlrpc@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |POST
--- Comment #3 from Fedora Admin user for bugzilla script actions fedora-admin-xmlrpc@fedoraproject.org --- The Pagure repository was created at https://src.fedoraproject.org/rpms/python-pybbi
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |MODIFIED
--- Comment #4 from Fedora Update System updates@fedoraproject.org --- FEDORA-2024-a9d380de48 (python-pybbi-0.4.0-2.fc41) has been submitted as an update to Fedora 41. https://bodhi.fedoraproject.org/updates/FEDORA-2024-a9d380de48
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Resolution|--- |ERRATA Status|MODIFIED |CLOSED Last Closed| |2024-06-18 21:14:28
--- Comment #5 from Fedora Update System updates@fedoraproject.org --- FEDORA-2024-a9d380de48 (python-pybbi-0.4.0-2.fc41) has been pushed to the Fedora 41 stable repository. If problem still persists, please make note of it in this bug report.
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
--- Comment #6 from Fedora Update System updates@fedoraproject.org --- FEDORA-2024-5fbd154599 (python-bioframe-0.7.1-5.fc40 and python-pybbi-0.4.0-2.fc40) has been submitted as an update to Fedora 40. https://bodhi.fedoraproject.org/updates/FEDORA-2024-5fbd154599
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
--- Comment #7 from Fedora Update System updates@fedoraproject.org --- FEDORA-2024-331a5826bd (python-bioframe-0.7.1-5.fc39 and python-pybbi-0.4.0-2.fc39) has been submitted as an update to Fedora 39. https://bodhi.fedoraproject.org/updates/FEDORA-2024-331a5826bd
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
--- Comment #8 from Fedora Update System updates@fedoraproject.org --- FEDORA-2024-5fbd154599 has been pushed to the Fedora 40 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-5fbd154599` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-5fbd154599
See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
--- Comment #9 from Fedora Update System updates@fedoraproject.org --- FEDORA-2024-331a5826bd has been pushed to the Fedora 39 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-331a5826bd` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-331a5826bd
See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
--- Comment #10 from Fedora Update System updates@fedoraproject.org --- FEDORA-2024-5fbd154599 (python-bioframe-0.7.1-5.fc40 and python-pybbi-0.4.0-2.fc40) has been pushed to the Fedora 40 stable repository. If problem still persists, please make note of it in this bug report.
https://bugzilla.redhat.com/show_bug.cgi?id=2282778
--- Comment #11 from Fedora Update System updates@fedoraproject.org --- FEDORA-2024-331a5826bd (python-bioframe-0.7.1-5.fc39 and python-pybbi-0.4.0-2.fc39) has been pushed to the Fedora 39 stable repository. If problem still persists, please make note of it in this bug report.
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