[Bug 1827948] New: Review Request: python-spyking-circus - Fast and scalable spike sorting of large-scale extracellular recordings
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
Bug ID: 1827948 Summary: Review Request: python-spyking-circus - Fast and scalable spike sorting of large-scale extracellular recordings Product: Fedora Version: rawhide Hardware: All OS: Linux Status: NEW Component: Package Review Severity: medium Priority: medium Assignee: nobody@fedoraproject.org Reporter: sanjay.ankur@gmail.com QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org Target Milestone: --- Classification: Fedora
Spec URL: https://ankursinha.fedorapeople.org/python-spyking-circus/python-spyking-cir... SRPM URL: https://ankursinha.fedorapeople.org/python-spyking-circus/python-spyking-cir...
Description: SpyKING CIRCUS is a python code to allow fast spike sorting on multi channel recordings. A publication on the algorithm can be found at https://elifesciences.org/articles/34518.
It has been tested on datasets coming from in vitro retina with 252 electrodes MEA, from in vivo hippocampus with tetrodes, in vivo and in vitro cortex data with 30 and up to 4225 channels, with good results. Synthetic tests on these data show that cells firing at more than 0.5Hz can be detected, and their spikes recovered with error rates at around 1%, even resolving overlapping spikes and synchronous firing. It seems to be compatible with optogenetic stimulation, based on experimental data obtained in the retina.
Fedora Account System Username: ankursinha
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1276941 (fedora-neuro) Alias| |python-spyking-circus 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=1827948
david08741@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |david08741@gmail.com
--- Comment #1 from david08741@gmail.com --- I tried to build the package, but that failed to print without ()
Is this using python2?
Also, why are the tests disabled? MPI is available ...
COPR build: https://copr.fedorainfracloud.org/coprs/davidsch/testing/package/python-spyk...
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
greg.hellings@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |greg.hellings@gmail.com Assignee|nobody@fedoraproject.org |greg.hellings@gmail.com Flags| |fedora-review?
--- Comment #2 from greg.hellings@gmail.com --- I'll hop on this review
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
--- Comment #3 from greg.hellings@gmail.com --- tl;dr My test machine is running Fedora 31, and I tested in F32 in a container. I couldn't get the package to install. Two other oddities that need an explanation or quick correction.
If you've got a minute, I could use a quick review on https://bugzilla.redhat.com/show_bug.cgi?id=1827887 as well.
Package Review ==============
Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed
Issues: ======= - Package installs properly. Fails to install with error "nothing provides python3.8dist(mpi4py) needed by python3-spyking-circus-0.9.7-1.fc32.noarch" - There are odd provides being picked up by rpmlint. python- and python38-. The python38- seems like it's targeting EPEL, while the bare python- doesn't seem right. But those must be auto-generated by the macros you use, as there are no explicit "provides" listed - README.rst is listed as %license but appears to be more of a README. This gives two files listed as license files
===== 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", "CeCILL License 2.1", "CeCILL License (v2.1)", "*No copyright* CeCILL License (v2.1)". 198 files have unknown license. Detailed output of licensecheck in /home/ghelling/src/packaging/1827948-python-spyking- circus/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. [x]: Macros in Summary, %description expandable at SRPM build time. Note: Macros in: python3-spyking-circus (description) [-]: 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. [-]: 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. [x]: Package complies to the Packaging Guidelines [x]: Package successfully compiles and builds into binary rpms on at least one supported primary architecture. [!]: Rpmlint is run on all rpms the build produces. Note: There are rpmlint messages (see attachment). [!]: 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]: 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]: Dist tag is present. [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 0 bytes in 0 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: [-]: Uses parallel make %{?_smp_mflags} macro. [-]: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [!]: Final provides and requires are sane (see attachments). [ ]: Fully versioned dependency in subpackages if applicable. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in python3-spyking-circus [x]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [x]: Patches link to upstream bugs/comments/lists or are otherwise justified. [-]: Sources are verified with gpgverify first in %prep if upstream publishes signatures. Note: gpgverify is not used. [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. [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: [!]: Rpmlint is run on all installed packages. Note: Mock build failed See: https://docs.fedoraproject.org/en-US/packaging- guidelines/#_use_rpmlint [x]: Spec file according to URL is the same as in SRPM.
Installation errors ------------------- INFO: mock.py version 2.2 starting (python version = 3.7.6)... Start: init plugins INFO: selinux disabled Finish: init plugins INFO: Signal handler active Start: run Start: chroot init INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin Mock Version: 2.2 INFO: Mock Version: 2.2 Finish: chroot init INFO: installing package(s): /home/ghelling/src/packaging/1827948-python-spyking-circus/results/python-spyking-circus-doc-0.9.7-1.fc33.noarch.rpm /home/ghelling/src/packaging/1827948-python-spyking-circus/results/python3-spyking-circus-0.9.7-1.fc33.noarch.rpm ERROR: Command failed: # /usr/bin/dnf --installroot /var/lib/mock/fedora-rawhide-x86_64/root/ --releasever 33 --setopt=deltarpm=False --allowerasing --disableplugin=local --disableplugin=spacewalk install /home/ghelling/src/packaging/1827948-python-spyking-circus/results/python-spyking-circus-doc-0.9.7-1.fc33.noarch.rpm /home/ghelling/src/packaging/1827948-python-spyking-circus/results/python3-spyking-circus-0.9.7-1.fc33.noarch.rpm
Rpmlint ------- Checking: python3-spyking-circus-0.9.7-1.fc33.noarch.rpm python-spyking-circus-doc-0.9.7-1.fc33.noarch.rpm python-spyking-circus-0.9.7-1.fc33.src.rpm python3-spyking-circus.noarch: W: spelling-error Summary(en_US) extracellular -> extra cellular, extra-cellular, extracurricular python3-spyking-circus.noarch: W: spelling-error %description -l en_US datasets -> data sets, data-sets, databases python3-spyking-circus.noarch: W: spelling-error %description -l en_US vitro -> vitriol python3-spyking-circus.noarch: W: spelling-error %description -l en_US vivo -> viva, vino, vivid python3-spyking-circus.noarch: W: spelling-error %description -l en_US hippocampus -> hippo campus, hippo-campus, hippopotamus python3-spyking-circus.noarch: W: spelling-error %description -l en_US tetrodes -> bestrode, strode python3-spyking-circus.noarch: W: spelling-error %description -l en_US optogenetic -> photogenic python3-spyking-circus.noarch: E: useless-provides python-spyking-circus python3-spyking-circus.noarch: E: useless-provides python38-spyking-circus python3-spyking-circus.noarch: W: no-documentation python3-spyking-circus.noarch: W: no-manual-page-for-binary circus-artefacts python3-spyking-circus.noarch: W: no-manual-page-for-binary circus-folders python3-spyking-circus.noarch: W: no-manual-page-for-binary circus-gui-matlab python3-spyking-circus.noarch: W: no-manual-page-for-binary circus-gui-python python3-spyking-circus.noarch: W: no-manual-page-for-binary circus-multi python3-spyking-circus.noarch: W: no-manual-page-for-binary spyking-circus python3-spyking-circus.noarch: W: no-manual-page-for-binary spyking-circus-launcher python3-spyking-circus.noarch: W: no-manual-page-for-binary spyking-circus-subtask python-spyking-circus.src: W: spelling-error Summary(en_US) extracellular -> extra cellular, extra-cellular, extracurricular python-spyking-circus.src: W: spelling-error %description -l en_US datasets -> data sets, data-sets, databases python-spyking-circus.src: W: spelling-error %description -l en_US vitro -> vitriol python-spyking-circus.src: W: spelling-error %description -l en_US vivo -> viva, vino, vivid python-spyking-circus.src: W: spelling-error %description -l en_US hippocampus -> hippo campus, hippo-campus, hippopotamus python-spyking-circus.src: W: spelling-error %description -l en_US tetrodes -> bestrode, strode python-spyking-circus.src: W: spelling-error %description -l en_US optogenetic -> photogenic 3 packages and 0 specfiles checked; 2 errors, 23 warnings.
Source checksums ---------------- https://files.pythonhosted.org/packages/source/s/spyking-circus/spyking-circ... : CHECKSUM(SHA256) this package : b0bce6f92fd38bf6e00cab2ae8f9d85bbe6b94cca9166bf8ce388a45a52d020d CHECKSUM(SHA256) upstream package : b0bce6f92fd38bf6e00cab2ae8f9d85bbe6b94cca9166bf8ce388a45a52d020d
Requires -------- python3-spyking-circus (rpmlib, GLIBC filtered): /usr/bin/python3 python(abi) python3.8dist(blosc) python3.8dist(colorama) python3.8dist(cython) python3.8dist(h5py) python3.8dist(matplotlib) python3.8dist(mpi4py) python3.8dist(numpy) python3.8dist(psutil) python3.8dist(scipy) python3.8dist(setuptools) python3.8dist(statsmodels) python3.8dist(tqdm)
python-spyking-circus-doc (rpmlib, GLIBC filtered): python3-spyking-circus
Provides -------- python3-spyking-circus: python-spyking-circus python3-spyking-circus python3.8dist(spyking-circus) python38-spyking-circus python3dist(spyking-circus)
python-spyking-circus-doc: python-spyking-circus-doc
Generated by fedora-review 0.7.5 (5fa5b7e) last change: 2020-02-16 Command line :/usr/bin/fedora-review -b 1827948 Buildroot used: fedora-rawhide-x86_64 Active plugins: Generic, Shell-api, Python Disabled plugins: fonts, Ocaml, R, PHP, Haskell, C/C++, SugarActivity, Java, Perl Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED
--- Comment #4 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Thanks for the review. I've made the necessary updates:
- Remove mpi4py from setup.py so that it isn't picked up from the automated dep generator. I include the mpi4py bit explicitly for the mpich/openmpi meta packages. - Move Readme.rst to %doc. - I filed a bug for the automated "useless" provides: https://bugzilla.redhat.com/show_bug.cgi?id=1828041
- david08741: MPI packages are available, but since our builders are isolated virtual machines, we can't really test MPI on them. Upstream uses the same code for py2 and py3, but are considering dropping support for py2, so that bug should be fixed soon. https://github.com/spyking-circus/spyking-circus/issues/177
Updated spec/srpm: Spec URL: https://ankursinha.fedorapeople.org/python-spyking-circus/python-spyking-cir... SRPM URL: https://ankursinha.fedorapeople.org/python-spyking-circus/python-spyking-cir...
Greg, I'll review your package now. Thanks very much.
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
--- Comment #5 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Note: Miro replied to the bug to say that the spurious provides are to be ignored on releases before F33. It's noted in the python guidelines now: https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/#_the_pytho...
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
greg.hellings@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags|fedora-review? |fedora-review+
--- Comment #6 from greg.hellings@gmail.com --- Looks good to me!
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
--- Comment #7 from greg.hellings@gmail.com --- For the sake of completeness I'll say: fedora-review still claims it can't install, but testing from a rawhide container the RPM installs just fine.
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |POST
--- Comment #8 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- (In reply to greg.hellings from comment #7)
For the sake of completeness I'll say: fedora-review still claims it can't install, but testing from a rawhide container the RPM installs just fine.
Thank you. I'd tested it out manually too, and it was OK. I'll double check why fedora-review is unhappy before building.
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
--- Comment #9 from Gwyn Ciesla gwync@protonmail.com --- (fedscm-admin): The Pagure repository was created at https://src.fedoraproject.org/rpms/python-spyking-circus
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |MODIFIED
--- Comment #10 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-14db45aad6 has been submitted as an update to Fedora 31. https://bodhi.fedoraproject.org/updates/FEDORA-2020-14db45aad6
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
--- Comment #11 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-f7314234a8 has been submitted as an update to Fedora 32. https://bodhi.fedoraproject.org/updates/FEDORA-2020-f7314234a8
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|MODIFIED |ON_QA
--- Comment #12 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-f7314234a8 has been pushed to the Fedora 32 testing repository. In short time you'll be able to install the update with the following command: `sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2020-f7314234a8 *` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-f7314234a8
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=1827948
--- Comment #13 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-14db45aad6 has been pushed to the Fedora 31 testing repository. In short time you'll be able to install the update with the following command: `sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2020-14db45aad6 *` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-14db45aad6
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=1827948
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ON_QA |CLOSED Resolution|--- |ERRATA Last Closed| |2020-05-06 03:07:25
--- Comment #14 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-14db45aad6 has been pushed to the Fedora 31 stable repository. If problem still persists, please make note of it in this bug report.
https://bugzilla.redhat.com/show_bug.cgi?id=1827948
--- Comment #15 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-f7314234a8 has been pushed to the Fedora 32 stable repository. If problem still persists, please make note of it in this bug report.
package-review@lists.fedoraproject.org
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