[Bug 1731592] New: Review Request: python-netpyne - Develop, simulate and analyse biological neuronal networks in NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
Bug ID: 1731592 Summary: Review Request: python-netpyne - Develop, simulate and analyse biological neuronal networks in NEURON 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-netpyne/python-netpyne.spec SRPM URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne-0.9.2-1.fc...
Description: NetPyNE is a python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator.
For more details, installation instructions, documentation, tutorials, forums, videos and more, please visit: www.netpyne.org
This package is developed and maintained by the Neurosim lab (www.neurosimlab.org).
Fedora Account System Username: ankursinha
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1276941 (fedora-neuro) Alias| |python-netpyne
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=1731592
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Depends On| |1731594 | |(python-matplotlib-scalebar | |)
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1731594 [Bug 1731594] Review Request: python-matplotlib-scalebar - Artist for matplotlib to display a scale bar
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
Elliott Sales de Andrade quantum.analyst@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED CC| |quantum.analyst@gmail.com Assignee|nobody@fedoraproject.org |quantum.analyst@gmail.com Flags| |fedora-review?
--- Comment #1 from Elliott Sales de Andrade quantum.analyst@gmail.com --- License check shows BSD and GPLv3 licenses. Please correct the License field and add a comment with the breakdown.
Tests do not pass even with python3-matplotlib-scalebar installed.
There are some hidden files in the docs (see rpmlint output) that you may wish to remove.
The URL should be https://pypi.org/project/%%7Bpypi_name%7D
Package Review ==============
Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed
Issues: ======= - Header files in -devel subpackage, if present. Note: python-netpyne-doc : /usr/share/doc/python-netpyne- doc/examples/LFPrecording/mod/misc.h python-netpyne-doc : /usr/share/doc/python-netpyne-doc/examples/M1detailed/mod/misc.h python- netpyne-doc : /usr/share/doc/python-netpyne- doc/examples/PTcell/mod/misc.h python-netpyne-doc : /usr/share/doc/python-netpyne-doc/examples/batchCell/misc.h python- netpyne-doc : /usr/share/doc/python-netpyne- doc/examples/rxd_net/mod/misc.h See: https://docs.fedoraproject.org/en-US/packaging- guidelines/#_devel_packages
===== 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", "Expat License", "BSD 2-clause "Simplified" License", "GPL (v3 or later)". 507 files have unknown license. Detailed output of licensecheck in 1731592-python-netpyne/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. [x]: 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. [?]: 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. [x]: 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]: 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]: 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 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]: 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: [x]: Avoid bundling fonts in non-fonts packages. Note: Package contains font files [-]: 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]: Fully versioned dependency in subpackages if applicable. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in python3-netpyne [?]: 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. [?]: Package should compile and build into binary rpms on all supported architectures. [?]: %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: python3-netpyne-0.9.2-1.fc31.noarch.rpm python-netpyne-doc-0.9.2-1.fc31.noarch.rpm python-netpyne-0.9.2-1.fc31.src.rpm python3-netpyne.noarch: W: spelling-error Summary(en_US) analyse -> analyses, analyst, analyze python3-netpyne.noarch: W: spelling-error %description -l en_US www -> WWW, wow python3-netpyne.noarch: W: spelling-error %description -l en_US neurosimlab -> neurosis python-netpyne-doc.noarch: W: spelling-error Summary(en_US) analyse -> analyses, analyst, analyze python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHH.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHHexport.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHybrid.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHybridexport.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exM1.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exM1export.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exSandbox.omt.broken python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exSandboxexport.omt.requires05noise python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.import.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.jnmlnetpyne.omt python-netpyne.src: W: spelling-error Summary(en_US) analyse -> analyses, analyst, analyze python-netpyne.src: W: spelling-error %description -l en_US www -> WWW, wow python-netpyne.src: W: spelling-error %description -l en_US neurosimlab -> neurosis 3 packages and 0 specfiles checked; 0 errors, 17 warnings.
Rpmlint (installed packages) ---------------------------- python3-netpyne.noarch: W: spelling-error Summary(en_US) analyse -> analyses, analyst, analyze python3-netpyne.noarch: W: spelling-error %description -l en_US www -> WWW, wow python3-netpyne.noarch: W: spelling-error %description -l en_US neurosimlab -> neurosis python3-netpyne.noarch: W: invalid-url URL: https://pypi.python.org/pypi/netpyne <urlopen error [Errno -2] Name or service not known> python-netpyne-doc.noarch: W: spelling-error Summary(en_US) analyse -> analyses, analyst, analyze python-netpyne-doc.noarch: W: description-shorter-than-summary python-netpyne-doc.noarch: W: invalid-url URL: https://pypi.python.org/pypi/netpyne <urlopen error [Errno -2] Name or service not known> python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHH.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHHexport.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHybrid.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHybridexport.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exM1.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exM1export.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exSandbox.omt.broken python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exSandboxexport.omt.requires05noise python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.import.omt python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.jnmlnetpyne.omt 2 packages and 0 specfiles checked; 0 errors, 17 warnings.
Source checksums ---------------- https://github.com/Neurosim-lab/netpyne/archive/v0.9.2/netpyne-0.9.2.tar.gz : CHECKSUM(SHA256) this package : 762a2354bdfa9b65488b36db401ca53fe15778159bd1d57f55502a068cf6ba83 CHECKSUM(SHA256) upstream package : 762a2354bdfa9b65488b36db401ca53fe15778159bd1d57f55502a068cf6ba83
Requires -------- python3-netpyne (rpmlib, GLIBC filtered): python(abi) python3.7dist(future) python3.7dist(matplotlib) python3.7dist(matplotlib-scalebar) python3.7dist(numpy) python3.7dist(pandas) python3.7dist(scipy)
python-netpyne-doc (rpmlib, GLIBC filtered):
Provides -------- python3-netpyne: python-netpyne python3-netpyne python3.7dist(netpyne) python3dist(netpyne)
python-netpyne-doc: python-netpyne-doc
Generated by fedora-review 0.7.2 (65d36bb) last change: 2019-04-09 Command line :/usr/bin/fedora-review -b 1731592 -m fedora-rawhide-x86_64 -L scalebar Buildroot used: fedora-rawhide-x86_64 Active plugins: Shell-api, Python, Generic Disabled plugins: C/C++, fonts, Java, Perl, Ocaml, Haskell, PHP, SugarActivity, R Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH
Built with local dependencies: review/scalebar/python3-matplotlib-scalebar-0.6.0-1.fc31.noarch.rpm
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
--- Comment #2 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- (In reply to Elliott Sales de Andrade from comment #1)
License check shows BSD and GPLv3 licenses. Please correct the License field and add a comment with the breakdown.
Corrected.
Tests do not pass even with python3-matplotlib-scalebar installed.
Turns out it also needs pyNeuroML which we haven't packaged yet. I'll go work on that now. https://github.com/Neurosim-lab/netpyne/blob/development/.travis.yml
There are some hidden files in the docs (see rpmlint output) that you may wish to remove.
Removed.
The URL should be https://pypi.org/project/%%7Bpypi_name%7D
Corrected.
Here's the updated spec/srpm in the meantime, but this review is now blocked until I get pyneuroml in:
Spec URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne.spec SRPM URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne-0.9.2-1.fc...
https://bugzilla.redhat.com/show_bug.cgi?id=1731592 Bug 1731592 depends on bug 1731594, which changed state.
Bug 1731594 Summary: Review Request: python-matplotlib-scalebar - Artist for matplotlib to display a scale bar https://bugzilla.redhat.com/show_bug.cgi?id=1731594
What |Removed |Added ---------------------------------------------------------------------------- Status|ON_QA |CLOSED Resolution|--- |ERRATA
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
Elliott Sales de Andrade quantum.analyst@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Whiteboard| |NotReady
--- Comment #3 from Elliott Sales de Andrade quantum.analyst@gmail.com --- I assume you're still waiting.
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
--- Comment #4 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- *** Bug 1886601 has been marked as a duplicate of this bug. ***
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
--- Comment #5 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Hi Elliott,
Sorry for the wait. Here's the updated spec/srpm:
Spec URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne.spec SRPM URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne-0.9.7-1.fc...
pyneuroml is an optional dependency (which depends on lots of java things and so only made it to the NeuroFedora extras COPR repository), so we can proceed here. I've run all the tests with the COPR enabled in mock to ensure that the tests that need pyneuroml also run fine.
Cheers, Ankur
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
--- Comment #6 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- I updated to the latest snapshot that includes a bunch of fixes:
Spec URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne.spec SRPM URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne-0.9.7-2.20...
(It needs the latest neuron build)
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
--- Comment #7 from Elliott Sales de Andrade quantum.analyst@gmail.com --- Why can't pyneuroml be packaged in Fedora?
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
--- Comment #8 from Elliott Sales de Andrade quantum.analyst@gmail.com --- - Replace %{__python3} with %{python3} - netpyne/support/stackedBarGraph.py is GPLv3, and not reflected in License
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
--- Comment #9 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- (In reply to Elliott Sales de Andrade from comment #7)
Why can't pyneuroml be packaged in Fedora?
pyneuroml is a wrapper around jneuroml and *bundles* its prebuilt jar. While I was able to unbundle that, jneuroml itself cannot currently be included in Fedora because building it from source requires one to package lots of java deps, like the whole spring framework. So neither jneuroml, nor packages that depend on it can currently be included in Fedora. They are all in the NeuroFedora copr:
https://docs.fedoraproject.org/en-US/neurofedora/copr/
(In reply to Elliott Sales de Andrade from comment #8)
- Replace %{__python3} with %{python3}
- netpyne/support/stackedBarGraph.py is GPLv3, and not reflected in License
Done.
Updated spec/srpm:
Spec URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne.spec SRPM URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne-0.9.7-2.20...
Changelog:
* Tue Oct 13 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.9.7-2.20201009git548ffc6 - Update license to include GPLv3+ - Add comment to explain why pyneuroml cannot be included in Fedora - use python3 instead of __python3
Cheers,
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
Elliott Sales de Andrade quantum.analyst@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |POST Whiteboard|NotReady | Flags|fedora-review? |fedora-review+
--- Comment #10 from Elliott Sales de Andrade quantum.analyst@gmail.com --- LGTM now; approved.
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
--- Comment #11 from Gwyn Ciesla gwync@protonmail.com --- (fedscm-admin): The Pagure repository was created at https://src.fedoraproject.org/rpms/python-netpyne
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |MODIFIED
--- Comment #12 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-febd6e24ac has been submitted as an update to Fedora 33. https://bodhi.fedoraproject.org/updates/FEDORA-2020-febd6e24ac
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |MODIFIED
--- Comment #12 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-febd6e24ac has been submitted as an update to Fedora 33. https://bodhi.fedoraproject.org/updates/FEDORA-2020-febd6e24ac
--- Comment #13 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-eead172880 has been submitted as an update to Fedora 32. https://bodhi.fedoraproject.org/updates/FEDORA-2020-eead172880
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|MODIFIED |ON_QA
--- Comment #14 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-febd6e24ac has been pushed to the Fedora 33 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-febd6e24ac *` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-febd6e24ac
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=1731592
--- Comment #15 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-eead172880 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-eead172880 *` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-eead172880
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=1731592
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ON_QA |CLOSED Resolution|--- |ERRATA Last Closed| |2020-11-11 01:19:20
--- Comment #16 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-febd6e24ac has been pushed to the Fedora 33 stable repository. If problem still persists, please make note of it in this bug report.
https://bugzilla.redhat.com/show_bug.cgi?id=1731592
--- Comment #17 from Fedora Update System updates@fedoraproject.org --- FEDORA-2020-eead172880 has been pushed to the Fedora 32 stable repository. If problem still persists, please make note of it in this bug report.
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