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Bug 2012917 - Review Request: python-probeinterface - Handles probe layout, geometry, and wiring to device
Summary: Review Request: python-probeinterface - Handles probe layout, geometry, and w...
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
Target Milestone: ---
Assignee: Sandro Mani
QA Contact: Fedora Extras Quality Assurance
: 2007997 (view as bug list)
Depends On:
Blocks: fedora-neuro, NeuroFedora
TreeView+ depends on / blocked
Reported: 2021-10-11 15:28 UTC by Ben Beasley
Modified: 2022-01-06 01:11 UTC (History)
4 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Last Closed: 2022-01-06 00:51:14 UTC
Type: ---
manisandro: fedora-review+

Attachments (Terms of Use)

Description Ben Beasley 2021-10-11 15:28:45 UTC
Spec URL:


A Python package to handle the layout, geometry, and wiring of silicon probes
for extracellular electrophysiology experiments.


Make a lightweight package to handle:

  • probe contact geometry (both 2D and 3D layouts)
  • probe shape (contour of the probe, shape of channel contact, …)
  • probe wiring to device (the physical layout often doesn’t match the channel
  • combining several probes into a device with global geometry + global wiring
  • exporting probe geometry data into JSON files
  • loading existing probe geometry files (Neuronexus, imec, Cambridge
    Neurotech…) Started here


  • optional plotting (based on matplotlib)
  • load/save geometry using common formats (PRB, CSV, NWB, …)
  • handle SI length units correctly um/mm/…

Target users/project:

  • spikeinterface team: integrate this into spikeextractor for channel
  • neo team: handle array_annotations for AnalogSignal
  • spikeforest team: use this package for plotting probe activity
  • phy team: integrate for probe display
  • spyking-circus team: handle probe with this package
  • kilosort team: handle probe with this package
  • tridesclous team: handle probe with this package
  • open ephys team: automatically generate channel map configuration files

Fedora Account System Username: music

Koji scratch builds:


This is a dependency for python-spikeinterface (, and @neuro-sig will have commit privileges.

Comment 1 Ben Beasley 2021-10-11 15:29:52 UTC
Already in progress at

Comment 2 Ben Beasley 2021-12-13 13:56:14 UTC
Reopened since the previous review request stalled and was closed blocking FE-DEADREVIEW.

Updated to 0.2.6, with a few minor packaging improvements.

Spec URL:

Koji scratch builds:


Comment 3 Ben Beasley 2021-12-13 13:56:41 UTC
*** Bug 2007997 has been marked as a duplicate of this bug. ***

Comment 4 Sandro Mani 2021-12-24 09:07:31 UTC
All good, only issue again the license. When importing, consider explicitly listing it as %license.


Package Review

[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed

===== MUST items =====

[x]: Package is licensed with an open-source compatible license and meets
     other legal requirements as defined in the legal section of Packaging
[x]: License field in the package spec file matches the actual license.
[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
[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.
[x]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of 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]: 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
[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
[x]: File names are valid UTF-8.
[x]: Packages must not store files under /srv, /opt or /usr/local

[-]: Binary eggs must be removed in %prep
[x]: Python eggs must not download any dependencies during the build
[-]: 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

===== SHOULD items =====

[-]: 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.
[?]: Package functions as described.
[?]: 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.
[-]: 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
[x]: %check is present and all tests pass.
[x]: Packages should try to preserve timestamps of original installed
[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
[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 =====

[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.


Source checksums
---------------- :
  CHECKSUM(SHA256) this package     : 91ed7389130134f0c0c96d96b7cf10c4b6b6f15be6b6145fb47478ecd36d3410
  CHECKSUM(SHA256) upstream package : 91ed7389130134f0c0c96d96b7cf10c4b6b6f15be6b6145fb47478ecd36d3410 :
  CHECKSUM(SHA256) this package     : a76ec1f35485b7717fb01d76530e97bfe41b3d5091675e3b9079cd0a14244283
  CHECKSUM(SHA256) upstream package : a76ec1f35485b7717fb01d76530e97bfe41b3d5091675e3b9079cd0a14244283 :
  CHECKSUM(SHA256) this package     : bfd6842dbf192c76dfb537a2588fda2f2a7ab1dfbd14808258c993dbdc2beae3
  CHECKSUM(SHA256) upstream package : bfd6842dbf192c76dfb537a2588fda2f2a7ab1dfbd14808258c993dbdc2beae3

python3-probeinterface (rpmlib, GLIBC filtered):

python-probeinterface-doc (rpmlib, GLIBC filtered):



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Command line :/usr/bin/fedora-review -b 2012917
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Comment 5 Ben Beasley 2021-12-24 14:26:21 UTC
Thanks for the review! Repository requested.

Regarding the license file—specifically, the status quo in which the license file is marked %license by %pyproject_save_files but resides in the dist-info directory rather than in /usr/share/licenses, and the question of whether it should be additionally installed in /usr/share/licenses—Miro Hrončok responded to my query on the packaging mailing list[1] agreeing that license files do not have to be installed in /usr/share/licenses, referencing an earlier thread on the same list[2] in which Jason L Tibbits III said he knew of no such requirement.

Since Miro and Jason are both current FPC members, I think this is a reasonably conclusive answer to the question of whether the additional “%license …” is required.


Comment 6 Gwyn Ciesla 2021-12-27 17:49:51 UTC
(fedscm-admin):  The Pagure repository was created at

Comment 7 Fedora Update System 2021-12-28 17:16:41 UTC
FEDORA-2021-1b8df94209 has been submitted as an update to Fedora 35.

Comment 8 Fedora Update System 2021-12-28 17:34:14 UTC
FEDORA-2021-f13606ff79 has been submitted as an update to Fedora 34.

Comment 9 Fedora Update System 2021-12-29 01:03:54 UTC
FEDORA-2021-f13606ff79 has been pushed to the Fedora 34 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2021-f13606ff79 \*`
You can provide feedback for this update here:

See also for more information on how to test updates.

Comment 10 Fedora Update System 2021-12-29 01:12:33 UTC
FEDORA-2021-1b8df94209 has been pushed to the Fedora 35 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2021-1b8df94209 \*`
You can provide feedback for this update here:

See also for more information on how to test updates.

Comment 11 Fedora Update System 2022-01-06 00:51:14 UTC
FEDORA-2021-f13606ff79 has been pushed to the Fedora 34 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 12 Fedora Update System 2022-01-06 01:11:21 UTC
FEDORA-2021-1b8df94209 has been pushed to the Fedora 35 stable repository.
If problem still persists, please make note of it in this bug report.

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