[Bug 1727491] New: Review Request: python-LFPy - A module for modeling extracellular potentials of multicompartment neuron models built on NEURON
7:26 p.m.
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Bug ID: 1727491
Summary: Review Request: python-LFPy - A module for modeling
extracellular potentials of multicompartment neuron
models built on NEURON
Product: Fedora
Version: rawhide
Hardware: All
OS: Linux
Status: NEW
Component: Package Review
Severity: medium
Assignee: nobody(a)fedoraproject.org
Reporter: victortyau(a)gmail.com
QA Contact: extras-qa(a)fedoraproject.org
CC: package-review(a)lists.fedoraproject.org
Target Milestone: ---
Classification: Fedora
Spec URL: https://victortyau.fedorapeople.org/python-LFPy/python-LFPy.spec
SRPM URL:
https://victortyau.fedorapeople.org/python-LFPy/python-LFPy-2.0.2-1.fc30....
Description: LFPy is a Python-module for calculation of extracellular
potentials from multi-compartment neuron models. It relies on the NEURON
simulator ( and uses
the Python interface ( it provides.LFPy provides a set of easy-to-use Python
classes for setting up your model, running your simulations and calculating the
extracellular potentials arising from activity in your model neuron
Fedora Account System Username:victortyau
I need to sponsor
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7:54 p.m.
New subject: [Bug 1727491] Review Request: python-LFPy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Luis Segundo <luis(a)blackfile.net> changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |luis(a)blackfile.net
Blocks| |1276941 (fedora-neuro)
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1276941
[Bug 1276941] Fedora NeuroImaging and NeuroScience tracking bug
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8:57 a.m.
New subject: [Bug 1727491] Review Request: python-LFPy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Luis Bazan <bazanluis20(a)gmail.com> changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |bazanluis20(a)gmail.com
Assignee|nobody(a)fedoraproject.org |bazanluis20(a)gmail.com
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8:57 a.m.
New subject: [Bug 1727491] Review Request: python-LFPy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Luis Bazan <bazanluis20(a)gmail.com> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |ASSIGNED
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8:58 a.m.
New subject: [Bug 1727491] Review Request: python-LFPy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Luis Bazan <bazanluis20(a)gmail.com> changed:
What |Removed |Added
----------------------------------------------------------------------------
Flags| |fedora-review?
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7:35 a.m.
New subject: [Bug 1727491] Review Request: python-LFPy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Zbigniew Jędrzejewski-Szmek <zbyszek(a)in.waw.pl> changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |zbyszek(a)in.waw.pl
--- Comment #1 from Zbigniew Jędrzejewski-Szmek <zbyszek(a)in.waw.pl> ---
Package name should be python-lfpy.
Please don't repeat the description text:
%description
LFPy is a Python-module for calculation of extracellular potentials from
...
have a model...
↓
%global %_description %{expand:
LFPy is a Python-module for calculation of extracellular potentials from
...
have a model...}
%description %_description
%description -n python3-%{pypi_name} %_description
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10:20 p.m.
New subject: [Bug 1727491] Review Request: python-LFPy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #2 from Victor Tejada Yau <victortyau(a)gmail.com> ---
Spec URL: https://victortyau.fedorapeople.org/python-LFPy/python-lfpy.spec
SRPM URL:
https://victortyau.fedorapeople.org/python-LFPy/python-lfpy-2.0.2-1.fc30....
thanks a lot
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12:35 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Zbigniew Jędrzejewski-Szmek <zbyszek(a)in.waw.pl> changed:
What |Removed |Added
----------------------------------------------------------------------------
Summary|Review Request: python-LFPy |Review Request: python-lfpy
|- A module for modeling |- A module for modeling
|extracellular potentials of |extracellular potentials of
|multicompartment neuron |multicompartment neuron
|models built on NEURON |models built on NEURON
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12:36 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #3 from Zbigniew Jędrzejewski-Szmek <zbyszek(a)in.waw.pl> ---
Hmm, now there are two description texts. Is this on purpose?
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8:52 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #4 from Victor Tejada Yau <victortyau(a)gmail.com> ---
Spec URL: https://victortyau.fedorapeople.org/python-LFPy/python-lfpy.spec
SRPM URL:
https://victortyau.fedorapeople.org/python-LFPy/python-lfpy-2.0.2-1.fc30....
thanks a lot
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11:49 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Aymen Qader <qader.aymen(a)gmail.com> changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |qader.aymen(a)gmail.com
--- Comment #5 from Aymen Qader <qader.aymen(a)gmail.com> ---
Hi, I'm not sponsored yet so these are just a few unofficial comments (not a
comprehensive review):
* Your summary is too long -- it shouldn't exceed 79 characters.
* The package doesn't build with mock, you need to list a BuildRequires against
gcc (for cython). Try make sure that the package builds using mock -- check out
https://fedoraproject.org/wiki/Using_Mock_to_test_package_builds
* Move the python3 specific BuildRequires statements to under the python3-
subpackage.
* Make sure that you are not using 'Requires' for dependencies which are only
needed during the build step (e.g. setuptools is likely not required outside of
building, so it should just be a BuildRequires). Likewise, BuildRequires
shouldn't be used for dependencies which are not needed for building but are
needed for the package to function.
* Upstream provides examples, which you can include with %doc. They also
provide sphinx docs, which you can build with sphinx-build and likewise include
with %doc.
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1:48 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #6 from Zbigniew Jędrzejewski-Szmek <zbyszek(a)in.waw.pl> ---
All good comments from Aymen, with one exception:
Move the python3 specific BuildRequires statements to under the
python3- subpackage.
Nah, not this. It is normal to keep all BRs at the top. It only
makes sense to
split
them out when there are optional subpackage and one wants to make clear which
BRs are
required for which subpackages. In this case, the python3- subpackage is "the"
subpackage,
that always needs to be built and the BRs for that should be at the top.
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2:11 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #7 from Aymen Qader <qader.aymen(a)gmail.com> ---
Nah, not this. It is normal to keep all BRs at the top.
Apologies for the misinformation, I had thought that this was the convention
because of the example spec in the guidelines
(https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/#_exampl...)
I'll make sure to keep this in mind for the future, thank you for the
correction.
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10:04 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #8 from Ankur Sinha (FranciscoD) <sanjay.ankur(a)gmail.com> ---
Victor, is this ready for a full review now?
Luis, would you have the cycles to do it this week please? I can take it up
otherwise since you're all going to be busy at Flock :P
Cheers!
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11:48 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #9 from Victor Tejada Yau <victortyau(a)gmail.com> ---
Spec URL: https://victortyau.fedorapeople.org/python-LFPy/python-lfpy.spec
SRPM URL:
https://victortyau.fedorapeople.org/python-LFPy/python-lfpy-2.0.2-1.fc30....
some changes waiting for comments.
Bless
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11:37 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #10 from Luis Bazan <bazanluis20(a)gmail.com> ---
Hi Victor
Please add on BuildRequires: gcc
and remove on Requires setuptools and Cython
and I can approve your package and them you add the %doc in spec
Cheers,
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11:11 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #11 from Victor Tejada Yau <victortyau(a)gmail.com> ---
Hi Luis
Spec URL: https://victortyau.fedorapeople.org/python-LFPy/python-lfpy.spec
SRPM URL:
https://victortyau.fedorapeople.org/python-LFPy/python-lfpy-2.0.3-1.fc30....
some changes waiting for comments.
Bless
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12:51 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #12 from Luis Bazan <bazanluis20(a)gmail.com> ---
Hi Victor
APPROVED!
Please continue with the next step.
Add the neuro-sig in members. :-)
Cheers,
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12:51 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Luis Bazan <bazanluis20(a)gmail.com> changed:
What |Removed |Added
----------------------------------------------------------------------------
Flags|fedora-review? |fedora-review+
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12:51 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #13 from Igor Gnatenko <i.gnatenko.brain(a)gmail.com> ---
(fedscm-admin): The Pagure repository was created at
https://src.fedoraproject.org/rpms/python-lfpy
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5:16 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Miro Hrončok <mhroncok(a)redhat.com> changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |mhroncok(a)redhat.com
Flags| |needinfo?(victortyau@gmail.
| |com)
--- Comment #14 from Miro Hrončok <mhroncok(a)redhat.com> ---
Why is the source package called python-lfpy and the subpacakge python3-LFPy
instead of python3-lfpy?
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9:43 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #15 from Ankur Sinha (FranciscoD) <sanjay.ankur(a)gmail.com> ---
Victor, please fix the sub-package as Miro pointed out, and then also build for
F31 and F30 and push updates to bodhi.
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10:50 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Fedora Update System <updates(a)fedoraproject.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|ASSIGNED |MODIFIED
--- Comment #16 from Fedora Update System <updates(a)fedoraproject.org> ---
FEDORA-2019-6f15ed9d48 has been submitted as an update to Fedora 30.
https://bodhi.fedoraproject.org/updates/FEDORA-2019-6f15ed9d48
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12:20 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #17 from Fedora Update System <updates(a)fedoraproject.org> ---
FEDORA-2019-8d739f7da7 has been submitted as an update to Fedora 29.
https://bodhi.fedoraproject.org/updates/FEDORA-2019-8d739f7da7
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12:21 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #18 from Luis Bazan <bazanluis20(a)gmail.com> ---
(In reply to Miro Hrončok from comment #14)
Why is the source package called python-lfpy and the subpacakge
python3-LFPy
instead of python3-lfpy?
Fixed!
Cheers,
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12:24 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #19 from Luis Bazan <bazanluis20(a)gmail.com> ---
https://koji.fedoraproject.org/koji/buildinfo?buildID=1365494
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1:21 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Fedora Update System <updates(a)fedoraproject.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|MODIFIED |ON_QA
--- Comment #20 from Fedora Update System <updates(a)fedoraproject.org> ---
python-lfpy-2.0.3-5.fc30 has been pushed to the Fedora 30 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-2019-53e7847129
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1:27 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #21 from Fedora Update System <updates(a)fedoraproject.org> ---
python-lfpy-2.0.3-4.fc29 has been pushed to the Fedora 29 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-2019-8d739f7da7
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4:14 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Fabio Valentini <decathorpe(a)gmail.com> changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |decathorpe(a)gmail.com
--- Comment #22 from Fabio Valentini <decathorpe(a)gmail.com> ---
I don't know why you think you need to define a whole lot of custom macros, but
at any rate the python3 sub-package is now named python3--lfpy with two
hyphens.
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10:14 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #23 from Luis Bazan <bazanluis20(a)gmail.com> ---
(In reply to Fabio Valentini from comment #22)
I don't know why you think you need to define a whole lot of
custom macros,
but at any rate the python3 sub-package is now named python3--lfpy with two
hyphens.
fixed!
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10:23 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #24 from Miro Hrončok <mhroncok(a)redhat.com> ---
only in master and there is no upgrade path at all.
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10:57 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Fedora Update System <updates(a)fedoraproject.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|ON_QA |MODIFIED
--- Comment #25 from Fedora Update System <updates(a)fedoraproject.org> ---
FEDORA-2019-5075fa927b has been submitted as an update to Fedora 29.
https://bodhi.fedoraproject.org/updates/FEDORA-2019-5075fa927b
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11:46 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #26 from Luis Bazan <bazanluis20(a)gmail.com> ---
(In reply to Miro Hrončok from comment #24)
only in master and there is no upgrade path at all.
https://src.fedoraproject.org/rpms/python-lfpy/c/d3cc39fc0bd44d3d7c3e7759...
https://src.fedoraproject.org/rpms/python-lfpy/c/d3cc39fc0bd44d3d7c3e7759...
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3:11 a.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Fedora Update System <updates(a)fedoraproject.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|MODIFIED |ON_QA
--- Comment #27 from Fedora Update System <updates(a)fedoraproject.org> ---
python-lfpy-2.0.3-6.fc30 has been pushed to the Fedora 30 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-2019-9a55c5aed6
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New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #28 from Fedora Update System <updates(a)fedoraproject.org> ---
python-lfpy-2.0.3-6.fc29 has been pushed to the Fedora 29 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-2019-5075fa927b
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9:21 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
Fedora Update System <updates(a)fedoraproject.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|ON_QA |CLOSED
Resolution|--- |ERRATA
Last Closed| |2019-09-09 02:21:55
--- Comment #29 from Fedora Update System <updates(a)fedoraproject.org> ---
python-lfpy-2.0.3-6.fc30 has been pushed to the Fedora 30 stable repository. If
problems still persist, please make note of it in this bug report.
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9:32 p.m.
New subject: [Bug 1727491] Review Request: python-lfpy - A module for modeling
extracellular potentials of multicompartment neuron models built on NEURON
https://bugzilla.redhat.com/show_bug.cgi?id=1727491
--- Comment #30 from Fedora Update System <updates(a)fedoraproject.org> ---
python-lfpy-2.0.3-6.fc29 has been pushed to the Fedora 29 stable repository. If
problems still persist, please make note of it in this bug report.
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