Issue #461: Tracker ticket: upstream contributions - NeuroFedora

ankursinha commented Aug 23, 2021

Gone through my GitHub history and found these to start with (probably going backwards in time):

iztokf commented Aug 23, 2021

My GitHub activities related to packages where I am maintainer of Fedora packages. More issues/pull requests will be added to the list ASAP (time constraints).

python-evopreprocess

python-pyswarms

python-nashpy

python-niapy

python-niaaml

python-niaclass

python-openant

vivoactive HR added to the list

Edited Aug 27, 2021 by iztokf

ankursinha commented Aug 31, 2021

0.5.2 Python3.10: failing tests: FAILED failures=11, skipped=10 · Issue 63 SmokinCaterpillar/pypet

ankursinha commented Aug 31, 2021

@sagitter opened this:

Support Python 3.10 · Issue 95 · thebjorn/pydeps

I've now opened a PR to include Py3.10 in stdlib_list:

Feat/py3.10 by sanjayankur31 · Pull Request 49 jackmaney/python-stdlib-list

ankursinha commented Sep 6, 2021

@music: https://github.com/FastTrackOrg/FastTrack/issues/20

music commented Sep 6, 2021

PR’s merged:

casc (for gamer): Update Free Software Foundation postal addresses
casc (for gamer): Support using an external GoogleTest library
earcut-hpp: Include headers for everything used in std::
libsbml: Do not use private unittest.TestCase.assert_() method
morphio: Rename CHANGLOG.md to CHANGELOG.md (typo fix)
morphio: Remove explicit template class instantiation
morphio: Remove unused python mock dependency
NiaAML-GUI: Fix LICENSE file installed directly in site-packages
NiaAML-GUI: Add a GUI script entry point
NiaAML-GUI: Add an icon file to AppData
python-airspeed: Remove shebang & execute bit from ⎽⎽init⎽⎽.py
python-bids-validator: Fix missing LICENSE on PyPI
python-cyipopt: Fix a couple of small documentation typos
python-cyipopt: A little consistency in shebangs and execute bits
python-grabbit: Update versioneer from 0.18 to 0.21
python-hdfs: Use unittest.mock where available
python-mapbox-earcut: Drop “message” keyword from pytest.raises(…)
python-mapbox-earcut: Fix out-of-bounds access on empty input
python-niaaml: Do not install text files in site-packages/
python-niaaml: Eschew deprecated numpy aliases for builtins
python-probeinterface: Fix a documentation typo (cvs for csv)
python-pyedflib: Correct “protokoll” to “protocol” in description
python-pyinstrument: Ensure test/ is not installed in site-packages
python-read-roi: Support either nose or nose2 as test runner
python-spyking-circus: Allow data_path to be set via environment variable
python-spyking-circus: Fix broken image link in Sphinx documentation
python-spyking-circus: Fix a doc typo: “CIRUCS” for “CIRCUS”
python-trimesh: Triangulation engine handling fixes in library and tests
shybrid: Remove useless or unused shebang lines

PR’s merged manually, or rewritten by upstream:

casc (for gamer): Fix uninitialized memory accesses
fasttrack: Respect NO_WEB in CLI project, too
fasttrack: Improvements to documentation generator script

PR’s declined by upstream:

edflib: Add support for big-endian platforms

PR’s pending review:

python-matplotlib-scalebar: Correct License trove classifier
python-matplotlib-scalebar: Remove useless shebangs
python-ppft: Simplify Python executable path guessing in examples

Open issues:

earcut-hpp: Test “self_touching” fails on aarch64, ppc64le, s390x
gamer: Triangle is nonfree
morphio: Support external pybind11
python-cyipopt: Empty, zero-length test files
python-pingouin: TestCorrelation::test_corr fails on some platforms
python-pingouin: TestRegression::test_linear_regression fails on 32-bit ARM
python-pingouin: TestParametric::test_pandas fails with dtype mismatch on 32-bit platforms
python-trimesh: Big-endian test failures

Closed issues — “won’t fix”:

edflib: Support big-endian architectures

Resolved issues:

casc (for gamer): Tests fail when libstdc++ assertions are enabled
fasttrack: Add AppStream metadata?
libsbml: Python 3.11 removes unittest.TestCase.assert_
NiaAML-GUI: GUI script entry point
python-airspeed: GitHub repository is behind PyPI
python-fastavro: test_ancient_datetime test fails in timezone with offset that changed since 1960
python-mapbox-earcut: Out-of-bounds array access with empty input
python-nilearn: Test failure on 32-bit platforms: test_resample_img_segmentation_fault
python-pandas: BUG: Spearman correlation is broken (dtype mismatch) on 32-bit platforms

(Updated 2022-02-03.)

Edited Feb 3, 2022 by music

alciregi commented Sep 6, 2021

Resolved issues:

major commented Oct 1, 2021

My contributions to a few packages so far:

python-mne
- Tests fail on s390x architecture
- test_xdawn_regularization fails on Fedora 34
python-pybv
- Tests fail with big-endian machines
python-owl_rl
- Test fails: test_cls_maxqc1
- Include the updated license text in the source.
snakemake
python-datrie
- Tests fail with Python 3.9
python-odml
- Test failure with Python 3.9
- Test failiure on Python 3.8
python-neurodsp
- Test failures with numpy 1.18.0
- Unable to build docs
pre-commit
- Running tests on a system-wide install.

ankursinha commented Oct 12, 2021

@shaneallcroft is working on pyplane at the moment, we opened:

ankursinha commented Oct 12, 2021

Two for annexremote:

ankursinha commented Mar 8, 2022

Did a quick search through all our repos, so this is a superset and may include stuff mentioned in comments that is now outdated:

alizams/alizams.spec:# https://github.com/AlizaMedicalImaging/AlizaMS/issues/2
arbor/arbor.spec:# https://github.com/arbor-sim/arbor/issues/916
auryn/auryn.spec:# https://github.com/fzenke/auryn/issues/4
catch22/catch22.spec:# https://github.com/chlubba/catch22/issues/12
ctk/ctk.spec:# (see https://github.com/commontk/CTKData/issues/1).
dcm2niix/dcm2niix.spec:# https://github.com/neurolabusc/dcm2niix/issues/8
dlib/dlib.spec:# and https://github.com/davisking/dlib/issues/111
earcut-hpp/earcut-hpp.spec:# https://github.com/mapbox/earcut.hpp/issues/97
earcut-hpp/earcut-hpp.spec:# https://github.com/mapbox/earcut.hpp/pull/96
earcut-hpp/earcut-hpp.spec:Patch0: https://github.com/mapbox/earcut.hpp/pull/96.patch
genesis-simulator/genesis-simulator.spec:# https://github.com/genesis-sim/genesis-2.4/issues/4
highfive/highfive.spec:# Issue filed upstream: https://github.com/BlueBrain/HighFive/issues/443
iv/iv.spec:# https://github.com/neuronsimulator/iv/issues/14: -Wstrict-aliasing
iv/iv.spec:# https://github.com/neuronsimulator/iv/issues/15: -Wchar-subscript
iv/iv.spec:# https://github.com/neuronsimulator/iv/issues/3
iv/iv.spec:# https://github.com/neuronsimulator/iv/pull/34
libneurosim/libneurosim.spec:- All explained in: https://github.com/INCF/libneurosim/issues/12
libneurosim/libneurosim.spec:# https://github.com/INCF/libneurosim/issues/11
libsbml/libsbml.spec:# https://github.com/sbmlteam/libsbml/pull/178
libsbml/libsbml.spec:Patch5: https://github.com/sbmlteam/libsbml/pull/178/commits/b12b7f9372424f5271a838c95605d9946c7ea1fb.patch
moose/moose.spec:# https://github.com/BhallaLab/moose-core/issues/437
moose/moose.spec:# https://github.com/BhallaLab/moose-core/pull/420
morphio/morphio.spec:# Some sent upstream: https://github.com/BlueBrain/MorphIO/pull/293
nest/nest.spec:# https://github.com/nest/nest-simulator/pull/2250
neuron/neuron.spec:# https://github.com/neuronsimulator/nrn/issues/113
neuron/neuron.spec:# https://github.com/neuronsimulator/nrn/issues/114
neuron/neuron.spec:# https://github.com/neuronsimulator/nrn/issues/145
neuron/neuron.spec:# https://github.com/neuronsimulator/nrn/issues/719#issuecomment-677501890
neuron/neuron.spec:# https://github.com/neuronsimulator/nrn/issues/719#issuecomment-677501890
neuron/neuron.spec:# https://github.com/neuronsimulator/nrn/issues/719#issuecomment-677501890
octave-iso2mesh/octave-iso2mesh.spec:# See also https://github.com/CGAL/cgal/issues/5857
openmeeg/openmeeg.spec:## https://github.com/openmeeg/openmeeg/issues/346
openmeeg/openmeeg.spec:# https://github.com/openmeeg/openmeeg/issues/421
openmeeg/openmeeg.spec:# See https://github.com/openmeeg/openmeeg/issues/441 for openmeeg_python_doc
pcg-cpp/pcg-cpp.spec:# https://github.com/imneme/pcg-cpp/issues/73.
pydeps/pydeps.spec:# https://github.com/thebjorn/pydeps/issues/118
pydeps/pydeps.spec:# https://github.com/thebjorn/pydeps/issues/71
python-airspeed/python-airspeed.spec:# https://github.com/purcell/airspeed/pull/53
python-airspeed/python-airspeed.spec:Patch0: https://github.com/purcell/airspeed/pull/53.patch
python-annexremote/python-annexremote.spec:# Sent upstream: https://github.com/Lykos153/AnnexRemote/pull/29
python-biopython/python-biopython.spec:# See https://github.com/biopython/biopython/issues/2128; https://github.com/biopython/biopython/issues/2120
python-biopython/python-biopython.spec:# See https://github.com/biopython/biopython/issues/855
python-biopython/python-biopython.spec:# See https://github.com/biopython/biopython/issues/855; https://github.com/biopython/biopython/issues/1889
python-brian2/python-brian2.spec:(https://github.com/brian-team/brian2/issues) or to the brian support mailing
python-chaospy/python-chaospy.spec:# https://github.com/jonathf/chaospy/issues/307#issuecomment-735379840
python-cro/python-cro.spec:# https://github.com/VictorPelaez/coral-reef-optimization-algorithm/issues/62
python-cro/python-cro.spec:# https://github.com/VictorPelaez/coral-reef-optimization-algorithm/pull/58
python-cro/python-cro.spec:# https://github.com/VictorPelaez/coral-reef-optimization-algorithm/pull/59
python-cro/python-cro.spec:# https://github.com/VictorPelaez/coral-reef-optimization-algorithm/pull/60
python-cro/python-cro.spec:# https://github.com/VictorPelaez/coral-reef-optimization-algorithm/pull/63
python-cyipopt/python-cyipopt.spec:# https://github.com/mechmotum/cyipopt/issues/135
python-cyipopt/python-cyipopt.spec:# https://github.com/mechmotum/cyipopt/pull/136
python-cyipopt/python-cyipopt.spec:# https://github.com/mechmotum/cyipopt/pull/137
python-cypy/python-cypy.spec:# Sent upstream: https://github.com/cyrus-/cypy/pull/3
python-datalad/python-datalad.spec:# https://github.com/datalad/datalad/issues/4090
python-datalad/python-datalad.spec:# https://github.com/datalad/datalad/pull/4232
python-datrie/python-datrie.spec:# https://github.com/pytries/datrie/issues/38
python-deap/python-deap.spec:Patch: https://github.com/DEAP/deap/pull/625.patch
python-devicely/python-devicely.spec:# already fixed in https://github.com/hpi-dhc/devicely/pull/60
python-devicely/python-devicely.spec:# https://github.com/hpi-dhc/devicely/issues/61
python-elephant/python-elephant.spec:# https://github.com/NeuralEnsemble/elephant/issues/408
python-elephant/python-elephant.spec:# https://github.com/NeuralEnsemble/elephant/issues/409
python-elephant/python-elephant.spec:# https://github.com/NeuralEnsemble/elephant/issues/410
python-fastavro/python-fastavro.spec:# Issue: https://github.com/fastavro/fastavro/issues/526
python-fsleyes/python-fsleyes.spec:# https://github.com/pauldmccarthy/fsleyes/issues/7
python-fsleyes/python-fsleyes.spec:# https://github.com/pauldmccarthy/fsleyes/issues/82
python-fsleyes-widgets/python-fsleyes-widgets.spec:- https://github.com/pauldmccarthy/fsleyes-widgets/issues/2
python-fslpy/python-fslpy.spec:# Ignore intermittently failing test: https://github.com/pauldmccarthy/fslpy/issues/10
python-grabbit/python-grabbit.spec:# https://github.com/grabbles/grabbit/pull/93
python-hdfs/python-hdfs.spec:# https://github.com/mtth/hdfs/pull/177
python-hdfs/python-hdfs.spec:Patch0: https://github.com/mtth/hdfs/pull/177.patch
python-hdmf/python-hdmf.spec:# https://github.com/hdmf-dev/hdmf/issues/663
python-indexed_gzip/python-indexed_gzip.spec:# (https://github.com/pauldmccarthy/indexed_gzip/issues/13). Still, we manage
python-indexed_gzip/python-indexed_gzip.spec:- Run tests, despite https://github.com/pauldmccarthy/indexed_gzip/issues/13
python-inspyred/python-inspyred.spec:# https://github.com/aarongarrett/inspyred/pull/22
python-inspyred/python-inspyred.spec:# upstream has been informed: https://github.com/aarongarrett/inspyred/pull/21#issue-1061517666
python-interfile/python-interfile.spec:# https://github.com/spedemon/interfile/pull/3
python-lazy-ops/python-lazy-ops.spec:# https://github.com/catalystneuro/lazy_ops/issues/26
python-lazy-ops/python-lazy-ops.spec:# https://github.com/catalystneuro/lazy_ops/pull/27
python-lfpy/python-lfpy.spec:# https://github.com/LFPy/LFPy/issues/173
python-libNeuroML/python-libNeuroML.spec:- Remove unneeded shebang (https://github.com/NeuralEnsemble/libNeuroML/issues/77)
python-llvmlite/python-llvmlite.spec:# https://github.com/numba/llvmlite/pull/769
python-llvmlite/python-llvmlite.spec:Patch0: https://github.com/numba/llvmlite/pull/769.patch
python-llvmlite/python-llvmlite.spec:# See also: https://github.com/numba/llvmlite/issues/740#issuecomment-937830985
python-matplotlib-scalebar/python-matplotlib-scalebar.spec:# https://github.com/ppinard/matplotlib-scalebar/pull/47
python-moss/python-moss.spec:# Disable tests forever due to: https://github.com/mwaskom/moss/issues/17
python-multiprocess/python-multiprocess.spec:https://github.com/uqfoundation/multiprocess/issues, with a legacy list
python-neurom/python-neurom.spec:# reported upstream: https://github.com/BlueBrain/NeuroM/issues/983
python-nitime/python-nitime.spec:# https://github.com/nipy/nitime/issues/136
python-nitime/python-nitime.spec:# https://github.com/nipy/nitime/issues/137
python-nixio/python-nixio.spec:# https://github.com/G-Node/nixpy/issues/528
python-nixio/python-nixio.spec:# https://github.com/G-Node/nixpy/pull/276
python-pathos/python-pathos.spec:https://github.com/uqfoundation/pathos/issues, with a legacy list maintained at
python-patsy/python-patsy.spec:# https://github.com/pydata/patsy/issues/143
python-pingouin/python-pingouin.spec:# https://github.com/pandas-dev/pandas/issues/43588
python-pingouin/python-pingouin.spec:# https://github.com/raphaelvallat/pingouin/issues/196
python-pingouin/python-pingouin.spec:# https://github.com/raphaelvallat/pingouin/issues/197
python-pox/python-pox.spec:https://github.com/uqfoundation/pox/issues, with a legacy list maintained at
python-ppft/python-ppft.spec:https://github.com/uqfoundation/ppft/issues, with a legacy list maintained at
python-probeinterface/python-probeinterface.spec:# https://github.com/SpikeInterface/probeinterface/issues/70.
python-probeinterface/python-probeinterface.spec:# https://github.com/SpikeInterface/probeinterface/issues/70.
python-pydicom/python-pydicom.spec:# reported upstream https://github.com/pydicom/pydicom/issues/1119
python-pydotplus/python-pydotplus.spec:# https://github.com/carlos-jenkins/pydotplus/issues/2
python-PyLEMS/python-PyLEMS.spec:# Sent upstream: https://github.com/LEMS/pylems/pull/64
python-pynetdicom/python-pynetdicom.spec:# https://github.com/pydicom/pynetdicom/issues/406 and https://github.com/pydicom/pynetdicom/issues/364
python-pynetdicom/python-pynetdicom.spec:# https://github.com/pydicom/pynetdicom/issues/498
python-pynn/python-pynn.spec:# https://github.com/NeuralEnsemble/PyNN/issues/707
python-pynn/python-pynn.spec:# https://github.com/neuronsimulator/nrn/issues/114
python-pynn/python-pynn.spec:# Issue filed upstream: https://github.com/NeuralEnsemble/PyNN/issues/705
python-pynn/python-pynn.spec:# Merged upstream: https://github.com/NeuralEnsemble/PyNN/pull/744
python-pyoptical/python-pyoptical.spec:### https://github.com/esc/pyoptical/issues/2
python-pypet/python-pypet.spec:# https://github.com/SmokinCaterpillar/pypet/issues/56
python-pypet/python-pypet.spec:# https://github.com/SmokinCaterpillar/pypet/issues/63
python-pyphi/python-pyphi.spec:# Also sent upstream: https://github.com/wmayner/pyphi/pull/22
python-pyphi/python-pyphi.spec:# https://github.com/wmayner/pyphi/pull/50
python-pyphi/python-pyphi.spec:# Tests fails on s390x: https://github.com/wmayner/pyphi/issues/41
python-pysb/python-pysb.spec:# https://github.com/pysb/pysb/issues/100
python-pysb/python-pysb.spec:# https://github.com/pysb/pysb/issues/555
python-pyspike/python-pyspike.spec:# https://github.com/mariomulansky/PySpike/issues/48
python-rangehttpserver/python-rangehttpserver.spec:# https://github.com/danvk/RangeHTTPServer/issues/21
python-ratelimiter/python-ratelimiter.spec:# https://github.com/RazerM/ratelimiter/issues/10
python-ratelimiter/python-ratelimiter.spec:# https://github.com/RazerM/ratelimiter/pull/11
python-shapely/python-shapely.spec:# https://github.com/shapely/shapely/issues/1145. The documentation is still
python-steps/python-steps.spec:# https://github.com/CNS-OIST/STEPS/issues/23
python-steps/python-steps.spec:# Sent upstream: https://github.com/CNS-OIST/STEPS/pull/24
python-stopit/python-stopit.spec:# https://github.com/glenfant/stopit/pull/23
python-trimesh/python-trimesh.spec:# https://github.com/BerkeleyAutomation/python-fcl/issues/19
python-trimesh/python-trimesh.spec:# https://github.com/cnr-isti-vclab/meshlab/issues/237
python-trimesh/python-trimesh.spec:# https://github.com/mikedh/trimesh/issues/1351
python-trimesh/python-trimesh.spec:# https://github.com/mikedh/trimesh/issues/690
python-trimesh/python-trimesh.spec:# (https://github.com/scopatz/pyembree/issues/28).
python-tvb-data/python-tvb-data.spec:# https://github.com/LTS5/cfflib/issues/7
smoldyn/smoldyn.spec:# See https://github.com/ssandrews/Smoldyn-official/issues/3
vxl/vxl.spec:- File upstream issue and use bundled openjpeg2: https://github.com/vxl/vxl/issues/627
vxl/vxl.spec:- Fix 32 bit arch builds: https://github.com/vxl/vxl/issues/638
vxl/vxl.spec:# Fixes https://github.com/vxl/vxl/issues/638
vxl/vxl.spec:# https://github.com/vxl/vxl/issues/550
vxl/vxl.spec:# https://github.com/vxl/vxl/issues/627
vxl/vxl.spec:# Submitted upstream https://github.com/vxl/vxl/pull/626
vxl/vxl.spec:- Temporarily use bundled dcmtk (https://github.com/vxl/vxl/issues/550)

To get this list, checkout all out repos using the scripts here: https://pagure.io/neuro-sig/NeuroFedora/blob/main/f/package-list and then run something like: rg -g "*.spec" -N "github.*(issues|pull)" | sort -h

ankursinha commented Feb 20, 2026

This ticket has been migrated to the forgejo instance. Please find the new ticket here
https://forge.fedoraproject.org/neuro/NeuroFedora//issues/461

neuro-sig / NeuroFedora

#461 Tracker ticket: upstream contributions

Opened Aug 23, 2021 by ankursinha. Modified Feb 20, 2026

python-evopreprocess

python-pyswarms

python-nashpy

python-niapy

python-niaaml

python-niaclass

python-openant

Metadata

neuro-sig / NeuroFedora

#461 Tracker ticket: upstream contributions Opened Aug 23, 2021 by ankursinha. Modified Feb 20, 2026

python-evopreprocess

python-pyswarms

python-nashpy

python-niapy

python-niaaml

python-niaclass

python-openant

Metadata

D: Easy S: Future meeting T: Community

#461 Tracker ticket: upstream contributions

Opened Aug 23, 2021 by ankursinha. Modified Feb 20, 2026