## START: Set by rpmautospec ## (rpmautospec version 0.7.3) ## RPMAUTOSPEC: autorelease, autochangelog %define autorelease(e:s:pb:n) %{?-p:0.}%{lua: release_number = 1; base_release_number = tonumber(rpm.expand("%{?-b*}%{!?-b:1}")); print(release_number + base_release_number - 1); }%{?-e:.%{-e*}}%{?-s:.%{-s*}}%{!?-n:%{?dist}} ## END: Set by rpmautospec # Sphinx-generated HTML documentation is not suitable for packaging; see # https://bugzilla.redhat.com/show_bug.cgi?id=2006555 for discussion. # # We can generate PDF documentation as a substitute. %bcond doc_pdf 1 Name: python-probeinterface Version: 0.2.24 Release: %autorelease Summary: Handles probe layout, geometry, and wiring to device # SPDX License: MIT URL: https://github.com/SpikeInterface/probeinterface # The GitHub tarball has documentation, examples, and tests; the PyPI one does # not. Source0: %{url}/archive/%{version}/probeinterface-%{version}.tar.gz # Probe definitions are normally downloaded at runtime. We can get tests and # examples that rely on probe definitions to work in an offline environment by # pre-populating the local cache. See also # https://github.com/SpikeInterface/probeinterface/issues/70. # # This URL comes from probeinterface/library.py, where it is called public_url. %global probe_url https://raw.githubusercontent.com/SpikeInterface/probeinterface_library/main Source1: %{probe_url}/neuronexus/A1x32-Poly3-10mm-50-177/A1x32-Poly3-10mm-50-177.json Source2: %{probe_url}/cambridgeneurotech/ASSY-156-P-1/ASSY-156-P-1.json BuildArch: noarch BuildRequires: python3-devel %if %{with doc_pdf} BuildRequires: make BuildRequires: python3dist(sphinx) BuildRequires: python3-sphinx-latex BuildRequires: latexmk BuildRequires: /usr/bin/xindy BuildRequires: tex-xetex-bin %endif %global common_description %{expand: A Python package to handle the layout, geometry, and wiring of silicon probes for extracellular electrophysiology experiments. Goals 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 ordering) • 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 Bonus: • 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 location • 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} %description %{common_description} %package -n python3-probeinterface Summary: %{summary} %description -n python3-probeinterface %{common_description} %package doc Summary: Documentation for probeinterface %description doc %{common_description} %prep %autosetup -n probeinterface-%{version} -p1 # Do not require an exact matplotlib version to build documentation: sed -r -i 's/(matplotlib)==/\1>=/' pyproject.toml # Drop coverage tools from test dependencies. # # https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/#_linters sed -r -i 's/^([[:blank:]])(.*pytest-cov.*,)$/\1# \2/' pyproject.toml # Pre-populate the probe definition cache PROBE_CACHE="${HOME}/.config/probeinterface/library" install -t "${PROBE_CACHE}/neuronexus" -p -m 0644 -D '%{SOURCE1}' install -t "${PROBE_CACHE}/cambridgeneurotech" -p -m 0644 -D '%{SOURCE2}' # Since pdflatex cannot handle Unicode inputs in general: echo "latex_engine = 'xelatex'" >> doc/conf.py %generate_buildrequires %pyproject_buildrequires -x test%{?with_doc_pdf:,docs} %build %pyproject_wheel %install %pyproject_install %pyproject_save_files -l probeinterface %if %{with doc_pdf} # Building this in %%install instead of %%build is a hack, but it is the # easiest workaround for the unusual fact that importing the package requires # proper distribution metadata. PYTHONPATH='%{buildroot}%{python3_sitelib}' %make_build -C doc latex \ SPHINXOPTS='-j%{?_smp_build_ncpus}' %make_build -C doc/_build/latex LATEXMKOPTS='-quiet' %endif %check # Skip tests that unconditionally download probe interface definitions and # bypass the cache. # https://github.com/SpikeInterface/probeinterface/issues/70. k="${k-}${k+ and }not test_download_probeinterface_file" k="${k-}${k+ and }not test_get_from_cache" %pytest -k "${k-}" %files -n python3-probeinterface -f %{pyproject_files} %doc README.md %files doc %license LICENSE %doc examples/ %if %{with doc_pdf} %doc doc/_build/latex/probeinterface.pdf %endif %changelog ## START: Generated by rpmautospec * Fri Sep 06 2024 Benjamin A. Beasley - 0.2.24-1 - Update to 0.2.24 (close RHBZ#2310398) * Thu Jul 18 2024 Benjamin A. Beasley - 0.2.23-1 - Update to 0.2.23 (close RHBZ#2298480) * Mon Jul 15 2024 Benjamin A. Beasley - 0.2.22-1 - Update to 0.2.22 (close RHBZ#2297975) * Mon Jun 17 2024 Python Maint - 0.2.21-3 - Rebuilt for Python 3.13 * Mon Feb 05 2024 Benjamin A. Beasley - 0.2.21-1 - Update to 0.2.21 (close RHBZ#2262778) * Fri Jan 26 2024 Fedora Release Engineering - 0.2.20-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Mon Jan 22 2024 Fedora Release Engineering - 0.2.20-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Mon Dec 18 2023 Benjamin A. Beasley - 0.2.20-2 - Assert that %%pyproject_files contains a license file * Tue Dec 12 2023 Benjamin A. Beasley - 0.2.20-1 - Update to 0.2.20 (close RHBZ#2254044) * Thu Nov 02 2023 Benjamin A. Beasley - 0.2.19-1 - Update to 0.2.19 * Tue Oct 31 2023 Benjamin A. Beasley - 0.2.18-1 - Update to 0.2.18 (close RHBZ#2247108) * Fri Jul 21 2023 Fedora Release Engineering - 0.2.17-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Wed Jul 12 2023 Benjamin A. Beasley - 0.2.17-3 - Use trailing slashes for directories in files lists * Wed Jun 28 2023 Python Maint - 0.2.17-2 - Rebuilt for Python 3.12 * Tue Jun 27 2023 Benjamin A. Beasley - 0.2.17-1 - Update to 0.2.17 (close RHBZ#2217884) * Mon Jun 19 2023 Benjamin A. Beasley - 0.2.16-3 - Use new (rpm 4.17.1+) bcond style * Sat Mar 18 2023 Benjamin A. Beasley - 0.2.16-2 - Don’t assume %%_smp_mflags is -j%%_smp_build_ncpus * Thu Feb 09 2023 Benjamin A. Beasley - 0.2.16-1 - Update to 0.2.16 (close RHBZ#2168525) * Fri Jan 20 2023 Fedora Release Engineering - 0.2.15-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Mon Dec 12 2022 Benjamin A. Beasley - 0.2.15-1 - Update to 0.2.15 (close RHBZ#2152539) * Thu Oct 27 2022 Benjamin A. Beasley - 0.2.14-1 - Update to 0.2.14 (close RHBZ#2138117) * Fri Oct 21 2022 Benjamin A. Beasley - 0.2.13-1 - Update to 0.2.13 (close RHBZ#2136599) * Mon Oct 10 2022 Benjamin A. Beasley - 0.2.12-1 - Update to 0.2.12 (close RHBZ#2133405) * Mon Oct 10 2022 Benjamin A. Beasley - 0.2.11-2 - Confirm License is SPDX MIT * Wed Sep 14 2022 Benjamin A. Beasley - 0.2.11-1 - Update to 0.2.11 (close RHBZ#2126799) * Thu Sep 01 2022 Benjamin A. Beasley - 0.2.10-1 - Update to 0.2.10 (close RHBZ#2123300) * Fri Jul 22 2022 Fedora Release Engineering - 0.2.9-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Wed Jun 15 2022 Python Maint - 0.2.9-2 - Rebuilt for Python 3.11 * Fri Apr 15 2022 Benjamin A. Beasley - 0.2.9-1 - Update to 0.2.9 (close RHBZ#2075767) * Wed Mar 23 2022 Benjamin A. Beasley - 0.2.8-1 - Update to 0.2.8 (close RHBZ#2067101) * Tue Mar 01 2022 Benjamin A. Beasley - 0.2.7-1 - Update to 0.2.7 (close RHBZ#2059621) * Fri Jan 21 2022 Fedora Release Engineering - 0.2.6-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Tue Dec 28 2021 Benjamin A. Beasley - 0.2.6-1 - Initial package (close RHBZ#2012917) ## END: Generated by rpmautospec