.gitignore

@@ -2,8 +2,3 @@
 /python-nixio-1.4.5.tar.gz
 /python-nixio-1.4.6.tar.gz
 /python-nixio-1.4.9.tar.gz
-/nixpy-1.5.1.tar.gz
-/nixpy-1.5.2.tar.gz
-/nixpy-1.5.3.tar.gz
-/nixpy-1.5.3-filtered.tar.gz
-/nixpy-1.5.4-filtered.tar.gz

0001-Remove-deprecated-pytest-runner-dependency.patch

@@ -1,34 +0,0 @@
-From b550f88e64c01194029a50b92d94955c39bf169f Mon Sep 17 00:00:00 2001
-From: Sandro <devel@penguinpee.nl>
-Date: Tue, 24 Dec 2024 09:08:28 +0100
-Subject: [PATCH] Remove deprecated pytest-runner dependency
-
-The `pytest-runner` project has been deprecated since 2019 and has been
-archived on git hub in December 2024.
-
-This removes the dependency on the deprecated package and also removes
-deprecated keywords from `setup.py` related to it.
----
- setup.py | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 16379a5..be594d5 100644
---- a/setup.py
-+++ b/setup.py
-@@ -75,9 +75,9 @@ setup(
-     packages=packages,
-     scripts=[],
-     python_requires=">=3.6",
--    tests_require=['pytest', 'scipy', 'pillow', 'matplotlib'],
--    test_suite='pytest',
--    setup_requires=['pytest-runner'],
-+    extras_require={
-+        "test": ['pytest', 'scipy', 'pillow', 'matplotlib'],
-+    },
-     install_requires=['numpy', 'h5py', 'six', 'enum34;python_version<"3.4"'],
-     package_data={'nixio': [license_text, description_text]},
-     include_package_data=True,
--- 
-2.48.1
-

changelog

@@ -1,91 +0,0 @@
-* Fri Jan 20 2023 Fedora Release Engineering <releng@fedoraproject.org> - 1.5.3-4
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
-
-* Fri Jul 22 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.5.3-3
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
-
-* Wed Jun 15 2022 Python Maint <python-maint@redhat.com> - 1.5.3-2
-- Rebuilt for Python 3.11
-
-* Sat Apr 02 2022 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.5.3-1
-- Update to latest release
-
-* Fri Jan 21 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.5.2-2
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
-
-* Thu Dec 30 2021 Vanessa Christopher <vanessaigwe1@gmail.com> - 1.5.2-1
-- Update to latest release
-
-* Sun Oct 03 2021 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.5.1-1
-- Update to latest release
-
-* Fri Jul 23 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.9-14
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
-
-* Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 1.4.9-13
-- Rebuilt for Python 3.10
-
-* Wed Jan 27 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.9-12
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
-
-* Wed Jul 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.9-11
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
-
-* Thu Jun 25 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.9-10
-- Explicitly BR setuptools
-
-* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 1.4.9-9
-- Rebuilt for Python 3.9
-
-* Thu Jan 30 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.9-8
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
-
-* Thu Oct 03 2019 Miro Hrončok <mhroncok@redhat.com> - 1.4.9-7
-- Rebuilt for Python 3.8.0rc1 (#1748018)
-
-* Mon Aug 19 2019 Miro Hrončok <mhroncok@redhat.com> - 1.4.9-6
-- Rebuilt for Python 3.8
-
-* Fri Jul 26 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.9-5
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
-
-* Wed Jul 10 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.9-4
-- Fix build: rhbz 1706159
-
-* Sat Feb 02 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.9-3
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
-
-* Tue Jan 15 2019 Igor Gnatenko <ignatenkobrain@fedoraproject.org> - 1.4.9-2
-- Enable python dependency generator
-
-* Sat Jan 12 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.9-1
-- Update to 1.4.9
-
-* Thu Oct 18 2018 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 1.4.6-2
-- Subpackage python2-nixio has been removed
-  See https://fedoraproject.org/wiki/Changes/Mass_Python_2_Package_Removal
-
-* Wed Jul 18 2018 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.6-1
-- Update to 1.4.6
-
-* Sat Jul 14 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.5-3
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
-
-* Tue Jun 19 2018 Miro Hrončok <mhroncok@redhat.com> - 1.4.5-2
-- Rebuilt for Python 3.7
-
-* Sat Jun 09 2018 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.5-1
-- Update to latest upstream release
-
-* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.3-2
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
-
-* Sun Jan 21 2018 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.3-1
-- Use newer release and GitHub sources
-- Run tests
-- Define summary macro
-- Add doc sub package
-
-* Fri Jan 12 2018 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.2-1
-- Initial build
-- use pydist macro

get_source

@@ -1,50 +0,0 @@
-#!/bin/sh
-set -o errexit
-set -o nounset
-
-if [ "$#" != '1' ]
-then
-	cat 1>&2 <<EOF
-Usage: $0 VERSION
-
-Downloads the requested version and creates a filtered source tarball.
-EOF
-	exit 1
-fi
-
-VERSION="${1}"
-OUTDIR="${PWD}"
-TMPDIR="$(mktemp -d)"
-trap "rm -rf '${TMPDIR}'" INT TERM EXIT
-
-cd "${TMPDIR}"
-REPO="https://github.com/G-node/nixpy"
-URL="${REPO}/archive/${VERSION}/nixpy-${VERSION}.tar.gz"
-echo "--> Downloading: ${URL}" 1>&2
-curl -L -O "${URL}"
-
-ARCHIVE="$(find . -mindepth 1 -maxdepth 1 -type f -name '*.tar.gz' -print -quit)"
-echo "--> Extracting: $(basename "${ARCHIVE}")" 1>&2
-tar -xzf "${ARCHIVE}"
-echo '--> Removing Lenna/Lena image due to licensing and other issues' 1>&2
-TARDIR="$(basename "${ARCHIVE}" '.tar.gz')"
-MTIME="$(stat -c '%Y' "${TARDIR}")"
-# https://github.com/G-Node/nixpy/issues/545
-find "${TARDIR}" -type f -name lenna.png -print -delete
-# Make sure the original mtime is preserved even if we modified the base
-# directory by removing something at the top level. (So far, we didn’t.)
-touch -d @"${MTIME}" "${TARDIR}"
-FILTERED="$(basename "${ARCHIVE}" .tar.gz)-filtered.tar.gz"
-echo "--> Re-archiving: ${FILTERED}" 1>&2
-# https://www.gnu.org/software/tar/manual/html_section/Reproducibility.html
-TZ=UTC LC_ALL=C tar \
-    --create \
-    --sort=name \
-    --format=posix \
-    --numeric-owner --owner=0 --group=0 \
-    --mode=go+u,go-w \
-    --pax-option='delete=atime,delete=ctime' \
-    "${TARDIR}/" |
-  gzip -9 > "${FILTERED}"
-mv -v "${FILTERED}" "${OUTDIR}"
-echo 'Done.' 1>&2

info.json

@@ -1,10 +0,0 @@
-{
-    "VERSION": "1.5.2",
-    "STATUS": "Release",
-    "RELEASE": "1.5.2 Release",
-    "AUTHOR": "Christian Kellner, Adrian Stoewer, Andrey Sobolev, Jan Grewe, Balint Morvai, Achilleas Koutsou",
-    "COPYRIGHT": "2014-2021, German Neuroinformatics Node, Christian Kellner, Adrian Stoewer, Andrey Sobolev, Jan Grewe, Balint Morvai, Achilleas Koutsou",
-    "CONTACT": "dev@g-node.org",
-    "BRIEF": "Python reimplementation of NIXIO (http://g-node.github.io/nix/)",
-    "HOMEPAGE": "https://github.com/G-Node/nixpy"
-}

python-nixio.spec

@@ -1,91 +1,118 @@
-%global forgeurl    https://github.com/G-node/nixpy
+%global srcname     nixio
 
-%global desc \
+Name:       python-%{srcname}
-The NIX project started as an initiative within the Electrophysiology Task \
+Version:    1.4.9
-Force a part of the INCF Data sharing Program. The NIX data model allows to \
+Release:    1%{?dist}
-store fully annotated scientific data-set, i.e. the data together with its \
-metadata within the same container. Our aim is to achieve standardization by \
-providing a common/generic data structure for a multitude of data types. See \
-the wiki for more information \
- \
-The current implementations store the actual data using the HDF5 file format as \
-a storage backend.
-
-Name:       python-nixio
-Version:    1.5.4
-Release:    %autorelease
 Summary:    Python bindings for NIX
 
-%global     tag     %version
+License:    BSD
-%forgemeta
+URL:        https://github.com/G-node/nixpy
+Source0:    https://github.com/G-node/nixpy/archive/%{version}/%{name}-%{version}.tar.gz
 
-License:    BSD-3-Clause
-URL:        %forgeurl
-# We need to upload a filtered version of the source archive because
-# docs/source/examples/lenna.png has several issues, including the lack of a
-# license. We have asked upstream to deal with this in
-#   Please consider replacing lenna.png
-#   https://github.com/G-Node/nixpy/issues/545
-# but for now, we must obtain the filtered archive by running the script in
-# Source2:
-#   ./get_source ${VERSION}
-%dnl Source0:    %forgesource
-Source0:    nixpy-%{version}-filtered.tar.gz
-# The tagged snapshot on GitHub still says "dev" but the manually uploaded
-# release does not, so use the info.json from there
-# https://github.com/G-Node/nixpy/issues/528
-Source1:    info.json
-# * Script used to obtain Source0: ./get_source %%{version}
-Source2:    get_source
-
-# Remove deprecated pytest-runner dependency
-# https://github.com/G-Node/nixpy/pull/547
-# Rebased on 1.5.4, without changes to GitHub CI configuration
-# https://fedoraproject.org/wiki/Changes/DeprecatePythonPytestRunner
-Patch:          0001-Remove-deprecated-pytest-runner-dependency.patch
 
 BuildArch:      noarch
 # No need for nix, they're uncoupling it from the C++
 # https://github.com/G-Node/nixpy/pull/276
 
-BuildRequires:  python3-devel
+%description
+The NIX project started as an initiative within the Electrophysiology Task
+Force a part of the INCF Data sharing Program. The NIX data model allows to
+store fully annotated scientific data-set, i.e. the data together with its
+metadata within the same container. Our aim is to achieve standardization by
+providing a common/generic data structure for a multitude of data types. See
+the wiki for more information
 
-%description %{desc}
+The current implementations store the actual data using the HDF5 file format as
+a storage backend.
 
-%package -n python3-nixio
+%package -n python3-%{srcname}
 Summary:        %{summary}
+BuildRequires:  python3-devel
+BuildRequires:  gcc
+BuildRequires:  %{py3_dist pytest numpy h5py pytest-runner}
+Requires:       %{py3_dist numpy h5py}
+%{?python_provide:%python_provide python3-%{srcname}}
 
-%description -n python3-nixio %{desc}
+%description -n python3-%{srcname}
+The NIX project started as an initiative within the Electrophysiology Task
+Force a part of the INCF Data sharing Program. The NIX data model allows to
+store fully annotated scientific data-set, i.e. the data together with its
+metadata within the same container. Our aim is to achieve standardization by
+providing a common/generic data structure for a multitude of data types. See
+the wiki for more information
+
+The current implementations store the actual data using the HDF5 file format as
+a storage backend.
+
+%package doc
+Summary:        %{summary}
+BuildRequires:  python3-sphinx
+
+%description doc
+Documentation files for %{name}.
 
 %prep
-%autosetup -n nixpy-%{version} -p1
+%autosetup -n nixpy-%{version}
-
+rm -fr *egg-info
-# it sets examples_path based on the name of the cwd
-sed -i "s/nixpy/nixpy-%{version}/" nixio/test/test_doc_examples.py
-
-cp %{SOURCE1} nixio/info.json -v -p
-
-%generate_buildrequires
-%pyproject_buildrequires -x test
 
 %build
-%pyproject_wheel
+%py3_build
+
+PYTHONPATH=. sphinx-build-3 docs/source html
+# Remove unneeded files
+rm -fr html/.{buildinfo,doctrees}
+
+# Remove shebang from documentation examples
+for f in html/_downloads/*.py; do
+    sed '1{\@^#!/usr/bin/env python@d}' $f > $f.new &&
+    touch -r $f $f.new &&
+    mv $f.new $f
+done
 
 %install
-%pyproject_install
+%py3_install
-%pyproject_save_files -l nixio
 
 %check
-# These require the removed lenna.png sample file:
+%{__python3} setup.py test
-k="${k-}${k+ and }not (TestDocumentationExamples and test_image_data)"
-k="${k-}${k+ and }not (TestDocumentationExamples and test_image_with_metadata)"
-k="${k-}${k+ and }not (TestDocumentationExamples and test_multiple_rois)"
-k="${k-}${k+ and }not (TestDocumentationExamples and test_single_roi)"
 
-%pytest -k "${k-}"
+%files -n python3-%{srcname}
+%license LICENSE
+%{python3_sitelib}/%{srcname}-%{version}-py?.?.egg-info
+%{python3_sitelib}/%{srcname}/
 
-%files -n python3-nixio -f %{pyproject_files}
+%files doc
-%{_bindir}/nixio
+%doc README.rst html
+%license LICENSE
 
 %changelog
-%autochangelog
+* Sat Jan 12 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.9-1
+- Update to 1.4.9
+
+* Thu Oct 18 2018 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 1.4.6-2
+- Subpackage python2-nixio has been removed
+  See https://fedoraproject.org/wiki/Changes/Mass_Python_2_Package_Removal
+
+* Wed Jul 18 2018 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.6-1
+- Update to 1.4.6
+
+* Sat Jul 14 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.5-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
+
+* Tue Jun 19 2018 Miro Hrončok <mhroncok@redhat.com> - 1.4.5-2
+- Rebuilt for Python 3.7
+
+* Sat Jun 09 2018 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.5-1
+- Update to latest upstream release
+
+* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.3-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
+
+* Sun Jan 21 2018 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.3-1
+- Use newer release and GitHub sources
+- Run tests
+- Define summary macro
+- Add doc sub package
+
+* Fri Jan 12 2018 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.4.2-1
+- Initial build
+- use pydist macro

sources

@@ -1 +1 @@
-SHA512 (nixpy-1.5.4-filtered.tar.gz) = 7842e1643df0b234b8de7f8c1c30875ad70ed2681561ecf570ffff2849f60ea9510e7dba3b6544e8f507eed2583925d52d29c348cc49b2d5da0a22c686e3173d
+SHA512 (python-nixio-1.4.9.tar.gz) = b7925ff6a0d04434c88f214dd7b557bf7ff9180b3d25fa639a289e0610e7c0abc6bbc34ecd7c03a97bec11c6b6e8268598b1b16345a7cc085479f44136e0f1ef