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@@ -1,74 +1,108 @@
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%bcond_without tests
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- %global _description %{expand:
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- PyPhi is a Python library for computing integrated information, and the
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- associated quantities and objects.
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-
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- If you use this code, please cite the manuscript:
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-
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- Mayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G (2017).
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- PyPhi: A toolbox for integrated information. arXiv:1712.09644 [q-bio.NC].
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-
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- The manuscript is available at https://arxiv.org/abs/1712.09644.}
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-
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- %global forgeurl https://github.com/wmayner/pyphi/
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+ # Sphinx-generated HTML documentation is not suitable for packaging; see
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+ # https://bugzilla.redhat.com/show_bug.cgi?id=2006555 for discussion.
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+ #
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+ # We can generate PDF documentation as a substitute.
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+ %bcond_without doc_pdf
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Name: python-pyphi
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Version: 1.2.1
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Release: %autorelease
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- Summary: A library for computing integrated information
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+ Summary: A toolbox for integrated information theory
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- %global tag %{version}
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- %forgemeta
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+ # The entire source is GPL-3.0-or-later, except:
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+ #
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+ # - docs/_themes/ contains “krTheme Sphinx Style,” which is BSD-3-Clause; but
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+ # we remove it in %%prep and do not use it.
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+ License: GPL-3.0-or-later
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+ URL: https://github.com/wmayner/pyphi/
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+ Source0: %{url}/%{version}/pyphi-%{version}.tar.gz
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- License: GPLv3
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- URL: %forgeurl
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- Source0: %forgesource
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# https://github.com/wmayner/pyphi/pull/50
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- Patch0: 0001-fix-py3.10-correct-collections-import.patch
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- BuildRequires: git-core
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- BuildArch: noarch
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+ Patch: 0001-fix-py3.10-correct-collections-import.patch
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+ # Remove sphinx-contrib-napoleon
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+ # https://github.com/wmayner/pyphi/pull/22
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+ Patch: %{url}/pull/22.patch
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# Tests fails on s390x: https://github.com/wmayner/pyphi/issues/41
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+ # https://bugzilla.redhat.com/show_bug.cgi?id=2010104
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ExcludeArch: s390x
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- %description %_description
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+ # The base package is arched so we can easily detect arch-dependent build
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+ # issues, but there is no compiled code.
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+ %global debug_package %{nil}
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- %package -n python3-pyphi
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- Summary: %{summary}
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- BuildRequires: make
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BuildRequires: python3-devel
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- BuildRequires: %{py3_dist pytest}
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- BuildRequires: %{py3_dist pytest-lazy-fixture}
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+
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+ %if %{with doc_pdf}
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+ # Documentation
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+ BuildRequires: make
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BuildRequires: %{py3_dist sphinx}
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+ BuildRequires: python3-sphinx-latex
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+ BuildRequires: latexmk
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+ BuildRequires: tex-xetex-bin
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+ BuildRequires: /usr/bin/xindy
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+ # HTML theme module is imported even when building LaTeX:
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BuildRequires: %{py3_dist sphinx_rtd_theme}
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+ %endif
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+
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+ %global _description %{expand:
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+ PyPhi is a Python library for computing integrated information (𝚽), and the
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+ associated quantities and objects.
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+
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+ If you use this code, please cite the paper:
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+
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+ Mayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G. (2018)
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+ PyPhi: A toolbox for integrated information theory. PLOS Computational
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+ Biology 14(7): e1006343. https://doi.org/10.1371/journal.pcbi.1006343}
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+
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+ %description %_description
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+
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+ %package -n python3-pyphi
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+ Summary: %{summary}
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+
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+ BuildArch: noarch
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%description -n python3-pyphi %_description
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%package doc
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Summary: %{summary}
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+ BuildArch: noarch
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+
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%description doc
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Documentation for %{name}
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-
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%prep
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- %autosetup -n pyphi-%{version} -S git
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+ %autosetup -n pyphi-%{version} -p1
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+
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+ # Strip unnecessary shebangs from non-script files
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+ find . -type f -name '*.py' -execdir sed -r -i '1{/^#!/d}' '{}' '+'
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- # sphinx 1.3+, it's an extension
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- # Also sent upstream: https://github.com/wmayner/pyphi/pull/22
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- sed -i "s/sphinxcontrib.napoleon/sphinx.ext.napoleon/" docs/conf.py
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+ # Remove a bundled copy of gprof2dot (packaged in Fedora, upstream at
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+ # https://github.com/jrfonseca/gprof2dot); we do not need to do profiling and
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+ # will not ship it in the binary RPMs.
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+ rm -v profiling/gprof2dot
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+ # Remove a bundled copy of “krTheme Sphinx Style”
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+ rm -rvf docs/_themes/*
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- find pyphi -name "*.py" -exec sed -i '/#!\/usr\/bin\/env python3/ d' '{}' \;
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+ # https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/#_linters
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+ sed -r '/^(coverage|asv|virtualenv)\b/d' test_requirements.txt |
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+ tee test_requirements.filtered.txt
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+
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+ # Since pdflatex cannot handle Unicode inputs in general:
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+ echo "latex_engine = 'xelatex'" >> docs/conf.py
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%generate_buildrequires
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- %pyproject_buildrequires -r
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+ %pyproject_buildrequires %{?with_tests:test_requirements.filtered.txt}
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%build
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%pyproject_wheel
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-
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- make -C docs SPHINXBUILD=sphinx-build-3 html
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- rm docs/_build/html/{.doctrees,.buildinfo} -vf
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+ %if %{with doc_pdf}
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+ %make_build -C docs latex SPHINXOPTS='-j%{?_smp_build_ncpus}'
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+ %make_build -C docs/_build/latex LATEXMKOPTS='-quiet'
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+ %endif
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%install
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%pyproject_install
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@@ -84,61 +118,9 @@
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%files doc
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%license LICENSE.md
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- %doc docs/_build/html/
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+ %if %{with doc_pdf}
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+ %doc docs/_build/latex/PyPhi.pdf
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+ %endif
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%changelog
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%autochangelog
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-
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- * Wed Aug 18 2021 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.2.0-13
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- - Correctly disable tests on s390x
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-
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- * Wed Aug 18 2021 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.2.0-12
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- - Fix build
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-
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- * Fri Jul 23 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.2.0-11
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- - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
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-
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- * Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 1.2.0-10
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- - Rebuilt for Python 3.10
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-
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- * Fri Jan 29 2021 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.2.0-9
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- - Update URL
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-
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- * Wed Jan 27 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.2.0-9
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- - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
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-
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- * Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.2.0-8
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- - Second attempt - Rebuilt for
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- https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
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-
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- * Wed Jul 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.2.0-7
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- - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
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-
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- * Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 1.2.0-6
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- - Rebuilt for Python 3.9
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-
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- * Thu Jan 30 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.2.0-5
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- - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
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-
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- * Mon Aug 19 2019 Miro Hrončok <mhroncok@redhat.com> - 1.2.0-4
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- - Rebuilt for Python 3.8
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-
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- * Fri Jul 26 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.2.0-3
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- - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
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-
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- * Fri Jul 12 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.2.0-2
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- - Enable tests
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-
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- * Sat Jun 22 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.2.0-1
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- - Update to 1.2.0
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-
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- * Sat Feb 02 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.1.0-3
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- - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
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-
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- * Mon Nov 19 2018 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.1.0-2
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- - Update license
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- - Fix doc generation
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- - Correct rpmlint errors
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-
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- * Wed Nov 14 2018 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.1.0-1
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- - Initial rpm build
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music
commented 6 months ago
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