[packit] 7.32.4 upstream release

Upstream tag: v7.32.4
Upstream commit: 0998cc57

.gitignore

@@ -16,3 +16,16 @@
 /snakemake-7.18.1.tar.gz
 /snakemake-7.18.2.tar.gz
 /snakemake-7.19.1.tar.gz
+/snakemake-7.20.0.tar.gz
+/snakemake-7.21.0.tar.gz
+/snakemake-7.22.0.tar.gz
+/snakemake-7.24.1.tar.gz
+/snakemake-7.25.2.tar.gz
+/snakemake-7.25.3.tar.gz
+/snakemake-7.26.0.tar.gz
+/snakemake-7.30.1.tar.gz
+/snakemake-7.31.1.tar.gz
+/snakemake-7.32.0.tar.gz
+/snakemake-7.32.2.tar.gz
+/snakemake-7.32.3.tar.gz
+/snakemake-7.32.4.tar.gz

README.packit

@@ -0,0 +1,3 @@
+This repository is maintained by packit.
+https://packit.dev/
+The file was generated using packit 0.80.0.post8+gf2b5fcbc.

snakemake.spec

@@ -1,7 +1,7 @@
-%bcond_without tests
+%bcond tests 1
 # Sphinx-generated HTML documentation is not suitable for packaging; see
 # https://bugzilla.redhat.com/show_bug.cgi?id=2006555 for discussion.
-%bcond_without doc_pdf
+%bcond doc_pdf 1
 
 %global _description %{expand:
 The Snakemake workflow management system is a tool to create reproducible and
@@ -12,15 +12,18 @@ Finally, Snakemake workflows can entail a description of required software,
 which will be automatically deployed to any execution environment.}
 
 Name:           snakemake
-Version:        7.19.1
+Version:        7.32.4
 Release:        %autorelease 
 Summary:        Workflow management system to create reproducible and scalable data analyses
 
 # The entire project is (SPDX) MIT, except:
-# - versioneer.py is LicenseRef-Fedora-Public-Domain (“License: Public Domain”)
-#   but does not contribute to the license of the binary RPM
-# SPDX
-License:        MIT
+# - versioneer.py is Unlicense
+# - snakemake/_version.py says:
+#     This file is released into the public domain.
+#   which would be LicenseRef-Fedora-Public-Domain, except that the comments in
+#   versioneer.py make it clear that Unlicense is intended for the generated
+#   files as well.
+License:        MIT AND Unlicense
 URL:            https://snakemake.readthedocs.io/en/stable/index.html
 Source0:        https://github.com/snakemake/snakemake/archive/v%{version}/snakemake-%{version}.tar.gz
 
@@ -32,6 +35,13 @@ Patch:          snakemake-7.11.0-docs-no-animated-demo.patch
 
 BuildRequires:  python3-devel
 
+BuildRequires:  help2man
+
+BuildRequires:  vim-filesystem
+Requires:       vim-filesystem
+
+Provides:       vim-snakemake = %{version}-%{release}
+
 %if %{with tests}
 # See test-environment.yml for a listing of test dependencies, along with a lot
 # of other cruft.
@@ -67,7 +77,7 @@ BuildRequires:  /usr/bin/rsvg-convert
 # No metapackage for “pep” extra because the following are not packaged:
 #   - python3-eido
 #   - python3-peppy
-%pyproject_extras_subpkg -n snakemake reports messaging google-cloud
+%pyproject_extras_subpkg -n snakemake reports messaging google-cloud azure
 
 %prep
 %autosetup -n snakemake-%{version} -p1
@@ -83,10 +93,16 @@ sed -r -i 's@"python"@"%{python3}"@g' tests/test_linting.py
 sed -r -i '/sphinxcontrib-napoleon/d' docs/requirements.txt
 # Since pdflatex cannot handle Unicode inputs in general:
 echo "latex_engine = 'xelatex'" >> docs/conf.py
+# Copy and rename nano and vim extensions readmes for use in the main
+# documentation directory.
+for editor in nano vim
+do
+  cp -vp "misc/${editor}/README.md" "README-${editor}.md"
+done
 
 %generate_buildrequires
 # Generate BR’s for all supported extras to ensure they do not FTI
-%pyproject_buildrequires -x reports,messaging,google-cloud %{?with_doc_pdf:docs/requirements.txt}
+%pyproject_buildrequires -x reports,messaging,google-cloud,azure %{?with_doc_pdf:docs/requirements.txt}
 
 %build
 %pyproject_wheel
@@ -108,6 +124,37 @@ PYTHONPATH="${PWD}" %make_build -C docs latexpdf SPHINXOPTS='%{?_smp_mflags}'
 %pyproject_install
 %pyproject_save_files snakemake
 
+# We wait until %%install to generate the man page so that we can use the
+# proper script entry point. The generated man page is not perfect, but it is
+# good enough to be useful.
+install -d %{buildroot}%{_mandir}/man1
+PATH="${PATH-}:%{buildroot}%{_bindir}" \
+    PYTHONPATH='%{buildroot}%{python3_sitelib}' \
+    help2man --no-info --name='%{summary}' snakemake \
+    > %{buildroot}%{_mandir}/man1/snakemake.1
+# No man page for snakemake-bash-completion since it is not intended for manual
+# invocation.
+
+# Generate and install shell completions.
+install -d %{buildroot}%{bash_completions_dir}
+# Since 7.29.0, snakemake --bash-completion no longer works without a Snakefile
+# https://github.com/snakemake/snakemake/issues/2336
+touch Snakefile
+PATH="${PATH-}:%{buildroot}%{_bindir}" \
+    PYTHONPATH='%{buildroot}%{python3_sitelib}' \
+    snakemake --bash-completion \
+    > %{buildroot}%{bash_completions_dir}/snakemake.bash
+
+# Install nano syntax highlighting
+install -t '%{buildroot}%{_datadir}/nano' -D -m 0644 -p \
+    misc/nano/syntax/snakemake.nanorc
+
+# Install vim syntax highlighting
+install -d '%{buildroot}%{_datadir}/vim/vimfiles'
+cp -vrp misc/vim/* '%{buildroot}%{_datadir}/vim/vimfiles'
+find '%{buildroot}%{_datadir}/vim/vimfiles' \
+    -type f -name 'README.*' -print -delete
+
 %check
 %if %{with tests}
 # Lint output “Migrate long run directives into scripts or notebooks …” is
@@ -120,19 +167,46 @@ k="${k-}${k+ and }not test_tes"
 # Require a running slurm instance; maybe this is possible to set up
 # temporarily in the offline build environment, but we don’t know how.
 k="${k-}${k+ and }not test_slurm_"
-# tests/test_google_lifesciences.py needs a network connection (and GCP credentials)
-%pytest -v -k "${k-}" --ignore tests/test_google_lifesciences.py
+
+# Needs a network connection (and GCP credentials):
+ignore="${ignore-} --ignore=tests/test_google_lifesciences.py"
+# ______ ERROR collecting tests/test_conda_python_script/test_script.py ______
+# import file mismatch:
+# imported module 'test_script' has this __file__ attribute:
+#   /builddir/build/BUILD/snakemake-7.31.1/tests/test_conda_python_3_7_script/test_script.py
+# which is not the same as the test file we want to collect:
+#   /builddir/build/BUILD/snakemake-7.31.1/tests/test_conda_python_script/test_script.py
+# HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules
+#
+# Plus, this would add an unwanted BuildRequires on %%{py3_dist Pillow}.
+ignore="${ignore-} --ignore-glob=tests/test_conda_python_3_7_script/*"
+
+%pytest -v -k "${k-}" ${ignore-}
 %endif
 
 %files -f %{pyproject_files}
 %{_bindir}/snakemake
+%{_mandir}/man1/snakemake.1*
+
 %{_bindir}/snakemake-bash-completion
+%{bash_completions_dir}/snakemake.bash
+
+# This is not owned by the filesystem package, and there is no nano-filesystem
+# subpackage, so we co-own the directory to avoid depending on nano.
+%dir %{_datadir}/nano/
+%{_datadir}/nano/snakemake.nanorc
+
+%{_datadir}/vim/vimfiles/ftdetect/snakemake.vim
+%{_datadir}/vim/vimfiles/ftplugin/snakemake/
+%{_datadir}/vim/vimfiles/syntax/snakemake.vim
 
 %files doc
 %license LICENSE.md
 %doc CHANGELOG.md
 %doc CODE_OF_CONDUCT.md
 %doc README.md
+%doc README-nano.md
+%doc README-vim.md
 %if %{with doc_pdf}
 %doc docs/_build/latex/Snakemake.pdf
 %endif

sources

@@ -1 +1 @@
-SHA512 (snakemake-7.19.1.tar.gz) = d35d4f61eef4f25a7f4b5f1869e10e259fe9aad11704ee59cd4f9c0ba1a2f58cde197be57eee6ed478bedc865971b584c1a3802e2044bb9817be5d5c4d1800d1
+SHA512 (snakemake-7.32.4.tar.gz) = 34fef61528b18facab798652c88ed5c698ef02161e023255fdd024b7c7781c4e582cdb04b2740fdff9b6f3600acaec719742984acee57920bb48ef3b5af99d9a