576 lines
24 KiB
RPMSpec
576 lines
24 KiB
RPMSpec
%global _with_bootstrap 1
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# Work around a series of circular test dependencies:
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#
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# python-snakemake-interface-report-plugins
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# ￬￪ ⬐───╮
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# snakemake → python-snakemake-interface-executor-plugins⬎
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# ￪￪￪ │ ⬑────────────────────python-snakemake-executor-plugin-cluster-generic
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# │││ ↳python-snakemake-interface-storage-plugins─────────────────╮
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# │││ ￬────────────────╮│
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# ││╰────────────────────────python-snakemake-storage-plugin-http││
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# │╰─────────────────────────python-snakemake-storage-plugin-s3🠔─╯│
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# ╰──────────────────────────python-snakemake-storage-plugin-fs🠔──╯
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#
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# A good build order is:
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#
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# 1. BOOTSTRAP: python-snakemake-interface-executor-plugins,
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# python-snakemake-interface-storage-plugins,
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# python-snakemake-interface-report-plugins
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# 2. BOOTSTRAP: snakemake
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# 3. python-snakemake-executor-plugin-cluster-generic,
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# python-snakemake-storage-plugin-http,
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# python-snakemake-storage-plugin-s3,
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# python-snakemake-storage-plugin-fs
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# 4. snakemake, python-snakemake-interface-executor-plugins,
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# python-snakemake-interface-storage-plugins,
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# python-snakemake-interface-report-plugins
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%bcond bootstrap 0
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%bcond tests %{without bootstrap}
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# Run tests that require network access? This only makes sense for local mock
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# builds in combination with --enable-network.
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%bcond network_tests 0
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# Almost all of the conda tests require network access, but there are also
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# other failures that are not straightforward to understand.
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%bcond conda_tests 0
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# F43FailsToInstall: python3-google-cloud-storage
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# https://bugzilla.redhat.com/show_bug.cgi?id=2371928
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%bcond gcs_tests 0
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Name: snakemake
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Version: 9.5.1
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Release: %autorelease
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Summary: Workflow management system to create reproducible and scalable data analyses
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# The primary license for Snakemake is MIT; web assets contribute a variety of
|
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# other licenses.
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#
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# Apache-2.0 AND BSD-2-Clause AND BSD-3-CLause AND ISC AND MIT AND MIT-0:
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# - src/snakemake/assets/data/vega/vega.js
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#
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# BSD-3-Clause AND MIT:
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# - src/snakemake/assets/data/vega-lite/vega-lite.js
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#
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# BSD-3-Clause AND ISC AND MIT:
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# - src/snakemake/assets/data/vega-embed/vega-embed.js
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#
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# MIT:
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# - All Snakemake code unless otherwise noted
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# - heroicons: It is unclear if anything derived from heroicons is actually
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# present in the package, but upstream carries a copy of its license file, so
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# we mention the possibility.
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# - src/snakemake/assets/data/prop-types/prop-types.min.js
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# - src/snakemake/assets/data/tailwindcss/tailwind.css
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#
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# == License breakdown: src/snakemake/assets/data/vega/vega.js ==
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#
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# The primary license for npm(vega) is BSD-3-Clause. The bundle contains:
|
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#
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# Apache-2.0:
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# - apache-commons-math, from which an implementation of erfinv is derived
|
||
# BSD-2-Clause:
|
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# - npm(esprima), bundled as a copied, derived, or adapted snippet
|
||
# BSD-3-Clause:
|
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# - npm(vega) and various npm(vega-*) libraries
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# - npm(d3-contour), bundled as a copied, derived, or adapted snippet
|
||
# - npm(d3-regression), bundled as a copied, derived, or adapted snippet
|
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# - npm(science), bundled as a copied, derived, or adapted snippet
|
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# - npm(shapefile), bundled as a copied, derived, or adapted snippet
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# ISC:
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# - various npm(d3-*) libraries
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# - npm(delaunator)
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# - npm(quickselect)
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# - npm(topojson-client)
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# ISC AND MIT:
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# - npm(d3-geo) (MIT is due to some code being derived from GeographicLib)
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||
# - npm(d3-geo-projection) (MIT is due to some code being derived from
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# https://github.com/scijs/integrate-adaptive-simpson)
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||
# MIT:
|
||
# - npm(@types/estree)
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# - npm(hashlru), bundled as a copied, derived, or adapted snippet
|
||
# - npm(regression), bundled as a copied, derived, or adapted snippet
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||
# MIT-0:
|
||
# - npm(fabric), bundled as a copied, derived, or adapted snippet
|
||
#
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||
# == License breakdown: src/snakemake/assets/data/vega-lite/vega-lite.js ==
|
||
#
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||
# The primary license for npm(vega-lite) is BSD-3-Clause. The bundle contains:
|
||
#
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||
# BSD-3-Clause:
|
||
# - npm(vega-lite) and various npm(vega-*) libraries
|
||
# MIT:
|
||
# - npm(@types/clone)
|
||
# - npm(@types/estree)
|
||
# - npm(clone)
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||
# - npm(fast-deep-equal)
|
||
# - npm(fast-json-stable-stringify)
|
||
# - npm(hashlru), bundled as a copied, derived, or adapted snippet
|
||
# - npm(json-stringify-pretty-compact)
|
||
#
|
||
# == License breakdown: src/snakemake/assets/data/vega-embed/vega-embed.js ==
|
||
#
|
||
# The primary license for npm(vega-embed) is BSD-3-Clause. The bundle contains:
|
||
#
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||
# BSD-3-Clause:
|
||
# - npm(vega-embed) and various npm(vega-*) libraries
|
||
# ISC:
|
||
# - npm(semver)
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||
# MIT:
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||
# - npm(fast-json-patch)
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||
# - npm(json-stringify-pretty-compact)
|
||
License: %{shrink:
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||
Apache-2.0 AND
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||
BSD-2-Clause AND
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||
BSD-3-Clause AND
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||
ISC AND
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MIT AND
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MIT-0
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||
}
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URL: https://snakemake.readthedocs.io/en/stable/index.html
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%global forgeurl https://github.com/snakemake/snakemake
|
||
# We could use the PyPI sdist, which already contains the HTML report assets,
|
||
# but we would lose at least the vim extensions and changelog, and we would
|
||
# have to nontrivially modify the sdist to remove a CC0-1.0-licensed polyfill
|
||
# before uploading it to the lookaside cache, so doing so would not be
|
||
# meaningfully easier than using the GitHub archive with an additional source
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# for the assets.
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Source0: %{forgeurl}/archive/v%{version}/snakemake-%{version}.tar.gz
|
||
# The assets for HTML reports are normally downloaded in setup.py when creating
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# the sdist. We use a script, Source2, executed with no arguments (implicitly
|
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# relying on the spec file in the same directory) to download the assets,
|
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# modify them as necessary, and pack them into an additional source archive.
|
||
Source1: snakemake-%{version}-assets.tar.zst
|
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Source2: get_assets
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|
||
# Downstream-only: adjust the asset metadata in the sources, including
|
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# checksums, for any adjustments that happened in the get_assets script.
|
||
#
|
||
# When the get_assets script unpacks and patches Source0 in order to use it to
|
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# download assets, it skips this patch, because we need to first fetch the
|
||
# original assets in order to then modify them. The signal for this behavior is
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||
# the substring "modified-assets" in the patch name.
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Patch: snakemake-9.1.1-modified-assets.patch
|
||
|
||
# chore: Allow PuLP 3.2
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||
# https://github.com/snakemake/snakemake/pull/3609
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Patch: %{forgeurl}/pull/3609.patch
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BuildSystem: pyproject
|
||
# Generate BR’s for all supported extras to ensure they do not FTI
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BuildOption(generate_buildrequires): -x reports,messaging
|
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BuildOption(install): -l snakemake
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BuildOption(check): %{shrink:
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-e '*.tests*'
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%{?!with_gcs_tests:-e 'snakemake.executors.google_lifesciences_helper'}
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||
}
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||
BuildArch: noarch
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||
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||
BuildRequires: help2man
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||
|
||
# Snakemake uses (unversioned) "python" as the default remote execution
|
||
# command. Because remote hosts could be Windows machines, and those are likely
|
||
# to lack "python3.exe" (see https://github.com/python/cpython/issues/99185),
|
||
# we didn’t try to convince upstream to change this. Instead, we (reluctantly)
|
||
# just make sure that our own Snakemake installations are compatible by
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||
# depending on python-unversioned-command.
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||
BuildRequires: python-unversioned-command
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||
Requires: python-unversioned-command
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||
|
||
BuildRequires: vim-filesystem
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||
Requires: vim-filesystem
|
||
|
||
# Required for snakemake.script.RScript, snakemake.notebook.RJupyterNotebook
|
||
# (Some of the tests in tests/tests_using_conda.py require this.)
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||
BuildRequires: R-core
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||
Recommends: R-core
|
||
|
||
Provides: vim-snakemake = %{version}-%{release}
|
||
|
||
# Regarding pre-compiled/pre-minified JavaScript, see:
|
||
# - https://pagure.io/fesco/issue/3177
|
||
# - https://pagure.io/packaging-committee/pull-request/1370
|
||
# Regarding CSS, see:
|
||
# - https://pagure.io/fesco/issue/3269
|
||
# - https://pagure.io/packaging-committee/pull-request/1402
|
||
|
||
# Styles from Pygments are bundled in generated HTML reports (thus the presence
|
||
# of a Pygments license file), but the styles come from the system
|
||
# python3-pygments package and are not actually bundled in this package.
|
||
|
||
# tailwind.css 3.4.16 is src/snakemake/assets/data/tailwindcss/tailwind.css,
|
||
# but we do not normally treat CSS frameworks as bundled dependencies, and it
|
||
# is not clear how we should name a virtusl Provides if we added one.
|
||
|
||
# src/snakemake/assets/data/react/react.production.min.js
|
||
Provides: bundled(npm(react)) = 18.2.0
|
||
# src/snakemake/assets/data/react/react-dom.production.min.js
|
||
Provides: bundled(npm(react-dom)) = 18.2.0
|
||
|
||
# src/snakemake/assets/data/vega/vega.js
|
||
Provides: bundled(npm(vega)) = 5.21.0
|
||
# Bundled in src/snakemake/assets/data/vega/vega.js as dependencies:
|
||
# For versions of vega-* packages, see:
|
||
# https://github.com/vega/vega/blob/v5.21.0/packages
|
||
Provides: bundled(npm(vega-crossfilter)) = 4.0.5
|
||
Provides: bundled(npm(vega-dataflow)) = 5.7.4
|
||
Provides: bundled(npm(vega-encode)) = 4.8.3
|
||
Provides: bundled(npm(vega-event-selector)) = 3.0.0
|
||
Provides: bundled(npm(vega-expression)) = 5.0.0
|
||
Provides: bundled(npm(vega-force)) = 4.0.7
|
||
Provides: bundled(npm(vega-format)) = 1.0.4
|
||
Provides: bundled(npm(vega-functions)) = 5.12.1
|
||
Provides: bundled(npm(vega-geo)) = 4.3.8
|
||
Provides: bundled(npm(vega-hierarchy)) = 4.0.9
|
||
Provides: bundled(npm(vega-label)) = 1.1.0
|
||
Provides: bundled(npm(vega-loader)) = 4.4.1
|
||
Provides: bundled(npm(vega-parser)) = 6.1.4
|
||
Provides: bundled(npm(vega-projection)) = 1.4.5
|
||
Provides: bundled(npm(vega-regression)) = 1.0.9
|
||
Provides: bundled(npm(vega-runtime)) = 6.1.3
|
||
Provides: bundled(npm(vega-scale)) = 7.1.1
|
||
Provides: bundled(npm(vega-scenegraph)) = 4.9.4
|
||
Provides: bundled(npm(vega-statistics)) = 5.3.1
|
||
Provides: bundled(npm(vega-time)) = 2.0.4
|
||
Provides: bundled(npm(vega-transforms)) = 4.9.5
|
||
Provides: bundled(npm(vega-typings)) = 0.22.0
|
||
Provides: bundled(npm(vega-util)) = 1.17.0
|
||
Provides: bundled(npm(vega-view)) = 5.10.1
|
||
Provides: bundled(npm(vega-view-transforms)) = 4.5.8
|
||
Provides: bundled(npm(vega-voronoi)) = 4.1.5
|
||
Provides: bundled(npm(vega-wordcloud)) = 4.1.3
|
||
# For these, see notes in src/snakemake/assets/__init__.py.
|
||
Provides: bundled(npm(@types/estree)) = 0.0.50
|
||
Provides: bundled(npm(d3-array)) = 2.12.1
|
||
Provides: bundled(npm(d3-color)) = 2.0.0
|
||
Provides: bundled(npm(d3-delaunay)) = 5.2.0
|
||
Provides: bundled(npm(d3-dispatch)) = 2.0.0
|
||
Provides: bundled(npm(d3-dsv)) = 2.0.0
|
||
Provides: bundled(npm(d3-force)) = 2.1.1
|
||
Provides: bundled(npm(d3-format)) = 2.0.0
|
||
Provides: bundled(npm(d3-geo)) = 2.0.2
|
||
Provides: bundled(npm(d3-geo-projection)) = 3.0.0
|
||
Provides: bundled(npm(d3-hierarchy)) = 2.0.0
|
||
Provides: bundled(npm(d3-interpolate)) = 2.0.1
|
||
Provides: bundled(npm(d3-path)) = 2.0.0
|
||
Provides: bundled(npm(d3-quadtree)) = 2.0.0
|
||
Provides: bundled(npm(d3-scale)) = 3.3.0
|
||
Provides: bundled(npm(d3-shape)) = 2.1.0
|
||
Provides: bundled(npm(d3-time)) = 2.1.1
|
||
Provides: bundled(npm(d3-time-format)) = 3.0.0
|
||
Provides: bundled(npm(d3-timer)) = 2.0.0
|
||
Provides: bundled(npm(delaunator)) = 4.0.1
|
||
Provides: bundled(npm(topojson-client)) = 3.1.0
|
||
# Present in src/snakemake/assets/data/vega/vega.js in the form of copied,
|
||
# derived, or adapted snippets. See notes in src/snakemake/assets/__init__.py.
|
||
# Implementation of erfinv is based on:
|
||
Provides: bundled(apache-commons-math) = 3.6.1
|
||
# Expression parser is based on:
|
||
Provides: bundled(esprima) = 2.2.0
|
||
Provides: bundled(fabric) = 2.4.5
|
||
Provides: bundled(npm(d3-contour)) = 1.3.2
|
||
Provides: bundled(npm(d3-regression)) = 1.2.1
|
||
Provides: bundled(npm(hashlru)) = 1.0.4
|
||
Provides: bundled(npm(quickselect)) = 2.0.0
|
||
Provides: bundled(npm(regression)) = 2.0.1
|
||
Provides: bundled(npm(science)) = 1.9.3
|
||
Provides: bundled(npm(shapefile)) = 0.6.2
|
||
|
||
# src/snakemake/assets/data/vega-lite/vega-lite.js
|
||
Provides: bundled(npm(vega-lite)) = 5.2.0
|
||
# NOTE: Some of the following virtual Provides are commented out. These are
|
||
# correct, and need to be considered when determining the license of
|
||
# vega-lite.js, but they do not need to be repeated in the spec file because
|
||
# they duplicate virtual Provides from vega.js.
|
||
#
|
||
# Bundled in src/snakemake/assets/data/vega-lite/vega-lite.js as dependencies:
|
||
# See notes in src/snakemake/assets/__init__.py.
|
||
Provides: bundled(npm(@types/clone)) = 2.1.1
|
||
Provides: bundled(npm(clone)) = 2.1.2
|
||
Provides: bundled(npm(fast-deep-equal)) = 3.1.3
|
||
Provides: bundled(npm(fast-json-stable-stringify)) = 2.1.0
|
||
Provides: bundled(npm(json-stringify-pretty-compact)) = 3.0.0
|
||
# See notes in src/snakemake/assets/__init__.py, as well as dependencies in
|
||
# https://github.com/vega/vega-lite/blob/v5.2.0/package.json, and for versions,
|
||
# see https://github.com/vega/vega-lite/blob/v5.2.0/yarn.lock; these correspond
|
||
# to those associated with vega 5.2.1.
|
||
#Provides: bundled(npm(@types/estree)) = 0.0.50
|
||
#Provides: bundled(npm(vega-event-selector)) = 3.0.0
|
||
#Provides: bundled(npm(vega-expression)) = 5.0.0
|
||
#Provides: bundled(npm(vega-util)) = 1.17.0
|
||
# Present in src/snakemake/assets/data/vega-lite/vega-lite.js in the form of
|
||
# copied, derived, or adapted snippets. See notes in
|
||
# src/snakemake/assets/__init__.py.
|
||
#Provides: bundled(npm(hashlru)) = 1.0.4
|
||
|
||
# src/snakemake/assets/data/vega-embed/vega-embed.js
|
||
Provides: bundled(npm(vega-embed)) = 6.20.8
|
||
# NOTE: Some of the following virtual Provides are commented out. These are
|
||
# correct, and need to be considered when determining the license of
|
||
# vega-embed.js, but they do not need to be repeated in the spec file because
|
||
# they duplicate virtual Provides from vega.js and/or vega-lite.js.
|
||
#
|
||
# Bundled in src/snakemake/assets/data/vega-embed/vega-embed.js as
|
||
# dependencies:
|
||
# See notes in src/snakemake/assets/__init__.py.
|
||
Provides: bundled(npm(fast-json-patch)) = 3.1.0
|
||
#Provides: bundled(npm(json-stringify-pretty-compact)) = 3.0.0
|
||
Provides: bundled(npm(semver)) = 7.3.5
|
||
# See notes in src/snakemake/assets/__init__.py, as well as dependencies in
|
||
# https://github.com/vega/vega-embed/blob/v6.20.8/package.json, and for
|
||
# versions, see https://github.com/vega/vega-embed/blob/v6.20.8/yarn.lock;
|
||
# these correspond to those associated with vega 5.2.1.
|
||
Provides: bundled(npm(vega-interpreter)) = 1.0.4
|
||
Provides: bundled(npm(vega-schema-url-parser)) = 2.2.0
|
||
Provides: bundled(npm(vega-themes)) = 2.10.0
|
||
Provides: bundled(npm(vega-tooltip)) = 0.28.0
|
||
#Provides: bundled(npm(vega-util)) = 1.17.0
|
||
# Present in src/snakemake/assets/data/vega-embed/vega-embed.js in the form of
|
||
# copied, derived, or adapted snippets. See notes in
|
||
# src/snakemake/assets/__init__.py.
|
||
#Provides: bundled(npm(hashlru)) = 1.0.4
|
||
# _areEquals() is based on:
|
||
#Provides: bundled(npm(fast-deep-equal)) = 3.1.3
|
||
|
||
# It is unclear if anything derived from heroicons is actually present in the
|
||
# package, but upstream carries a copy of its license file, so we dutifully add
|
||
# the virtual Provides, just in case we have missed something.
|
||
Provides: bundled(npm(heroicons)) = 1.0.3
|
||
|
||
# src/snakemake/assets/data/prop-types/prop-types.min.js
|
||
Provides: bundled(npm(prop-types)) = 15.7.2
|
||
|
||
# These extras were removed upstream in Snakemake 8.0.0. Retain the Obsoletes
|
||
# until F40 reaches EOL so we have a clean upgrade path.
|
||
Obsoletes: snakemake+azure < 8.1.0-1
|
||
Obsoletes: snakemake+google-cloud < 8.1.0-1
|
||
# We no longer build Sphinx-generated PDF documentation. Beginning with 8.2.3,
|
||
# this would require patching out sphinxawesome-theme from docs/conf.py. It’s
|
||
# possible but tedious.
|
||
Obsoletes: snakemake-doc < 8.2.1-2
|
||
|
||
%if %{with tests}
|
||
# For several tests (either apptainer or singularity-ce should work):
|
||
BuildRequires: (apptainer or singularity-ce)
|
||
%if %{with conda_tests}
|
||
# For tests/tests_using_conda.py
|
||
BuildRequires: conda
|
||
# For test_conda_pin_file, test_conda_named, test_conda_function
|
||
BuildRequires: ripgrep
|
||
# For test_script_xsh
|
||
BuildRequires: xonsh
|
||
%endif
|
||
# For test_env_modules:
|
||
BuildRequires: environment-modules
|
||
# For test_filegraph and test_env_modules, which use dot:
|
||
BuildRequires: graphviz
|
||
# For test_github_issue1158:
|
||
BuildRequires: strace
|
||
# For test_benchmark and test_benchmark_jsonl:
|
||
BuildRequires: stress-ng
|
||
|
||
# See test-environment.yml for a listing of test dependencies, along with a lot
|
||
# of other cruft.
|
||
BuildRequires: %{py3_dist boto3}
|
||
BuildRequires: %{py3_dist pandas}
|
||
BuildRequires: %{py3_dist pytest}
|
||
BuildRequires: %{py3_dist pytest-mock}
|
||
BuildRequires: %{py3_dist snakemake-executor-plugin-cluster-generic}
|
||
BuildRequires: %{py3_dist snakemake-storage-plugin-http}
|
||
BuildRequires: %{py3_dist snakemake-storage-plugin-fs}
|
||
BuildRequires: %{py3_dist snakemake-storage-plugin-s3}
|
||
%endif
|
||
# For import-testing snakemake.gui
|
||
BuildRequires: %{py3_dist flask}
|
||
%if %{with google_cloud_storage_tests}
|
||
# For import-testing snakemake.executors.google_lifesciences_helper:
|
||
BuildRequires: %{py3_dist google-cloud-storage}
|
||
%endif
|
||
|
||
%global _description %{expand:
|
||
The Snakemake workflow management system is a tool to create reproducible and
|
||
scalable data analyses. Workflows are described via a human readable, Python
|
||
based language. They can be seamlessly scaled to server, cluster, grid and
|
||
cloud environments, without the need to modify the workflow definition.
|
||
Finally, Snakemake workflows can entail a description of required software,
|
||
which will be automatically deployed to any execution environment.}
|
||
|
||
%description %_description
|
||
|
||
|
||
# No metapackage for “pep” extra because the following are not packaged:
|
||
# - python3-eido
|
||
# - python3-peppy
|
||
%pyproject_extras_subpkg -n snakemake reports messaging
|
||
|
||
|
||
%prep
|
||
%autosetup -n snakemake-%{version} -p1
|
||
%setup -q -T -D -a 1 -c -n snakemake-%{version}
|
||
|
||
# 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
|
||
|
||
# The CDN URL for tailwind.css does not deliver a file with a stable checksum,
|
||
# so upstream has not recorded a checksum in src/snakemake/assets/__init__.py.
|
||
# A consequence of this is that setup.py will *always* re-download
|
||
# tailwind.css, even if it is already present, when building an sdist or
|
||
# bdist/wheel. Of course, this is not acceptable in an offline build, so we
|
||
# record the actual checksum of the tailwind.css file we are packaging.
|
||
cat >> src/snakemake/assets/__init__.py <<EOF
|
||
|
||
# Fedora patch: Upstream does not record a checksum for tailwind.css because
|
||
# they report that the CDN URL may serve trivially different copies. Since we
|
||
# package a copy of the file, we record the checksum of the actual packaged
|
||
# file.
|
||
Assets.spec["tailwindcss/tailwind.css"].sha256 = "$(
|
||
sha256sum -b src/snakemake/assets/data/tailwindcss/tailwind.css |
|
||
awk '{print $1}'
|
||
)"
|
||
EOF
|
||
|
||
|
||
%generate_buildrequires -p
|
||
export SETUPTOOLS_SCM_PRETEND_VERSION='%{version}'
|
||
|
||
|
||
%build -p
|
||
export SETUPTOOLS_SCM_PRETEND_VERSION='%{version}'
|
||
|
||
|
||
%install -a
|
||
# Fix shebangs (no /usr/env shebangs)
|
||
%py3_shebang_fix %{buildroot}%{python3_sitelib} %{buildroot}%{_bindir}
|
||
|
||
# Remove shebangs from non-executable scripts. The Python script is executable
|
||
# in the source tree but will be installed without executable permissions.
|
||
sed -r -i '1{/^#!/d}' \
|
||
%{buildroot}%{python3_sitelib}/snakemake/executors/jobscript.sh \
|
||
%{buildroot}%{python3_sitelib}/snakemake/executors/google_lifesciences_helper.py
|
||
|
||
# Mark license files in the asset bundle.
|
||
sed -r -i 's@^.*/(LICEN[CS]E|NOTICE)[^/]*$@%%license &@' %{pyproject_files}
|
||
|
||
# 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="${PATH-}:%{buildroot}%{_bindir}" \
|
||
PYTHONPATH='%{buildroot}%{python3_sitelib}' \
|
||
help2man --no-info --name='%{summary}' snakemake \
|
||
> %{buildroot}%{_mandir}/man1/snakemake.1
|
||
|
||
# Install nano syntax highlighting
|
||
install -t '%{buildroot}%{_datadir}/nano' -D -m 0644 -p \
|
||
misc/nano/syntax/snakemake.nanorc
|
||
|
||
# Install vim syntax highlighting
|
||
install -d '%{buildroot}%{_datadir}/vim/vimfiles'
|
||
cp -vrp misc/vim/* '%{buildroot}%{_datadir}/vim/vimfiles'
|
||
find '%{buildroot}%{_datadir}/vim/vimfiles' \
|
||
-type f -name 'README.*' -print -delete
|
||
|
||
|
||
%check -a
|
||
%if %{with tests}
|
||
%if %{without network_tests}
|
||
# The following require network access (at least DNS) and pass if it is
|
||
# available.
|
||
k="${k-}${k+ and }not test_ancient"
|
||
k="${k-}${k+ and }not test_dynamic_container"
|
||
k="${k-}${k+ and }not test_github_issue78"
|
||
k="${k-}${k+ and }not test_issue1083"
|
||
k="${k-}${k+ and }not test_issue3361_pass"
|
||
k="${k-}${k+ and }not test_keep_local"
|
||
k="${k-}${k+ and }not test_modules_prefix"
|
||
k="${k-}${k+ and }not test_report_after_run"
|
||
k="${k-}${k+ and }not test_retrieve"
|
||
k="${k-}${k+ and }not test_shell_exec"
|
||
%endif
|
||
|
||
# These use the s3_storage test fixture, which sets up a server on the local
|
||
# loopback interface. For some reason, this does not seem to work in mock, with
|
||
# or without network access enabled. It is very likely that this is a quirk of
|
||
# the build environment rather than a real issue.
|
||
k="${k-}${k+ and }not test_default_storage"
|
||
k="${k-}${k+ and }not test_default_storage_local_job"
|
||
k="${k-}${k+ and }not test_output_file_cache_storage"
|
||
k="${k-}${k+ and }not test_storage"
|
||
|
||
# The following requires cwltool,
|
||
# https://github.com/common-workflow-language/cwltool, which is not packaged.
|
||
k="${k-}${k+ and }not test_cwl_singularity"
|
||
|
||
# The following requires polars, which is not packaged.
|
||
k="${k-}${k+ and }not test_params_pickling"
|
||
k="${k-}${k+ and }not test_validate"
|
||
|
||
# The following require the “pep” extra. They might also require network
|
||
# access.
|
||
k="${k-}${k+ and }not test_modules_peppy"
|
||
k="${k-}${k+ and }not test_pep_pathlib"
|
||
k="${k-}${k+ and }not test_peppy"
|
||
|
||
# Flaky; so far, we have not attempted to understand or report this.
|
||
#
|
||
# FAILED ../tests/tests.py::test_update_flag - AssertionError: wrong result
|
||
# produced for file 'test.txt':
|
||
# ------found------
|
||
# foo
|
||
# -----expected-----
|
||
# foo
|
||
# bar
|
||
# -----------------
|
||
k="${k-}${k+ and }not test_update_flag"
|
||
|
||
# Hangs on s390x; we have not attempted to understand or report this, although
|
||
# it would be nice to do so. For simplicity, we just skip it on all
|
||
# architectures.
|
||
k="${k-}${k+ and }not test_github_issue1158"
|
||
|
||
# Workaround for Python path issues
|
||
cd src/
|
||
|
||
# See discussion in https://github.com/snakemake/snakemake/issues/2961
|
||
# regarding running individual tests explicitly rather than letting pytest
|
||
# discover them freely, and see the “Running the full test suite” section in
|
||
# docs/project_info/contributing.rst for the list of tests that should be run.
|
||
# - tests/test_api.py requires network access and S3 credentials
|
||
%pytest -v -k "${k-}" ${ignore-} \
|
||
../tests/tests.py \
|
||
%if %{with conda_tests}
|
||
../tests/tests_using_conda.py \
|
||
%endif
|
||
../tests/test_expand.py \
|
||
../tests/test_io.py \
|
||
../tests/test_schema.py \
|
||
../tests/test_linting.py \
|
||
../tests/test_executor_test_suite.py \
|
||
../tests/test_internals.py
|
||
%endif
|
||
|
||
|
||
%files -f %{pyproject_files}
|
||
%doc CHANGELOG.md
|
||
%doc README.md
|
||
%doc README-nano.md
|
||
%doc README-vim.md
|
||
|
||
%{_bindir}/snakemake
|
||
%{_mandir}/man1/snakemake.1*
|
||
|
||
# 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
|
||
|
||
|
||
%changelog
|
||
%autochangelog
|