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dev-python/snakemake and deps: version bumps #1296

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dev-python/snakemake and deps: version bumps #1296

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1478df7
dev-python/snakemake-interface-common: version bump 1.17.4
mschubert Nov 11, 2024
7a1cb96
dev-python/snakemake-interface-executor-plugins: version bump 9.3.2
mschubert Nov 11, 2024
075929a
dev-python/snakemake-interface-report-plugins: version bump 1.1.0
mschubert Nov 11, 2024
c5b960d
dev-python/snakemake-interface-storage-plugins: version bump 3.3.0
mschubert Nov 11, 2024
0930f26
dev-python/snakemake: version bump 8.25.3 and enable tests
mschubert Nov 11, 2024
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2 changes: 1 addition & 1 deletion dev-python/snakemake-interface-common/Manifest
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DIST snakemake_interface_common-1.17.2.tar.gz 9928 BLAKE2B 91be90640adb5f19fb97185ef84954cececd9e26e9c64f59b4ff014eca257575c5d5501ea7a8d74d9de2bb3280e88be500d1a2df2ec3296f2ecd30acbda27c87 SHA512 08d1688f70863825e76832250ee9da0be3a8baae9e67eb9bafaab30d862fe33fb9508eb4571f39322579699a4cd98d8878854ad9a94615e3b73255d18fe38c14
DIST snakemake_interface_common-1.17.4.tar.gz 9897 BLAKE2B d81df168b25f482a02e132a7d2ac34d348dba136509f1ed4f5196fc08454e713c86829e8d48da03e23f472a42a54408022a980508b7fd646c994bd25a9f2f56c SHA512 8af34099f5db0d6c49af2e4da1f9ed1b862ff5dbba2f19e9dc98a93558850ee1cfdd83f83623a677f30d7030bc738fec9da201229d980926404b80fe168c0253
2 changes: 1 addition & 1 deletion .../snakemake-interface-common-1.17.2.ebuild → .../snakemake-interface-common-1.17.4.ebuild
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# Copyright 1999-2018 Gentoo Foundation
# Copyright 1999-2024 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2

EAPI=8
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2 changes: 1 addition & 1 deletion dev-python/snakemake-interface-executor-plugins/Manifest
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DIST snakemake_interface_executor_plugins-9.2.0.tar.gz 16490 BLAKE2B e239c68edbb14c89322a2bd91bb60beb73a939e523e01bec882ee6762412478bc28d856182cf82d62a7879b65797b299cce34aa69cea6d216b6e3bfb3aa59bca SHA512 d6f6ec6cba2649b801bf2352ac60a66bfdc419e53987c77ce64aa37ed08aebec54d07d0e99b1ef212f122b87b40e7f0cb0a0713a2b756e28228dbb9b27b27fce
DIST snakemake_interface_executor_plugins-9.3.2.tar.gz 16714 BLAKE2B 0ae26f520a81fae4a35cddc059bf76da49f558fffda41e1f29db4ab5bc17d6c6f29c3b01961d683b7fc6be05a9e2541a7f6a853f44b94b68ede0033bb9f42a3f SHA512 c516cc2b0aac2fda7f6ae3cd092e626e72591e5810cd11c4f990d297da9407fb98290b8636a7c5ac9e491cb5b89710b03d97746b8d9fd5007fa60b5fcceced8b
0 ...e-interface-executor-plugins-9.2.0.ebuild → ...e-interface-executor-plugins-9.3.2.ebuild
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2 changes: 1 addition & 1 deletion dev-python/snakemake-interface-report-plugins/Manifest
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DIST snakemake_interface_report_plugins-1.0.0.tar.gz 4239 BLAKE2B efda3664614d123b0cd0f3d246d324ef7a4e67b2a069a5b1dde929921cf7e2251f67d6fcc1806864488dcc9c9b586681908e5a11b13f78206342ff0383efdbdc SHA512 2f5ac7e0ccd02c10aebcbe0eebfdb617cb32f66204e91316e3bc2b0053c3606207baa5de5bdda570f5559db366c637adf614f9ac23c7a33fb06d64560bd780aa
DIST snakemake_interface_report_plugins-1.1.0.tar.gz 4383 BLAKE2B 3e7201d3f0d3b18389838e3f06ff38feca7b710d26a8848b378c2d5f18a93e9e1c7e6cfb771bc644c1193d76836a35531a6f5bafc0d05b03008ce9a69ae667a1 SHA512 0d664bac65c412ab8492b731d5e23cff1c38fceb7a0fde2037d094f4bc451431b8c05f860fc1355e7eb048b89714f86e8cd7cc810e94abc4b7ab0c0c2e8b0f54
0 ...ake-interface-report-plugins-1.0.0.ebuild → ...ake-interface-report-plugins-1.1.0.ebuild
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2 changes: 1 addition & 1 deletion dev-python/snakemake-interface-storage-plugins/Manifest
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DIST snakemake_interface_storage_plugins-3.2.3.tar.gz 11930 BLAKE2B 5f46a52d46c11a2feb9840e5a3eb67374ad4a148ff2366953be0285877d1a33c344fcf9930a8145fccd1987995ddaf177997e393a9f21bbd316102d620b4bc9d SHA512 7692c9cacc5ece8e76dab67be3a8ed1a32930b27ce7edaa3998b23305723e7e01b3c04954b61585d876b5410caf3036efd0cb9569e159abcc5a95d9ab2446494
DIST snakemake_interface_storage_plugins-3.3.0.tar.gz 12244 BLAKE2B 353c247d139e10bfe4a2dbf45a0af1dbea0e545a668f7c47d71f063262e2c1695ed2e33a2eab2d94ea7084b586542674fc4011f16c4e960857e649e7ffbd527f SHA512 54aab99808f8c896d4ddbccc3dd3fd4522ddfbf20f505916e4ae29086af0404178e2733f3b1bebb1eeb7a48ad08046727d954f4cd71ca7d40b9e5f02ccb7e8a6
0 ...ke-interface-storage-plugins-3.2.3.ebuild → ...ke-interface-storage-plugins-3.3.0.ebuild
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2 changes: 1 addition & 1 deletion dev-python/snakemake/Manifest
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@@ -1,2 +1,2 @@
DIST snakemake-7.32.4.gh.tar.gz 8885863 BLAKE2B 6bb7ff4722dd06f0edf5e8079b42f5e54d6f55f41e2987b7dae7f9b75df0d4d836138e28340e5977107a5cc0b5afe793b0d7897c501246cc1b4340eb4eca2f17 SHA512 34fef61528b18facab798652c88ed5c698ef02161e023255fdd024b7c7781c4e582cdb04b2740fdff9b6f3600acaec719742984acee57920bb48ef3b5af99d9a
DIST snakemake-8.16.0.gh.tar.gz 8665306 BLAKE2B 76d3455ce9a7ccc749adb5a729ab954d7a3fd97dc2432c3a0e9aba1ace1cb08e377244a2a2527c676b9709f9bb8b5af29948c0385657755bbbc8449b136fc26d SHA512 29b6ba6da5dbbd347dee45114b949c976973555c9234f8a150dcd83e4af1638c1773590320bc44284cf20ea445efb377dcf9199921ed2b4d62bad3a60a41af3c
DIST snakemake-8.25.3.gh.tar.gz 8693083 BLAKE2B 8d5070d5c78f560bc714da189454776ea87a8403075da98b45b021ac304053cb08763c929846d4c8f949c71245566bdb012b78d8807f40a584805cd08917af14 SHA512 f769c89e98130c738bb43931f240eaa93482d19403c6bcda65334910ccf4cac2e11257ed8b133d220d645ea39b0af8aa580fe24c57221478ea7dd0fb4d21d4e7
33 changes: 15 additions & 18 deletions dev-python/snakemake/snakemake-8.16.0.ebuild → dev-python/snakemake/snakemake-8.25.3.ebuild
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Expand Up @@ -16,21 +16,6 @@ LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64"

# cannot import name '_helpers' from 'google.cloud'
RESTRICT="test"

BDEPEND="
dev-python/tomli[${PYTHON_USEDEP}]
test? (
dev-python/requests-mock[${PYTHON_USEDEP}]
dev-python/google-api-python-client[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/pygments[${PYTHON_USEDEP}]
dev-python/pygraphviz[${PYTHON_USEDEP}]
net-libs/google-cloud-cpp
)
"

RDEPEND="
dev-python/appdirs[${PYTHON_USEDEP}]
dev-python/immutables[${PYTHON_USEDEP}]
Expand All @@ -50,13 +35,12 @@ RDEPEND="
dev-python/reretry[${PYTHON_USEDEP}]
>=dev-python/smart-open-4.0[${PYTHON_USEDEP}]
>=dev-python/snakemake-interface-common-1.17.0[${PYTHON_USEDEP}]
>=dev-python/snakemake-interface-executor-plugins-9.2.0[${PYTHON_USEDEP}]
>=dev-python/snakemake-interface-executor-plugins-9.3.2[${PYTHON_USEDEP}]
>=dev-python/snakemake-interface-storage-plugins-3.2.3[${PYTHON_USEDEP}]
>=dev-python/snakemake-interface-report-plugins-1.0.0[${PYTHON_USEDEP}]
>=dev-python/snakemake-interface-report-plugins-1.1.0[${PYTHON_USEDEP}]
dev-python/stopit[${PYTHON_USEDEP}]
dev-python/tabulate[${PYTHON_USEDEP}]
dev-python/throttler[${PYTHON_USEDEP}]
>=dev-python/toposort-1.10[${PYTHON_USEDEP}]
dev-python/wrapt[${PYTHON_USEDEP}]
>=dev-python/yte-1.5.1[${PYTHON_USEDEP}]
>=dev-python/dpath-2.1.6[${PYTHON_USEDEP}]
Expand All @@ -71,4 +55,17 @@ RDEPEND="
# dev-python/docutils \
# dev-python/recommonmark \
# dev-python/myst-parser

EPYTEST_IGNORE=(
# __file__ attribute does not match test name ('python_3_7')
tests/test_conda_python_3_7_script/test_script.py
# ModuleNotFoundError: No module named 'snakemake_executor_plugin_cluster_generic'
tests/test_executor_test_suite.py
# ImportError: cannot import name 'snakemake' from 'snakemake.script'
tests/test_script_py/scripts/test_explicit_import.py
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Does setting PYTHONPATH (or similar) help for this one?

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If I understand this comment correctly, it is not a matter of simply adding to PYTHONPATH:

running from snakemake.script import snakemake outside of a Snakemake "context", since snakemake.script.snakemake (lower case) is simply a type hint that can be used by editor. At execution time, the snakemake object needs to be created by snakemake, which is done by the boilerplate/preamble

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That comment seems to suggest that passing some path to epytest would resolve the problem, have you tried this?

)
EPYTEST_DESELECT=(
# No module named 'snakemake_storage_plugin_s3'
tests/test_api.py::test_deploy_sources
)
distutils_enable_tests pytest
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