[med-svn] [Git][med-team/snakemake][master] 5 commits: New upstream version 7.8.3
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Tue Jul 5 17:53:52 BST 2022
Nilesh Patra pushed to branch master at Debian Med / snakemake
Commits:
64f24f80 by Nilesh Patra at 2022-06-25T15:34:40+05:30
New upstream version 7.8.3
- - - - -
b13a075b by Nilesh Patra at 2022-07-05T21:49:38+05:30
New upstream version 7.8.5
- - - - -
5fea6205 by Nilesh Patra at 2022-07-05T21:50:08+05:30
Update upstream source from tag 'upstream/7.8.5'
Update to upstream version '7.8.5'
with Debian dir d51c8d38cdaef78bfc8c898a1282194a6291ae53
- - - - -
c8d5b989 by Nilesh Patra at 2022-07-05T21:51:00+05:30
Refresh patches
- - - - -
8ba67e61 by Nilesh Patra at 2022-07-05T21:51:46+05:30
Upload to unstable
- - - - -
10 changed files:
- + .wci.yml
- CHANGELOG.md
- debian/changelog
- debian/patches/cirumvent-retry.patch
- debian/patches/remove-yte.patch
- + pyproject.toml
- setup.py
- snakemake/_version.py
- snakemake/deployment/conda.py
- snakemake/workflow.py
Changes:
=====================================
.wci.yml
=====================================
@@ -0,0 +1,17 @@
+name: Snakemake
+language: Python
+documentation:
+ general: https://snakemake.readthedocs.io
+ installation: https://snakemake.readthedocs.io/en/stable/getting_started/installation.html
+ tutorial: https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html
+
+social:
+ twitter: johanneskoester
+
+execution_environment:
+ resource_managers:
+ - any DRM providing a script based submission interface (e.g. slurm, lsf, pbs, ...)
+ - kubernetes
+ - google life sciences API
+ - tibanna
+ - TES
\ No newline at end of file
=====================================
CHANGELOG.md
=====================================
@@ -1,5 +1,26 @@
# Changelog
+## [7.8.5](https://github.com/snakemake/snakemake/compare/v7.8.4...v7.8.5) (2022-06-30)
+
+
+### Documentation
+
+* fix long description type for pypi (set to markdown) ([d8d9b8f](https://github.com/snakemake/snakemake/commit/d8d9b8f284d2863f672cd96fd96d2034806d52de))
+
+## [7.8.4](https://github.com/snakemake/snakemake/compare/v7.8.3...v7.8.4) (2022-06-30)
+
+
+### Bug Fixes
+
+* only display a warning in case of non-strict channel priorities ([#1752](https://github.com/snakemake/snakemake/issues/1752)) ([b84fa33](https://github.com/snakemake/snakemake/commit/b84fa337f5c417360fc744202a419da3f37594b5))
+* pass triggers and resources to subworkflow ([#1733](https://github.com/snakemake/snakemake/issues/1733)) ([fa7fb75](https://github.com/snakemake/snakemake/commit/fa7fb75d2314cd2965a9f578506e27aae4b07349))
+* add pyproject.toml to use setuptools features ([#1725](https://github.com/snakemake/snakemake/issues/1725)) ([454bfd1](https://github.com/snakemake/snakemake/commit/454bfd17aba8631ea34d6a8971b1db60b2955965))
+
+
+### Documentation
+
+* add workflows.community metadata ([#1736](https://github.com/snakemake/snakemake/issues/1736)) ([8a42afc](https://github.com/snakemake/snakemake/commit/8a42afc053e3f398f1a299fb3234ca0ee847faae))
+
### [7.8.3](https://www.github.com/snakemake/snakemake/compare/v7.8.2...v7.8.3) (2022-06-20)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+snakemake (7.8.5-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version 7.8.5
+ * Refresh patches
+
+ -- Nilesh Patra <nilesh at debian.org> Tue, 05 Jul 2022 21:51:30 +0530
+
snakemake (7.8.3-2) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/cirumvent-retry.patch
=====================================
@@ -146,7 +146,7 @@ Last-Update: 2022-06-25
return self._open(source_file, mode)
--- a/setup.py
+++ b/setup.py
-@@ -84,7 +84,6 @@
+@@ -74,7 +74,6 @@
"tabulate",
"yte >=1.0,<2.0",
"jinja2 >=3.0,<4.0",
=====================================
debian/patches/remove-yte.patch
=====================================
@@ -3,7 +3,7 @@ Author: Nilesh Patra <nilesh at debian.org>
Last-Update: 2022-06-25
--- a/setup.py
+++ b/setup.py
-@@ -82,7 +82,6 @@
+@@ -72,7 +72,6 @@
"smart_open >=3.0",
"stopit",
"tabulate",
=====================================
pyproject.toml
=====================================
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=42"]
+build-backend = "setuptools.build_meta"
=====================================
setup.py
=====================================
@@ -1,26 +1,14 @@
-# -*- coding: UTF-8 -*-
-
-from __future__ import print_function
-
-__author__ = "Johannes Köster"
-__copyright__ = "Copyright 2022, Johannes Köster"
-__email__ = "johannes.koester at uni-due.de"
-__license__ = "MIT"
-
+import os
import sys
-import versioneer
-
-if sys.version_info < (3, 7):
- print("At least Python 3.7 is required for Snakemake.\n", file=sys.stderr)
- exit(1)
+from setuptools import setup
+# ensure the current directory is on sys.path so versioneer can be imported
+# when pip uses PEP 517/518 build rules.
+# https://github.com/python-versioneer/python-versioneer/issues/193
+sys.path.append(os.path.dirname(__file__))
-try:
- from setuptools import setup
-except ImportError:
- print("Please install setuptools before installing snakemake.", file=sys.stderr)
- exit(1)
+import versioneer # noqa: E402
setup(
@@ -34,6 +22,7 @@ setup(
"together with a clean and modern specification language in python style. "
"Snakemake workflows are essentially Python scripts extended by declarative "
"code to define rules. Rules describe how to create output files from input files.",
+ long_description_content_type="text/markdown",
zip_safe=False,
license="MIT",
url="https://snakemake.readthedocs.io",
@@ -63,6 +52,7 @@ setup(
]
},
package_data={"": ["*.css", "*.sh", "*.html", "*.jinja2", "*.js", "*.svg"]},
+ python_requires=">=3.7",
install_requires=[
"wrapt",
"requests",
=====================================
snakemake/_version.py
=====================================
@@ -22,9 +22,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
- git_refnames = " (tag: v7.8.3)"
- git_full = "9b5ee38001f1b19dbbe6805a99c0b570af545d4b"
- git_date = "2022-06-20 12:52:22 +0200"
+ git_refnames = " (HEAD -> main, tag: v7.8.5)"
+ git_full = "531ef4a6b962b06ef865ba34ea6e952a7d4b3a2b"
+ git_date = "2022-06-30 15:19:34 +0200"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
snakemake/deployment/conda.py
=====================================
@@ -751,11 +751,11 @@ class Conda:
)
)
if res["get"].get("channel_priority") != "strict":
- raise CreateCondaEnvironmentException(
+ logger.warning(
"Your conda installation is not configured to use strict channel priorities. "
"This is however crucial for having robust and correct environments (for details, "
"see https://conda-forge.org/docs/user/tipsandtricks.html). "
- "Please configure strict priorities by executing 'conda config --set channel_priority strict'."
+ "Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'."
)
def bin_path(self):
=====================================
snakemake/workflow.py
=====================================
@@ -833,10 +833,12 @@ class Workflow:
targets=subworkflow_targets,
cores=self._cores,
nodes=self.nodes,
+ resources=self.global_resources,
configfiles=[subworkflow.configfile]
if subworkflow.configfile
else None,
updated_files=updated,
+ rerun_triggers=self.rerun_triggers,
):
return False
dag.updated_subworkflow_files.update(
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/6a2d13d14d9adb81412bfe96a32f7028e4d7fe6f...8ba67e61856f4452be5419fe27bc30e8266b260a
--
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/6a2d13d14d9adb81412bfe96a32f7028e4d7fe6f...8ba67e61856f4452be5419fe27bc30e8266b260a
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