From 5fe9c91537a1ad532572af1173dfe2a10177fd48 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 30 Nov 2020 13:49:09 +0000 Subject: [PATCH 1/2] Cast ``ncores`` to str for ``subprocess.call()`` Fix https://github.com/galaxyproject/galaxy/issues/10824 . --- lib/galaxy/objectstore/s3.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py index 327988be7be..1a4f4c3d36a 100644 --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -437,7 +437,7 @@ class S3ObjectStore(ObjectStore, CloudConfigMixin): log.debug("Parallel pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path)) ncores = multiprocessing.cpu_count() url = key.generate_url(7200) - ret_code = subprocess.call(['axel', '-a', '-n', ncores, url]) + ret_code = subprocess.call(['axel', '-a', '-n', str(ncores), url]) if ret_code == 0: return True else: From 7d1569ed472d7381bcacecbbee883cbc97d97a01 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 30 Nov 2020 16:48:42 +0000 Subject: [PATCH 2/2] Update `sphinx-markdown-tables` to fix conflict `sphinx-markdown-tables` 0.0.12 had a strict pin which is causing a conflict error with the new pip 20.3: ``` ERROR: Cannot install -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55) and markdown==3.1.1 because these package versions have conflicting dependencies. ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies The conflict is caused by: The user requested markdown==3.1.1 The user requested markdown==3.1.1 sphinx-markdown-tables 0.0.12 depends on markdown==3.0.1 To fix this you could try to: 1. loosen the range of package versions you've specified 2. remove package versions to allow pip attempt to solve the dependency conflict ``` See https://github.com/galaxyproject/galaxy/pull/10825/checks?check_run_id=1474883413 --- .../dependencies/pipfiles/default/pinned-dev-requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt index 1b53e2b2826..9a382962cbd 100644 --- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt +++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt @@ -52,7 +52,7 @@ scandir==1.10.0 ; python_version < '3.5' selenium==3.141.0 six==1.11.0 snowballstemmer==2.0.0 -sphinx-markdown-tables==0.0.12 +sphinx-markdown-tables==0.0.13 sphinx-rtd-theme==0.4.3 sphinx==1.8.5 sphinxcontrib-websupport==1.1.2