From 4f099fc836399a95e29c96a2106e866b9dfe1f77 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Fri, 1 Mar 2024 14:45:19 +0000 Subject: [PATCH 1/3] Using packaging.version instead of pkg_resources --- nf_core/download.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/download.py b/nf_core/download.py index d08e0ba40e..74331db48d 100644 --- a/nf_core/download.py +++ b/nf_core/download.py @@ -20,7 +20,7 @@ import rich import rich.progress from git.exc import GitCommandError, InvalidGitRepositoryError -from pkg_resources import parse_version as version_parser +from packaging.version import Version as Version_parser import nf_core import nf_core.list @@ -1664,7 +1664,7 @@ def tidy_tags_and_branches(self): else: # desired revisions may contain arbitrary branch names that do not correspond to valid sematic versioning patterns. valid_versions = [ - version_parser(v) + Version_parser(v) for v in desired_revisions if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v) ] From ae59ec01d53afee02b67fd5d883991574ba53194 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 1 Mar 2024 14:47:31 +0000 Subject: [PATCH 2/3] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a16db59e56..10fdb1ffe7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ - Update CI to use nf-core/setup-nextflow v2 - Changelog bot: handle also patch version before dev suffix ([#2820](https://github.com/nf-core/tools/pull/2820)) +- Using packaging.version instead of pkg_resources ([#2825](https://github.com/nf-core/tools/pull/2825)) ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29] From be4351153e2fc63ab69662a03dda098a46480c5c Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 1 Mar 2024 15:54:47 +0100 Subject: [PATCH 3/3] fix type --- nf_core/download.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/nf_core/download.py b/nf_core/download.py index 74331db48d..5b06f37192 100644 --- a/nf_core/download.py +++ b/nf_core/download.py @@ -20,7 +20,7 @@ import rich import rich.progress from git.exc import GitCommandError, InvalidGitRepositoryError -from packaging.version import Version as Version_parser +from packaging.version import Version import nf_core import nf_core.list @@ -1664,9 +1664,7 @@ def tidy_tags_and_branches(self): else: # desired revisions may contain arbitrary branch names that do not correspond to valid sematic versioning patterns. valid_versions = [ - Version_parser(v) - for v in desired_revisions - if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v) + str(Version(v)) for v in desired_revisions if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v) ] # valid versions sorted in ascending order, last will be aliased as "latest". latest = sorted(valid_versions)[-1]