Merge pull request #3058 from mashehu/update-to-pytest8

Update to pytest v8 and move it to dev dependencies

CHANGELOG.md

@@ -47,6 +47,7 @@
 - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052))
 - update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054))
+- Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

nf_core/pipelines/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
 
 import nf_core
 import nf_core.pipelines.list
@@ -1693,13 +1693,11 @@ 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)
+                            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]
-                        self.repo.create_head("latest", latest)
+                        self.repo.create_head("latest", str(latest))
                         self.checkout(latest)
                     if self.repo.head.is_detached:
                         self.repo.head.reset(index=True, working_tree=True)

requirements-dev.txt

@@ -7,7 +7,6 @@ ruff
 Sphinx
 sphinx-rtd-theme
 textual-dev==1.5.1
-mypy
 types-PyYAML
 types-requests
 types-jsonschema
@@ -16,4 +15,6 @@ types-PyYAML
 types-requests
 types-setuptools
 pytest-textual-snapshot==0.4.0
+pytest-workflow>=2.0.0
+pytest>=8.0.0
 ruff

requirements.txt

@@ -11,8 +11,6 @@ pdiff
 pre-commit
 prompt_toolkit>=3.0.3
 pydantic>=2.2.1
-pytest-workflow>=2.0.0
-pytest>=7.0.0
 pyyaml
 questionary>=1.8.0
 refgenie