diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 480495de..e3634513 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -50,8 +50,8 @@ jobs: matrix: python-version: - '3.10' - # - "3.11" # no compatible pysam yet - # - "3.12" # no compatible pysam yet + - '3.11' + - '3.12' needs: linting steps: - name: Install Python via conda diff --git a/setup.py b/setup.py index ec3f1487..b02b8f1a 100644 --- a/setup.py +++ b/setup.py @@ -47,10 +47,8 @@ def parse_requirements(path): "Topic :: Scientific/Engineering :: Bio-Informatics", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10", - # We are missing bioconda pysam packages for 3.11 and 3.12, cf. - # https://github.com/bioconda/bioconda-recipes/issues/37805 - # "Programming Language :: Python :: 3.11", - # "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", ], entry_points={"console_scripts": ("cubi-tk = cubi_tk.__main__:main",)}, description="Tooling for connecting GitLab, pipelines, and SODAR at CUBI.", diff --git a/tests/test_seasnap_itransfer_results.py b/tests/test_seasnap_itransfer_results.py index dbcc0488..3c879808 100644 --- a/tests/test_seasnap_itransfer_results.py +++ b/tests/test_seasnap_itransfer_results.py @@ -37,7 +37,7 @@ def test_run_seasnap_itransfer_results_nothing(capsys): assert res.err -def test_run_seasnap_itransfer_results_smoke_test(mocker): +def test_run_seasnap_itransfer_results_smoke_test(mocker, fs): # --- setup arguments dest_path = "/irods/dest" fake_base_path = "/base/path" @@ -57,7 +57,6 @@ def test_run_seasnap_itransfer_results_smoke_test(mocker): # Setup fake file system but only patch selected modules. We cannot use the Patcher approach here as this would # break biomedsheets. - fs = fake_filesystem.FakeFilesystem() fake_os = fake_filesystem.FakeOsModule(fs) fake_pl = fake_pathlib.FakePathlibModule(fs) @@ -83,7 +82,6 @@ def test_run_seasnap_itransfer_results_smoke_test(mocker): fs.remove(fake_file_paths[3]) # --- mock modules - mocker.patch("glob.os", fake_os) mocker.patch("cubi_tk.sea_snap.itransfer_results.pathlib", fake_pl) mocker.patch("cubi_tk.sea_snap.itransfer_results.os", fake_os) mocker.patch("cubi_tk.snappy.itransfer_common.os", fake_os)