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ci: Update Python versions we test against. #215

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ci: Update Python versions we test against. #215

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12d5df9
ci: Update Python versions we test against.
sellth Jan 23, 2024
36880f5
do not install pysam from bioconda
sellth Jan 23, 2024
708fbb8
remove Python 3.12 due to SNAPPY conflict
sellth Jan 23, 2024
0fe149a
Merge remote-tracking branch 'origin/main' into update_python
sellth Jan 24, 2024
2de4065
fix pyfakefs usage
sellth Jan 24, 2024
4a43396
linting
sellth Jan 24, 2024
228723c
add Python 3.12 because of snappy-pipeline #485
sellth Jan 25, 2024
695d085
Merge branch 'main' into update_python
sellth Jun 25, 2024
2bc0aaf
pysam was fixed
sellth Jun 25, 2024
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10 changes: 6 additions & 4 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -77,8 +77,10 @@ jobs:
- name: Update environment using mamba
run: mamba env update --name root --file /tmp/environment.yaml

- name: Save time by installing packages via mamba.
run: mamba install -y pysam
# We are missing bioconda pysam packages for 3.11 and 3.12, cf.
# https://github.com/bioconda/bioconda-recipes/issues/37805
# - name: Save time by installing packages via mamba.
# run: mamba install -y pysam
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Maybe we should open an issue, so this doesn't get lost?


- name: Install dependencies
run: |
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6 changes: 2 additions & 4 deletions setup.py
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Expand Up @@ -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.",
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4 changes: 1 addition & 3 deletions tests/test_seasnap_itransfer_results.py
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Expand Up @@ -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"
Expand All @@ -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)

Expand All @@ -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)
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