From 12d5df92c5574ab34b5ca2a9fe553d88508e0ff1 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Tue, 23 Jan 2024 14:18:45 +0100 Subject: [PATCH 1/7] ci: Update Python versions we test against. --- .github/workflows/main.yml | 6 +++--- setup.py | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f1aade92..e3634513 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -26,7 +26,7 @@ jobs: - name: Install Python uses: actions/setup-python@v2 with: - python-version: "3.8" + python-version: "3.10" - name: Install dependencies run: | @@ -49,9 +49,9 @@ jobs: strategy: matrix: python-version: - - '3.8' - - '3.9' - '3.10' + - '3.11' + - '3.12' needs: linting steps: - name: Install Python via conda diff --git a/setup.py b/setup.py index 2a244a04..a1b65713 100644 --- a/setup.py +++ b/setup.py @@ -42,9 +42,9 @@ def parse_requirements(path): "Natural Language :: English", "Topic :: Scientific/Engineering :: Bio-Informatics", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", + "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.", From 36880f5e22f47122c96c1248eb538b1af99f1ad1 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Tue, 23 Jan 2024 17:14:30 +0100 Subject: [PATCH 2/7] do not install pysam from bioconda --- .github/workflows/main.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e3634513..c96ca8c3 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -77,9 +77,6 @@ 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 - - name: Install dependencies run: | pip install -r requirements/test_black.txt From 708fbb804aa2248f31ddcbe29688af9a5632a4ae Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Tue, 23 Jan 2024 17:35:50 +0100 Subject: [PATCH 3/7] remove Python 3.12 due to SNAPPY conflict --- .github/workflows/main.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c96ca8c3..badc30a0 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -51,7 +51,6 @@ jobs: python-version: - '3.10' - '3.11' - - '3.12' needs: linting steps: - name: Install Python via conda From 2de40657949a22e55bb77654aac8e64f95432eed Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Wed, 24 Jan 2024 16:59:02 +0100 Subject: [PATCH 4/7] fix pyfakefs usage --- tests/test_seasnap_itransfer_results.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) 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) From 4a4339680fb757b7e5e0beb4646371c5ebbe657d Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Wed, 24 Jan 2024 17:27:42 +0100 Subject: [PATCH 5/7] linting --- .github/workflows/main.yml | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 4220c895..47af8c00 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -51,7 +51,7 @@ jobs: python-version: - '3.10' - '3.11' - #- '3.12' # blocked by snappy-pipeline #483 + # - '3.12' # blocked by snappy-pipeline #483 needs: linting steps: - name: Install Python via conda diff --git a/setup.py b/setup.py index 7797d407..bb8870c4 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ def parse_requirements(path): "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", - #"Programming Language :: Python :: 3.12", # blocked by snappy-pipeline #483 + # "Programming Language :: Python :: 3.12", # blocked by snappy-pipeline #483 ], entry_points={"console_scripts": ("cubi-tk = cubi_tk.__main__:main",)}, description="Tooling for connecting GitLab, pipelines, and SODAR at CUBI.", From 228723c7f450c21c9fe603b59f99fe614230712f Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Thu, 25 Jan 2024 13:42:04 +0100 Subject: [PATCH 6/7] add Python 3.12 because of snappy-pipeline #485 --- .github/workflows/main.yml | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 47af8c00..2c1221fa 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -51,7 +51,7 @@ jobs: python-version: - '3.10' - '3.11' - # - '3.12' # blocked by snappy-pipeline #483 + - '3.12' needs: linting steps: - name: Install Python via conda diff --git a/setup.py b/setup.py index bb8870c4..a1b65713 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ def parse_requirements(path): "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", - # "Programming Language :: Python :: 3.12", # blocked by snappy-pipeline #483 + "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.", From 2bc0aaf44890336e6a9db0aac4e130d40f0d80fb Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Tue, 25 Jun 2024 18:36:40 +0200 Subject: [PATCH 7/7] pysam was fixed --- .github/workflows/main.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 2c1221fa..e3634513 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -77,10 +77,8 @@ jobs: - name: Update environment using mamba run: mamba env update --name root --file /tmp/environment.yaml - # 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 + - name: Save time by installing packages via mamba. + run: mamba install -y pysam - name: Install dependencies run: |