diff --git a/poetryinstall.output b/poetryinstall.output new file mode 100644 index 00000000..5a155a05 --- /dev/null +++ b/poetryinstall.output @@ -0,0 +1,170 @@ +Installing dependencies from lock file + +Package operations: 123 installs, 25 updates, 0 removals + + • Updating certifi (2023.5.7 -> 2021.10.8) + • Updating charset-normalizer (3.1.0 /home/conda/feedstock_root/build_artifacts/charset-normalizer_1678108872112/work -> 2.0.12) + • Updating idna (3.4 /home/conda/feedstock_root/build_artifacts/idna_1663625384323/work -> 3.3) + • Installing markupsafe (2.0.1) + • Installing pyparsing (3.0.9) + • Installing pytz (2022.1) + • Updating six (1.16.0 /home/conda/feedstock_root/build_artifacts/six_1620240208055/work -> 1.16.0) + • Updating urllib3 (1.26.15 /home/conda/feedstock_root/build_artifacts/urllib3_1678635778344/work -> 1.26.9) + • Updating zipp (3.15.0 /home/conda/feedstock_root/build_artifacts/zipp_1677313463193/work -> 3.8.0) + • Installing alabaster (0.7.12) + • Installing asttokens (2.0.5) + • Installing babel (2.10.1) + • Installing docutils (0.16) + • Updating attrs (23.1.0 /home/conda/feedstock_root/build_artifacts/attrs_1683424013410/work -> 21.4.0) + • Installing imagesize (1.3.0) + • Installing iniconfig (1.1.1) + • Installing jinja2 (2.11.3) + • Updating packaging (23.1 /home/conda/feedstock_root/build_artifacts/packaging_1681337016113/work -> 21.3) + • Installing parso (0.8.3) + • Installing pluggy (1.0.0) + • Installing executing (0.8.3) + • Installing pure-eval (0.2.2) + • Updating importlib-resources (5.12.0 /home/conda/feedstock_root/build_artifacts/importlib_resources_1676919000169/work -> 5.7.1) + • Installing pygments (2.12.0) + • Updating pyrsistent (0.19.3 /home/conda/feedstock_root/build_artifacts/pyrsistent_1672681475076/work -> 0.18.1) + • Updating ptyprocess (0.7.0 /home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl -> 0.7.0) + • Installing py (1.11.0) + • Installing smmap (5.0.0) + • Updating requests (2.31.0 /home/conda/feedstock_root/build_artifacts/requests_1684774241324/work -> 2.27.1) + • Installing snowballstemmer (2.2.0) + • Installing sphinxcontrib-applehelp (1.0.2) + • Installing sphinxcontrib-devhelp (1.0.2) + • Installing sphinxcontrib-htmlhelp (2.0.0) + • Installing sphinxcontrib-jsmath (1.0.1) + • Installing sphinxcontrib-qthelp (1.0.3) + • Installing sphinxcontrib-serializinghtml (1.1.5) + • Installing toml (0.10.2) + • Updating tomli (2.0.1 /home/conda/feedstock_root/build_artifacts/tomli_1644342247877/work -> 2.0.1) + • Installing traitlets (5.2.1.post0) + • Installing wcwidth (0.2.5) + • Installing appdirs (1.4.4) + • Installing backcall (0.2.0) + • Installing cycler (0.11.0) + • Installing decorator (5.1.1) + • Updating distlib (0.3.6 /home/conda/feedstock_root/build_artifacts/distlib_1668356257807/work -> 0.3.4) + • Installing fastjsonschema (2.15.3) + • Installing click (7.1.2) + • Installing gitdb (4.0.9) + • Installing entrypoints (0.4) + • Installing jsonpointer (2.3) + • Installing jedi (0.18.1) + • Updating filelock (3.12.0 /home/conda/feedstock_root/build_artifacts/filelock_1681839547898/work -> 3.7.0) + • Installing jupyter-core (4.10.0) + • Installing kiwisolver (1.4.2) + • Installing mypy-extensions (0.4.3) + • Installing nest-asyncio (1.5.5) + • Installing pathspec (0.9.0) + • Updating pexpect (4.8.0 /home/conda/feedstock_root/build_artifacts/pexpect_1667297516076/work -> 4.8.0) + • Installing pickleshare (0.7.5) + • Installing pillow (9.0.1) + • Installing matplotlib-inline (0.1.3) + • Installing prompt-toolkit (3.0.29) + • Installing fonttools (4.33.3) + • Installing pyyaml (6.0) + • Updating jsonschema (4.17.3 /home/conda/feedstock_root/build_artifacts/jsonschema-meta_1669810440410/work -> 4.5.1) + • Installing pyzmq (22.3.0) + • Installing setuptools-scm (6.4.2) + • Installing stack-data (0.2.0) + • Installing tornado (6.1) + • Updating typing-extensions (4.6.3 /home/conda/feedstock_root/build_artifacts/typing_extensions_1685704949284/work -> 4.2.0) + • Installing python-dateutil (2.8.2) + • Installing ruamel-yaml-clib (0.2.6) + • Installing sphinx (3.5.4) + • Updating platformdirs (3.5.1 /home/conda/feedstock_root/build_artifacts/platformdirs_1683850015520/work -> 2.5.2) + • Updating numpy (1.24.3 /home/conda/feedstock_root/build_artifacts/numpy_1682210232610/work -> 1.22.3) + • Installing regex (2022.4.24) + • Installing pytest (6.2.5) + • Installing typed-ast (1.4.3) + • Installing argcomplete (1.12.3) + • Installing black (20.8b1) + • Updating colorama (0.4.6 /home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work -> 0.4.4) + • Installing configargparse (1.5.3) + • Installing cfgv (3.3.1) + • Installing datrie (0.8.2) + • Installing et-xmlfile (1.1.0) + • Installing gitpython (3.1.27) + • Installing identify (2.5.0) + • Installing decli (0.5.2) + • Installing connection-pool (0.0.3) + • Installing matplotlib (3.5.2) + • Installing mccabe (0.6.1) + • Installing execnet (1.9.0) + • Installing pandas (1.4.2) + • Installing psutil (5.9.0) + • Installing pulp (2.6.0) + • Installing pycodestyle (2.7.0) + • Installing pyflakes (2.3.1) + • Installing pytest-forked (1.4.0) + • Installing questionary (1.10.0) + • Installing nbformat (5.4.0) + • Installing ruamel-std-argparse (0.8.3) + • Installing nodeenv (1.6.0) + • Installing scipy (1.6.1) + • Installing smart-open (6.0.0) + • Installing sphinx-jsonschema (1.15) + • Installing stopit (1.1.2) + • Installing tabulate (0.8.9) + • Updating tomlkit (0.11.8 /home/conda/feedstock_root/build_artifacts/tomlkit_1683028165096/work -> 0.10.2) + • Installing pydantic (1.9.0) + • Installing wrapt (1.14.1) + • Installing ratelimiter (1.2.0.post0) + • Installing ruamel-appconfig (0.5.5) + • Installing ruamel-yaml (0.17.21) + • Updating importlib-metadata (6.6.0 /home/conda/feedstock_root/build_artifacts/importlib-metadata_1682176699712/work -> 1.7.0) + • Installing sphinx-prompt (1.5.0) + • Installing termcolor (1.1.0) + • Updating virtualenv (20.23.0 /home/conda/feedstock_root/build_artifacts/virtualenv_1682674264573/work -> 20.14.1) + • Installing ruamel-std-pathlib (0.9.2) + • Installing ipython (8.3.0) + • Installing toposort (1.7) + • Installing ipython-genutils (0.2.0) + • Installing jupyter-client (7.3.1) + • Installing commitizen (2.27.0) + • Installing flake8 (3.9.2) + • Installing ipykernel (5.5.6) + • Installing isort (5.10.1) + • Installing mypy (0.812) + • Updating more-itertools (9.1.0 /home/conda/feedstock_root/build_artifacts/more-itertools_1677514956219/work -> 8.13.0) + • Installing networkx (2.8) + • Installing pre-commit (2.19.0) + • Installing openpyxl (3.0.9) + • Installing pysam (0.16.0.1) + • Installing pytest-mock (3.7.0) + • Installing pytest-xdist (2.5.0) + • Installing rope (0.19.0) + • Installing rstcheck (3.5.0) + • Installing python-ternary (1.0.8) + • Installing seaborn (0.11.2) + • Installing snakefmt (0.4.2) + • Installing sphinx-click (3.1.0) + • Installing sphinx-pydantic (0.1.1) + • Installing sphinx-rtd-theme (0.5.2) + • Installing ryd (0.4.1) + • Installing snakemake (6.15.5) + • Installing sphinx-substitution-extensions (2020.9.30.0) + • Installing sphinxcontrib-mermaid (0.4.0) + • Installing typer (0.3.2) + • Installing ptvsd (4.3.2) +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 +Connection pool is full, discarding connection: pypi.org. Connection pool size: 10 + +Installing the current project: cgr_gwas_qc (0.1.2) diff --git a/tests/cli/test_submit.py b/tests/cli/test_submit.py index e0411703..06e67596 100644 --- a/tests/cli/test_submit.py +++ b/tests/cli/test_submit.py @@ -5,42 +5,30 @@ from cgr_gwas_qc.testing.data import FakeData -# [(True, False, None), (False, True, None), (False, False, "./test")], @pytest.mark.parametrize( - "cgems,biowulf,ccad2,cluster_profile", - [ - (True, False, False, None), - (False, True, False, None), - (False, False, True, None), - (False, False, False, "./test"), - ], + "cgems,biowulf,cluster_profile", + [(True, False, None), (False, True, None), (False, False, "./test")], ) -def test_check_exclusive_options_no_error(cgems, biowulf, ccad2, cluster_profile): +def test_check_exclusive_options_no_error(cgems, biowulf, cluster_profile): from cgr_gwas_qc.cli.submit import check_exclusive_options - check_exclusive_options(cgems, biowulf, ccad2, cluster_profile) + check_exclusive_options(cgems, biowulf, cluster_profile) -# [(True, True, "./test"), (True, True, None), (True, False, "./test"), (False, True, "./test")], @pytest.mark.parametrize( - "cgems,biowulf,ccad2,cluster_profile", - [ - (True, True, True, "./test"), - (True, True, True, None), - (True, False, False, "./test"), - (False, True, False, "./test"), - ], + "cgems,biowulf,cluster_profile", + [(True, True, "./test"), (True, True, None), (True, False, "./test"), (False, True, "./test")], ) -def test_check_exclusive_options_raises_error(cgems, biowulf, ccad2, cluster_profile): +def test_check_exclusive_options_raises_error(cgems, biowulf, cluster_profile): from click.exceptions import Exit as ClickExit from cgr_gwas_qc.cli.submit import check_exclusive_options with pytest.raises(ClickExit): - check_exclusive_options(cgems, biowulf, ccad2, cluster_profile) + check_exclusive_options(cgems, biowulf, cluster_profile) -@pytest.mark.parametrize("cluster", ["cgems", "biowulf", "ccad2"]) +@pytest.mark.parametrize("cluster", ["cgems", "biowulf"]) def test_get_profile(cluster): from pathlib import Path @@ -144,44 +132,19 @@ def test_create_submission_script_biowulf(tmp_path): @pytest.mark.parametrize( - "cluster,cmd", - [("cgems", "qsub"), ("biowulf", "sbatch"), ("ccad2", "sbatch"), ("custom", "pbs")], + "cluster,cmd", [("cgems", "qsub"), ("biowulf", "sbatch"), ("custom", "pbs")] ) def test_run_submit_with_right_command(cluster, cmd, tmp_path, mocker: MockerFixture): from cgr_gwas_qc.cli import submit if cluster == "cgems": - cgems, biowulf, ccad2, cluster_profile, queue, submission_cmd = ( - True, - False, - False, - None, - None, - None, - ) + cgems, biowulf, cluster_profile, queue, submission_cmd = True, False, None, None, None elif cluster == "biowulf": # Biowulf - cgems, biowulf, ccad2, cluster_profile, queue, submission_cmd = ( - False, - True, - False, - None, - None, - None, - ) - elif cluster == "ccad2": - cgems, biowulf, ccad2, cluster_profile, queue, submission_cmd = ( - False, - False, - True, - None, - None, - None, - ) + cgems, biowulf, cluster_profile, queue, submission_cmd = False, True, None, None, None else: profile_dir = tmp_path / "test_profile" profile_dir.mkdir() - cgems, biowulf, ccad2, cluster_profile, queue, submission_cmd = ( - False, + cgems, biowulf, cluster_profile, queue, submission_cmd = ( False, False, profile_dir, @@ -195,7 +158,6 @@ def test_run_submit_with_right_command(cluster, cmd, tmp_path, mocker: MockerFix submit.main( cgems=cgems, biowulf=biowulf, - ccad2=ccad2, cluster_profile=cluster_profile, subworkflow=None, time_hr=12, diff --git a/tests/data b/tests/data index 73eddd8a..5def846f 160000 --- a/tests/data +++ b/tests/data @@ -1 +1 @@ -Subproject commit 73eddd8a496a083038bd9b15d0a03ba5e4cccc4e +Subproject commit 5def846ff2b0459b3bee4711a32481e14c5e2f58