Jake Fennick

I'm not sure if this will solve the problem, but `/usr/bin/clang --version` yields: ``` Apple clang version 13.1.6 (clang-1316.0.21.2.5) Target: x86_64-apple-darwin21.6.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin ``` whereas `conda search...

Is there a reason cwltool needs mypyc instead of just regular mypy? i.e. is this line in tox.ini necessary? `make mypy mypyc PYTEST_EXTRA={posargs}` I see there are some commented out...

I'm still getting a few test failures: ``` ========================================================================================================================== FAILURES ========================================================================================================================== ________________________________________________________________________________________________________________ TestMpiRun.test_mpi_workflow ________________________________________________________________________________________________________________ [gw4] darwin -- Python 3.10.5 /Users/jakefennick/opt/anaconda3/envs/cwltool_test/bin/python3.10 self = , fake_mpi_conf = '/Users/jakefennick/cwltool/tmp/popen-gw4/fake_mpi0/plat_mpi.yml', tmp_path = PosixPath('/Users/jakefennick/cwltool/tmp/popen-gw4/test_mpi_workflow0') @needs_docker...

FYI the two errors about tabs can be fixed by replacing the tabs with spaces in `tests/subgraph/count-lines17-wf.cwl.json`. The other error about Docker and MPI being mutually exclusive seems to be...

`pytest` now works on my machine, but `tox` still gives 3 failures: ``` ========================================================================================================================== FAILURES ========================================================================================================================== ___________________________________________________________________________________________________________________ test_iwdr_permutations ___________________________________________________________________________________________________________________ [gw3] darwin -- Python 3.10.5 /Users/jakefennick/cwltool/.tox/py310-unit/bin/python tmp_path_factory = TempPathFactory(_given_basetemp=PosixPath('/Users/jakefennick/cwltool/tmp/popen-gw3'), _trace=, _basetemp=PosixPath('/Users/jakefennick/cwltool/tmp/popen-gw3'))...

FYI now I'm getting a pytest failure on test_bioconda: ``` UnavailableInvalidChannel: The channel is not accessible or is invalid. channel name: pkgs/main channel url: https://repo.anaconda.com/pkgs/main error code: 404 You will...

Looks like we're just about done. With this change, both pytest and tox work on my machine. ``` diff --git a/tests/test_examples.py b/tests/test_examples.py index b6a7edab..0516a6df 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@...

pytest and tox are now both working on my machine. However, I'm still running into #1694

Sure. Here is the relevant command line + stack trace from my log file. ``` /Users/jakefennick/workflow_inference_compiler/cachedir/fe47d299645b0f71eff2e8cbf791dcf9$ docker \ run \ -i \ --mount=type=bind,source=/Users/jakefennick/workflow_inference_compiler/cachedir/fe47d299645b0f71eff2e8cbf791dcf9,target=/RvczZO \ --mount=type=bind,source=/private/tmp/docker_tmpyrn_kcgl,target=/tmp \ --mount=type=bind,source=/Users/jakefennick/workflow_inference_compiler/cachedir/1b588cb52801df5be9d783bad2d2cb63/npt.gro,target=/var/lib/cwl/stgdce8320f-73ef-4a3a-8db9-ea43afcfd074/npt.gro,readonly \ --mount=type=bind,source=/Users/jakefennick/workflow_inference_compiler/cachedir/ae541201128048b4defdf1875c5dfa42/prod.trr,target=/var/lib/cwl/stg7d3f8150-98a4-4051-aed6-3f480f6cf22a/prod.trr,readonly \...

I guess I should clarify that `cwltool` automatically generates the above command and it includes the `--read-only=true` flag.