Connexion can't install with new Werkzeug and also MiniWDL

[adamnovak]

It looks like #4925 was merged even though it did not pass CI.

Now CI is failing because there's no version of connexion before 3 that works with the new Werkzeug 3, and also with a pyyaml that MiniWDL will accept. See https://ucsc-ci.com/databiosphere/toil/-/jobs/68399#L691

ERROR: Cannot install None, connexion and toil[all]==7.0.0a1 because these package versions have conflicting dependencies.
The conflict is caused by:
    toil[all] 7.0.0a1 depends on werkzeug<4 and >=3.0.3; extra == "all"
    connexion 2.14.2 depends on werkzeug<2.3 and >=1.0
    toil[all] 7.0.0a1 depends on werkzeug<4 and >=3.0.3; extra == "all"
    connexion 2.14.1 depends on werkzeug<3 and >=1.0
    toil[all] 7.0.0a1 depends on werkzeug<4 and >=3.0.3; extra == "all"
    connexion 2.14.0 depends on werkzeug<3 and >=1.0
    toil[all] 7.0.0a1 depends on werkzeug<4 and >=3.0.3; extra == "all"
    connexion 2.13.1 depends on werkzeug<3 and >=1.0
    toil[all] 7.0.0a1 depends on werkzeug<4 and >=3.0.3; extra == "all"
    connexion 2.13.0 depends on werkzeug<3 and >=1.0
    toil[all] 7.0.0a1 depends on pyyaml<7 and >=6
    miniwdl 1.12.0 depends on PyYAML<7 and >=5.4.1
    connexion 2.12.0 depends on PyYAML<6 and >=5.1
    toil[all] 7.0.0a1 depends on pyyaml<7 and >=6
    miniwdl 1.12.0 depends on PyYAML<7 and >=5.4.1
    connexion 2.11.2 depends on PyYAML<6 and >=5.1
    toil[all] 7.0.0a1 depends on pyyaml<7 and >=6
    miniwdl 1.12.0 depends on PyYAML<7 and >=5.4.1
    connexion 2.11.1 depends on PyYAML<6 and >=5.1
    toil[all] 7.0.0a1 depends on pyyaml<7 and >=6
    miniwdl 1.12.0 depends on PyYAML<7 and >=5.4.1
    connexion 2.11.0 depends on PyYAML<6 and >=5.1
    toil[all] 7.0.0a1 depends on pyyaml<7 and >=6
    miniwdl 1.12.0 depends on PyYAML<7 and >=5.4.1
    connexion 2.10.0 depends on PyYAML<6 and >=5.1

We need to probably update to Connexion 3, and also make sure that it actually passes the Toil WES server tests because there will be breaking changes in Connexion.

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1565

[adamnovak]

We can't actually adopt the new connexion because our wes-service dependency requires an older version: common-workflow-language/workflow-service#134

[adamnovak]

It looks like we depend on wes-service for its wes_client module, which we use to implement a toil-wes-cwl-runner CLI command to send a CWL workflow to a WES server, which we use in the test_wes_server_cwl_conformance() test. Which I'm not sure we ever run.

It might make sense to cut toil-wes-cwl-runner and just use some third-party CWL submission tool.

[adamnovak]

To properly fix this, we need Werkzeug 3 and also a compatible connexion and wes-service.