Missing argument 'CLS' when Running Workflow

[ACastanza]

Trying to run the workflow for Ensembl 110 (also tried with 'latest', which seemed to default to 109) and getting the following error (same error for all species):

Run poetry run ensembl_genes all --species="human" --release=[11](https://github.com/ACastanza/ensembl-genes/actions/runs/6254378054/job/16981773658#step:5:12)0
Usage: ensembl_genes all [OPTIONS] CLS
Try 'ensembl_genes all --help' for help.
╭─ Error ──────────────────────────────────────────────────────────────────────╮
│ Missing argument 'CLS'.                                                      │
╰──────────────────────────────────────────────────────────────────────────────╯
Error: Process completed with exit code 2.

Trying to get the "_old_to_newest" tables for our MSigDB build somewhat urgently

[dhimmel]

We haven't built release 110 via GitHub actions due to https://github.com/related-sciences/ensembl-genes/issues/22, which is supposed to be fixed in 111. If you're okay with release 109 that data is available on the homo_sapiens_core_109_38.

The Missing argument 'CLS' error is strange. I cannot see the link at https://github.com/ACastanza/ensembl-genes/actions/runs/6254378054/job/16981773658, but possible I could debug better with that log.

[ACastanza]

All I did was run the workflow the same way as with previous releases but with 110 as the build number, after PR'ing in your latest changes. Could you try running the workflow for that latest Ensembl release on the main repository to see if it errors there as well?

-Anthony

On Wed, Sep 20, 2023, 8:33 PM Daniel Himmelstein @.***> wrote:

We haven't built release 110 via GitHub actions due to #22 https://github.com/related-sciences/ensembl-genes/issues/22, which is supposed to be fixed in 111. If you're okay with release 109 that data is available on the homo_sapiens_core_109_38 https://github.com/related-sciences/ensembl-genes/tree/output/homo_sapiens_core_109_38 .

The Missing argument 'CLS' error is strange. I cannot see the link at https://github.com/ACastanza/ensembl-genes/actions/runs/6254378054/job/16981773658, but possible I could debug better with that log.

— Reply to this email directly, view it on GitHub https://github.com/related-sciences/ensembl-genes/issues/23#issuecomment-1728714577, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGGOVD4HAACBBYEKX3SLJITX3OYRJANCNFSM6AAAAAA5ASI4FA . You are receiving this because you authored the thread.Message ID: @.***>

[dhimmel]

Could you try running the workflow for that latest Ensembl release on the main repository to see if it errors there as well?

Ah yes happening on this repo too! Let me look into it.

BTW the reason this didn't happen in an automated/schedule way is that GitHub disabled the scheduled workflow after 60 days of inactivity. A separate annoying thing we should address.

[dhimmel]

Similar problem at https://stackoverflow.com/questions/70793842/writing-command-line-for-class-methods-using-python-and-typer. Looks like typer / click have problems making a command out of class or instance methods. Will look into fixing.

[dhimmel]

the workflow for Ensembl 110 (also tried with 'latest', which seemed to default to 109)

Confirming that latest is resolving to 109 with this command:

poetry run ensembl_genes ensembl_release --release=latest

This is due to bioversions being outdated. Reported at https://github.com/biopragmatics/bioversions/issues/33

[dhimmel]

Kicked off a functional build after 4b1a4d89444b66c238f55abfa49e89803e657e77. Human fails as expected, but at least gets to the computation.