khanlab / khanlab/hippunfold

v2.0.0: docker build fails with KeyError 'dseg_dentate' in import_template_dseg_dentate (--use-template-seg)

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Dominant language
Python
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Forks
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Description

Building v2.0.0 (ffb1e85) via podman on macOS (apple silicon; using the `podman-rootful` vm template from lima).

Build fails at the 9th `/app/entrypoint.sh` call in the second `RUN` block. The prior 8 calls ran successfully.

Dockerfile line:

```shell
/app/entrypoint.sh hippunfold test_data/bids_T1w test_out participant --modality T1w --use-template-seg --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba
```

Traceback:

```
Building DAG of jobs...
InputFunctionException in rule import_template_dseg_dentate in file "/src/hippunfold/workflow/rules/download.smk", line 142:
Error:
KeyError: 'dseg_dentate'
Wildcards:
subject=001
hemi=L
Traceback:
File "/src/hippunfold/workflow/rules/download.smk", line 149, in (rule import_template_dseg_dentate, line 232, /src/hippunfold/workflow/rules/download.smk)
Error: building at STEP "RUN set -e && /app/entrypoint.sh hippunfold test_data/bids_singleT2w test_out participant --modality T2w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_multiT2w test_out participant --modality T2w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_T1w test_out participant --modality T1w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_hippb500 test_out participant --modality hippb500 --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_singleT2w_longitudinal test_out participant --modality T2w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_dsegtissue test_out participant --modality dsegtissue --derivatives test_data/bids_dsegtissue --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_singleT2w test_out participant --modality T2w --t1_reg_template --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_singleT2w test_out participant --modality T2w --output_space T1w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_T1w test_out participant --modality T1w --use-template-seg --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_singleT2w test_out participant --modality T2w --generate-myelin-map --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_dsegtissue test_out group_create_atlas --modality dsegtissue --derivatives test_data/bids_dsegtissue --new-atlas-name mytestatlas --new_atlas_subfields_from native --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && rm -rf /root/.cache": while running runtime: exit status 1
```

Contributor guide

No contributing guide indexed for this repository

Research direction

Reproduce the failing Dockerfile RUN sequence, then inspect workflow/rules/download.smk around lines 142 and 149 and the /app/entrypoint.sh invocation using --use-template-seg. Trace why the dseg_dentate key is missing for subject 001 and hemisphere L; done means the v2.0.0 build completes that command without the KeyError.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, python
Domain
build-system, devops
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
45/100

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