Merge branch 'main' into enh/default_root

Author: mattcieslak

.circleci/config.yml

@@ -4,7 +4,7 @@ version: 2.1
 
 .dockersetup: &dockersetup
   docker:
-    - image: pennlinc/babs_testing:0.3
+    - image: pennlinc/slurm-docker-ci:0.9
 
 jobs:
   download_test_data:
@@ -51,6 +51,33 @@ jobs:
             pip install .[tests]
             pytest -n 4 -sv --durations=0 --timeout=300 --log-cli-level=DEBUG
 
+  e2e-slurm:
+    machine:
+      image: ubuntu-2204:current
+    # docker:
+    #   - image: pennlinc/slurm-docker-ci:0.8
+    working_directory: /home/circleci/src/babs
+    steps:
+      - checkout:
+          path: /home/circleci/src/babs
+      - restore_cache:
+          keys:
+            - test-data-v1
+      - run:
+          name: pytest of BABS
+          no_output_timeout: 1h
+          command: |
+            docker build \
+            -t pennlinc/slurm-docker-ci:unstable \
+            -f Dockerfile_testing .
+
+            docker run -it \
+                -v ${PWD}:/tests \
+                -h slurmctl --cap-add sys_admin \
+                --privileged \
+                pennlinc/slurm-docker-ci:unstable \
+                /tests/tests/e2e-slurm/container/walkthrough-tests.sh
+
   deployable: # checkpoint of deployable: requires all success
     <<: *dockersetup
     steps:
@@ -87,9 +114,16 @@ workflows:
           filters:
             tags:
               only: /.*/
+      - e2e-slurm:
+          requires:
+            - download_test_data
+          filters:
+            tags:
+              only: /.*/
       - deployable:
           requires:
             - pytest
+            - e2e-slurm
           filters:
             branches:
               only: main

.github/workflows/shellcheck.yml

@@ -17,8 +17,4 @@ jobs:
     - name: Run shellcheck
       run: |
         shellcheck -x \
-        tests/e2e-slurm/container/babs-user-script.sh \
-        tests/e2e-slurm/container/ensure-env.sh \
-        tests/e2e-slurm/container/walkthrough-tests.sh \
-        tests/e2e-slurm/install-babs.sh \
-        tests/e2e-slurm/main.sh
+        tests/e2e-slurm/container/walkthrough-tests.sh

DockerfileSLURM

@@ -0,0 +1,31 @@
+FROM giovtorres/docker-centos7-slurm:latest
+
+WORKDIR /
+RUN echo "2024.04.11"
+RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+
+COPY docker/environment.yml /tmp/environment.yml
+ENV MAMBA_ROOT_PREFIX="/opt/conda" \
+    MAMBA_NO_LOW_SPEED_LIMIT=1 \
+    PIP_DEFAULT_TIMEOUT=100
+
+RUN micromamba config set extract_threads 1 \
+    && micromamba create -vv -y -f /tmp/environment.yml \
+    && micromamba clean -y -a
+
+ENV PATH=/opt/conda/envs/babs/bin:$PATH
+
+# Configure the git user name and email
+RUN git config --global user.name "CircleCI" \
+    && git config --global user.email "circleci@example.com"
+
+# Create toy bids app
+RUN mkdir -p /singularity_images \
+    && /opt/conda/envs/babs/bin/apptainer build \
+    /singularity_images/toybidsapp_0.0.7.sif \
+    docker://pennlinc/toy_bids_app:0.0.7
+
+# # install BABS
+# COPY . /babs
+# WORKDIR /babs
+# RUN pip install .[tests]

Dockerfile_testing

@@ -0,0 +1,6 @@
+FROM pennlinc/slurm-docker-ci:0.9
+
+# # install BABS
+COPY . /babs
+WORKDIR /babs
+RUN pip install .[tests]

docker/docker-entrypoint.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+exec "$@"

docker/environment.yml

@@ -6,6 +6,7 @@ dependencies:
   - git
   - git-annex
   - pip
+  - p7zip
   - python=3.11
   - pip:
       - backoff

pyproject.toml

@@ -71,9 +71,9 @@ allow-direct-references = true
 exclude = [".git_archival.txt"] # No longer needed in sdist
 
 [tool.hatch.build.targets.wheel]
-packages = ["qsiprep"]
+packages = ["babs"]
 exclude = [
-    "qsiprep/tests/data", # Large test data directory
+    "babs/tests/data", # Large test data directory
 ]
 
 ##  The following two sections configure setuptools_scm in the hatch way

tests/e2e-slurm/container/babs-user-script.sh

@@ -1,5 +1,6 @@
 # Arguments in `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     --no-zipped: ""
     --dummy: "2"
     -v: ""
@@ -11,11 +12,10 @@ zip_foldernames:
 # How much cluster resources it needs:
 cluster_resources:
     interpreting_shell: /bin/bash
-    hard_memory_limit: 2G
 
 script_preamble: |
-    . ~/miniconda.env
-    conda activate babs
+    PATH=/opt/conda/envs/babs/bin:$PATH
+    which python
 
 # Where to run the jobs:
 job_compute_space: "/tmp"