FIX: Adjust the implementation of the python wrappers

.circleci/config.yml

@@ -533,6 +533,20 @@ jobs:
               pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
               docker images
             fi
+      - run:
+          name: Setup miniconda environment and install connectomemapper3 with Python wrappers
+          command: |
+            apt update
+            apt install -y wget
+            wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+            echo $(sha256sum miniconda.sh)
+            bash miniconda.sh -b -p $HOME/miniconda
+            export PATH="$HOME/miniconda/bin:$PATH"
+            conda update -y conda
+            conda env create -f environment.yml --name connectomemapper3
+            source activate connectomemapper3
+            echo $(which pip)
+            pip install .
       - run:
           name: Remove any config file present in ds-sample/code and create ds-sample/test
           no_output_timeout: 1h
@@ -553,19 +567,20 @@ jobs:
             mkdir -p /tmp/data/${CIRCLE_JOB}/ds-sample
             cp -R /tmp/data/ds-sample/* /tmp/data/${CIRCLE_JOB}/ds-sample
       - run:
-          name: Run anatomical pipeline on ds-sample (test 5 - NativeFreesurfer)
+          name: Run anatomical pipeline on ds-sample (test 5 - NativeFreesurfer - Python wrapper)
           no_output_timeout: 5h
           command: |
-            # Execute BIDS App
-            docker run -it --rm \
-                --entrypoint /app/run_coverage_cmp3.sh \
-                -v /tmp/data/${CIRCLE_JOB}/ds-sample:/bids_dir \
-                -v /tmp/data/${CIRCLE_JOB}/ds-sample/derivatives:/output_dir \
-                -v /home/circleci/src/connectomemapper3/.circleci/tests/configuration_files:/config \
-                sebastientourbier/connectomemapper3 \
-                /bids_dir /output_dir participant --participant_label 01 --session_label 01 \
-                --anat_pipeline_config /config/ref_anatomical_config_2.ini \
-                --fs_license /bids_dir/code/license.txt \
+            # Activate the conda environment with the wrapper installed
+            source activate connectomemapper3
+            # Execute BIDS App via the docker python wrapper
+            bids_dir="/tmp/data/${CIRCLE_JOB}/ds-sample"
+            output_dir="${bids_dir}/derivatives"
+            config_dir="/home/circleci/src/connectomemapper3/.circleci/tests/configuration_files"
+            connectomemapper3_docker \
+                "${bids_dir}" "${output_dir}" participant --participant_label 01 --session_label 01 \
+                --config_dir "${config_dir}" \
+                --anat_pipeline_config "ref_anatomical_config_2.ini" \
+                --fs_license "${bids_dir}/code/license.txt" \
                 --coverage
 
             # Rename partial coverage
@@ -829,6 +844,12 @@ jobs:
               echo "Skipping test_singularity_parcellation job"
               circleci step halt
             fi
+      - attach_workspace:
+          at: /tmp
+      - singularity/install-go:
+          go-version: '1.13'
+      - singularity/debian-install-3:
+          singularity-version: 3.7.3
       - run:
           name: Setup miniconda environment and install connectomemapper3 with Python wrappers
           command: |
@@ -843,12 +864,6 @@ jobs:
             source activate connectomemapper3
             echo $(which pip)
             pip install .
-      - attach_workspace:
-          at: /tmp
-      - singularity/install-go:
-          go-version: '1.13'
-      - singularity/debian-install-3:
-          singularity-version: 3.7.3
       - run:
           name: Remove any config file present in ds-sample/code and create ds-sample/test
           no_output_timeout: 1h
@@ -881,8 +896,10 @@ jobs:
             connectomemapper3_singularity \
                 "${bids_dir}" "${output_dir}" participant --participant_label 01 --session_label 01 \
                 --singularity_image "/tmp/cache/connectomemapper3.simg" \
-                --anat_pipeline_config "${config_dir}/ref_anatomical_config_2.ini" \
-                --fs_license "${bids_dir}/code/license.txt"
+                --config_dir "${config_dir}" \
+                --anat_pipeline_config "ref_anatomical_config_2.ini" \
+                --fs_license "${bids_dir}/code/license.txt" \
+                --coverage
       - run:
           name: Checking outputs of Connectome Mapper run (test 5)
           command: |

cmp/cli/connectomemapper3_docker.py

@@ -8,6 +8,7 @@
 
 # General imports
 import sys
+from pathlib import Path
 
 # Own imports
 from cmp.info import __version__
@@ -28,6 +29,16 @@ def create_docker_cmd(args):
                 'output_dir': "/path/to/output/directory",
                 'analysis_level': "participant",
                 'participant_label': ['01', '02', '03'],
+                'anat_pipeline_config': "/path/to/ref_anatomical_config.json",
+                'dwi_pipeline_config': "/path/to/ref_diffusion_config.json",
+                'func_pipeline_config': "/path/to/ref_fMRI_config.json",
+                ('number_of_threads': 1,)
+                ('number_of_participants_processed_in_parallel': 1,)
+                ('mrtrix_random_seed': 1234,)
+                ('ants_random_seed': 1234,)
+                ('ants_number_of_threads': 2,)
+                ('fs_license': "/path/to/license.txt",)
+                ('notrack': True)
             }
 
     Returns
@@ -38,38 +49,50 @@ def create_docker_cmd(args):
     # Docker run command prelude
     cmd = 'docker run -t --rm '
     cmd += '-u $(id -u):$(id -g) '
-    cmd += f'-bind {args.bids_dir}:/bids_dir '
-    cmd += f'-bind {args.output_dir}:/output_dir '
-    # cmd += f'-v {args.param_file}:/bids_dir/code/participants_params.json '
-    # cmd += f'sebastientourbier/mialsuperresolutiontoolkit-bidsapp:v{__version__} '
-    cmd += args.docker_image
+    if args.coverage:
+        cmd += '--entrypoint /app/run_coverage_cmp3.sh '
+    cmd += f'-v {args.bids_dir}:/bids_dir '
+    cmd += f'-v {args.output_dir}:/output_dir '
+    if args.config_dir:
+        cmd += f'-v {args.config_dir}:/config '
+    else:
+        cmd += f'-v {args.bids_dir}/code:/config '
+    if args.fs_license:
+        cmd += f'-v {args.fs_license}:/bids_dir/code/license.txt '
+
+    cmd += f'{args.docker_image} '
 
     # Standard BIDS App inputs
     cmd += '/bids_dir '
     cmd += '/output_dir '
     cmd += f'{args.analysis_level} '
-
     if args.participant_label:
         cmd += '--participant_label '
         for label in args.participant_label:
             cmd += f'{label} '
-
     if args.session_label:
         cmd += '--session_label '
         for label in args.session_label:
             cmd += f'{label} '
-
+    if args.anat_pipeline_config:
+        cmd += f'/config/{args.anat_pipeline_config} '
+    if args.dwi_pipeline_config:
+        cmd += f'/config/{args.dwi_pipeline_config} '
+    if args.func_pipeline_config:
+        cmd += f'/config/{args.func_pipeline_config} '
+    cmd += f'--fs_license /bids_dir/code/license.txt '
     optional_single_args = (
-        "anat_pipeline_config", "dwi_pipeline_config", "func_pipeline_config",
         "number_of_threads", "number_of_participants_processed_in_parallel",
         "mrtrix_random_seed", "ants_random_seed", "ants_number_of_threads",
-        "fs_license", "notrack"
     )
-
     for arg_name in optional_single_args:
         argument_value = getattr(args, arg_name)
         if argument_value:
             cmd += f'--{arg_name} {argument_value} '
+    if args.notrack:
+        cmd += "--notrack "
+    if args.coverage:
+        cmd += "--coverage"
 
     return cmd
 

cmp/cli/connectomemapper3_singularity.py

@@ -8,6 +8,7 @@
 
 # General imports
 import sys
+from pathlib import Path
 
 # Own imports
 from cmp.info import __version__
@@ -50,13 +51,19 @@ def create_singularity_cmd(args):
     cmd = 'singularity run --containall '
     cmd += f'--bind {args.bids_dir}:/bids_dir '
     cmd += f'--bind {args.output_dir}:/output_dir '
-    cmd += args.singularity_image
+    if args.config_dir:
+        cmd += f'--bind {args.config_dir}:/config '
+    else:
+        cmd += f'--bind {args.bids_dir}/code:/config '
+    if args.fs_license:
+        cmd += f'--bind {args.fs_license}:/bids_dir/code/license.txt '
+
+    cmd += f'{args.singularity_image} '
 
     # Standard BIDS App inputs
     cmd += '/bids_dir '
     cmd += '/output_dir '
     cmd += f'{args.analysis_level} '
-
     if args.participant_label:
         cmd += '--participant_label '
         for label in args.participant_label:
@@ -65,18 +72,25 @@ def create_singularity_cmd(args):
         cmd += '--session_label '
         for label in args.session_label:
             cmd += f'{label} '
-
+    if args.anat_pipeline_config:
+        cmd += f'/config/{args.anat_pipeline_config} '
+    if args.dwi_pipeline_config:
+        cmd += f'/config/{args.dwi_pipeline_config} '
+    if args.func_pipeline_config:
+        cmd += f'/config/{args.func_pipeline_config} '
+    cmd += f'--fs_license /bids_dir/code/license.txt '
     optional_single_args = (
-        "anat_pipeline_config", "dwi_pipeline_config", "func_pipeline_config",
         "number_of_threads", "number_of_participants_processed_in_parallel",
         "mrtrix_random_seed", "ants_random_seed", "ants_number_of_threads",
-        "fs_license", "notrack"
     )
-
     for arg_name in optional_single_args:
         argument_value = getattr(args, arg_name)
         if argument_value:
             cmd += f'--{arg_name} {argument_value} '
+    if args.notrack:
+        cmd += "--notrack "
+    if args.coverage:
+        cmd += "--coverage"
 
     return cmd
 

cmp/parser.py

@@ -108,9 +108,15 @@ def get_docker_wrapper_parser():
     p.add_argument(
         '--docker_image',
         type=str,
-        default=f'sebastientourbier/connectomemapper-bidsapp:{__version__} ',
+        default=f'sebastientourbier/connectomemapper-bidsapp:{__version__}',
         help="The path to the docker image.",
     )
+    p.add_argument(
+        '--config_dir',
+        type=str,
+        default=None,
+        help="The path to the directory containing the configuration files.",
+    )
     return p
 
 
@@ -130,4 +136,10 @@ def get_singularity_wrapper_parser():
         default=f'library://connectomicslab/default/connectomemapper-bidsapp:{__version__}',
         help="The path to the singularity image.",
     )
+    p.add_argument(
+        '--config_dir',
+        type=str,
+        default=None,
+        help="The path to the directory containing the configuration files.",
+    )
     return p

docs/usage.rst

@@ -37,25 +37,27 @@ When you run ``connectomemapper3_docker``, it will generate a Docker command lin
     .. code-block:: console
 
        $ connectomemapper_docker \
-            /home/user/data/ds001 /home/user/data/ds001/derivatives \
+            "/home/user/data/ds001" "/home/user/data/ds001/derivatives" \
             participant --participant_label 01 --session_label 01 \
-            --fs_license /usr/local/freesurfer/license.txt \
-            --anat_pipeline_config /home/user/data/ds001/code/ref_anatomical_config.json \
-            (--dwi_pipeline_config /home/user/data/ds001/code/ref_diffusion_config.json \)
-            (--func_pipeline_config /home/user/data/ds001/code/ref_fMRI_config.json \)
+            --fs_license "/usr/local/freesurfer/license.txt" \
+            --config_dir "/home/user/data/ds001/code" \
+            --anat_pipeline_config "ref_anatomical_config.json" \
+            (--dwi_pipeline_config "ref_diffusion_config.json" \)
+            (--func_pipeline_config "ref_fMRI_config.json" \)
             (--number_of_participants_processed_in_parallel 1)
 
 When you run ``connectomemapper3_singularity``, it will generate a Singularity command line for you, print it out for reporting purposes, and then execute it without further action needed, e.g.:
 
     .. code-block:: console
 
        $ connectomemapper3_singularity \
-            /home/user/data/ds001 /home/user/data/ds001/derivatives \
+            "/home/user/data/ds001" "/home/user/data/ds001/derivatives" \
             participant --participant_label 01 --session_label 01 \
-            --fs_license /usr/local/freesurfer/license.txt \
-            --anat_pipeline_config /home/user/data/ds001/code/ref_anatomical_config.json \
-            (--dwi_pipeline_config /home/user/data/ds001/code/ref_diffusion_config.json \)
-            (--func_pipeline_config /home/user/data/ds001/code/ref_fMRI_config.json \)
+            --fs_license "/usr/local/freesurfer/license.txt" \
+            --config_dir "/home/user/data/ds001/code" \
+            --anat_pipeline_config "ref_anatomical_config.json" \
+            (--dwi_pipeline_config "ref_diffusion_config.json" \)
+            (--func_pipeline_config "ref_fMRI_config.json" \)
             (--number_of_participants_processed_in_parallel 1)