Merge pull request #90 from PennLINC/enh/docker_version_4test

[ENH] update toy BIDS App version used for CircleCI testing

.circleci/config.yml

@@ -4,7 +4,7 @@ version: 2.1
 
 .dockersetup: &dockersetup
   docker:
-    - image: pennlinc/babs_tests:datalad0.17.2_v4
+    - image: pennlinc/babs_tests:datalad0.17.2_v5
 
 # TODO:
 # runinstall: &runinstall

.readthedocs.yaml

@@ -1,13 +1,16 @@
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
 sphinx:
    configuration: docs/source/conf.py
 
 python:
-  version: 3.8
   install:
     - method: pip
       path: .
       extra_requirements:
         - doc
-  system_packages: true

.vscode/launch.json

@@ -30,7 +30,7 @@
                 "--container_ds",
                 "/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/data/toybidsapp-container-docker",
                 "--container_name",
-                "toybidsapp-0-0-6", // "fmriprep-20-2-3", 
+                "toybidsapp-0-0-7", // "fmriprep-20-2-3", 
                 "--container_config_yaml_file",
                 "/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/babs/notebooks/example_container_toybidsapp.yaml",
                 // "/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/babs/notebooks/example_container_fmriprep.yaml",
@@ -49,7 +49,7 @@
             //     // "--list_sub_file", "/cbica/projects/BABS/babs/notebooks/initial_sub_list_multi-ses.csv",
             //     // "--container_ds", "/cbica/projects/BABS/data/toybidsapp-container",
             //     "--container_ds", "/cbica/projects/BABS/data/fmriprep-container",
-            //     // "--container_name", "toybidsapp-0-0-6",
+            //     // "--container_name", "toybidsapp-0-0-7",
             //     "--container_name", "fmriprep-20-2-3",
             //     // "--container_config_yaml_file", "/cbica/projects/BABS/babs/notebooks/example_container_toybidsapp.yaml",
             //     "--container_config_yaml_file", "/cbica/projects/BABS/babs/notebooks/example_container_fmriprep_anatonly.yaml",

docs/source/babs-init.rst

@@ -137,7 +137,7 @@ an SGE cluster:
         --project_name my_BABS_project \
         --input BIDS /path/to/BIDS_datalad_dataset \
         --container_ds /path/to/toybidsapp-container \
-        --container_name toybidsapp-0-0-6 \
+        --container_name toybidsapp-0-0-7 \
         --container_config_yaml_file /path/to/container_toybidsapp.yaml \
         --type_session multi-ses \
         --type_system sge

notebooks/example_container_toybidsapp.yaml

@@ -1,4 +1,7 @@
-# This is an example config yaml file for toy BIDS App "toy_bids_app" version 0.0.6.
+# This is an example config yaml file for:
+#   toy BIDS App "toy_bids_app"
+#   whose version = 0.0.7
+#   for application to raw BIDS dataset ("unzipped")
 # Toy BIDS App's Docker image is publicly available at: https://hub.docker.com/r/pennlinc/toy_bids_app
 # This BIDS App counts number of non-hidden files in a subject's (or a session's) folder;
 #     More details please see: https://github.com/PennLINC/babs_tests/blob/main/docker/README.md#toy-bids-app-toy_bids_app
@@ -12,8 +15,8 @@
 
 singularity_run:
     --no-zipped: ""  # for raw BIDS dataset
-    # --zipped: ""    # for zipped input dataset
-    -v: ""
+    --dummy: "2"   # this is a dummy variable, accepting values
+    -v: ""    # this is also a dummy variable, not accepting values
 
 # Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
 zip_foldernames:

notebooks/example_container_zipped_toybidsapp.yaml

@@ -1,9 +1,12 @@
-# Below is example config yaml file for toy BIDS App:
+# This is an example config yaml file for:
+#   toy BIDS App "toy_bids_app"
+#   whose version = 0.0.7
+#   for application to zipped BIDS derivatives dataset ("zipped")
 
 singularity_run:
-    # --no-zipped: ""  # for raw BIDS dataset
     --zipped: ""    # for zipped input dataset
-    -v: ""
+    --dummy: "2"   # this is a dummy variable, accepting values
+    -v: ""    # this is also a dummy variable, not accepting values
 
 # Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
 zip_foldernames:
@@ -31,9 +34,6 @@ script_preamble: |
 # Where to run the jobs:
 job_compute_space: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
 
-# Below is to filter out subjects (or sessions)
-#   right now we only filter based on unzipped dataset
-# required_files:
-#     $INPUT_DATASET_#1:
-#         - ""
+# 'required_files' section is not needed for toy BIDS App.
 
+# 'alert_log_messages' section is usually not needed for toy BIDS App.

tests/get_data.py

@@ -17,7 +17,7 @@
 
 # containers:
 LIST_WHICH_BIDSAPP = ["toybidsapp", "fmriprep", "qsiprep"]
-TOYBIDSAPP_VERSION = "0.0.6"   # +++++++++++++++++++++++
+TOYBIDSAPP_VERSION = "0.0.7"   # +++++++++++++++++++++++
 TOYBIDSAPP_VERSION_DASH = TOYBIDSAPP_VERSION.replace(".", "-")
 FN_TOYBIDSAPP_SIF_CIRCLECI = op.join("/singularity_images",
                                      "toybidsapp_" + TOYBIDSAPP_VERSION + ".sif")
@@ -180,16 +180,16 @@ def container_ds_path(where_now, tmp_path_factory):
             # datalad containers-add --url ${fn_sif} toybidsapp-${version_tag_dash}
             # API help: in python env: `help(dlapi.containers_add)`
             container_ds_handle.containers_add(
-                name=which_bidsapp+"-"+TOYBIDSAPP_VERSION_DASH,  # e.g., "toybidsapp-0-0-6"
+                name=which_bidsapp+"-"+TOYBIDSAPP_VERSION_DASH,  # e.g., "toybidsapp-0-0-7"
                 url=fn_toybidsapp_sif)
             # # can remove the original sif file now:
             # os.remove(fn_toybidsapp_sif)
         elif where_now == "on_local":   # add docker image:
             # datalad containers-add --url dhub://pennlinc/toy_bids_app:${version_tag} \
             #   toybidsapp-${version_tag_dash}
             container_ds_handle.containers_add(
-                name=which_bidsapp+"-"+TOYBIDSAPP_VERSION_DASH,  # e.g., "toybidsapp-0-0-6"
-                url="dhub://"+docker_addr   # e.g., "dhub://pennlinc/toy_bids_app:0.0.6"
+                name=which_bidsapp+"-"+TOYBIDSAPP_VERSION_DASH,  # e.g., "toybidsapp-0-0-7"
+                url="dhub://"+docker_addr   # e.g., "dhub://pennlinc/toy_bids_app:0.0.7"
             )
 
     return origin_container_ds