From 955ac44ff6aabae72cac1b07557b405236819962 Mon Sep 17 00:00:00 2001 From: Chenying Zhao Date: Wed, 3 May 2023 19:05:48 -0400 Subject: [PATCH] change toybidsapp version to 0.0.7 in docker image for testing; add --dummy in YAML file --- .circleci/config.yml | 2 +- .vscode/launch.json | 4 ++-- docs/source/babs-init.rst | 2 +- notebooks/example_container_toybidsapp.yaml | 8 +++++--- tests/get_data.py | 8 ++++---- 5 files changed, 13 insertions(+), 11 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a3762c48..4634e8dc 100644 --- a/.circleci/config.yml +++ b/.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 diff --git a/.vscode/launch.json b/.vscode/launch.json index 23d2f251..5e7a0d84 100644 --- a/.vscode/launch.json +++ b/.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", diff --git a/docs/source/babs-init.rst b/docs/source/babs-init.rst index 1ef68c58..bad6881d 100644 --- a/docs/source/babs-init.rst +++ b/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 diff --git a/notebooks/example_container_toybidsapp.yaml b/notebooks/example_container_toybidsapp.yaml index 387238c8..c75b09f8 100644 --- a/notebooks/example_container_toybidsapp.yaml +++ b/notebooks/example_container_toybidsapp.yaml @@ -1,4 +1,6 @@ -# 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 # 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 +14,8 @@ 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: diff --git a/tests/get_data.py b/tests/get_data.py index c4c4bdaa..42e02848 100644 --- a/tests/get_data.py +++ b/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") @@ -180,7 +180,7 @@ 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) @@ -188,8 +188,8 @@ def container_ds_path(where_now, tmp_path_factory): # 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