From 955ac44ff6aabae72cac1b07557b405236819962 Mon Sep 17 00:00:00 2001 From: Chenying Zhao Date: Wed, 3 May 2023 19:05:48 -0400 Subject: [PATCH 1/6] 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 From 7123aa0b259a05e6ca0396ce297303d7e9619cb0 Mon Sep 17 00:00:00 2001 From: Chenying Zhao Date: Wed, 3 May 2023 20:51:07 -0400 Subject: [PATCH 2/6] update example zipped_toybidsapp yaml file --- notebooks/example_container_toybidsapp.yaml | 1 + .../example_container_zipped_toybidsapp.yaml | 16 ++++++++-------- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/notebooks/example_container_toybidsapp.yaml b/notebooks/example_container_toybidsapp.yaml index c75b09f8..2d9a09bd 100644 --- a/notebooks/example_container_toybidsapp.yaml +++ b/notebooks/example_container_toybidsapp.yaml @@ -1,6 +1,7 @@ # 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 diff --git a/notebooks/example_container_zipped_toybidsapp.yaml b/notebooks/example_container_zipped_toybidsapp.yaml index 09468054..9ab0e811 100644 --- a/notebooks/example_container_zipped_toybidsapp.yaml +++ b/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. From 656196a24585f56fc03c2808012a63f0f259d9d4 Mon Sep 17 00:00:00 2001 From: Chenying Zhao Date: Thu, 4 May 2023 14:36:07 -0400 Subject: [PATCH 3/6] try fixing RTD: remove system_packages: true --- .readthedocs.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index b0775e49..7d89571f 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -10,4 +10,3 @@ python: path: . extra_requirements: - doc - system_packages: true From 4071631beee956109a0804c7a34cb81d0ead63ec Mon Sep 17 00:00:00 2001 From: Chenying Zhao Date: Thu, 4 May 2023 14:38:39 -0400 Subject: [PATCH 4/6] try fixing RTD: add build os --- .readthedocs.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 7d89571f..963d4023 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,5 +1,8 @@ version: 2 +build: + os: ubuntu-22.04 + sphinx: configuration: docs/source/conf.py From 51d97d39a0f7339ee6a7aec594c65e92bf683409 Mon Sep 17 00:00:00 2001 From: Chenying Zhao Date: Thu, 4 May 2023 14:43:59 -0400 Subject: [PATCH 5/6] try fixing RTD: remove python version --- .readthedocs.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 963d4023..55748d1d 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,7 +7,6 @@ sphinx: configuration: docs/source/conf.py python: - version: 3.8 install: - method: pip path: . From 1970f410b8fb51a5b80ab78b369ea0e79a7d2b40 Mon Sep 17 00:00:00 2001 From: Chenying Zhao Date: Thu, 4 May 2023 14:45:32 -0400 Subject: [PATCH 6/6] try fixing RTD: move python version to build tools --- .readthedocs.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 55748d1d..f5468ece 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -2,6 +2,8 @@ version: 2 build: os: ubuntu-22.04 + tools: + python: "3.8" sphinx: configuration: docs/source/conf.py