FCP-INDI · shnizzedy · Oct 15, 2024 · Oct 15, 2024 · Oct 15, 2024 · Oct 22, 2024
diff --git a/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile
@@ -14,7 +14,7 @@
 
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
-FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.8.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.8.dev2
 LABEL org.opencontainers.image.description "Full C-PAC image"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root

diff --git a/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile
@@ -14,7 +14,7 @@
 
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
-FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.8.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.8.dev2
 LABEL org.opencontainers.image.description "Full C-PAC image without FreeSurfer"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root

diff --git a/.github/Dockerfiles/base-standard.Dockerfile b/.github/Dockerfiles/base-standard.Dockerfile
@@ -16,7 +16,7 @@
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 FROM ghcr.io/fcp-indi/c-pac/freesurfer:6.0.0-min.neurodocker-jammy as FreeSurfer
 
-FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.8.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.8.dev2
 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 Standard software dependencies for C-PAC standard images"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC

diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml
@@ -318,7 +318,6 @@ jobs:
     uses: ./.github/workflows/build_C-PAC.yml
     with:
       variant: lite
-
   smoke-tests-participant:
     name: Run participant-level smoke tests
     needs:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -30,13 +30,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Moved `pygraphviz` from requirements to `graphviz` optional dependencies group.
 - Automatically tag untagged `subject_id` and `unique_id` as `!!str` when loading data config files.
 - Made orientation configurable (was hard-coded as "RPI").
+- Disabled variant image builds.
 
 ### Fixed
 
 - A bug in which AWS S3 encryption was looked for in Nipype config instead of pipeline config (only affected uploading logs).
 - Restored `bids-validator` functionality.
 - Fixed empty `shell` variable in cluster run scripts.
 - A bug in which bandpass filters always assumed 1D regressor files have exactly 5 header rows.
+- Supplied missing `subject_id` for longitudinal workflow logger and make that field optional for the logger.
 
 ### Removed
 

diff --git a/CPAC/info.py b/CPAC/info.py
@@ -47,7 +47,7 @@
 _version_major = 1
 _version_minor = 8
 _version_micro = 8
-_version_extra = "dev1"
+_version_extra = "dev2"
 
 
 def get_cpac_gitversion():

diff --git a/CPAC/longitudinal_pipeline/longitudinal_workflow.py b/CPAC/longitudinal_pipeline/longitudinal_workflow.py
@@ -38,6 +38,7 @@
     create_wf_calculate_ants_warp,
 )
 from CPAC.registration.registration import apply_transform
+from CPAC.utils.configuration.configuration import Configuration
 from CPAC.utils.datasource import (
     resolve_resolution,
 )
@@ -380,24 +381,25 @@ def warp_longitudinal_seg_to_T1w(wf, cfg, strat_pool, pipe_num, opt=None):
     return (wf, outputs)
 
 
-def anat_longitudinal_wf(subject_id, sub_list, config):
+def anat_longitudinal_wf(
+    subject_id: str, sub_list: list[dict], config: Configuration
+) -> None:
     """
+    Create and run anatomical longitudinal workflow(s).
+
     Parameters
     ----------
-    subject_id : str
+    subject_id
         the id of the subject
-    sub_list : list of dict
+    sub_list
         this is a list of sessions for one subject and each session if the same dictionary as the one given to
         prep_workflow
-    config : configuration
+    config
         a configuration object containing the information of the pipeline config. (Same as for prep_workflow)
-
-    Returns
-    -------
-        None
     """
-    # list of lists for every strategy
-    session_id_list = []
+    config["subject_id"] = subject_id
+    session_id_list: list[list] = []
+    """List of lists for every strategy"""
     session_wfs = {}
 
     cpac_dirs = []

diff --git a/CPAC/pipeline/engine.py b/CPAC/pipeline/engine.py
@@ -1073,7 +1073,9 @@ def post_process(self, wf, label, connection, json_info, pipe_idx, pipe_x, outs)
     def gather_pipes(self, wf, cfg, all=False, add_incl=None, add_excl=None):
         excl = []
         substring_excl = []
-        outputs_logger = getLogger(f'{cfg["subject_id"]}_expectedOutputs')
+        outputs_logger = getLogger(
+            f'{cfg.get("subject_id", getattr(wf, "name", ""))}_expectedOutputs'
+        )
         expected_outputs = ExpectedOutputs()
 
         if add_excl:

diff --git a/CPAC/resources/configs/data_config_S3-BIDS-ABIDE.yml b/CPAC/resources/configs/data_config_S3-BIDS-ABIDE.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/data_config_S3-BIDS-ADHD200.yml b/CPAC/resources/configs/data_config_S3-BIDS-ADHD200.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/data_config_S3-BIDS-ADHD200_only2.yml b/CPAC/resources/configs/data_config_S3-BIDS-ADHD200_only2.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/data_config_S3-BIDS-NKI-RocklandSample.yml b/CPAC/resources/configs/data_config_S3-BIDS-NKI-RocklandSample.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/data_config_cpac_benchmark.yml b/CPAC/resources/configs/data_config_cpac_benchmark.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/data_settings_template.yml b/CPAC/resources/configs/data_settings_template.yml
@@ -1,5 +1,5 @@
 # CPAC Data Settings File
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/group_config_template.yml b/CPAC/resources/configs/group_config_template.yml
@@ -1,5 +1,5 @@
 # CPAC Group-Level Analysis Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_abcd-options.yml b/CPAC/resources/configs/pipeline_config_abcd-options.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_abcd-prep.yml b/CPAC/resources/configs/pipeline_config_abcd-prep.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_anat-only.yml b/CPAC/resources/configs/pipeline_config_anat-only.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml b/CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml b/CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_blank.yml b/CPAC/resources/configs/pipeline_config_blank.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_ccs-options.yml b/CPAC/resources/configs/pipeline_config_ccs-options.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_default-deprecated.yml b/CPAC/resources/configs/pipeline_config_default-deprecated.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_default.yml b/CPAC/resources/configs/pipeline_config_default.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_fmriprep-ingress.yml b/CPAC/resources/configs/pipeline_config_fmriprep-ingress.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_fmriprep-options.yml b/CPAC/resources/configs/pipeline_config_fmriprep-options.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_fx-options.yml b/CPAC/resources/configs/pipeline_config_fx-options.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_monkey-ABCD.yml b/CPAC/resources/configs/pipeline_config_monkey-ABCD.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_monkey.yml b/CPAC/resources/configs/pipeline_config_monkey.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_ndmg.yml b/CPAC/resources/configs/pipeline_config_ndmg.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_nhp-macaque.yml b/CPAC/resources/configs/pipeline_config_nhp-macaque.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_preproc.yml b/CPAC/resources/configs/pipeline_config_preproc.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_rbc-options.yml b/CPAC/resources/configs/pipeline_config_rbc-options.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_regtest-1.yml b/CPAC/resources/configs/pipeline_config_regtest-1.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_regtest-2.yml b/CPAC/resources/configs/pipeline_config_regtest-2.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_regtest-3.yml b/CPAC/resources/configs/pipeline_config_regtest-3.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_regtest-4.yml b/CPAC/resources/configs/pipeline_config_regtest-4.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/pipeline_config_rodent.yml b/CPAC/resources/configs/pipeline_config_rodent.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/system_config.yml b/CPAC/resources/configs/system_config.yml
@@ -1,5 +1,5 @@
 # C-PAC System Configuration YAML file
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/test_configs/data-test_S3-ADHD200_1.yml b/CPAC/resources/configs/test_configs/data-test_S3-ADHD200_1.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/test_configs/data-test_S3-ADHD200_no-params.yml b/CPAC/resources/configs/test_configs/data-test_S3-ADHD200_no-params.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #

diff --git a/CPAC/resources/configs/test_configs/data-test_S3-NKI-RS_fmap.yml b/CPAC/resources/configs/test_configs/data-test_S3-NKI-RS_fmap.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.8.8.dev1
+# Version 1.8.8.dev2
 #
 # http://fcp-indi.github.io for more info.
 #