[pre-commit.ci] auto fixes from pre-commit.com hooks

pre-commit-ci[bot] · pre-commit-ci[bot] · commit 651cfa57a14e · 2025-09-12T18:30:14.000Z
for more information, see https://pre-commit.ci
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-v
 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-v
 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-v
 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/CPAC/anat_preproc/ants.py b/CPAC/anat_preproc/ants.py
@@ -295,12 +295,22 @@ def init_brain_extraction_wf(  # noqa: PLR0913
         init_aff.inputs.search_grid = (40, (0, 40, 40))
 
     # Set up spatial normalization
-    settings_file = (f'antsBrainExtraction_{normalization_quality}.json' if use_laplacian else f'antsBrainExtractionNoLaplacian_{normalization_quality}.json')
-    norm = pe.Node(Registration(from_file=str(files('CPAC.anat_preproc').joinpath('data').joinpath(settings_file))),
-        name='norm',
+    settings_file = (
+        f"antsBrainExtraction_{normalization_quality}.json"
+        if use_laplacian
+        else f"antsBrainExtractionNoLaplacian_{normalization_quality}.json"
+    )
+    norm = pe.Node(
+        Registration(
+            from_file=str(
+                files("CPAC.anat_preproc").joinpath("data").joinpath(settings_file)
+            )
+        ),
+        name="norm",
         n_procs=omp_nthreads,
         mem_gb=1.7,
-        mem_x=(1233286593342025 / 151115727451828646838272, 'moving_image'))
+        mem_x=(1233286593342025 / 151115727451828646838272, "moving_image"),
+    )
     norm.inputs.float = use_float
     fixed_mask_trait = "fixed_image_mask"
     if _ants_version and parseversion(_ants_version) >= Version("2.2.0"):
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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # 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 
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/data_config_S3_CoRR_5only_mult-scan.yml b/CPAC/resources/configs/test_configs/data_config_S3_CoRR_5only_mult-scan.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.8.8.dev1
+# Version 
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/data_config_S3_CoRR_5only_mult-sess.yml b/CPAC/resources/configs/test_configs/data_config_S3_CoRR_5only_mult-sess.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.8.8.dev1
+# Version 
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_ABCD.yml b/CPAC/resources/configs/test_configs/pipe-test_ABCD.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-AllNuis.yml b/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-AllNuis.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-DistCorr3dSk.yml b/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-DistCorr3dSk.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-DistCorrBET.yml b/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-DistCorrBET.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_ANTs-BET-AllNuis.yml b/CPAC/resources/configs/test_configs/pipe-test_ANTs-BET-AllNuis.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.8.dev1
+# Version 
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-3dSk-AllNuis.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-3dSk-AllNuis.yml
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-BASC.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-BASC.yml
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-ISC-voxel.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-ISC-voxel.yml
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-ISC.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-ISC.yml
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-MDMR.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-MDMR.yml
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis.yml
diff --git a/CPAC/resources/configs/test_configs/pipe-test_all.yml b/CPAC/resources/configs/test_configs/pipe-test_all.yml
diff --git a/Dockerfile b/Dockerfile
diff --git a/variant-lite.Dockerfile b/variant-lite.Dockerfile
diff --git a/version b/version

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# CPAC Data Configuration File`
`2`		`-# Version 1.8.8.dev1`
	`2`	`+# Version`
`3`	`3`	`#`
`4`	`4`	`# http://fcp-indi.github.io for more info.`
`5`	`5`	`#`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# CPAC Data Settings File`
`2`		`-# Version 1.8.8.dev1`
	`2`	`+# Version`
`3`	`3`	`#`
`4`	`4`	`# http://fcp-indi.github.io for more info.`
`5`	`5`	`#`