Merge pull request #1764 from FCP-INDI/fix/pipeline-config-versions

sgiavasis · web-flow · commit 9586d7146eff · 2022-09-19T21:31:01.000-04:00
🔖 Hotfix: Update version to 1.8.4
diff --git a/CPAC/pipeline/engine.py b/CPAC/pipeline/engine.py
@@ -1949,9 +1949,6 @@ def initiate_rpool(wf, cfg, data_paths=None, part_id=None):
                 ingress_raw_func_data(wf, rpool, cfg, data_paths, unique_id,
                                       part_id, ses_id)
 
-    # grab already-processed data from the output directory
-    rpool = ingress_output_dir(cfg, rpool, unique_id, creds_path)
-
     # grab any file paths from the pipeline config YAML
     rpool = ingress_pipeconfig_paths(cfg, rpool, unique_id, creds_path)
 
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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 for RBC options
-# Version 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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 1.8.4.dev
+# Version 1.8.4
 #
 # 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
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.4.dev
+# Version 1.8.4
 #
 # http://fcp-indi.github.io for more info.
 #
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
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.4.dev
+# Version 1.8.4
 #
 # http://fcp-indi.github.io for more info.
 #
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
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.4.dev
+# Version 1.8.4
 #
 # http://fcp-indi.github.io for more info.
 #
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
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.4.dev
+# Version 1.8.4
 #
 # http://fcp-indi.github.io for more info.
 #
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
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.4.dev
+# Version 1.8.4
 #
 # http://fcp-indi.github.io for more info.
 #
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
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.4.dev
+# Version 1.8.4
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_all.yml b/CPAC/resources/configs/test_configs/pipe-test_all.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.4.dev
+# Version 1.8.4
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/README.md b/README.md
@@ -40,7 +40,7 @@ Documentation pertaining to this latest release can be found here: https://fcp-i
 Discussion Forum
 ---------------
 
-If you are stuck and need help or have any other questions or comments about C-PAC, there is a C-PAC discussion forum here: ttps://neurostars.org/tag/cpac
+If you are stuck and need help or have any other questions or comments about C-PAC, there is a C-PAC discussion forum here: https://neurostars.org/tag/cpac
 
 Issue Tracker and Bugs
 ----------------------
diff --git a/dev/docker_data/default_pipeline.yml b/dev/docker_data/default_pipeline.yml
@@ -1,7 +1,7 @@
 %YAML 1.1
 ---
 # CPAC Pipeline Configuration YAML file
-# Version 1.8.4.dev
+# Version 1.8.4
 #
 # http://fcp-indi.github.io for more info.
 #

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# CPAC Data Configuration File`
`2`		`-# Version 1.8.4.dev`
	`2`	`+# Version 1.8.4`
`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 1.8.4.dev`
	`2`	`+# Version 1.8.4`
`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 Group-Level Analysis Configuration YAML file`
`2`		`-# Version 1.8.4.dev`
	`2`	`+# Version 1.8.4`
`3`	`3`	`#`
`4`	`4`	`# http://fcp-indi.github.io for more info.`
`5`	`5`	`#`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`%YAML 1.1`
`2`	`2`	`---`
`3`	`3`	`# CPAC Pipeline Configuration YAML file`
`4`		`-# Version 1.8.4.dev`
	`4`	`+# Version 1.8.4`
`5`	`5`	`#`
`6`	`6`	`# http://fcp-indi.github.io for more info.`
`7`	`7`	`#`