👔 Persist longitudinal resource pool

Author: shnizzedy

CHANGELOG.md

@@ -14,15 +14,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.8.7.post1.dev1] - unreleased
+## [1.8.7.post1] - unreleased
 
 ### Changed
 
 - Disabled variant image builds.
 
 ### Fixed
 
-- Supplied missing `subject_id` for longitudinal workflow logger and make that field optional for the logger.
+- Graph-building bugs that prevented longitudinal workflows from running.
 
 ## [1.8.7] - 2024-05-03
 
@@ -304,7 +304,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 See [Version 1.8.1 Beta](https://fcp-indi.github.io/docs/user/release_notes/v1.8.1) for release notes for v1.8.1 and [Release Notes](https://fcp-indi.github.io/docs/user/release_notes) for all release notes back to v0.1.1.
 
-[1.8.7.post1.dev1]: https://github.com/FCP-INDI/C-PAC/compare/v1.8.7...v1.8.7.post1.dev1
+[1.8.7.post1]: https://github.com/FCP-INDI/C-PAC/compare/v1.8.7...v1.8.7.post1.dev3
 [1.8.7]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.7
 [1.8.6]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.6
 [1.8.5]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.5

CPAC/info.py

@@ -43,7 +43,7 @@
 _version_major = 1
 _version_minor = 8
 _version_micro = 7
-_version_extra = 'post1.dev2'
+_version_extra = 'post1.dev3'
 
 
 def get_cpac_gitversion():

CPAC/longitudinal_pipeline/longitudinal_workflow.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright (C) 2020-2022  C-PAC Developers
+# Copyright (C) 2020-2024  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -15,10 +15,12 @@
 
 # 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/>.
-import os
 import copy
-import time
+import os
 import shutil
+import time
+from typing import Optional
+
 from CPAC.pipeline.nodeblock import nodeblock
 
 from nipype import config
@@ -41,7 +43,7 @@
 from CPAC.pipeline.cpac_pipeline import initialize_nipype_wf, \
     connect_pipeline, build_anat_preproc_stack, build_T1w_registration_stack,\
     build_segmentation_stack
-from CPAC.pipeline.engine import initiate_rpool, ingress_output_dir
+from CPAC.pipeline.engine import initiate_rpool, ingress_output_dir, ResourcePool
 
 from CPAC.registration import (
     create_fsl_flirt_linear_reg,
@@ -492,6 +494,8 @@ def anat_longitudinal_wf(subject_id, sub_list, config):
                             strats_head_dct[tag].append(os.path.join(cpac_dir,
                                                                      head_file))
 
+    longitudinal_rpool: Optional[ResourcePool] = None
+
     for strat in strats_brain_dct.keys():
 
         wf = initialize_nipype_wf(config, sub_list[0],
@@ -567,6 +571,8 @@ def anat_longitudinal_wf(subject_id, sub_list, config):
         # once for every strategy!
         wf.run()
 
+        longitudinal_rpool = rpool.copy_rpool()
+
         # now, just write out a copy of the above to each session
         config.pipeline_setup['pipeline_name'] = orig_pipe_name
         for session in sub_list:
@@ -591,7 +597,7 @@ def anat_longitudinal_wf(subject_id, sub_list, config):
 
             wf = initialize_nipype_wf(config, sub_list[0])
 
-            wf, rpool = initiate_rpool(wf, config, session)
+            wf, rpool = initiate_rpool(wf, config, session, rpool=longitudinal_rpool)
 
             config.pipeline_setup[
                 'pipeline_name'] = f'longitudinal_{orig_pipe_name}'
@@ -627,6 +633,7 @@ def anat_longitudinal_wf(subject_id, sub_list, config):
 
             rpool.gather_pipes(wf, config, add_excl=excl)
             wf.run()
+            longitudinal_rpool = rpool.copy_rpool()
 
     # begin single-session stuff again
     for session in sub_list:
@@ -651,7 +658,7 @@ def anat_longitudinal_wf(subject_id, sub_list, config):
 
         wf = initialize_nipype_wf(config, sub_list[0])
 
-        wf, rpool = initiate_rpool(wf, config, session)
+        wf, rpool = initiate_rpool(wf, config, session, rpool=longitudinal_rpool)
 
         pipeline_blocks = [warp_longitudinal_T1w_to_template,
                            warp_longitudinal_seg_to_T1w]