Merge pull request #1944 from FCP-INDI/develop-1.8.6

Merge develop-1.8.6 into develop

Author: nx10

.github/README.md

@@ -0,0 +1,121 @@
+# C-PAC/.github README
+
+This directory contains Dockerfiles, scripts, requirements files, and workflow configurations for [this repository's GitHub Actions](https://github.com/FCP-INDI/C-PAC/actions).
+
+When updating these files, please update this README as necessary.
+
+[The `workflows` directory](./workflows) contains the configurations for the Actions themselves. The other directories support these configs.
+
+```mermaid
+flowchart TD
+    subgraph Dockerfiles
+      base[base-.*]
+
+      cpacdockerfiles["C-PAC.develop-(?!lite).*"]
+
+      cpaclitedockerfile[C-PAC.develop-lite.*]
+
+      stagedockerfiles[AFNI.*\nANTs.*\nc3d.*\nconnectome-workbench.*\nFSL.*\nICA-AROMA.*\nmsm.*]
+
+      ubuntudockerfiles[Ubuntu.*]
+    end
+    subgraph scripts
+      get_package_id.py
+      get_pr_base_shas
+      local_ghcr
+    end
+    subgraph smoke_test_participant.yml
+      smoke_test_human
+      smoke_test_nhp
+      smoke_test_rodent
+    end
+    subgraph stage_requirements
+      .*.txt
+    end
+    subgraph workflows
+      subgraph build_stages.yml
+
+        ubuntu[[Ubnutu]]-->stages[[stages]]-->build-base[[build-base]]
+
+      end
+      subgraph build_C-PAC.yml
+        bCPAC[[C-PAC]]
+      end
+      subgraph build_and_test.yml
+        Circle_tests[[Circle_tests]]
+      
+        C-PAC[[C-PAC]]-->bCPAC
+        C-PAC-->Circle_tests
+        C-PAC-->smoke-tests-participant
+        C-PAC-->C-PAC-lite
+
+        C-PAC-lite[[C-PAC-lite]]-->bCPAC
+        C-PAC-lite-->Circle_tests
+        C-PAC-lite-->smoke-tests-participant
+
+        C-PAC-ABCD-HCP[[C-PAC-ABCD-HCP]]-->bCPAC
+        C-PAC-ABCD-HCP-->Circle_tests
+        C-PAC-ABCD-HCP-->smoke-tests-participant
+
+        C-PAC-fMRIPrep[[C-PAC-fMRIPrep-LTS]]-->bCPAC
+        C-PAC-fMRIPrep-->Circle_tests
+        C-PAC-fMRIPrep-->smoke-tests-participant
+
+        smoke-tests-participant[[smoke-tests-participant]]
+      end
+
+      check_updated_preconfigs.yml-->build_stages.yml
+
+      delete_images.yml
+    end
+
+    subgraph yaml_template[CPAC/utils/configuration/yaml_template.py]
+
+      update_all_preconfigs[[update_all_preconfigs]]
+    end
+
+    base<-->build-base
+
+    Circle_tests-->CircleCI((Run tests on Circle CI))
+
+    build_stages.yml-->build_and_test.yml
+
+    check_updated_preconfigs.yml<-->get_pr_base_shas
+    check_updated_preconfigs.yml-->update_all_preconfigs
+
+    cpacdockerfiles<-->C-PAC
+    cpacdockerfiles<-->C-PAC-ABCD-HCP
+    cpacdockerfiles<-->C-PAC-fMRIPrep
+
+    cpaclitedockerfile<-->C-PAC-lite
+
+    delete>delete branch]-->delete_images.yml
+
+    delete_images.yml<-->get_package_id.py
+
+    build-base<-->local_ghcr
+    bCPAC<-->local_ghcr
+    stages<-->local_ghcr
+
+    push>git push]-->check_updated_preconfigs.yml
+
+    smoke-tests-participant-->smoke_test_human
+    smoke-tests-participant-->smoke_test_nhp
+    smoke-tests-participant-->smoke_test_rodent
+
+    stagedockerfiles<-->stages
+
+    build-base<-->.*.txt
+
+    ubuntudockerfiles<-->ubuntu
+```
+
+In this [Mermaid flowchart](https://mermaid.js.org/syntax/flowchart.html), these shapes are used:
+
+concept | shape
+---|---
+directory | `subgraph`
+file | rectangle (`[]`) or `subgraph`
+workflow job | subprocess (`[[]]`)
+trigger action | asymetric (`>]`)
+external API | circle (`(())`)

.gitignore

@@ -38,16 +38,9 @@ bids-examples
 .project
 .pydevproject
 
-# Other project files
-.idea/*.xml
-
-# Transpiling and compiling
-*.c
-*.so
-
-
- .vscode/launch.json
- .vscode/settings.json
+# IDE configs
+.vscode/
+.idea/
 
 cpac_runs/
 

.vscode/run_nose.py

@@ -413,17 +413,6 @@ def workflows():
     pass
 
 
-@workflows.command()
-@click.argument('func_ts')
-@click.argument('func_brain_mask')
-@click.option('--hp', default=0.01)
-@click.option('--lp', default=0.1)
-def alff(func_ts, func_brain_mask, hp=0.01, lp=0.1):
-    from CPAC.alff.alff import run_alff
-    paths = run_alff(func_ts, func_brain_mask, hp, lp)
-    print(paths)
-
-
 @utils.command()
 @click.argument('directory')
 def repickle(directory):