Fix packaging (#14)

* bug (was data/results)  + removed T1 (erode_skin too long) for macaque + no n_procs 1

* added segment_petra in workflows, plus added init in root dir (for segment_skull) to check if one  on them is understood correctly in the pypi version

.github/workflows/build_on_prerelease.yml

@@ -96,7 +96,7 @@ jobs:
 
       - name: Running all test pipelines (ANTS cenir macaque petra)
         run: |
-            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull -data /data/cenir-macaque-petra -out /data/cenir-macaque-petra/results -soft ANTS_prep_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad -nprocs 1
+            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull -data /data/cenir-macaque-petra -out /data/cenir-macaque-petra/results -soft ANTS_prep_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt petra -deriv -pad
 
             ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results
 
@@ -143,7 +143,7 @@ jobs:
       - name: Running all test pipelines (ANTS cerimed macaque CT)
         run: |
 
-            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull  -data /data/cerimed-macaque-ct -out /datat/cerimed-macaque-ct/results -soft ANTS_prep_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT -deriv -pad
+            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull  -data /data/cerimed-macaque-ct -out /data/cerimed-macaque-ct/results -soft ANTS_prep_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt CT -deriv -pad
 
             ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results
 
@@ -190,7 +190,7 @@ jobs:
 
       - name: Running all test pipelines (ANTS cerimed marmo petra)
         run: |
-            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull -data /data/cerimed-marmo-petra -out /data/results -soft ANTS_noseg_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad
+            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull -data /data/cerimed-marmo-petra -out /data/cerimed-marmo-petra/results -soft ANTS_noseg_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad
 
             ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results
 

TODO.txt

@@ -0,0 +1,38 @@
+
+29/08/2022
+Bug report
+- Issue when using _spm docker versions (at least the latest rc7_spm and rc8_spm versions) with the -soft ANTS option
+
+Road map to v0.3.2:
+- replace in default params (used with -species, located in workflows) short_preparation_pipe -> preparation pipe, and modify params only if -params is not used
+
+
+24/08/2022
+Bug report
+Issues with padding, works only if short_preparation_pipe / crop_T1 (not with long preparation_prep / prep_T1 / crop in params.json)
+
+29/06/2022 Added the following issues:
+
+Road map to v0.3.2
+- -template to provide user template.
+
+19/05/2022: with params, if long_prep, do not work with ANTS_T1.
+    also with -species, problem if crop_T1 and crop_T2 is available, -soft ANTS_T1 will crash
+
+17/05/2022 Added the following issues
+
+Road map to v0.3.2
+- make use of macapype_CI.zip in the examples + build the doc at all the release
+- reframe automated definition of short_preparation_pipe based on the content indiv_params.json
+- add more command line options (in the default, but interfering with the params):
+    -no_crop if data are already cropped (see previous point)
+    -export_5tt for exporting 5tt
+- 5tt with 6 priors -> gm cortical and subcortical as 2 first tissus
+
+
+Road map to v0.4
+- better reorientation tools
+- better bet-cropping
+
+
+16/05/2022 Release v0.3.1

segment_skull.py

@@ -63,9 +63,10 @@
     create_full_ants_subpipes,
     create_full_T1_ants_subpipes,)
 
-from macapype.utils.utils_bids import (create_datasource,
-                                       create_datasource_indiv_params,
-                                       create_datasink)
+from macapype.utils.utils_bids import (
+    create_datasource,
+    create_datasource_indiv_params,
+    create_datasink)
 
 from macapype.utils.utils_tests import load_test_data, format_template
 
@@ -75,13 +76,15 @@
 
 from macapype.pipelines.rename import rename_all_brain_derivatives
 
-from skullTo3d.pipelines.skull_pipe import (create_skull_petra_pipe,
-                                       create_skull_ct_pipe,
-                                       create_skull_t1_pipe)
+from skullTo3d.pipelines.skull_pipe import (
+    create_skull_petra_pipe,
+    create_skull_ct_pipe,
+    create_skull_t1_pipe)
 
-from skullTo3d.pipelines.rename import (rename_all_skull_petra_derivatives,
-                                        rename_all_skull_t1_derivatives,
-                                        rename_all_skull_ct_derivatives)
+from skullTo3d.pipelines.rename import (
+    rename_all_skull_petra_derivatives,
+    rename_all_skull_t1_derivatives,
+    rename_all_skull_ct_derivatives)
 
 
 fsl.FSLCommand.set_default_output_type('NIFTI_GZ')

setup.py

@@ -39,6 +39,8 @@
     long_description_content_type='text/markdown',
     license='BSD 3',
     entry_points={
-        'console_scripts': ['segment_skull = segment_skull:main']},
+        'console_scripts': ['segment_skull = segment_skull:main',
+                            'segment_petra = workflows.segment_petra:main']
+        },
     install_requires=required_packages,
     include_package_data=True)

skullTo3d/_version.py

@@ -1,2 +1 @@
-
-__version__ = '0.0.1-rc12'
+__version__ = '0.0.1-rc13'