create isolated conda env for each rule

.dryrun_test_all.sh

@@ -1,16 +1,16 @@
 #!/bin/bash
 set -euxo pipefail
 HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --use-conda
-# hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R 
-# hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L 
-# hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w 
-# hippunfold test_data/bids_T1w test_out participant -np --modality T1w 
-# hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500 
-# hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w 
-# hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w 
-# hippunfold test_data/bids_manualseg test_out participant -np --modality manualseg --path_manualseg test_data/bids_manualseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
-# hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality manualseg --hemi L
-# hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template 
-# hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w 
-# hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L 
+hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w 
+hippunfold test_data/bids_T1w test_out participant -np --modality T1w 
+hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500 
+hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w 
+hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w 
+hippunfold test_data/bids_manualseg test_out participant -np --modality manualseg --path_manualseg test_data/bids_manualseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz 
+hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality manualseg --hemi L 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w 
+hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg 

hippunfold/workflow/envs/env10.yaml

@@ -0,0 +1,9 @@
+name: env10
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - matplotlib
+  - pandas=2.2.3
+  - seaborn

hippunfold/workflow/envs/env11.yaml

@@ -0,0 +1,7 @@
+name: env11
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - pandas=2.2.3

hippunfold/workflow/envs/env12.yaml

@@ -0,0 +1,7 @@
+name: env12
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - greedyreg

hippunfold/workflow/envs/env13.yaml

@@ -0,0 +1,9 @@
+name: env13
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - nibabel=5.2.1
+  - numpy=2.1.2
+  - scipy=1.13.1

hippunfold/workflow/envs/env14.yaml

@@ -0,0 +1,7 @@
+name: env14
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - niftyreg

hippunfold/workflow/envs/env15.yaml

@@ -0,0 +1,10 @@
+name: env15
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - nibabel=5.2.1
+  - numpy=2.1.2
+  - scipy=1.13.1
+  - naturalneighbor

hippunfold/workflow/envs/env5.yaml

@@ -0,0 +1,7 @@
+name: env5
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - convert3d

hippunfold/workflow/envs/env6.yaml

@@ -0,0 +1,7 @@
+name: env6
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - niftyreg

hippunfold/workflow/envs/env7.yaml

@@ -0,0 +1,8 @@
+name: env7
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - convert3d
+  - niftyreg

hippunfold/workflow/envs/env8.yaml

@@ -0,0 +1,8 @@
+name: env8
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - nilearn
+  - matplotlib

hippunfold/workflow/envs/env9.yaml

@@ -0,0 +1,9 @@
+name: env9
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - nibabel=5.2.1
+  - numpy=2.1.2
+  - pandas=2.2.3

hippunfold/workflow/rules/gifti.smk

@@ -1463,6 +1463,8 @@ rule create_spec_file_hipp:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:

hippunfold/workflow/rules/myelin_map.smk

@@ -29,6 +29,8 @@ rule divide_t1_by_t2:
             suffix="T1wDividedByT2w.nii.gz",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env5.yaml"
     group:
         "subj"
     container:
@@ -61,6 +63,8 @@ rule create_ribbon:
             hemi="{hemi}",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env5.yaml"
     group:
         "subj"
     container:
@@ -133,6 +137,8 @@ rule sample_myelin_map_surf:
             label="{autotop}",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     container:

hippunfold/workflow/rules/nnunet.smk

@@ -206,6 +206,8 @@ rule unflip_nnunet_nii:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env5.yaml"
     group:
         "subj"
     shell:
@@ -282,6 +284,8 @@ rule qc_nnunet_f3d:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env6.yaml"
     log:
         bids(
             root="logs",
@@ -331,6 +335,8 @@ rule qc_nnunet_dice:
             caption="../report/nnunet_qc.rst",
             category="Segmentation QC",
         ),
+    conda:
+        "../envs/env1.yaml"
     group:
         "subj"
     container:

hippunfold/workflow/rules/preproc_hippb500.smk

@@ -23,6 +23,8 @@ rule resample_hippdwi_to_template:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env5.yaml"
     group:
         "subj"
     shell:
@@ -56,6 +58,8 @@ rule lr_flip_b500:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env5.yaml"
     group:
         "subj"
     shell:

hippunfold/workflow/rules/preproc_manualseg.smk

@@ -20,6 +20,8 @@ rule import_manualseg_to_corobl:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env4.yaml"
     group:
         "subj"
     shell:
@@ -48,6 +50,8 @@ rule lr_flip_seg:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env5.yaml"
     group:
         "subj"
     shell:

hippunfold/workflow/rules/preproc_t1.smk

@@ -52,6 +52,8 @@ else:
         threads: 8
         container:
             config["singularity"]["autotop"]
+        conda:
+            "../envs/env4.yaml"
         group:
             "subj"
         shell:
@@ -97,6 +99,8 @@ rule warp_t1_to_corobl_crop:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env4.yaml"
     group:
         "subj"
     shell:
@@ -127,6 +131,8 @@ rule lr_flip_t1:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env5.yaml"
     group:
         "subj"
     shell:

hippunfold/workflow/rules/preproc_t2.smk

@@ -33,6 +33,8 @@ rule n4_t2:
     threads: 8
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env4.yaml"
     group:
         "subj"
     shell:
@@ -111,6 +113,8 @@ rule reg_t2_to_ref:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env7.yaml"
     group:
         "subj"
     shell:
@@ -179,6 +183,8 @@ else:
             ),
         container:
             config["singularity"]["autotop"]
+        conda:
+            "../envs/env5.yaml"
         group:
             "subj"
         shell:
@@ -242,6 +248,8 @@ rule reg_t2_to_t1:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env7.yaml"
     group:
         "subj"
     shell:
@@ -345,6 +353,8 @@ rule compose_t2_xfm_corobl:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env5.yaml"
     group:
         "subj"
     shell:
@@ -407,6 +417,8 @@ rule warp_t2_to_corobl_crop:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env4.yaml"
     group:
         "subj"
     shell:
@@ -437,6 +449,8 @@ rule lr_flip_t2:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env5.yaml"
     group:
         "subj"
     shell:

hippunfold/workflow/rules/qc.smk

@@ -29,6 +29,8 @@ rule qc_reg_to_template:
             caption="../report/t1w_template_regqc.rst",
             category="Registration QC",
         ),
+    conda:
+        "../envs/env8.yaml"
     group:
         "subj"
     container:
@@ -72,6 +74,8 @@ rule get_subfield_vols_subj:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env9.yaml"
     script:
         "../scripts/gen_volume_tsv.py"
 
@@ -105,6 +109,8 @@ rule plot_subj_subfields:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env10.yaml"
     script:
         "../scripts/plot_subj_subfields.py"
 
@@ -188,6 +194,8 @@ rule qc_subfield:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env8.yaml"
     script:
         "../scripts/vis_qc_dseg.py"
 
@@ -224,6 +232,8 @@ rule qc_subfield_surf:
         "subj"
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env8.yaml"
     script:
         "../scripts/vis_qc_surf.py"
 
@@ -260,5 +270,7 @@ rule concat_subj_vols_tsv:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env11.yaml"
     script:
         "../scripts/concat_tsv.py"