fix conflicts

Author: yibeichan

pydra/tasks/fsl/model/cluster.py

@@ -8,14 +8,12 @@ def Cluster_output(inputs):
     from pydra.engine.helpers_file import split_filename
 
     in_file = inputs.in_file
-    
+
     if in_file not in [None, attr.NOTHING]:
         pth, fname, ext = split_filename(in_file)
         return f"{fname}_localmax.txt"
     else:
-        raise Exception(
-            f"this function should be run only for out_localmax_txt_file not {name}"
-        )
+        raise Exception(f"this function should be run only for out_localmax_txt_file not {name}")
 
 
 input_fields = [
@@ -67,7 +65,6 @@ def Cluster_output(inputs):
             "help_string": "output of local maxima volume",
             "argstr": "--olmaxim={out_localmax_vol_file}",
             "output_file_template": "{in_file}_localmax",
-
         },
     ),
     (
@@ -76,7 +73,7 @@ def Cluster_output(inputs):
         {
             "help_string": "filename for output of size image",
             "argstr": "--osize={out_size_file}",
-            "output_file_template": "{in_file}_size"
+            "output_file_template": "{in_file}_size",
         },
     ),
     (
@@ -85,7 +82,7 @@ def Cluster_output(inputs):
         {
             "help_string": "filename for output of max image",
             "argstr": "--omax={out_max_file}",
-            "output_file_template": "{in_file}_max"
+            "output_file_template": "{in_file}_max",
         },
     ),
     (
@@ -94,7 +91,7 @@ def Cluster_output(inputs):
         {
             "help_string": "filename for output of mean image",
             "argstr": "--omean={out_mean_file}",
-            "output_file_template": "{in_file}_mean"
+            "output_file_template": "{in_file}_mean",
         },
     ),
     (
@@ -103,7 +100,7 @@ def Cluster_output(inputs):
         {
             "help_string": "filename for image output of log pvals",
             "argstr": "--opvals={out_pval_file}",
-            "output_file_template": "{in_file}_pval"
+            "output_file_template": "{in_file}_pval",
         },
     ),
     (
@@ -214,13 +211,9 @@ def Cluster_output(inputs):
         },
     ),
 ]
-Cluster_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+Cluster_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
-output_fields = [
-    
-]
+output_fields = []
 Cluster_output_spec = specs.SpecInfo(
     name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
 )
@@ -240,4 +233,4 @@ class Cluster(ShellCommandTask):
 
     input_spec = Cluster_input_spec
     output_spec = Cluster_output_spec
-    executable = "cluster"
+    executable = "cluster"

pydra/tasks/fsl/model/feat.py

@@ -39,16 +39,12 @@ def FEAT_output(fsf_file):
         },
     )
 ]
-FEAT_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+FEAT_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = [
     ("feat_dir", specs.Directory, {"requires": ["fsf_file"], "callable": FEAT_output})
 ]
-FEAT_output_spec = specs.SpecInfo(
-    name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
-)
+FEAT_output_spec = specs.SpecInfo(name="Output", fields=output_fields, bases=(specs.ShellOutSpec,))
 
 
 class FEAT(ShellCommandTask):
@@ -63,4 +59,4 @@ class FEAT(ShellCommandTask):
 
     input_spec = FEAT_input_spec
     output_spec = FEAT_output_spec
-    executable = "feat"
+    executable = "feat"

pydra/tasks/fsl/model/featmodel.py

@@ -64,9 +64,7 @@ def FEATModel_output(field, fsf_file):
         },
     ),
 ]
-FEATModel_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+FEATModel_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = [
     (
@@ -118,4 +116,4 @@ def FEATModel_output(field, fsf_file):
 class FEATModel(ShellCommandTask):
     input_spec = FEATModel_input_spec
     output_spec = FEATModel_output_spec
-    executable = "feat_model"
+    executable = "feat_model"

pydra/tasks/fsl/model/filmgls.py

@@ -2,6 +2,7 @@
 from pydra import ShellCommandTask
 import typing as ty
 
+
 def FILMGLS_output(field, inputs):
     import os, attr
 
@@ -39,7 +40,7 @@ def _get_numcons(inputs):
         return numtcons, numfcons
 
     name = field.name
-    pth = inputs.results_dir       
+    pth = inputs.results_dir
     if name == "results_dir":
         return pth
     elif name == "param_estimates":
@@ -57,7 +58,7 @@ def _get_numcons(inputs):
         return os.path.join(pth, "threshac1.nii.gz")
     elif name == "logfile":
         return os.path.join(pth, "logfile")
-    
+
     numtcons, numfcons = _get_numcons(inputs)
     base_contrast = 1
     copes = []
@@ -90,9 +91,7 @@ def _get_numcons(inputs):
             return zfstats
 
 
-
 input_fields = [
-    
     (
         "in_file",
         specs.File,
@@ -263,15 +262,10 @@ def _get_numcons(inputs):
         "results_dir",
         str,
         "results",
-        {
-            "help_string": "directory to store results in",
-            "argstr": "--rn={results_dir}"
-        },
+        {"help_string": "directory to store results in", "argstr": "--rn={results_dir}"},
     ),
 ]
-FILMGLS_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+FILMGLS_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = [
     (
@@ -327,32 +321,56 @@ def _get_numcons(inputs):
     (
         "copes",
         specs.MultiOutputFile,
-        {"help_string": "Contrast estimates for each contrast", "requires": ["tcon_file"], "callable": FILMGLS_output},
+        {
+            "help_string": "Contrast estimates for each contrast",
+            "requires": ["tcon_file"],
+            "callable": FILMGLS_output,
+        },
     ),
     (
         "varcopes",
         specs.MultiOutputFile,
-        {"help_string": "Variance estimates for each contrast", "requires": ["tcon_file"], "callable": FILMGLS_output},
+        {
+            "help_string": "Variance estimates for each contrast",
+            "requires": ["tcon_file"],
+            "callable": FILMGLS_output,
+        },
     ),
     (
         "zstats",
         specs.MultiOutputFile,
-        {"help_string": "z-stat file for each contrast", "requires": ["tcon_file"], "callable": FILMGLS_output},
+        {
+            "help_string": "z-stat file for each contrast",
+            "requires": ["tcon_file"],
+            "callable": FILMGLS_output,
+        },
     ),
     (
         "tstats",
         specs.MultiOutputFile,
-        {"help_string": "t-stat file for each contrast","requires": ["tcon_file"], "callable": FILMGLS_output},
+        {
+            "help_string": "t-stat file for each contrast",
+            "requires": ["tcon_file"],
+            "callable": FILMGLS_output,
+        },
     ),
     (
         "fstats",
         specs.MultiOutputFile,
-        {"help_string": "f-stat file for each contrast", "requires": ["fcon_file"],"callable": FILMGLS_output},
+        {
+            "help_string": "f-stat file for each contrast",
+            "requires": ["fcon_file"],
+            "callable": FILMGLS_output,
+        },
     ),
     (
         "zfstats",
         specs.MultiOutputFile,
-        {"help_string": "z-stat file for each F contrast", "requires": ["fcon_file"], "callable": FILMGLS_output},
+        {
+            "help_string": "z-stat file for each F contrast",
+            "requires": ["fcon_file"],
+            "callable": FILMGLS_output,
+        },
     ),
 ]
 FILMGLS_output_spec = specs.SpecInfo(
@@ -375,4 +393,4 @@ class FILMGLS(ShellCommandTask):
 
     input_spec = FILMGLS_input_spec
     output_spec = FILMGLS_output_spec
-    executable = "film_gls"
+    executable = "film_gls"

pydra/tasks/fsl/model/flameo.py

@@ -16,7 +16,7 @@ def atoi(text):
 
         def natural_keys(text):
             import re
-            
+
             if isinstance(text, tuple):
                 text = text[0]
             return [atoi(c) for c in re.split(r"(\d+)", text)]
@@ -25,7 +25,7 @@ def natural_keys(text):
 
     pth = inputs.log_dir
     name = field.name
-    
+
     if name == "pes":
         pes = human_order_sorted(glob.glob(os.path.join(pth, "pe[0-9]*.*")))
         if len(pes) >= 1:
@@ -51,9 +51,7 @@ def natural_keys(text):
         if len(tstats) >= 1:
             return tstats
     elif name == "mrefvars":
-        mrefs = human_order_sorted(
-            glob.glob(os.path.join(pth, "mean_random_effects_var[0-9]*.*"))
-        )
+        mrefs = human_order_sorted(glob.glob(os.path.join(pth, "mean_random_effects_var[0-9]*.*")))
         if len(mrefs) >= 1:
             return mrefs
     elif name == "tdof":
@@ -211,9 +209,7 @@ def natural_keys(text):
     ),
     ("log_dir", ty.Any, "stats", {"help_string": "", "argstr": "--ld={log_dir}"}),
 ]
-FLAMEO_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+FLAMEO_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = [
     (
@@ -337,4 +333,4 @@ class FLAMEO(ShellCommandTask):
 
     input_spec = FLAMEO_input_spec
     output_spec = FLAMEO_output_spec
-    executable = "flameo"
+    executable = "flameo"

pydra/tasks/fsl/model/glm.py

@@ -172,14 +172,10 @@
         },
     ),
 ]
-GLM_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+GLM_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = []
-GLM_output_spec = specs.SpecInfo(
-    name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
-)
+GLM_output_spec = specs.SpecInfo(name="Output", fields=output_fields, bases=(specs.ShellOutSpec,))
 
 
 class GLM(ShellCommandTask):
@@ -195,4 +191,4 @@ class GLM(ShellCommandTask):
 
     input_spec = GLM_input_spec
     output_spec = GLM_output_spec
-    executable = "fsl_glm"
+    executable = "fsl_glm"

pydra/tasks/fsl/model/melodic.py

@@ -320,9 +320,7 @@ def MELODIC_output(field, inputs):
         },
     ),
 ]
-MELODIC_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+MELODIC_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = [
     ("out_dir", specs.Directory, {"callable": MELODIC_output}),
@@ -355,4 +353,4 @@ class MELODIC(ShellCommandTask):
 
     input_spec = MELODIC_input_spec
     output_spec = MELODIC_output_spec
-    executable = "melodic"
+    executable = "melodic"

pydra/tasks/fsl/model/tests/test_run_cluster.py

@@ -3,9 +3,7 @@
 from ..cluster import Cluster
 
 
-@pytest.mark.xfail(
-    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
-)
+@pytest.mark.xfail("FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError)
 @pytest.mark.parametrize(
     "inputs, outputs",
     [
@@ -51,9 +49,7 @@ def test_Cluster(test_data, inputs, outputs):
             except:
                 pass
         task = Cluster(**inputs)
-    assert set(task.generated_output_names) == set(
-        ["return_code", "stdout", "stderr"] + outputs
-    )
+    assert set(task.generated_output_names) == set(["return_code", "stdout", "stderr"] + outputs)
     res = task()
     print("RESULT: ", res)
     for out_nm in outputs:

pydra/tasks/fsl/model/tests/test_run_feat.py

@@ -3,9 +3,7 @@
 from ..feat import FEAT
 
 
-@pytest.mark.xfail(
-    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
-)
+@pytest.mark.xfail("FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError)
 @pytest.mark.parametrize("inputs, outputs", [])
 def test_FEAT(test_data, inputs, outputs):
     if inputs is None:
@@ -33,9 +31,7 @@ def test_FEAT(test_data, inputs, outputs):
             except:
                 pass
         task = FEAT(**inputs)
-    assert set(task.generated_output_names) == set(
-        ["return_code", "stdout", "stderr"] + outputs
-    )
+    assert set(task.generated_output_names) == set(["return_code", "stdout", "stderr"] + outputs)
     res = task()
     print("RESULT: ", res)
     for out_nm in outputs: