ran make specs after python install to generate auto tests

Author: JensNRAD

nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py

@@ -56,14 +56,18 @@ def test_ProcStreamlines_inputs():
     position=-1,
     ),
     outputacm=dict(argstr='-outputacm',
+    requires=['outputroot', 'seedfile'],
     ),
     outputcbs=dict(argstr='-outputcbs',
+    requires=['outputroot', 'targetfile', 'seedfile'],
     ),
     outputcp=dict(argstr='-outputcp',
+    requires=['outputroot', 'seedfile'],
     ),
     outputroot=dict(argstr='-outputroot %s',
     ),
     outputsc=dict(argstr='-outputsc',
+    requires=['outputroot', 'seedfile'],
     ),
     outputtracts=dict(argstr='-outputtracts',
     ),
@@ -103,7 +107,8 @@ def test_ProcStreamlines_inputs():
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
 
 def test_ProcStreamlines_outputs():
-    output_map = dict(proc=dict(),
+    output_map = dict(outputroot_files=dict(),
+    proc=dict(),
     )
     outputs = ProcStreamlines.output_spec()
 

nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py

@@ -16,20 +16,28 @@ def test_ApplyTOPUP_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    in_files=dict(argstr='%s',
+    in_files=dict(argstr='--imain=%s',
     mandatory=True,
+    sep=',',
     ),
-    in_index=dict(argstr='%s',
+    in_index=dict(argstr='--inindex=%s',
     mandatory=True,
+    sep=',',
     ),
-    in_topup=dict(argstr='--topup=%s',
-    mandatory=True,
+    in_topup_fieldcoef=dict(argstr='--topup=%s',
+    copyfile=False,
+    requires=['in_topup_movpar'],
+    ),
+    in_topup_movpar=dict(copyfile=False,
+    requires=['in_topup_fieldcoef'],
     ),
     interp=dict(argstr='--interp=%s',
     ),
     method=dict(argstr='--method=%s',
     ),
-    out_base=dict(argstr='--out=%s',
+    out_corrected=dict(argstr='--out=%s',
+    name_source=['in_files'],
+    name_template='%s_corrected',
     ),
     output_type=dict(),
     terminal_output=dict(mandatory=True,

nipype/interfaces/fsl/tests/test_auto_DTIFit.py

@@ -17,7 +17,7 @@ def test_DTIFit_inputs():
     mandatory=True,
     position=3,
     ),
-    cni=dict(argstr='-cni %s',
+    cni=dict(argstr='--cni=%s',
     ),
     dwi=dict(argstr='-k %s',
     mandatory=True,

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -33,7 +33,12 @@ def test_Eddy_inputs():
     in_mask=dict(argstr='--mask=%s',
     mandatory=True,
     ),
-    in_topup=dict(argstr='--topup=%s',
+    in_topup_fieldcoef=dict(argstr='--topup=%s',
+    copyfile=False,
+    requires=['in_topup_movpar'],
+    ),
+    in_topup_movpar=dict(copyfile=False,
+    requires=['in_topup_fieldcoef'],
     ),
     method=dict(argstr='--resamp=%s',
     ),

nipype/interfaces/fsl/tests/test_auto_FIRST.py

@@ -18,6 +18,7 @@ def test_FIRST_inputs():
     usedefault=True,
     ),
     in_file=dict(argstr='-i %s',
+    copyfile=False,
     mandatory=True,
     position=-2,
     ),

nipype/interfaces/fsl/tests/test_auto_MELODIC.py

@@ -32,6 +32,7 @@ def test_MELODIC_inputs():
     in_files=dict(argstr='-i %s',
     mandatory=True,
     position=0,
+    sep=',',
     ),
     log_power=dict(argstr='--logPower',
     ),

nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py

@@ -0,0 +1,152 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.fsl.dti import ProbTrackX2
+
+def test_ProbTrackX2_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    avoid_mp=dict(argstr='--avoid=%s',
+    ),
+    c_thresh=dict(argstr='--cthr=%.3f',
+    ),
+    colmask4=dict(argstr='--colmask4=%s',
+    ),
+    correct_path_distribution=dict(argstr='--pd',
+    ),
+    dist_thresh=dict(argstr='--distthresh=%.3f',
+    ),
+    distthresh1=dict(argstr='--distthresh1=%.3f',
+    ),
+    distthresh3=dict(argstr='--distthresh3=%.3f',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    fibst=dict(argstr='--fibst=%d',
+    ),
+    fopd=dict(argstr='--fopd=%s',
+    ),
+    force_dir=dict(argstr='--forcedir',
+    usedefault=True,
+    ),
+    fsamples=dict(mandatory=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    inv_xfm=dict(argstr='--invxfm=%s',
+    ),
+    loop_check=dict(argstr='--loopcheck',
+    ),
+    lrtarget3=dict(argstr='--lrtarget3=%s',
+    ),
+    mask=dict(argstr='-m %s',
+    mandatory=True,
+    ),
+    meshspace=dict(argstr='--meshspace=%s',
+    ),
+    mod_euler=dict(argstr='--modeuler',
+    ),
+    n_samples=dict(argstr='--nsamples=%d',
+    usedefault=True,
+    ),
+    n_steps=dict(argstr='--nsteps=%d',
+    ),
+    network=dict(argstr='--network',
+    ),
+    omatrix1=dict(argstr='--omatrix1',
+    ),
+    omatrix2=dict(argstr='--omatrix2',
+    requires=['target2'],
+    ),
+    omatrix3=dict(argstr='--omatrix3',
+    requires=['target3', 'lrtarget3'],
+    ),
+    omatrix4=dict(argstr='--omatrix4',
+    ),
+    onewaycondition=dict(argstr='--onewaycondition',
+    ),
+    opd=dict(argstr='--opd',
+    usedefault=True,
+    ),
+    os2t=dict(argstr='--os2t',
+    ),
+    out_dir=dict(argstr='--dir=%s',
+    genfile=True,
+    ),
+    output_type=dict(),
+    phsamples=dict(mandatory=True,
+    ),
+    rand_fib=dict(argstr='--randfib=%d',
+    ),
+    random_seed=dict(argstr='--rseed',
+    ),
+    s2tastext=dict(argstr='--s2tastext',
+    ),
+    sample_random_points=dict(argstr='--sampvox',
+    ),
+    samples_base_name=dict(argstr='--samples=%s',
+    usedefault=True,
+    ),
+    seed=dict(argstr='--seed=%s',
+    mandatory=True,
+    ),
+    seed_ref=dict(argstr='--seedref=%s',
+    ),
+    simple=dict(argstr='--simple',
+    usedefault=False,
+    ),
+    step_length=dict(argstr='--steplength=%.3f',
+    ),
+    stop_mask=dict(argstr='--stop=%s',
+    ),
+    target2=dict(argstr='--target2=%s',
+    ),
+    target3=dict(argstr='--target3=%s',
+    ),
+    target4=dict(argstr='--target4=%s',
+    ),
+    target_masks=dict(argstr='--targetmasks=%s',
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    thsamples=dict(mandatory=True,
+    ),
+    use_anisotropy=dict(argstr='--usef',
+    ),
+    verbose=dict(argstr='--verbose=%d',
+    ),
+    waycond=dict(argstr='--waycond=%s',
+    ),
+    wayorder=dict(argstr='--wayorder',
+    ),
+    waypoints=dict(argstr='--waypoints=%s',
+    ),
+    xfm=dict(argstr='--xfm=%s',
+    ),
+    )
+    inputs = ProbTrackX2.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_ProbTrackX2_outputs():
+    output_map = dict(fdt_paths=dict(),
+    log=dict(),
+    lookup_tractspace=dict(),
+    matrix1_dot=dict(),
+    matrix2_dot=dict(),
+    matrix3_dot=dict(),
+    network_matrix=dict(),
+    particle_files=dict(),
+    targets=dict(),
+    way_total=dict(),
+    )
+    outputs = ProbTrackX2.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/fsl/tests/test_auto_TOPUP.py

@@ -8,8 +8,14 @@ def test_TOPUP_inputs():
     config=dict(argstr='--config=%s',
     usedefault=True,
     ),
-    encoding_direction=dict(),
+    encoding_direction=dict(argstr='--datain=%s',
+    mandatory=True,
+    requires=['readout_times'],
+    xor=['encoding_file'],
+    ),
     encoding_file=dict(argstr='--datain=%s',
+    mandatory=True,
+    xor=['encoding_direction'],
     ),
     environ=dict(nohash=True,
     usedefault=True,
@@ -33,15 +39,31 @@ def test_TOPUP_inputs():
     numprec=dict(argstr='--numprec=%s',
     ),
     out_base=dict(argstr='--out=%s',
+    hash_files=False,
+    name_source=['in_file'],
+    name_template='%s_base',
     ),
     out_corrected=dict(argstr='--iout=%s',
+    hash_files=False,
+    name_source=['in_file'],
+    name_template='%s_corrected',
     ),
     out_field=dict(argstr='--fout=%s',
+    hash_files=False,
+    name_source=['in_file'],
+    name_template='%s_field',
     ),
     out_logfile=dict(argstr='--logout=%s',
+    hash_files=False,
+    keep_extension=True,
+    name_source=['in_file'],
+    name_template='%s_topup.log',
     ),
     output_type=dict(),
-    readout_times=dict(),
+    readout_times=dict(mandatory=True,
+    requires=['encoding_direction'],
+    xor=['encoding_file'],
+    ),
     regrid=dict(argstr='--regrid=%d',
     ),
     scale=dict(argstr='--scale=%d',
@@ -69,7 +91,6 @@ def test_TOPUP_outputs():
     out_fieldcoef=dict(),
     out_logfile=dict(),
     out_movpar=dict(),
-    out_topup=dict(),
     )
     outputs = TOPUP.output_spec()
 

nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py

@@ -16,12 +16,13 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     usedefault=True,
     ),
     exclude_file=dict(argstr='-exclude %s',
-    position=2,
+    xor=['exclude_file', 'exclude_spec'],
     ),
-    exclude_spec=dict(argstr='-seed %s',
+    exclude_spec=dict(argstr='-exclude %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['exclude_file', 'exclude_spec'],
     ),
     gradient_encoding_file=dict(argstr='-grad %s',
     mandatory=True,
@@ -35,12 +36,13 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     position=-2,
     ),
     include_file=dict(argstr='-include %s',
-    position=2,
+    xor=['include_file', 'include_spec'],
     ),
-    include_spec=dict(argstr='-seed %s',
+    include_spec=dict(argstr='-include %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['include_file', 'include_spec'],
     ),
     initial_cutoff_value=dict(argstr='-initcutoff %s',
     units='NA',
@@ -52,13 +54,14 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     position=-3,
     usedefault=True,
     ),
-    mask_file=dict(argstr='-exclude %s',
-    position=2,
+    mask_file=dict(argstr='-mask %s',
+    xor=['mask_file', 'mask_spec'],
     ),
-    mask_spec=dict(argstr='-seed %s',
+    mask_spec=dict(argstr='-mask %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['mask_file', 'mask_spec'],
     ),
     maximum_number_of_tracks=dict(argstr='-maxnum %d',
     ),
@@ -74,21 +77,24 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     no_mask_interpolation=dict(argstr='-nomaskinterp',
     ),
     out_file=dict(argstr='%s',
-    genfile=True,
+    name_source=['in_file'],
+    name_template='%s_tracked.tck',
+    output_name='tracked.tck',
     position=-1,
     ),
     seed_file=dict(argstr='-seed %s',
-    position=2,
+    xor=['seed_file', 'seed_spec'],
     ),
     seed_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['seed_file', 'seed_spec'],
     ),
     step_size=dict(argstr='-step %s',
     units='mm',
     ),
-    stop=dict(argstr='-gzip',
+    stop=dict(argstr='-stop',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,