Merge pull request #108 from oesteban/enh/new-datasinks

ENH: Use new ``DerivativesDataSink`` from NiWorkflows 1.2.0

Author: oesteban

MANIFEST.in

@@ -1,7 +1 @@
-# General
-include CHANGES.rst
-include LICENSE
-
-# versioneer
 include versioneer.py
-include dmriprep/_version.py

dmriprep/cli/run.py

@@ -129,7 +129,6 @@ def main():
         failed_reports = generate_reports(
             config.execution.participant_label,
             config.execution.output_dir,
-            config.execution.work_dir,
             config.execution.run_uuid,
             config=pkgrf("dmriprep", "config/reports-spec.yml"),
             packagename="dmriprep",

dmriprep/cli/workflow.py

@@ -57,7 +57,6 @@ def build_workflow(config_file, retval):
         retval["return_code"] = generate_reports(
             subject_list,
             config.execution.output_dir,
-            config.execution.work_dir,
             config.execution.run_uuid,
             config=pkgrf("dmriprep", "config/reports-spec.yml"),
             packagename="dmriprep",

dmriprep/config/reports-spec.yml

@@ -2,40 +2,40 @@ package: dmriprep
 sections:
 - name: Summary
   reportlets:
-  - bids: {datatype: anat, desc: summary, suffix: T1w}
+  - bids: {datatype: figures, desc: summary, suffix: T1w}
 - name: Anatomical
   reportlets:
   - bids:
-      datatype: anat
+      datatype: figures
       desc: conform
       extension: [.html]
       suffix: T1w
-  - bids: {datatype: anat, suffix: dseg}
+  - bids: {datatype: figures, suffix: dseg}
     caption: This panel shows the template T1-weighted image (if several T1w images
       were found), with contours delineating the detected brain mask and brain tissue
       segmentations.
     subtitle: Brain mask and brain tissue segmentation of the T1w
-  - bids: {datatype: anat, space: .*, suffix: T1w, regex_search: True}
+  - bids: {datatype: figures, space: .*, suffix: T1w, regex_search: True}
     caption: Spatial normalization of the T1w image to the <code>{space}</code> template.
     description: Results of nonlinear alignment of the T1w reference one or more template
       space(s). Hover on the panels with the mouse pointer to transition between both
       spaces.
     static: false
     subtitle: Spatial normalization of the anatomical T1w reference
-  - bids: {datatype: anat, desc: reconall, suffix: T1w}
+  - bids: {datatype: figures, desc: reconall, suffix: T1w}
     caption: Surfaces (white and pial) reconstructed with FreeSurfer (<code>recon-all</code>)
       overlaid on the participant's T1w template.
     subtitle: Surface reconstruction
 - name: Diffusion
   ordering: session,acquisition,run
   reportlets:
-  - bids: {datatype: dwi, desc: validation, suffix: dwi}
-  - bids: {datatype: dwi, desc: brain, suffix: mask}
+  - bids: {datatype: figures, desc: validation, suffix: dwi}
+  - bids: {datatype: figures, desc: brain, suffix: mask}
     caption: Average b=0 that serves for reference in early preprocessing steps.
     descriptions: The reference b=0 is obtained as the voxel-wise median across
       all b=0 found in the dataset, after accounting for signal drift.
       The red contour shows the brain mask calculated using this reference b=0.
     subtitle: Reference b=0 and brain mask
 - name: About
   reportlets:
-  - bids: {datatype: anat, desc: about, suffix: T1w}
+  - bids: {datatype: figures, desc: about, suffix: T1w}

dmriprep/workflows/base.py

@@ -165,7 +165,7 @@ def init_single_subject_wf(subject_id):
 
 """
     spaces = config.workflow.spaces
-    reportlets_dir = str(config.execution.work_dir / "reportlets")
+    output_dir = config.execution.output_dir
 
     fsinputnode = pe.Node(niu.IdentityInterface(fields=["subjects_dir"]),
                           name="fsinputnode")
@@ -185,13 +185,11 @@ def init_single_subject_wf(subject_id):
                     name="about", run_without_submitting=True)
 
     ds_report_summary = pe.Node(
-        DerivativesDataSink(base_directory=reportlets_dir,
-                            desc="summary", keep_dtype=True),
+        DerivativesDataSink(base_directory=str(output_dir), desc="summary", datatype="figures"),
         name="ds_report_summary", run_without_submitting=True)
 
     ds_report_about = pe.Node(
-        DerivativesDataSink(base_directory=reportlets_dir,
-                            desc="about", keep_dtype=True),
+        DerivativesDataSink(base_directory=str(output_dir), desc="about", datatype="figures"),
         name="ds_report_about", run_without_submitting=True)
 
     anat_derivatives = config.execution.anat_derivatives
@@ -214,8 +212,7 @@ def init_single_subject_wf(subject_id):
         hires=config.workflow.hires,
         longitudinal=config.workflow.longitudinal,
         omp_nthreads=config.nipype.omp_nthreads,
-        output_dir=str(config.execution.output_dir),
-        reportlets_dir=reportlets_dir,
+        output_dir=str(output_dir),
         skull_strip_fixed_seed=config.workflow.skull_strip_fixed_seed,
         skull_strip_mode="force",
         skull_strip_template=Reference.from_string(

dmriprep/workflows/dwi/base.py

@@ -88,8 +88,7 @@ def init_early_b0ref_wf(
     ])
 
     # REPORTING ############################################################
-    reportlets_dir = str(config.execution.work_dir / 'reportlets')
-    reportlets_wf = init_reportlets_wf(reportlets_dir)
+    reportlets_wf = init_reportlets_wf(str(config.execution.output_dir))
     workflow.connect([
         (inputnode, reportlets_wf, [('dwi_file', 'inputnode.source_file')]),
         (dwi_reference_wf, reportlets_wf, [

dmriprep/workflows/dwi/outputs.py

@@ -5,7 +5,7 @@
 from ...interfaces import DerivativesDataSink
 
 
-def init_reportlets_wf(reportlets_dir, name='reportlets_wf'):
+def init_reportlets_wf(output_dir, name='reportlets_wf'):
     """Set up a battery of datasinks to store reports in the right location."""
     from niworkflows.interfaces.masks import SimpleShowMaskRPT
     workflow = Workflow(name=name)
@@ -17,12 +17,11 @@ def init_reportlets_wf(reportlets_dir, name='reportlets_wf'):
     mask_reportlet = pe.Node(SimpleShowMaskRPT(), name='mask_reportlet')
 
     ds_report_mask = pe.Node(
-        DerivativesDataSink(base_directory=reportlets_dir,
-                            desc='brain', suffix='mask'),
+        DerivativesDataSink(base_directory=output_dir, desc='brain', suffix='mask',
+                            datatype="figures"),
         name='ds_report_mask', run_without_submitting=True)
     ds_report_validation = pe.Node(
-        DerivativesDataSink(base_directory=reportlets_dir,
-                            desc='validation', keep_dtype=True),
+        DerivativesDataSink(base_directory=output_dir, desc='validation', datatype="figures"),
         name='ds_report_validation', run_without_submitting=True)
 
     workflow.connect([

docs/requirements.txt

@@ -2,11 +2,11 @@ git+https://github.com/AleksandarPetrov/napoleon.git@0dc3f28a309ad602be5f44a9049
 git+https://github.com/rwblair/sphinxcontrib-versioning.git@39b40b0b84bf872fc398feff05344051bbce0f63#egg=sphinxcontrib-versioning
 nbsphinx
 nipype ~= 1.4
-niworkflows >=1.2.0rc1,<1.3
+git+https://github.com/nipreps/niworkflows.git@master#egg=niworkflows
 packaging
 pydot>=1.2.3
 pydotplus
-smriprep >=0.6.0rc2
+git+https://github.com/poldracklab/smriprep.git@master#egg=smriprep
 sphinx-argparse
 sphinx >=2.1.2,<3.0
 sphinx_rtd_theme

pyproject.toml

@@ -1,2 +1,4 @@
 [build-system]
+# setuptools can be configured with setup.cfg when >=30.3
+# Most bugfixes regarding setup.cfg are included before 38.3
 requires = ["setuptools >= 40.8.0", "wheel"]

setup.cfg

@@ -1,13 +1,6 @@
 [metadata]
-url = https://github.com/nipreps/dmriprep
-author = The dMRIPrep developers
-author_email = [email protected]
-maintainer = Oscar Esteban
-maintainer_email = [email protected]
-description = dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data.
-long_description = file:README.rst
-long_description_content_type = text/x-rst; charset=UTF-8
-license = Apache License, Version 2.0
+author = The NiPreps developers
+author_email = [email protected]
 classifiers =
     Development Status :: 3 - Alpha
     Intended Audience :: Science/Research
@@ -16,28 +9,51 @@ classifiers =
     Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
+description = dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data.
+license = Apache License, Version 2.0
+long_description = file:README.rst
+long_description_content_type = text/x-rst; charset=UTF-8
+name = dmriprep
+project_urls =
+    Home = https://github.com/nipreps/dmriprep
+    Documentation = https://www.nipreps.org/dmriprep
 
 [options]
-python_requires = >=3.5
+python_requires = >=3.6
 install_requires =
     dipy >=1.0.0
     indexed_gzip >=0.8.8
     nibabel ~= 3.0
     nipype ~= 1.4
-    niworkflows >=1.2.0rc4,<1.3
+    niworkflows @ git+https://github.com/nipreps/niworkflows.git@master
     numpy
     pybids >=0.10.2
     pyyaml
-    sdcflows >= 1.2.3
-    smriprep >=0.6.0rc4,<0.7
-    templateflow >= 0.4.2
+    sdcflows @ git+https://github.com/nipreps/sdcflows.git@master
+    smriprep @ git+https://github.com/poldracklab/smriprep.git@master
+    templateflow ~= 0.6
     toml
+setup_requires =
+    setuptools >= 40.8.0
 test_requires =
     codecov
     coverage
     pytest
 packages = find:
-include_package_data = True
+
+[options.packages.find]
+exclude =
+    *.tests
+
+[options.package_data]
+dmriprep =
+    VERSION
+    config/reports-spec.yml
+    data/boilerplate.bib
+    data/tests/config.toml
+    data/tests/THP/*
+    data/tests/THP/sub-THP0005/anat/*
+    data/tests/THP/sub-THP0005/dwi/*
 
 [options.exclude_package_data]
 * = tests
@@ -77,16 +93,6 @@ all =
     %(popylar)s
     %(tests)s
 
-[options.package_data]
-dmriprep =
-    VERSION
-    config/reports-spec.yml
-    data/boilerplate.bib
-    data/tests/config.toml
-    data/tests/THP/*
-    data/tests/THP/sub-THP0005/anat/*
-    data/tests/THP/sub-THP0005/dwi/*
-
 [options.entry_points]
 console_scripts =
     dmriprep=dmriprep.cli.run:main