Merge pull request #5 from PennLINC/enh/acres

Use acres for loading package data

ingress2qsirecon/cli/main.py

@@ -6,8 +6,8 @@
 
 from beartype import beartype
 
-import ingress2qsirecon
 from ingress2qsirecon.cli.parser import _build_parser
+from ingress2qsirecon.data import load_resource
 from ingress2qsirecon.utils.functions import create_layout
 from ingress2qsirecon.utils.workflows import create_ingress2qsirecon_wf
 
@@ -43,9 +43,9 @@ def _ingress2qsirecon(**kwargs):
         output_dir.mkdir(parents=True)
 
     # Move BIDS scaffold files to output directory
-    ingress2recon_dir = os.path.dirname(ingress2qsirecon.__file__)
+    bids_scaffold = str(load_resource('bids_scaffold/'))
     if not os.path.exists(os.path.join(output_dir, "dataset_description.json")):
-        shutil.copytree(os.path.join(ingress2recon_dir, "data", "bids_scaffold"), output_dir, dirs_exist_ok=True)
+        shutil.copytree(bids_scaffold, output_dir, dirs_exist_ok=True)
 
     # If participant_label not defined, make it empty list
     if participant_label is None:

ingress2qsirecon/data/__init__.py

@@ -0,0 +1,14 @@
+'''Data package
+
+.. autofunction:: load_resource
+
+.. automethod:: load_resource.readable
+
+.. automethod:: load_resource.as_path
+
+.. automethod:: load_resource.cached
+'''
+
+from acres import Loader
+
+load_resource = Loader(__package__)

ingress2qsirecon/utils/interfaces.py

@@ -3,12 +3,12 @@
 """
 
 import os
-import pandas as pd
 import shutil
 from textwrap import indent
 
 import nibabel as nb
 import numpy as np
+import pandas as pd
 import SimpleITK as sitk
 from nilearn import image as nim
 from nipype import logging
@@ -609,14 +609,17 @@ def _convert_fsl_to_mrtrix(bval_file, bvec_file, output_fname):
     gtab = np.column_stack([vecs.T, vals]) * np.array([-1, -1, 1, 1])
     np.savetxt(output_fname, gtab, fmt=["%.8f", "%.8f", "%.8f", "%d"])
 
+
 class _ScansTSVWriterInputSpec(BaseInterfaceInputSpec):
     filenames = traits.List(traits.Str, mandatory=True, desc="List of filenames")
     source_files = traits.List(traits.Str, mandatory=True, desc="List of source files")
     out_file = File("output.tsv", usedefault=True, desc="Output TSV file")
 
+
 class _ScansTSVWriterOutputSpec(TraitedSpec):
     out_file = File(desc="Output TSV file")
 
+
 class ScansTSVWriter(BaseInterface):
     input_spec = _ScansTSVWriterInputSpec
     output_spec = _ScansTSVWriterOutputSpec
@@ -630,10 +633,7 @@ def _run_interface(self, runtime):
             raise ValueError("filenames and source_files must have the same length")
 
         # Create DataFrame
-        df = pd.DataFrame({
-            "filename": filenames,
-            "source_file": source_files
-        })
+        df = pd.DataFrame({"filename": filenames, "source_file": source_files})
 
         # Write to TSV
         df.to_csv(self.inputs.out_file, sep='\t', index=False)
@@ -642,4 +642,4 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self.output_spec().get().copy()
         outputs['out_file'] = self.inputs.out_file
-        return outputs
+        return outputs

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "Ingress2QSIRecon"
-version = "0.1.3"
+version = "0.1.4"
 description = "Tool to ingress data from other pipelines for use in QSIRecon"
 authors = ["Steven Meisler <[email protected]>"]
 readme = "README.md"