Merge pull request #59 from frheault/trx_integration_dipy_2

Trx integration to Dipy (part 2)

.github/workflows/python-package.yml

@@ -12,8 +12,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
-
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}

pyproject.toml

@@ -10,6 +10,3 @@ __version__ = "{version}"
 """
 fallback_version = "0.0"
 local_scheme = "no-local-version"
-authors = [
-    "Francois Rheault @FrancoisRheault",
-]

scripts/tff_manipulate_datatype.py

@@ -78,7 +78,6 @@ def main():
         dtype_dict['positions'] = np.dtype(args.positions_dtype)
     if args.offsets_dtype:
         dtype_dict['offsets'] = np.dtype(args.offsets_dtype)
-
     if args.dpv:
         dtype_dict['dpv'] = {}
         for name, dtype in args.dpv:

setup.cfg

@@ -21,19 +21,21 @@ include_package_data = True
 
 
 [options]
-python_requires = >=3.7
+python_requires = >=3.8
 setup_requires =
     packaging >= 19.0
     cython >= 0.29
 install_requires =
     setuptools_scm
     deepdiff
-    nibabel >= 3
-    dipy@git+https://git@github.com/arokem/dipy@11a94c0fcf9b3
+    nibabel >= 5
+    numpy >= 1.22
+    dipy@git+https://git@github.com/frheault/dipy@cf4338d
     fury
 
 [options.extras_require]
-doc = sphinx <= 6
+doc = astroid==2.15.8
+    sphinx
     pydata-sphinx-theme
     sphinx-autoapi
     numpydoc

trx/trx_file_memmap.py

@@ -1065,8 +1065,15 @@ def _create_trx_from_pointer(
                 ext = ".bool"
             mem_adress, size = dict_pointer_size[elem_filename]
 
-            if root is not None and folder.startswith(root.rstrip("/")):
-                folder = folder.replace(root, "").lstrip("/")
+            if root is not None:
+                # This is for Unix
+                if os.name != 'nt' and folder.startswith(root.rstrip("/")):
+                    folder = folder.replace(root, "").lstrip("/")
+                # These two are for Windows
+                elif os.path.isdir(folder) and os.path.basename(folder) in ['dpg', 'dpv', 'dps']:
+                    folder = os.path.basename(folder)
+                else:
+                    folder = ''
 
             # Parse/walk the directory tree
             if base == "positions" and folder == "":
@@ -1089,7 +1096,10 @@ def _create_trx_from_pointer(
                     shape=(trx.header["NB_STREAMLINES"]+1,),
                     dtype=ext[1:],
                 )
-                lengths = _compute_lengths(offsets)
+                if offsets[-1] != 0:
+                    lengths = _compute_lengths(offsets)
+                else:
+                    lengths = [0]
             elif folder == "dps":
                 nb_scalar = size / trx.header["NB_STREAMLINES"]
                 if not nb_scalar.is_integer() or nb_scalar != dim: