REF: Adopt pathlib for path manipulation

.spin/cmds.py

@@ -1,7 +1,7 @@
 """Custom spin commands for trx-python development."""
 
-import glob
 import os
+from pathlib import Path
 import shutil
 import subprocess
 import sys
@@ -223,35 +223,32 @@ def docs(_clean, open_browser):
     open_browser : bool
         If True, open documentation in browser after building.
     """
-    import os
 
-    docs_dir = "docs"
+    docs_dir = Path("docs")
 
     if _clean:
         click.echo("Cleaning build directory...")
-        build_dir = os.path.join(docs_dir, "_build")
-        if os.path.exists(build_dir):
+        build_dir = docs_dir / "_build"
+        if build_dir.exists():
             shutil.rmtree(build_dir)
 
         # Clean sphinx-gallery generated files
-        gallery_dir = os.path.join(docs_dir, "source", "auto_examples")
-        if os.path.exists(gallery_dir):
+        gallery_dir = docs_dir / "source" / "auto_examples"
+        if gallery_dir.exists():
             click.echo("Cleaning sphinx-gallery generated files...")
             shutil.rmtree(gallery_dir)
 
         # Clean sphinx-gallery execution times file
-        sg_times = os.path.join(docs_dir, "source", "sg_execution_times.rst")
-        if os.path.exists(sg_times):
+        sg_times = docs_dir / "source" / "sg_execution_times.rst"
+        if sg_times.exists():
             os.remove(sg_times)
 
     click.echo("Building documentation...")
-    cmd = ["make", "-C", docs_dir, "html"]
+    cmd = ["make", "-C", str(docs_dir), "html"]
     result = run(cmd, capture=False, check=False)
 
     if result == 0:
-        index_path = os.path.abspath(
-            os.path.join(docs_dir, "_build", "html", "index.html")
-        )
+        index_path = (docs_dir / "_build" / "html" / "index.html").resolve()
         click.echo("\nDocs built successfully!")
         click.echo(f"Open: {index_path}")
 
@@ -270,27 +267,26 @@ def clean():  # noqa: C901
 
     # Clean TRX temp directory
     trx_tmp_dir = os.getenv("TRX_TMPDIR", tempfile.gettempdir())
-    if os.path.exists(trx_tmp_dir):
-        temp_files = glob.glob(os.path.join(trx_tmp_dir, "trx_*"))
-        for temp_dir in temp_files:
-            if os.path.isdir(temp_dir):
-                click.echo(f"Removing temporary directory: {temp_dir}")
-                shutil.rmtree(temp_dir)
+    if trx_tmp_dir.exists():
+        for temp_name in trx_tmp_dir.glob("trx_*"):
+            if temp_name.is_dir():
+                click.echo(f"Removing temporary directory: {temp_name}")
+                shutil.rmtree(temp_name)
 
     # Clean build artifacts
     for build_pattern in ["build", "dist", "*.egg-info"]:
-        for path in glob.glob(build_pattern):
-            if os.path.isdir(path):
+        for path in Path(".").glob(build_pattern):
+            if path.is_dir():
                 click.echo(f"Removing build directory: {path}")
                 shutil.rmtree(path)
-            elif os.path.isfile(path):
+            elif path.is_file():
                 click.echo(f"Removing build file: {path}")
-                os.remove(path)
+                path.unlink()
 
     # Clean Python cache
     for cache_dir in ["**/__pycache__", "**/.pytest_cache"]:
-        for path in glob.glob(cache_dir, recursive=True):
-            if os.path.isdir(path):
+        for path in Path(".").glob(cache_dir):
+            if path.is_dir():
                 click.echo(f"Removing cache directory: {path}")
                 shutil.rmtree(path)
 

docs/source/conf.py

@@ -17,6 +17,7 @@
 import warnings
 import os
 from datetime import datetime as dt
+from pathlib import Path
 
 # -- Version information -----------------------------------------------------
 # Get version from environment variable (set by CI) or package
@@ -191,5 +192,5 @@ def _validate_reference_urls(urls, timeout=5):
     'gallery_dirs': 'auto_examples',
     'within_subsection_order': 'NumberOfCodeLinesSortKey',
     'reference_url': _validate_reference_urls(_reference_urls),
-    'default_thumb_file': os.path.join(os.path.dirname(__file__), '..', '_static', 'trx_logo.png'),
+    'default_thumb_file': str(Path(__file__).parent / '..' / '_static' / 'trx_logo.png'),
 }

examples/plot_dps_dpv.py

@@ -39,8 +39,6 @@
 #
 # Let's load a TRX file and explore its metadata.
 
-import os
-
 import numpy as np
 
 from trx.fetcher import fetch_data, get_home, get_testing_files_dict
@@ -49,7 +47,7 @@
 # Download test data
 fetch_data(get_testing_files_dict(), keys="gold_standard.zip")
 trx_home = get_home()
-trx_path = os.path.join(trx_home, "gold_standard", "gs.trx")
+trx_path = trx_home / "gold_standard" / "gs.trx"
 
 # Load the TRX file
 tgm = load(trx_path)

examples/plot_groups.py

@@ -35,8 +35,6 @@
 #
 # Let's load a TRX file that contains group information.
 
-import os
-
 import numpy as np
 
 from trx.fetcher import fetch_data, get_home, get_testing_files_dict
@@ -45,7 +43,7 @@
 # Download test data
 fetch_data(get_testing_files_dict(), keys="gold_standard.zip")
 trx_home = get_home()
-trx_path = os.path.join(trx_home, "gold_standard", "gs.trx")
+trx_path = trx_home / "gold_standard" / "gs.trx"
 
 # Load the TRX file
 tgm = load(trx_path)

examples/plot_read_write_trx.py

@@ -24,7 +24,6 @@
 # Let's start by loading an existing TRX file. First, we need to download
 # some test data.
 
-import os
 import tempfile
 
 from trx.fetcher import fetch_data, get_home, get_testing_files_dict
@@ -33,7 +32,7 @@
 # Download test data
 fetch_data(get_testing_files_dict(), keys="gold_standard.zip")
 trx_home = get_home()
-trx_path = os.path.join(trx_home, "gold_standard", "gs.trx")
+trx_path = trx_home / "gold_standard" / "gs.trx"
 
 # Load the TRX file
 tgm = load(trx_path)
@@ -109,10 +108,10 @@
 
 with tempfile.TemporaryDirectory() as tmpdir:
     # Save as TRX file (zip archive)
-    output_path = os.path.join(tmpdir, "output.trx")
+    output_path = tmpdir / "output.trx"
     save(tgm, output_path)
     print(f"Saved TRX file to: {output_path}")
-    print(f"File size: {os.path.getsize(output_path)} bytes")
+    print(f"File size: {output_path.stat().st_size} bytes")
 
     # Reload to verify
     reloaded = load(output_path)

trx/fetcher.py

@@ -4,6 +4,7 @@
 import hashlib
 import logging
 import os
+from pathlib import Path
 import shutil
 import urllib.request
 
@@ -24,13 +25,13 @@ def get_home():
 
     Returns
     -------
-    str
+    Path
         Path to the TRX home directory.
     """
     if "TRX_HOME" in os.environ:
-        trx_home = os.environ["TRX_HOME"]
+        trx_home = Path(os.environ["TRX_HOME"])
     else:
-        trx_home = os.path.join(os.path.expanduser("~"), ".tee_ar_ex")
+        trx_home = Path("~").expanduser() / ".tee_ar_ex"
     return trx_home
 
 
@@ -132,7 +133,7 @@ def fetch_data(files_dict, keys=None):  # noqa: C901
     """
     trx_home = get_home()
 
-    if not os.path.exists(trx_home):
+    if not trx_home.exists():
         os.makedirs(trx_home)
 
     if keys is None:
@@ -147,10 +148,10 @@ def fetch_data(files_dict, keys=None):  # noqa: C901
             expected_sha = None
         else:
             url, expected_md5, expected_sha = file_entry
-        full_path = os.path.join(trx_home, fname)
+        full_path = trx_home / fname
 
         logging.info(f"Downloading {fname} to {trx_home}")
-        if not os.path.exists(full_path):
+        if not full_path.exists():
             urllib.request.urlretrieve(url, full_path)
 
         actual_md5 = md5sum(full_path)
@@ -169,5 +170,5 @@ def fetch_data(files_dict, keys=None):  # noqa: C901
                 )
 
         if fname.endswith(".zip"):
-            dst_dir = os.path.join(trx_home, fname[:-4])
+            dst_dir = trx_home / fname[:-4]
             shutil.unpack_archive(full_path, extract_dir=dst_dir, format="zip")

trx/io.py

@@ -3,6 +3,7 @@
 
 import logging
 import os
+from pathlib import Path
 import sys
 import tempfile
 
@@ -32,26 +33,30 @@ def get_trx_tmp_dir():
     """
     if os.getenv("TRX_TMPDIR") is not None:
         if os.getenv("TRX_TMPDIR") == "use_working_dir":
-            trx_tmp_dir = os.getcwd()
+            trx_tmp_dir = str(Path.cwd())
         else:
             trx_tmp_dir = os.getenv("TRX_TMPDIR")
     else:
         trx_tmp_dir = tempfile.gettempdir()
 
     if sys.version_info[1] >= 10:
-        return tempfile.TemporaryDirectory(
+        tmp_dir = tempfile.TemporaryDirectory(
             dir=trx_tmp_dir, prefix="trx_", ignore_cleanup_errors=True
         )
     else:
-        return tempfile.TemporaryDirectory(dir=trx_tmp_dir, prefix="trx_")
+        tmp_dir = tempfile.TemporaryDirectory(dir=trx_tmp_dir, prefix="trx_")
+
+    # Keep the TemporaryDirectory instance, but provide a Path-compatible name
+    tmp_dir.name = Path(tmp_dir.name)
+    return tmp_dir
 
 
 def load_sft_with_reference(filepath, reference=None, bbox_check=True, from_space=None):
     """Load a tractogram as a StatefulTractogram with an explicit reference.
 
     Parameters
     ----------
-    filepath : str
+    filepath : str or Path
         Path to the tractogram file (.trk, .tck, .fib, .vtk, .dpy).
     reference : str or nibabel.Nifti1Image, optional
         Reference image used for formats without embedded affine information.
@@ -81,7 +86,7 @@ def load_sft_with_reference(filepath, reference=None, bbox_check=True, from_spac
     from dipy.io.streamline import load_tractogram
 
     # Force the usage of --reference for all file formats without an header
-    _, ext = os.path.splitext(filepath)
+    ext = "".join(Path(filepath).suffixes)
     if ext == ".trk":
         if reference is not None and reference != "same":
             logging.warning(f"Reference is discarded for this file format {filepath}.")
@@ -122,7 +127,7 @@ def load(tractogram_filename, reference=None, from_space=None):
     import trx.trx_file_memmap as tmm
 
     in_ext = split_name_with_gz(tractogram_filename)[1]
-    if in_ext != ".trx" and not os.path.isdir(tractogram_filename):
+    if in_ext != ".trx" and not tractogram_filename.is_dir():
         tractogram_obj = load_sft_with_reference(
             tractogram_filename, reference, bbox_check=False, from_space=from_space
         )
@@ -140,7 +145,7 @@ def save(tractogram_obj, tractogram_filename, bbox_valid_check=False):
     tractogram_obj : TrxFile or StatefulTractogram
         Tractogram to persist. Non-TRX inputs are converted to StatefulTractogram
         before saving to non-TRX formats.
-    tractogram_filename : str
+    tractogram_filename : str or Path
         Destination file name. ``.trx`` will be saved using the TRX writer; all
         other extensions are handled by ``dipy.save_tractogram``.
     bbox_valid_check : bool, optional
@@ -153,6 +158,7 @@ def save(tractogram_obj, tractogram_filename, bbox_valid_check=False):
         The function writes to disk and returns ``None``. Returns ``None``
         immediately when ``dipy`` is unavailable.
     """
+    tractogram_filename = Path(tractogram_filename)
     if not dipy_available:
         logging.error(
             "Dipy library is missing, cannot use functions related "