From 3ba4b3cd86ca0886e62ae2d3559a83437df4c4e4 Mon Sep 17 00:00:00 2001
From: William T Clarke <william.clarke@ndcn.ox.ac.uk>
Date: Thu, 31 Oct 2024 14:54:03 +0000
Subject: [PATCH] REL: 0.8.5 (#155)

* Prep for release, test 3.13 compatibility

* Wheels for python 3.13 not availible for scipy 1.13, bump to >=1.14

* Change test install strategy to avoid pypi conda conflicts.

* Fix mistake in pytest call for orientation marker.

* Try adding PIL as dependency.

* move from package_resources to importlib.resources for python 3.12+ compat
---
 .github/workflows/push_pr.yml |  8 ++---
 CHANGELOG.md                  |  6 ++++
 setup.py                      |  1 +
 spec2nii/bruker.py            | 57 ++++++++++++++++++-----------------
 4 files changed, 41 insertions(+), 31 deletions(-)

diff --git a/.github/workflows/push_pr.yml b/.github/workflows/push_pr.yml
index f05b272..0e85c55 100644
--- a/.github/workflows/push_pr.yml
+++ b/.github/workflows/push_pr.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: [ "3.9", "3.10", "3.11", "3.12"]
+        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -38,6 +38,6 @@ jobs:
       - name: Run pytest
         shell: bash -l {0}
         run: |
-            conda install pytest h5py
-            pip install .
-            pytest -k "not orientation" tests
+            conda install pytest h5py pillow
+            pip install --no-deps .
+            pytest -m "not orientation" tests
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e8c49f4..1c66664 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,11 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
+0.8.5 (Thursday 31st October 2024)
+----------------------------------
+- Add special case handling for DICOM dkd_svs_mslaser_msspnav sequence
+- More GE HBCD sequence adjustments.
+- Python 3.13 compatibility and testing, scipy dependency now >=1.13
+
 0.8.4 (Monday 23rd September 2024)
 -------------------------------
 - GE HBCD sequence adjustments.
diff --git a/setup.py b/setup.py
index 61871f0..b1e1972 100644
--- a/setup.py
+++ b/setup.py
@@ -31,6 +31,7 @@
           "Programming Language :: Python :: 3.10",
           "Programming Language :: Python :: 3.11",
           "Programming Language :: Python :: 3.12",
+          "Programming Language :: Python :: 3.13",
           "License :: OSI Approved :: BSD License",
           "Operating System :: OS Independent"],
       python_requires='>=3.9',
diff --git a/spec2nii/bruker.py b/spec2nii/bruker.py
index 9bf2d0e..a3367f7 100644
--- a/spec2nii/bruker.py
+++ b/spec2nii/bruker.py
@@ -7,7 +7,7 @@
 Copyright (C) 2021 Institute of Scientific Instruments of the CAS, v. v. i.
 """
 import os
-import pkg_resources
+import importlib.resources as importlib_resources
 import warnings
 from datetime import datetime
 
@@ -64,40 +64,43 @@ def yield_bruker(args):
     2/ Directory - function yields data and properties and data of all datasets compliant to the queries
 
     """
-    # get location of the spec2nii Bruker properties configuration file
-    bruker_properties_path = pkg_resources.resource_filename('spec2nii', 'bruker_properties.json')
-    bruker_fid_override_path = pkg_resources.resource_filename('spec2nii', 'bruker_fid_override.json')
-
     # get a list of queries to filter datasets
     queries = _get_queries(args)
 
-    # case of Bruker dataset
-    if os.path.isfile(args.file):
-        d = Dataset(
-            args.file,
-            property_files=[bruker_fid_override_path, bruker_properties_path],
-            parameter_files=['method'])
-        try:
-            d.query(queries)
-        except FilterEvalFalse:
-            raise ValueError(f'Bruker dataset {d.path} is not suitable for conversion to mrs_nifti')
-        yield from _proc_dataset(d, args)
-
-    # case of folder containing Bruker datasets
-    elif os.path.isdir(args.file):
-
-        # process individual datasets
-        for dataset in Folder(args.file, dataset_state={
-            "parameter_files": ['method'],
-            "property_files": [bruker_properties_path]
-        }).get_dataset_list_rec():
-            with dataset as d:
+    # get location of the spec2nii Bruker properties configuration file
+    ref1 = importlib_resources.files('spec2nii') / 'bruker_properties.json'
+    ref2 = importlib_resources.files('spec2nii') / 'bruker_fid_override.json'
+
+    with importlib_resources.as_file(ref1) as bruker_properties_path:
+        with importlib_resources.as_file(ref2) as bruker_fid_override_path:
+
+            # case of Bruker dataset
+            if os.path.isfile(args.file):
+                d = Dataset(
+                    args.file,
+                    property_files=[bruker_fid_override_path, bruker_properties_path],
+                    parameter_files=['method'])
                 try:
                     d.query(queries)
                 except FilterEvalFalse:
-                    continue
+                    raise ValueError(f'Bruker dataset {d.path} is not suitable for conversion to mrs_nifti')
                 yield from _proc_dataset(d, args)
 
+            # case of folder containing Bruker datasets
+            elif os.path.isdir(args.file):
+
+                # process individual datasets
+                for dataset in Folder(args.file, dataset_state={
+                    "parameter_files": ['method'],
+                    "property_files": [bruker_properties_path]
+                }).get_dataset_list_rec():
+                    with dataset as d:
+                        try:
+                            d.query(queries)
+                        except FilterEvalFalse:
+                            continue
+                        yield from _proc_dataset(d, args)
+
 
 def _get_queries(args):
     """