Merge pull request #339 from ericpre/python3.13

Python 3.13

.github/workflows/tests.yml

@@ -26,37 +26,48 @@ jobs:
           # test oldest supported version of main dependencies on python 3.8
           - os: ubuntu
             os_version: latest
-            PYTHON_VERSION: '3.8'
+            PYTHON_VERSION: '3.9'
             # Set pillow and scikit-image version to be compatible with imageio and scipy
-            # matplotlib needs 3.5 to support markers in hyperspy 2.0 (requires `collection.set_offset_transform`)
-            DEPENDENCIES: matplotlib==3.5 numpy==1.20.0 tifffile==2022.7.28 dask[array]==2021.5.1 distributed==2021.5.1 numba==0.52 imageio==2.16 pillow==8.3.2 scikit-image==0.18.0 python-box==6.0.0
+            # align matplotlib dependency with hyperspy
+            DEPENDENCIES: matplotlib==3.6 numpy==1.20.0 tifffile==2022.7.28 dask[array]==2021.5.1 distributed==2021.5.1 numba==0.53 imageio==2.16 pillow==8.3.2 scikit-image==0.18.0 python-box==6.0.0
             LABEL: '-oldest'
           # test minimum requirement
           - os: ubuntu
             os_version: latest
-            PYTHON_VERSION: '3.9'
+            PYTHON_VERSION: '3.10'
             LABEL: '-minimum'
           - os: ubuntu
             os_version: latest
             PYTHON_VERSION: '3.12'
-            LABEL: '-minimum-without-hyperspy'
+            LABEL: '-hyperspy-dev'
           - os: ubuntu
             os_version: latest
-            PYTHON_VERSION: '3.11'
-            LABEL: '-hyperspy-dev'
+            PYTHON_VERSION: '3.10'
+            LABEL: '-without-hyperspy'
           - os: ubuntu
             os_version: latest
             PYTHON_VERSION: '3.9'
-            LABEL: '-without-hyperspy'
           - os: ubuntu
             os_version: latest
-            PYTHON_VERSION: '3.8'
+            PYTHON_VERSION: '3.12'
           - os: ubuntu
             os_version: latest
-            PYTHON_VERSION: '3.11'
+            PYTHON_VERSION: '3.13'
+            # can remove minimum dependencies when numba supports 3.13
+            LABEL: '-minimum'
+          - os: macos
+            os_version: latest
+            PYTHON_VERSION: '3.13'
+            # can remove minimum dependencies when numba supports 3.13
+            LABEL: '-minimum'
+          - os: windows
+            os_version: latest
+            PYTHON_VERSION: '3.13'
+            # can remove minimum dependencies when numba supports 3.13
+            LABEL: '-minimum'
           - os: macos
             os_version: '13'
-            PYTHON_VERSION: '3.11'
+            PYTHON_VERSION: '3.12'
 
     steps:
       - uses: actions/checkout@v4
@@ -79,6 +90,7 @@ jobs:
         name: Install Python
         with:
           python-version: ${{ matrix.PYTHON_VERSION }}
+          cache: 'pip'
 
       - name: Get the number of CPUs
         id: cpus
@@ -91,7 +103,7 @@ jobs:
           with open(output_file, "a", encoding="utf-8") as output_stream:
               output_stream.write(f"count={num_cpus}\n")
         shell: python
-          
+
       - name: Set Environment Variable
         shell: bash
         # Set PIP_SELECTOR environment variable according to matrix.LABEL
@@ -108,8 +120,14 @@ jobs:
           python --version
           pip --version
 
+      - name: Install traits dev for python 3.13
+        if: ${{ matrix.PYTHON_VERSION == '3.13' }}
+        run: |
+          # traits release with python 3.13 pending
+          pip install git+https://github.com/enthought/traits.git
+
       - name: Install hyperspy and exspy
-        if: ${{ ! contains(matrix.LABEL, 'without-hyperspy') }}
+        if: ${{ ! contains(matrix.LABEL, 'without-hyperspy') && matrix.PYTHON_VERSION != '3.13'}}
         run: |
           pip install hyperspy exspy
 
@@ -119,14 +137,20 @@ jobs:
           pip install git+https://github.com/hyperspy/hyperspy.git
           pip install git+https://github.com/hyperspy/exspy.git
 
-      - name: Install pint and python-mrcz dev
+      - name: Install hyperspy (python 3.13) and exspy (dev)
+        if: ${{ matrix.PYTHON_VERSION == '3.13' }}
+        run: |
+          # speed up installing scikit-image using pre-release with python 3.13 wheels
+          pip install scikit-image --pre 
+          pip install git+https://github.com/ericpre/hyperspy.git@python313
+          pip install git+https://github.com/hyperspy/exspy.git
+
+      - name: Install python-mrcz dev
         # for numpy 2.0 support for python >= 3.9
         # https://github.com/em-MRCZ/python-mrcz/pull/15
-        # https://github.com/hgrecco/pint/issues/1974
-        if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }}
+        if: ${{ ! contains(matrix.LABEL, 'oldest') && ! contains(matrix.LABEL, 'minimum') }}
         run: |
           pip install git+https://github.com/ericpre/[email protected]_and_deprecation_fixes
-          pip install git+https://github.com/hgrecco/pint
 
       - name: Install
         shell: bash
@@ -147,7 +171,7 @@ jobs:
       - name: Install numpy 2.0 
         if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }}
         run: |
-          pip install numpy==2
+          pip install numpy>=2
 
       - name: Pip list
         run: |

azure-pipelines.yml

@@ -23,6 +23,10 @@ resources:
 
 strategy:
   matrix:
+    Linux_Python312:
+      vmImage: 'ubuntu-latest'
+      PYTHON_VERSION: '3.12'
+      MINIFORGE_PATH: $(Agent.BuildDirectory)/miniforge3
     Linux_Python310:
       vmImage: 'ubuntu-latest'
       PYTHON_VERSION: '3.10'
@@ -31,25 +35,21 @@ strategy:
       vmImage: 'ubuntu-latest'
       PYTHON_VERSION: '3.9'
       MINIFORGE_PATH: $(Agent.BuildDirectory)/miniforge3
-    Linux_Python38:
-      vmImage: 'ubuntu-latest'
-      PYTHON_VERSION: '3.8'
-      MINIFORGE_PATH: $(Agent.BuildDirectory)/miniforge3
-    MacOS_Python38:
+    MacOS_Python39:
       vmImage: 'macOS-latest'
-      PYTHON_VERSION: '3.8'
+      PYTHON_VERSION: '3.9'
       MINIFORGE_PATH: $(Agent.BuildDirectory)/miniforge3
-    MacOS_Python310:
+    MacOS_Python312:
       vmImage: 'macOS-latest'
-      PYTHON_VERSION: '3.10'
+      PYTHON_VERSION: '3.12'
       MINIFORGE_PATH: $(Agent.BuildDirectory)/miniforge3
-    Windows_Python38:
+    Windows_Python39:
       vmImage: 'windows-latest'
-      PYTHON_VERSION: '3.8'
+      PYTHON_VERSION: '3.9'
       MINIFORGE_PATH: $(Agent.BuildDirectory)\miniforge3
-    Windows_Python310:
+    Windows_Python312:
       vmImage: 'windows-latest'
-      PYTHON_VERSION: '3.10'
+      PYTHON_VERSION: '3.12'
       MINIFORGE_PATH: $(Agent.BuildDirectory)\miniforge3
 
 pool:

pyproject.toml

@@ -5,19 +5,19 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "rosettasciio"
 description = "Reading and writing scientific file formats"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 readme = "README.md"
 classifiers = [
   "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
   "Operating System :: OS Independent",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Topic :: Scientific/Engineering",
   "Topic :: Scientific/Engineering :: Physics",
   "Topic :: Software Development :: Libraries",
@@ -94,8 +94,8 @@ eds-stream = ["sparse"]
 hdf5 = ["h5py>=2.3"]
 image = ["imageio>=2.16"]
 mrcz = ["blosc>=1.5", "mrcz>=0.3.6"]
-scalebar_export = ["matplotlib-scalebar", "matplotlib>=3.5"]
-speed = ["numba>=0.52"]
+scalebar_export = ["matplotlib-scalebar", "matplotlib>=3.6"]
+speed = ["numba>=0.53"]
 tiff = ["tifffile>=2022.7.28", "imagecodecs"]
 usid = ["pyUSID>=0.0.11"]
 zspy = ["zarr", "msgpack"]

rsciio/bruker/_api.py

@@ -490,9 +490,9 @@ def __init__(self, spectrum):
             self.detector_metadata["DetLayers"][i.tag] = dict(i.attrib)
 
         # map stuff from esma xml branch:
-        if esma_header:
+        if esma_header is not None:
             self.esma_metadata = x2d.dictionarize(esma_header)
-        if xrf_header:
+        if xrf_header is not None:
             xrf_header_dict = x2d.dictionarize(xrf_header)
             self.esma_metadata = {
                 "PrimaryEnergy": xrf_header_dict["Voltage"],

rsciio/digitalsurf/_api.py

@@ -714,7 +714,9 @@ def _split_signal_dict(self):
                 self._split_surfaceserie()
         elif (n_nav, n_sig) == (2, 0):
             warnings.warn(
-                f"Signal dimension {n_sig} and navigation dimension {n_nav} exported as surface type. Consider transposing signal object before exporting if this is intentional."
+                f"Signal dimension {n_sig} and navigation dimension {n_nav} exported "
+                "as surface type. Consider transposing signal object before exporting "
+                "if this is intentional."
             )
             if self._is_binary():
                 self._split_binary_img()

rsciio/edax/_api.py

@@ -591,7 +591,7 @@ def get_ipr_dtype_list(endianess="<", version=333):
     dtype_list = [
         ("version", end + "u2"),
         ("imageType", end + "u2"),
-        ("label", end + "a8"),
+        ("label", end + "S8"),
         ("sMin", end + "u2"),
         ("sMax", end + "u2"),
         ("color", end + "u2"),
@@ -618,7 +618,7 @@ def get_ipr_dtype_list(endianess="<", version=333):
         ("mppX", end + "f4"),
         ("mppY", end + "f4"),
         ("nTextLines", end + "u2"),
-        ("charText", end + "4a32"),
+        ("charText", end + "4S32"),
         ("reserved3", end + "4f4"),
         ("nOverlayElements", end + "u2"),
         ("overlayColors", end + "16u2"),

rsciio/emd/_emd_ncem.py

@@ -203,8 +203,10 @@ def _read_dataset(dataset):
         if h5py.check_string_dtype(dataset.dtype) and hasattr(dataset, "asstr"):
             # h5py 3.0 and newer
             # https://docs.h5py.org/en/3.0.0/strings.html
-            dataset = dataset.asstr()[:]
-        return dataset, chunks
+            data = dataset.asstr()[:]
+        else:
+            data = dataset[:]
+        return data, chunks
 
     def _read_emd_version(self, group):
         """Return the group version if the group is an EMD group, otherwise
@@ -225,38 +227,38 @@ def _read_data_from_groups(
         axes = []
         transpose_required = True if dataset_name != "datacube" else False
 
-        array_list = [self.file.get(f"{key}/{dataset_name}") for key in group_path]
+        dataset_list = [self.file.get(f"{key}/{dataset_name}") for key in group_path]
 
-        if None in array_list:
+        if None in dataset_list:
             raise IOError("Dataset can't be found.")
 
-        if len(array_list) > 1:
+        if len(dataset_list) > 1:
             # Squeeze the data only when
             if self.lazy:
-                data_list = [da.from_array(*self._read_dataset(d)) for d in array_list]
+                data_list = [
+                    da.from_array(*self._read_dataset(d)) for d in dataset_list
+                ]
                 if transpose_required:
                     data_list = [da.transpose(d) for d in data_list]
                 data = da.stack(data_list)
                 data = da.squeeze(data)
             else:
-                data_list = [
-                    np.asanyarray(self._read_dataset(d)[0]) for d in array_list
-                ]
+                data_list = [self._read_dataset(d)[0] for d in dataset_list]
                 if transpose_required:
                     data_list = [np.transpose(d) for d in data_list]
                 data = np.stack(data_list).squeeze()
         else:
-            d = array_list[0]
+            d = dataset_list[0]
             if self.lazy:
                 data = da.from_array(*self._read_dataset(d))
             else:
-                data = np.asanyarray(self._read_dataset(d)[0])
+                data = self._read_dataset(d)[0]
             if transpose_required:
                 data = data.transpose()
 
         shape = data.shape
 
-        if len(array_list) > 1:
+        if len(dataset_list) > 1:
             offset, scale, units = 0, 1, None
             if self._is_prismatic_file and "depth" in stack_key:
                 simu_om = original_metadata.get("simulation_parameters", {})
@@ -274,7 +276,7 @@ def _read_data_from_groups(
                     simu_om.get("tile", 0)[2] * simu_om.get("cellDimension", 0)[0]
                 )
                 if not math.isclose(
-                    total_thickness, len(array_list) * scale, rel_tol=1e-4
+                    total_thickness, len(dataset_list) * scale, rel_tol=1e-4
                 ):
                     _logger.warning(
                         "Depth axis is non-uniform and its offset "
@@ -289,7 +291,7 @@ def _read_data_from_groups(
                     "name": stack_key if stack_key is not None else None,
                     "offset": offset,
                     "scale": scale,
-                    "size": len(array_list),
+                    "size": len(dataset_list),
                     "units": units,
                     "navigate": True,
                 }

rsciio/tests/generate_dm_testing_files.py

@@ -136,9 +136,10 @@ def generate_4D_files(f, data_types, dmversion):
 
 
 if __name__ == "__main__":
-    with open("generate_dm3_test_files.s", "w") as f1, open(
-        "generate_dm4_test_files.s", "w"
-    ) as f2:
+    with (
+        open("generate_dm3_test_files.s", "w") as f1,
+        open("generate_dm4_test_files.s", "w") as f2,
+    ):
         for f in (f1, f2):
             f.write("image im\n")
             f.write("string filename, path\n")