Merge pull request #281 from ericpre/numpy2.0

Numpy 2

.github/workflows/tests.yml

@@ -118,18 +118,31 @@ jobs:
           pip install git+https://github.com/hyperspy/hyperspy.git
           pip install git+https://github.com/hyperspy/exspy.git
 
-      - name: Install latest python-box
-        # When installing hyperspy, python-box 6 is installed (rosettasciio pinning)
-        # Remove when rosettasciio >0.4.0 is released
-        if: ${{ ! contains(matrix.LABEL, 'oldest') }}
+      - name: Install pint and 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' }}
         run: |
-          pip install --upgrade python-box
+          pip install git+https://github.com/ericpre/[email protected]_and_deprecation_fixes
+          pip install git+https://github.com/hgrecco/pint
 
       - name: Install
         shell: bash
         run: |
           pip install --upgrade -e .'${{ env.PIP_SELECTOR }}'
 
+      - name: Uninstall pyUSID
+        # remove when pyUSID supports numpy 2 
+        if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }}
+        run: |
+          pip uninstall -y pyUSID
+
+      - name: Install numpy 2.0 
+        if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }}
+        run: |
+          pip install numpy==2
+
       - name: Pip list
         run: |
           pip list

pyproject.toml

@@ -23,13 +23,13 @@ classifiers = [
   "Topic :: Software Development :: Libraries",
 ]
 dependencies = [
-  "dask[array]>=2021.3.1",
+  "dask[array] >=2021.3.1",
   "python-dateutil",
-  "numpy>=1.20.0,<2.0.0",
-  "pint>=0.8",
+  "numpy >=1.20",
+  "pint >=0.8",
   # python-box API changed on major release
   # and compatibility needs to be checked
-  "python-box>=6,<8",
+  "python-box >=6,<8",
   "pyyaml",
 ]
 dynamic = ["version"]
@@ -97,9 +97,7 @@ mrcz = ["blosc>=1.5", "mrcz>=0.3.6"]
 scalebar_export = ["matplotlib-scalebar", "matplotlib>=3.5"]
 speed = ["numba>=0.52"]
 tiff = ["tifffile>=2022.7.28", "imagecodecs"]
-# Add sidpy dependency and pinning as workaround to fix pyUSID import
-# Remove sidpy dependency once https://github.com/pycroscopy/pyUSID/issues/85 is fixed.
-usid = ["pyUSID", "sidpy<=0.12.0"]
+usid = ["pyUSID>=0.0.11"]
 zspy = ["zarr", "msgpack"]
 tests = [
   "filelock",

rsciio/dens/_api.py

@@ -27,7 +27,10 @@
 
 def _cnv_time(timestr):
     try:
-        t = datetime.strptime(timestr.decode(), "%H:%M:%S.%f")
+        if not isinstance(timestr, str):
+            # for numpy < 2.0
+            timestr = timestr.decode()
+        t = datetime.strptime(timestr, "%H:%M:%S.%f")
         dt = t - datetime(t.year, t.month, t.day)
         r = float(dt.seconds) + float(dt.microseconds) * 1e-6
     except ValueError:

rsciio/renishaw/_api.py

@@ -922,9 +922,7 @@ def _parse_ORGN(self, header_orgn_count):
         for _ in range(origin_count):
             ax_tmp_dict = {}
             ## ignore first bit of dtype read (sometimes 0, sometimes 1 in testfiles)
-            dtype = DataType(
-                self.__read_numeric("uint32", convert=False) & ~(0b1 << 31)
-            ).name
+            dtype = DataType(self.__read_numeric("uint32") & ~(0b1 << 31)).name
             ax_tmp_dict["units"] = str(UnitType(self.__read_numeric("uint32")))
             ax_tmp_dict["annotation"] = self.__read_utf8(0x10)
             ax_tmp_dict["data"] = self._set_data_for_ORGN(dtype)

rsciio/semper/_api.py

@@ -218,7 +218,11 @@ def _read_label(cls, unf_file):
         assert label["SEMPER"] == "Semper"
         # Process dimensions:
         for key in ["NCOL", "NROW", "NLAY", "ICCOLN", "ICROWN", "ICLAYN"]:
-            value = 256**2 * label.pop(key + "H") + 256 * label[key][0] + label[key][1]
+            value = (
+                256**2 * np.int32(label.pop(key + "H"))
+                + 256 * label[key][0]
+                + label[key][1]
+            )
             label[key] = value
         # Process date:
         date = "{}-{}-{} {}:{}:{}".format(label["DATE"][0] + 1900, *label["DATE"][1:])

upcoming_changes/281.maintenance.rst

@@ -0,0 +1 @@
+Add support for numpy 2 in Renishaw, Semper and Dens reader.