Update pynxtools

.github/workflows/benchmark.yml

@@ -28,10 +28,10 @@ jobs:
           private_key: ${{ secrets.APP_PRIVATE_KEY }}
 
       # Setup python
-      - name: Set up Python 3.10
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
@@ -42,7 +42,7 @@ jobs:
           uv pip install ".[dev]"
 
       # Run benchmarks
-      - name: Run benchmarks on python 3.10
+      - name: Run benchmarks on python 3.12
         run: |
           pytest --full-trace --show-capture=no -sv benchmarks/benchmark_*.py
 

.github/workflows/documentation.yml

@@ -34,10 +34,10 @@ jobs:
           fetch-depth: 0
 
       # Setup python
-      - name: Set up Python 3.10
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |

.github/workflows/linting.yml

@@ -17,10 +17,10 @@ jobs:
           fetch-depth: 0
 
       # Setup python
-      - name: Set up Python 3.10
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |

.github/workflows/testing_coverage.yml

@@ -20,10 +20,10 @@ jobs:
           fetch-depth: 0
 
       # Setup python
-      - name: Set up Python 3.10
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
@@ -34,7 +34,7 @@ jobs:
           uv pip install -e ".[dev]"
 
       # Run pytest with coverage report, saving to xml
-      - name: Run tests on python 3.10
+      - name: Run tests on python 3.12
         run: |
           pytest --cov --cov-report xml:cobertura.xml --full-trace --show-capture=no -sv -n auto tests/
 

.github/workflows/testing_multiversion.yml

@@ -17,7 +17,7 @@ jobs:
     # Using matrix strategy
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
       # Check out repo and set up Python

pyproject.toml

@@ -19,9 +19,8 @@ authors = [
 readme = "README.md"
 keywords = ["sed", "mpes", "flash", "arpes"]
 license = { file = "LICENSE" }
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -41,12 +40,12 @@ dependencies = [
     "matplotlib>=3.5.1",
     "natsort>=8.1.0",
     "numba>=0.55.1",
-    "numpy>=1.18",
+    "numpy>=2.0.0",
     "pandas>=1.4.1",
     "photutils<2.0",
     "psutil>=5.9.0",
-    "pynxtools-mpes>=0.2.5",
-    "pynxtools>=0.11.1",
+    "pynxtools-mpes>=0.2.6",
+    "pynxtools>=0.12.0",
     "pyyaml>=6.0.0",
     "scipy>=1.8.0",
     "symmetrize>=0.5.5",

src/sed/binning/binning.py

@@ -178,7 +178,7 @@ def bin_partition(
             ranges=ranges,
         )
     elif hist_mode == "numpy":
-        hist_partition, edges = np.histogramdd(
+        hist_partition, edges = np.histogramdd(  # type: ignore
             vals,
             bins=bins,
             range=ranges,

src/sed/binning/numba_bin.py

@@ -195,7 +195,7 @@ def numba_histogramdd(
         num_rows, num_cols = sample.shape  # pylint: disable=unused-variable
 
     if isinstance(bins, (int, np.int_)):  # bins provided as a single number
-        bins = num_cols * [bins]
+        bins = cast(int, num_cols) * [bins]
     num_bins = len(bins)  # Number of dimensions in bins
 
     if num_bins != num_cols:  # check number of dimensions

tests/test_processor.py

@@ -1236,13 +1236,13 @@ def test_save(caplog) -> None:
         )
         assert (
             caplog.messages[0]
-            == "WARNING: The data entry corresponding to /ENTRY[entry]/SAMPLE[sample]/name is "
-            "required and hasn't been supplied by the reader."
+            == "WARNING: The required field /ENTRY[entry]/SAMPLE[sample]/name hasn't been "
+            "supplied."
         )
         assert (
             caplog.messages[1]
-            == "WARNING: Field /ENTRY[entry]/INSTRUMENT[instrument]/undocumented_field written "
-            "without documentation."
+            == "WARNING: Field /ENTRY[entry]/INSTRUMENT[instrument]/undocumented_field has no "
+            "documentation."
         )
     os.remove("output.nxs")
     os.remove("temp_eln.yaml")