Merge branch 'released'

.github/workflows/test.yml

@@ -16,16 +16,26 @@ jobs:
   build:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-20.04, ubuntu-latest, macos-11, macos-latest, windows-2019, windows-latest]
-        python-version: [ '3.8', '3.x' ]
+        os: [ubuntu-20.04, ubuntu-latest, macos-13, macos-latest, windows-2019, windows-latest]
+        python-version: [ '3.9', '3.x' ]
 
     steps:
     - uses: actions/checkout@v3
     - name: Setup python
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install libhdf5 (macOS)
+      # See https://stackoverflow.com/questions/73029883
+      if: runner.os == 'macOS'
+      run: |
+        brew install hdf5
+        brew install c-blosc
+        export HDF5_DIR=/opt/homebrew/opt/hdf5
+        export BLOSC_DIR=/opt/homebrew/opt/c-blosc
+        export LZO_DIR=/opt/homebrew/opt/lzo
     - name: Upgrade pip
       run: python -m pip install --upgrade pip
     - name: Build and install flydra_core
@@ -37,8 +47,9 @@ jobs:
   test-ubuntu-system-python:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-20.04, ubuntu-latest]
+        os: [ubuntu-24.04, ubuntu-latest]
     steps:
     - uses: actions/checkout@v3
     - name: Update package index

flydra_analysis/conftest.py

@@ -0,0 +1,8 @@
+import numpy as np
+import pytest
+
+
+@pytest.fixture(scope="session", autouse=True)
+def set_numpy_printoptions():
+    np.set_printoptions(legacy="1.25")
+

flydra_analysis/flydra_analysis/version.py

@@ -1 +1 @@
-__version__ = "0.7.18"  # keep in sync with pyproject.toml
+__version__ = "0.7.19"  # keep in sync with pyproject.toml

flydra_analysis/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "flydra_analysis"
-version = "0.7.18"                     # keep in sync with flydra_analysis/version.py
+version = "0.7.19"                     # keep in sync with flydra_analysis/version.py
 description = "flydra analysis tools"
 readme = "README.md"
 requires-python = ">= 3.8"
@@ -106,7 +106,7 @@ wt0803 = "flydra_analysis.a2.conditions_draw:wt0803"
 
 [build-system]
 # following advice in https://stackoverflow.com/a/66479252
-requires = ["setuptools >= 61", "cython >= 0.29", "numpy"]
+requires = ["setuptools >= 61", "cython >= 0.29.32", "numpy"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]

flydra_core/conftest.py

@@ -0,0 +1,8 @@
+import numpy as np
+import pytest
+
+
+@pytest.fixture(scope="session", autouse=True)
+def set_numpy_printoptions():
+    np.set_printoptions(legacy="1.25")
+

flydra_core/flydra_core/reconstruct.py

@@ -921,8 +921,8 @@ def SingleCameraCalibration_from_xml(elem, helper=None):
     assert ET.iselement(elem)
     assert elem.tag == "single_camera_calibration"
     cam_id = elem.find("cam_id").text
-    pmat = numpy.array(numpy.mat(elem.find("calibration_matrix").text))
-    res = numpy.array(numpy.mat(elem.find("resolution").text))[0, :]
+    pmat = numpy.array(np.asmatrix(elem.find("calibration_matrix").text))
+    res = numpy.array(np.asmatrix(elem.find("resolution").text))[0, :]
     scale_elem = elem.find("scale_factor")
     if NO_BACKWARDS_COMPAT:
         assert scale_elem is None, "XML file has outdated <scale_factor>"
@@ -2102,12 +2102,13 @@ def add_element(self, parent):
         for cam_id in self.cam_ids:
             scc = self.get_SingleCameraCalibration(cam_id)
             scc.add_element(elem)
-        if 1:
-            me_elem = ET.SubElement(elem, "minimum_eccentricity")
-            me_elem.text = repr(self.minimum_eccentricity)
-        if self.wateri is not None:
-            water_elem = ET.SubElement(elem, "water")
-            water_elem.text = repr(self.wateri.n2)
+        with np.printoptions(legacy='1.25'):
+            if 1:
+                me_elem = ET.SubElement(elem, "minimum_eccentricity")
+                me_elem.text = repr(self.minimum_eccentricity)
+            if self.wateri is not None:
+                water_elem = ET.SubElement(elem, "water")
+                water_elem.text = repr(self.wateri.n2)
 
 
 def align_calibration():

flydra_core/flydra_core/version.py

@@ -1 +1 @@
-__version__ = "0.7.16"  # keep in sync with pyproject.toml
+__version__ = "0.7.18"  # keep in sync with pyproject.toml

flydra_core/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "flydra_core"
-version = "0.7.16"                            # keep in sync with flydra_core/version.py
+version = "0.7.18"                            # keep in sync with flydra_core/version.py
 description = "flydra mainbrain and core lib"
 readme = "README.md"
 requires-python = ">= 3.8"
@@ -13,7 +13,7 @@ urls.homepage = "https://github.com/strawlab/flydra"
 dependencies = [
     "numpy >= 1.19",
 
-    "tables",
+    "tables>=3.9.0",
     "cgkit1 >= 1.3.0",
     "pymvg >= 2.1.0",
     "adskalman",
@@ -29,7 +29,7 @@ flydra_analysis_flip_calibration = "flydra_core.reconstruct:flip_calibration"
 
 [build-system]
 # following advice in https://stackoverflow.com/a/66479252
-requires = ["setuptools >= 61", "cython >= 0.29", "numpy"]
+requires = ["setuptools >= 61", "cython >= 0.29.32", "numpy"]
 build-backend = "setuptools.build_meta"
 
 [tool.pytest.ini_options]