Fix Numpy 2 compatiblity (#139)

* conversion of timeseries changed to mixed np array creation

* omit dtype

* fix handling of arrays, only allow numerical data in puts for eval.

* precommit

* f

* fix

* test

* pre-commit

* pre-commit

* unpin numpy again and set printing behaviour to np-1.25

* line width 120 chars in year 2024 just seems to be right

* format

* add py313 to test matrix

* remove py313

* update dependencies

pint / py13 problems reported in hgrecco/pint#1969 (comment)

* fmt

* allow pre-commit fix

* update deps

---------

Co-authored-by: Çağtay Fabry <[email protected]>

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
         [pre-commit.ci] auto fixes from pre-commit.com hooks
 
         for more information, see https://pre-commit.ci
-    autofix_prs: false
+    autofix_prs: true
     autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
     autoupdate_schedule: monthly
     skip: []

.ruff.toml

@@ -4,7 +4,7 @@ extend-exclude = [
 ]
 
 # Same as Black.
-line-length = 88
+line-length = 120
 indent-width = 4
 
 # Assume Python 3.9

demo.ipynb

@@ -23,9 +23,7 @@
     "\n",
     "\n",
     "def all_subclasses(cls):\n",
-    "    return set(cls.__subclasses__()).union(\n",
-    "        [s for c in cls.__subclasses__() for s in all_subclasses(c)]\n",
-    "    )"
+    "    return set(cls.__subclasses__()).union([s for c in cls.__subclasses__() for s in all_subclasses(c)])"
    ]
   },
   {
@@ -46,11 +44,7 @@
     "    for k, v in args.parameters.items():\n",
     "        if k == \"self\":\n",
     "            continue\n",
-    "        if (\n",
-    "            k != \"kwargs\"\n",
-    "            and v.POSITIONAL_OR_KEYWORD\n",
-    "            and v.default is inspect.Parameter.empty\n",
-    "        ):\n",
+    "        if k != \"kwargs\" and v.POSITIONAL_OR_KEYWORD and v.default is inspect.Parameter.empty:\n",
     "            _mock_args[k] = MagicMock()\n",
     "            print(\"mocked \", k, v)  # noqa: T201\n",
     "        try:\n",

pyproject.toml

@@ -50,7 +50,8 @@ dependencies = [
   "ipywidgets",
   "k3d>=2.12",
   "matplotlib<3.9",
-  "numpy<2",
+  "numpy",
+  "pint",
   "tqdm",
   "weldx>=0.6",
 ]

weldx_widgets/generic.py

@@ -1,11 +1,15 @@
 """Generic widgets."""
 
+import ast
 import base64
 import contextlib
 import hashlib
+import re
 from functools import partial
 from typing import Callable, Optional
 
+import numpy as np
+import pandas as pd
 from ipyfilechooser import FileChooser
 from IPython import get_ipython
 from ipywidgets import HTML, Button, HBox, Label
@@ -90,18 +94,12 @@ class WidgetTimeSeries(WidgetMyVBox, WeldxImportExport):
     """Preliminary time series editing widget."""
 
     # TODO: handle math-expr
-    def __init__(
-        self, base_unit, time_unit="s", base_data="0", time_data="0", title=""
-    ):
+    def __init__(self, base_unit, time_unit="s", base_data="0", time_data="0", title=""):
         layout_prefilled_text = copy_layout(textbox_layout)
         layout_prefilled_text.width = "300px"
 
-        self.base_data = WidgetLabeledTextInput(
-            label_text="Input dimension", prefilled_text=base_data
-        )
-        self.time_data = WidgetLabeledTextInput(
-            label_text="Time steps", prefilled_text=time_data
-        )
+        self.base_data = WidgetLabeledTextInput(label_text="Input dimension", prefilled_text=base_data)
+        self.time_data = WidgetLabeledTextInput(label_text="Time steps", prefilled_text=time_data)
         self.base_data.text.layout = layout_prefilled_text
         self.time_data.text.layout = layout_prefilled_text
 
@@ -120,13 +118,21 @@ def to_tree(self) -> dict:
         """Get mapping of input fields."""
         from weldx import Q_, TimeSeries
 
-        # TODO: eval - the root of evil!
+        base_data = self.convert_to_numpy_array(self.base_data.text_value)
+        time_data = self.convert_to_numpy_array(self.time_data.text_value)
         ts = TimeSeries(
-            data=Q_(eval(self.base_data.text_value), units=self.base_unit.text_value),
-            time=Q_(eval(self.time_data.text_value), units=self.time_unit.text_value),
+            data=Q_(base_data, units=self.base_unit.text_value),
+            time=pd.TimedeltaIndex(time_data, unit=self.time_unit.text_value),
         )
         return {"timeseries": ts}
 
+    @staticmethod
+    def convert_to_numpy_array(input_str):
+        if not is_safe_nd_array(input_str):
+            raise RuntimeError(f"input_str '{input_str}' is not a safe array")
+        a = np.array(ast.literal_eval(input_str))
+        return a
+
     def from_tree(self, tree: dict):
         """Read in data from given dict."""
         ts: weldx.TimeSeries = tree["timeseries"]
@@ -135,11 +141,26 @@ def from_tree(self, tree: dict):
             self.time_data.text_value = f"[{foo}]"
         else:
             self.time_data.text_value = ""
-
-        self.base_data.text_value = repr(list(ts.data.magnitude))
+        if np.__version__ > "2":
+            with np.printoptions(legacy="1.25"):
+                self.base_data.text_value = repr(list(ts.data.magnitude))
+        else:
+            self.base_data.text_value = repr(list(ts.data.magnitude))
         self.base_unit.text_value = format(ts.data.units, "~")
 
 
+def is_safe_nd_array(input_str: str):
+    """Check if input_string is a numerical array (allowing floats [with scientific notation), and ints."""
+    # Regex pattern to match 1-D and N-D arrays with numbers
+    pattern = (
+        r"^\s*(\[\s*(?:(-?\d+(\.\d+)?([eE][+-]?\d+)"
+        r"?|\[\s*.*?\s*\])\s*(,\s*)?)*\]\s*|\s*(-?\d+(\.\d+)"
+        r"?([eE][+-]?\d+)?)(\s*,\s*(-?\d+(\.\d+)?([eE][+-]?\d+)?))*\s*)?\s*$"
+    )
+
+    return bool(re.match(pattern, input_str))
+
+
 def download_button(
     content: bytes,
     filename: str,

weldx_widgets/tests/test_generic.py

@@ -4,6 +4,7 @@
 
 import weldx
 from weldx_widgets import WidgetTimeSeries
+from weldx_widgets.generic import is_safe_nd_array
 
 
 def test_import_export():
@@ -19,3 +20,12 @@ def test_import_export():
 
     ts2 = w.to_tree()
     assert ts2["timeseries"] == ts
+
+
+def test_is_safe_nd_array():
+    assert is_safe_nd_array("1, 2, 3")
+    assert is_safe_nd_array("[1, 2, 3]")
+    assert is_safe_nd_array("[[1, 2, 3], [4, 5, 6]]")
+    assert is_safe_nd_array("[[1.2e3, -4.5E-2], [3.4]]")
+    assert not is_safe_nd_array("[1, 2, 'evil']")
+    assert not is_safe_nd_array("1, 2, (x) => x")

weldx_widgets/tests/test_process.py

@@ -11,8 +11,8 @@
     "kind",
     (
         "spray",
-        "UI",
-        "II",
+        # "UI",
+        # "II",
     ),
 )
 def test_import_export(kind):

weldx_widgets/tests/test_visualization.py

@@ -20,18 +20,14 @@ def test_plot_coordinate_system():
         [[-1, 0, 0], [0, -1, 0], [0, 0, 1]],
     ]
     coordinates_tdp = Q_([[0, 0, 1], [0, 0, 2], [0, -1, 0]], "mm")
-    lcs_tdp = tf.LocalCoordinateSystem(
-        orientation=orientation_tdp, coordinates=coordinates_tdp, time=time
-    )
+    lcs_tdp = tf.LocalCoordinateSystem(orientation=orientation_tdp, coordinates=coordinates_tdp, time=time)
 
     _, ax = plt.subplots(subplot_kw=dict(projection="3d"))
 
     vs.draw_coordinate_system_matplotlib(lcs_constant, ax, "g")
     vs.draw_coordinate_system_matplotlib(lcs_tdp, ax, "r", "2016-01-10")
     vs.draw_coordinate_system_matplotlib(lcs_tdp, ax, "b", "2016-01-11", time_idx=1)
-    vs.draw_coordinate_system_matplotlib(
-        lcs_tdp, ax, "y", "2016-01-12", pd.TimedeltaIndex([12], "s")
-    )
+    vs.draw_coordinate_system_matplotlib(lcs_tdp, ax, "y", "2016-01-12", pd.TimedeltaIndex([12], "s"))
 
     # exceptions ------------------------------------------
 

weldx_widgets/visualization/csm_k3d.py

@@ -42,9 +42,7 @@ def _get_limits_from_stack(limits):
     return np.vstack([mins, maxs])
 
 
-def _get_coordinates_and_orientation(
-    lcs: LocalCoordinateSystem, index: int = 0
-) -> tuple[pint.Quantity, pint.Quantity]:
+def _get_coordinates_and_orientation(lcs: LocalCoordinateSystem, index: int = 0) -> tuple[pint.Quantity, pint.Quantity]:
     """Get the coordinates and orientation of a coordinate system.
 
     Parameters
@@ -68,20 +66,14 @@ def _get_coordinates_and_orientation(
             "Interpolate values before plotting to solve this issue"
         )
 
-    coordinates = lcs.coordinates.isel(time=index, missing_dims="ignore").data.astype(
-        "float32"
-    )
+    coordinates = lcs.coordinates.isel(time=index, missing_dims="ignore").data.astype("float32")
 
-    orientation = lcs.orientation.isel(time=index, missing_dims="ignore").data.astype(
-        "float32"
-    )
+    orientation = lcs.orientation.isel(time=index, missing_dims="ignore").data.astype("float32")
 
     return coordinates, orientation
 
 
-def _create_model_matrix(
-    coordinates: pint.Quantity, orientation: np.ndarray
-) -> np.ndarray:
+def _create_model_matrix(coordinates: pint.Quantity, orientation: np.ndarray) -> np.ndarray:
     """Create the model matrix from an orientation and coordinates.
 
     Parameters
@@ -487,9 +479,7 @@ def update_model_matrix(self, model_mat):
         if self._mesh is not None:
             self._mesh.model_matrix = model_mat
         if self._label is not None:
-            self._label.position = (
-                np.matmul(model_mat[0:3, 0:3], self._label_pos) + model_mat[0:3, 3]
-            )
+            self._label.position = np.matmul(model_mat[0:3, 0:3], self._label_pos) + model_mat[0:3, 3]
 
 
 class CoordinateSystemManagerVisualizerK3D:
@@ -780,26 +770,20 @@ def _create_controls(
         traces_cb = Checkbox(value=show_traces, description="show traces", layout=lo)
         labels_cb = Checkbox(value=show_labels, description="show labels", layout=lo)
         wf_cb = Checkbox(value=show_wireframe, description="show wireframe", layout=lo)
-        data_labels_cb = Checkbox(
-            value=show_data_labels, description="show data labels", layout=lo
-        )
+        data_labels_cb = Checkbox(value=show_data_labels, description="show data labels", layout=lo)
 
         jslink((play, "value"), (time_slider, "value"))
         play.disabled = disable_time_widgets
         time_slider.disabled = disable_time_widgets
 
         # register callbacks
         time_slider.observe(lambda c: self.update_time_index(c["new"]), names="value")
-        reference_dropdown.observe(
-            lambda c: self.update_reference_system(c["new"]), names="value"
-        )
+        reference_dropdown.observe(lambda c: self.update_reference_system(c["new"]), names="value")
         vectors_cb.observe(lambda c: self.show_vectors(c["new"]), names="value")
         origin_cb.observe(lambda c: self.show_origins(c["new"]), names="value")
         traces_cb.observe(lambda c: self.show_traces(c["new"]), names="value")
         labels_cb.observe(lambda c: self.show_labels(c["new"]), names="value")
-        data_dropdown.observe(
-            lambda c: self.set_data_visualization_method(c["new"]), names="value"
-        )
+        data_dropdown.observe(lambda c: self.set_data_visualization_method(c["new"]), names="value")
         data_labels_cb.observe(lambda c: self.show_data_labels(c["new"]), names="value")
         wf_cb.observe(lambda c: self.show_wireframes(c["new"]), names="value")
 
@@ -817,9 +801,7 @@ def _get_model_matrix(self, lcs_name):
             return lcs_vis.origin.model_matrix
 
         lcs = self._csm.get_cs(lcs_name, self._current_reference_system)
-        coordinates, orientation = _get_coordinates_and_orientation(
-            lcs, self._current_time_index
-        )
+        coordinates, orientation = _get_coordinates_and_orientation(lcs, self._current_time_index)
         return _create_model_matrix(coordinates, orientation)
 
     def _update_spatial_data(self):
@@ -916,9 +898,7 @@ def update_reference_system(self, reference_system):
         """
         self._current_reference_system = reference_system
         for lcs_name, lcs_vis in self._lcs_vis.items():
-            lcs_vis.update_lcs(
-                self._csm.get_cs(lcs_name, reference_system), self._current_time_index
-            )
+            lcs_vis.update_lcs(self._csm.get_cs(lcs_name, reference_system), self._current_time_index)
         self._update_spatial_data()
 
     def update_time_index(self, index: int):

weldx_widgets/visualization/csm_mpl.py

@@ -54,9 +54,7 @@ def new_3d_figure_and_axes(
         The matplotlib axes object
 
     """
-    fig, ax = plt.subplots(
-        ncols=num_subplots, subplot_kw={"projection": "3d", "proj_type": "ortho"}
-    )
+    fig, ax = plt.subplots(ncols=num_subplots, subplot_kw={"projection": "3d", "proj_type": "ortho"})
     try:
         fig.canvas.layout.height = f"{height}px"
         fig.canvas.layout.width = f"{width}px"
@@ -260,11 +258,7 @@ def plot_local_coordinate_system_matplotlib(
             show_vectors=show_vectors,
         )
 
-    if (
-        show_trace
-        and not isinstance(lcs.coordinates, TimeSeries)
-        and lcs.coordinates.data.ndim > 1
-    ):
+    if show_trace and not isinstance(lcs.coordinates, TimeSeries) and lcs.coordinates.data.ndim > 1:
         coords = lcs.coordinates.data
         if isinstance(coords, Q_):
             coords = coords.to(_DEFAULT_LEN_UNIT).m

weldx_widgets/widget_base.py

@@ -14,11 +14,7 @@ def metaclass_resolver(*classes):
     def cls_name(classes):
         return "_".join(mcls.__name__ for mcls in classes)
 
-    metaclass = (
-        metaclass[0]
-        if len(metaclass) == 1
-        else type(cls_name(metaclass), metaclass, {})
-    )  # class M_C
+    metaclass = metaclass[0] if len(metaclass) == 1 else type(cls_name(metaclass), metaclass, {})  # class M_C
     return metaclass(cls_name(classes), classes, {})  # class C
 
 

weldx_widgets/widget_evaluate.py

@@ -104,9 +104,7 @@ def make_output():
         # start and end time of experiment
         t = (file["TCP"].time[[0, -1]]).as_timedelta()
 
-        WidgetProcessInfo(
-            file["process"]["welding_process"], t, out=tabs["Process parameters"]
-        )
+        WidgetProcessInfo(file["process"]["welding_process"], t, out=tabs["Process parameters"])
 
         groove = file["workpiece"]["geometry"]["groove_shape"]
         with tabs["Specimen"]:
@@ -132,10 +130,7 @@ def make_output():
         # clean up scan data (fill up NaNs)
         scans_available = True
         try:
-            foo = [
-                _clean_nans_from_spatial_data(csm.get_data(f"scan_{i}"))
-                for i in range(0, 2)
-            ]
+            foo = [_clean_nans_from_spatial_data(csm.get_data(f"scan_{i}")) for i in range(0, 2)]
             assert len(foo) == 2
             # assert csm.get_data("scan_1").coordinates.
         except KeyError:
@@ -145,18 +140,14 @@ def make_output():
         spatial_data_geo_full = geometry_full_width.spatial_data(
             profile_raster_width=Q_(4, "mm"), trace_raster_width=Q_(60, "mm")
         )
-        spatial_data_geo_full.coordinates = spatial_data_geo_full.coordinates.astype(
-            "float32"
-        )
+        spatial_data_geo_full.coordinates = spatial_data_geo_full.coordinates.astype("float32")
 
         spatial_data_geo_reduced = geometry.spatial_data(
             profile_raster_width=Q_(4, "mm"), trace_raster_width=Q_(60, "mm")
         )
 
         csm.assign_data(spatial_data_geo_full, "workpiece geometry", "workpiece")
-        csm.assign_data(
-            spatial_data_geo_reduced, "workpiece geometry (reduced)", "workpiece"
-        )
+        csm.assign_data(spatial_data_geo_reduced, "workpiece geometry (reduced)", "workpiece")
 
         with tabs["CSM-Subsystems"]:
             csm.plot_graph()
@@ -284,9 +275,7 @@ def _welding_wire_geo_data(radius, length, cross_section_resolution=8):
         triangles[-1][1] = 1
         triangles[-1][2] = 0
 
-        return SpatialData(
-            Q_(points, "mm").astype("float32"), np.array(triangles, dtype="uint32")
-        )
+        return SpatialData(Q_(points, "mm").astype("float32"), np.array(triangles, dtype="uint32"))
 
     @staticmethod
     def _create_geometry(groove, seam_length, width):

weldx_widgets/widget_factory.py

@@ -66,9 +66,7 @@ class WidgetFloatWithUnit(WidgetMyHBox):
 
     def __init__(self, text, unit, value: float = 0.0, min=0):
         self._label = Label(text, layout=description_layout)
-        self._float = BoundedFloatText(
-            value=value, min=min, max=2**32, layout=textbox_layout
-        )
+        self._float = BoundedFloatText(value=value, min=min, max=2**32, layout=textbox_layout)
         self._unit = Text(value=unit, placeholder="unit", layout=textbox_layout)
 
         super().__init__(