Merge branch 'master' into feat/tags

.github/dependabot/constraints.txt

@@ -1,18 +1,18 @@
 EXtra-data==1.18.0
-ipython==8.29.0
+ipython==8.30.0
 kafka-python==2.0.2
-matplotlib==3.9.2
+matplotlib==3.10.0
 mplcursors==0.6
 mpl-pan-zoom==1.0.0
-numpy==2.1.3
+numpy==2.2.0
 openpyxl==3.1.5
 pandas==2.2.3
 pyflakes==3.2.0
 PyQt5==5.15.11
-pytest==8.3.3
+pytest==8.3.4
 pytest-qt==4.4.0
 pytest-xvfb==3.0.0
 QScintilla==2.13.0
 supervisor==4.2.5
 termcolor==2.5.0
-xarray==2024.10.0
+xarray==2024.11.0

damnit/ctxsupport/ctxrunner.py

@@ -415,7 +415,11 @@ def generate_thumbnail(image):
     fig.subplots_adjust(left=0, right=1, bottom=0, top=1)
     vmin = np.nanquantile(image, 0.01)
     vmax = np.nanquantile(image, 0.99)
-    ax.imshow(image, vmin=vmin, vmax=vmax, extent=(0, 1, 1, 0))
+    if isinstance(image, np.ndarray):
+        ax.imshow(image, vmin=vmin, vmax=vmax)
+    else:
+        # Use DataArray's own plotting method
+        image.plot(ax=ax, vmin=vmin, vmax=vmax, add_colorbar=False)
     ax.axis('tight')
     ax.axis('off')
     ax.margins(0, 0)
@@ -519,7 +523,12 @@ def summarise(self, name):
             if data.ndim == 0:
                 return data
             elif data.ndim == 2:
-                return generate_thumbnail(np.nan_to_num(data))
+                if isinstance(data, np.ndarray):
+                    data = np.nan_to_num(data)
+                else:
+                    data = data.fillna(0)
+
+                return generate_thumbnail(data)
             else:
                 return f"{data.dtype}: {data.shape}"
 

damnit/gui/editor.py

@@ -1,4 +1,5 @@
 import sys
+import traceback
 from enum import Enum
 from io import StringIO
 from pathlib import Path
@@ -26,12 +27,17 @@ class ContextFileCheckerThread(QThread):
     # ContextTestResult, traceback, lineno, offset, checked_code
     check_result = pyqtSignal(object, str, int, int, str)
 
-    def __init__(self, code, db_dir, context_python, parent=None):
+    def __init__(self, code, db_dir, context_python, context_getter, parent=None):
         super().__init__(parent)
         self.code = code
         self.db_dir = db_dir
         self.context_python = context_python
 
+        # This is a hack to allow us to test throwing an exception when checking
+        # the context file. It'll always be get_context_file() except when
+        # replaced with a Mock by the tests.
+        self.context_getter = context_getter
+
     def run(self):
         error_info = None
 
@@ -51,7 +57,16 @@ def run(self):
                 ctx_path = Path(ctx_file.name)
                 ctx_path.write_text(self.code)
 
-                ctx, error_info = get_context_file(ctx_path, self.context_python)
+                try:
+                    ctx, error_info = self.context_getter(ctx_path, self.context_python)
+                except:
+                    # Not a failure to evalute the context file, but a failure
+                    # to *attempt* to evaluate the context file (e.g. because of
+                    # a missing dependency).
+                    help_msg = "# This is a partial error, please check the terminal for the full error message and ask for help from DA or the DOC."
+                    traceback_str = f"{help_msg}\n\n{traceback.format_exc()}"
+                    self.check_result.emit(ContextTestResult.ERROR, traceback_str, 0, 0, self.code)
+                    return
 
         if error_info is not None:
             stacktrace, lineno, offset = error_info
@@ -110,7 +125,7 @@ def __init__(self):
 
     def launch_test_context(self, db):
         context_python = db.metameta.get("context_python")
-        thread = ContextFileCheckerThread(self.text(), db.path.parent, context_python, parent=self)
+        thread = ContextFileCheckerThread(self.text(), db.path.parent, context_python, get_context_file, parent=self)
         thread.check_result.connect(self.on_test_result)
         thread.finished.connect(thread.deleteLater)
         thread.start()

docs/changelog.md

@@ -5,6 +5,9 @@
 Fixed:
 
 - Added back grid lines for plots of `DataArray`'s (!334).
+- Fixed thumbnails of 2D `DataArray`'s to match what is displayed when the
+  variable is plotted (!355).
+- Fixed crashes when the context file environment is missing dependencies (!356).
 
 ## [0.1.4]
 

tests/test_backend.py

@@ -325,13 +325,18 @@ def foo(run): return xr.DataArray([1, 2, 3])
 
     figure_code = """
     import numpy as np
+    import xarray as xr
     from damnit_ctx import Variable
     from matplotlib import pyplot as plt
 
-    @Variable("2D array")
+    @Variable("2D ndarray")
     def twodarray(run):
         return np.random.rand(1000, 1000)
 
+    @Variable("2D xarray")
+    def twodxarray(run):
+        return xr.DataArray(np.random.rand(100, 100))
+
     @Variable(title="Axes")
     def axes(run):
         _, ax = plt.subplots()
@@ -359,8 +364,9 @@ def figure(run):
         assert f["axes/data"].ndim == 3
 
         # Test that the summaries are the right size
-        twodarray_png = Image.open(io.BytesIO(f[".reduced/twodarray"][()]))
-        assert np.asarray(twodarray_png).shape == (THUMBNAIL_SIZE, THUMBNAIL_SIZE, 4)
+        for var in ["twodarray", "twodxarray"]:
+            png = Image.open(io.BytesIO(f[f".reduced/{var}"][()]))
+            assert np.asarray(png).shape == (THUMBNAIL_SIZE, THUMBNAIL_SIZE, 4)
 
         figure_png = Image.open(io.BytesIO(f[".reduced/figure"][()]))
         assert max(np.asarray(figure_png).shape) == THUMBNAIL_SIZE

tests/test_gui.py

@@ -1,5 +1,6 @@
 import os
 import re
+import sys
 import textwrap
 from contextlib import contextmanager
 from pathlib import Path
@@ -151,6 +152,15 @@ def test_editor(mock_db, mock_ctx, qtbot):
         win.save_context()
     assert ctx_path.read_text() == warning_code
 
+    # Throwing an exception when evaluating the context file in a different
+    # environment should be handled gracefully. This can happen if running the
+    # ctxrunner itself fails, e.g. because of a missing dependency.
+    db.metameta["context_python"] = sys.executable
+    with qtbot.waitSignal(editor.check_result) as sig, \
+         patch("damnit.gui.editor.get_context_file", side_effect=Exception("foo")):
+        editor.launch_test_context(db)
+    assert sig.args[0] == ContextTestResult.ERROR
+
 def test_settings(mock_db_with_data, mock_ctx, tmp_path, monkeypatch, qtbot):
     db_dir, db = mock_db_with_data
     monkeypatch.chdir(db_dir)