Merge remote-tracking branch 'origin/develop' into bugfix/fix-single-smooth

Author: SBlokhuizen

.github/workflows/ci.yml

@@ -83,3 +83,4 @@ jobs:
       with:
         name: html-docs
         path: docs/_build/html/
+        retention-days: 1

tests/tendencies/periodic/test_sine_wave.py

@@ -52,7 +52,7 @@ def test_generate():
         user_start=0, user_duration=1, user_base=2, user_amplitude=3, user_phase=1
     )
     time, values = tendency.get_value()
-    assert np.all(time == np.linspace(0, 1, 101))
+    assert np.all(time == np.linspace(0, 1, 32 + 1))
     assert np.allclose(values, 2 + 3 * np.sin(2 * np.pi * time + 1))
     assert not tendency.annotations
 

tests/tendencies/test_repeat.py

@@ -166,3 +166,12 @@ def test_filled(repeat_waveform):
     assert tendencies[2].base == 2
     assert tendencies[2].amplitude == -1
     assert tendencies[2].frequency == 0.25
+
+
+def test_too_short(repeat_waveform):
+    """Check for warning in annotations if repeated waveform has not completed a
+    single repetition."""
+    repeat_waveform["user_duration"] = 2
+    repeat_tendency = RepeatTendency(**repeat_waveform)
+    assert repeat_tendency.annotations
+    assert repeat_tendency.annotations[0]["type"] == "warning"

tests/test_yaml_parser.py

@@ -91,3 +91,30 @@ def assert_tendencies_correct(tendencies):
     assert tendencies[6].duration == approx(2)
     assert tendencies[6].from_ == approx(8)
     assert tendencies[6].to == approx(0)
+
+
+def test_scientific_notation():
+    """Test if scientific notation is parsed correctly."""
+    waveforms = {
+        "waveform:\n- {type: linear, to: 1.5e5}": 1.5e5,
+        "waveform:\n- {type: linear, to: 1.5e+5}": 1.5e5,
+        "waveform:\n- {type: linear, to: 1.5E+5}": 1.5e5,
+        "waveform:\n- {type: linear, to: 1.5e-5}": 1.5e-5,
+        "waveform:\n- {type: linear, to: 1.5E-5}": 1.5e-5,
+        "waveform:\n- {type: linear, to: 1e5}": 1e5,
+        "waveform:\n- {type: linear, to: 1e+5}": 1e5,
+        "waveform:\n- {type: linear, to: 1E+5}": 1e5,
+        "waveform:\n- {type: linear, to: 1e-5}": 1e-5,
+        "waveform:\n- {type: linear, to: 1E-5}": 1e-5,
+        "waveform:\n- {type: linear, to: 0e5}": 0.0,
+        "waveform:\n- {type: linear, to: 0E0}": 0.0,
+        "waveform:\n- {type: linear, to: -1.5e5}": -1.5e5,
+        "waveform:\n- {type: linear, to: -1E+5}": -1e5,
+        "waveform:\n- {type: linear, to: -1.5e-5}": -1.5e-5,
+    }
+
+    yaml_parser = YamlParser()
+
+    for waveform, expected_value in waveforms.items():
+        yaml_parser.parse_waveforms(waveform)
+        assert yaml_parser.waveform.tendencies[0].to == expected_value

waveform_editor/annotations.py

@@ -3,6 +3,12 @@
 
 
 class Annotations(UserList):
+    def __str__(self):
+        sorted_annotations = sorted(self, key=lambda ann: ann["row"])
+        return "\n".join(
+            f"Line {a['row'] + 1}: {a['text']}" for a in sorted_annotations
+        )
+
     def add_annotations(self, annotations):
         """Merge another Annotations instance into this instance by appending its
         annotations.

waveform_editor/tendencies/base.py

@@ -87,16 +87,26 @@ def __init__(self, **kwargs):
         super().__init__()
         with param.parameterized.batch_call_watchers(self):
             for param_name, value in kwargs.items():
+                if param_name not in self.param:
+                    unknown_kwargs.append(param_name.replace("user_", ""))
+                    continue
+
                 if value is None:
                     self.annotations.add(
                         self.line_number,
                         f"The value of {param_name.replace('user_', '')!r} cannot be "
                         "empty.\nIt will be set to its default value.\n",
                         is_warning=True,
                     )
+                    continue
 
-                if param_name not in self.param:
-                    unknown_kwargs.append(param_name.replace("user_", ""))
+                if isinstance(value, (int, float)) and not np.isfinite(value):
+                    self.annotations.add(
+                        self.line_number,
+                        f"The value for {param_name.replace('user_', '')!r} is not a "
+                        "valid number.\nIt will be set to its default value.\n",
+                        is_warning=True,
+                    )
                     continue
 
                 try:
@@ -132,6 +142,14 @@ def _handle_unknown_kwargs(self, unknown_kwargs):
             word.replace("user_", "") for word in self.param if "user_" in word
         ]
         for unknown_kwarg in unknown_kwargs:
+            if ":" in unknown_kwarg:
+                error_msg = (
+                    f"Found ':' in {unknown_kwarg!r}. "
+                    "Did you forget a space after the ':'?\n"
+                )
+                self.annotations.add(self.line_number, error_msg, is_warning=True)
+                continue
+
             suggestion = self.annotations.suggest(unknown_kwarg, params_list)
             error_msg = (
                 f"Unknown keyword passed: {unknown_kwarg!r}. {suggestion}"

waveform_editor/tendencies/linear.py

@@ -124,8 +124,8 @@ def _calc_values(self):
             values = solve_with_constraints(inputs, constraint_matrix)
         except InconsistentInputsError:
             error_msg = (
-                "Inputs are inconsistent: from + duration * rate != end\n"
-                "The 'from', 'to', and 'rate' values are set to 0.\n"
+                "Inputs are inconsistent: from + duration * rate != to\n"
+                "The 'from', 'to', and 'rate' values will be set to 0.\n"
             )
             self.annotations.add(self.line_number, error_msg, is_warning=True)
             values = (0.0, 0.0, 0.0)

waveform_editor/tendencies/periodic/sine_wave.py

@@ -22,8 +22,10 @@ def get_value(
             Tuple containing the time and its tendency values.
         """
         if time is None:
-            sampling_rate = 100
+            sampling_rate = 32 * self.frequency
             num_steps = int(self.duration * sampling_rate) + 1
+            # Choosing prime number instead of 100k to reduce aliasing artifacts
+            num_steps = min(num_steps, 100003)
             time = np.linspace(float(self.start), float(self.end), num_steps)
         values = self._calc_sine(time)
         return time, values

waveform_editor/tendencies/piecewise.py

@@ -20,12 +20,18 @@ class PiecewiseLinearTendency(BaseTendency):
     )
 
     def __init__(self, user_time=None, user_value=None, **kwargs):
-        user_start, user_end = self._handle_user_time(user_time)
-        annotations = self._remove_user_time_params(kwargs)
-
-        super().__init__(user_start=user_start, user_end=user_end, **kwargs)
-        self.annotations.add_annotations(annotations)
-        self._validate_time_value(user_time, user_value)
+        self.pre_check_annotations = Annotations()
+        self.line_number = kwargs.get("line_number", 0)
+        time, value = self._validate_time_value(user_time, user_value)
+        self._remove_user_time_params(kwargs)
+        super().__init__(
+            user_start=time[0],
+            user_end=time[-1],
+            time=time,
+            value=value,
+            **kwargs,
+        )
+        self.annotations.add_annotations(self.pre_check_annotations)
 
         self.start_value_set = True
         self.param.update(values_changed=True)
@@ -76,37 +82,42 @@ def _validate_time_value(self, time, value):
         Args:
             time: List of time values.
             value: List of values defined on each time step.
+
+        Returns:
+            Tuple containing the validated time and value arrays. If any errors are
+            encountered during the validation, the self.time and self.value defaults are
+            returned instead.
         """
         if time is None or value is None:
             error_msg = "Both the `time` and `value` arrays must be specified.\n"
-            self.annotations.add(self.line_number, error_msg)
+            self.pre_check_annotations.add(self.line_number, error_msg)
         elif len(time) != len(value):
             error_msg = (
                 "The provided time and value arrays are not of the same length.\n"
             )
-            self.annotations.add(self.line_number, error_msg)
+            self.pre_check_annotations.add(self.line_number, error_msg)
         elif len(time) < 2:
             error_msg = (
                 "The provided time and value arrays should have a length "
                 "of at least 2.\n"
             )
+            self.pre_check_annotations.add(self.line_number, error_msg)
 
-            self.annotations.add(self.line_number, error_msg)
-        else:
+        try:
+            time = np.asarray_chkfinite(time, dtype=float)
+            value = np.asarray_chkfinite(value, dtype=float)
             is_monotonic = np.all(np.diff(time) > 0)
             if not is_monotonic:
                 error_msg = "The provided time array is not monotonically increasing.\n"
-                self.annotations.add(self.line_number, error_msg)
-
-        try:
-            time = np.asarray(time, dtype=float)
-            value = np.asarray(value, dtype=float)
+                self.pre_check_annotations.add(self.line_number, error_msg)
         except Exception as error:
-            self.annotations.add(self.line_number, str(error))
-        # Only update the time and value arrays if there are no errors
-        if not self.annotations:
-            self.time = np.array(time)
-            self.value = np.array(value)
+            self.pre_check_annotations.add(self.line_number, str(error))
+
+        # If there are any errors, use the default values instead
+        if not self.pre_check_annotations:
+            return time, value
+        else:
+            return self.time, self.value
 
     def _remove_user_time_params(self, kwargs):
         """Remove user_start, user_duration, and user_end if they are passed as kwargs,
@@ -115,37 +126,13 @@ def _remove_user_time_params(self, kwargs):
 
         Args:
             kwargs: the keyword arguments.
-
-        Returns:
-            annotations containing the errors, or an empty annotations object.
         """
         line_number = kwargs.get("user_line_number", 0)
-        annotations = Annotations()
 
-        error_msg = "is not allowed in a piecewise tendency\nIt will be ignored.\n"
+        error_msg = "is not allowed in a piecewise tendency\n"
         for key in ["user_start", "user_duration", "user_end"]:
             if key in kwargs:
                 kwargs.pop(key)
-                annotations.add(
+                self.pre_check_annotations.add(
                     line_number, f"'{key.replace('user_', '')}' {error_msg}"
                 )
-
-        return annotations
-
-    def _handle_user_time(self, user_time):
-        """Get the start and end of the time array.
-
-        Args:
-            user_time: Time array provided by the user.
-        """
-        if (
-            user_time is not None
-            and len(user_time) > 1
-            and (user_time[-1] - user_time[0]) > 0
-        ):
-            user_start = user_time[0]
-            user_end = user_time[-1]
-        else:
-            user_start = self.time[0]
-            user_end = self.time[-1]
-        return user_start, user_end

waveform_editor/tendencies/repeat.py

@@ -18,14 +18,21 @@ def __init__(self, **kwargs):
 
         self.waveform = Waveform(waveform=waveform, is_repeated=True)
         if not self.waveform.tendencies:
-            error_msg = "There are no tendencies in the repeated waveform."
+            error_msg = "There are no tendencies in the repeated waveform.\n"
             self.annotations.add(self.line_number, error_msg)
             return
 
         if self.waveform.tendencies[0].start != 0:
-            error_msg = "The starting point of the first repeated must be set to 0."
+            error_msg = "The starting point of the first repeated must be set to 0.\n"
             self.annotations.add(self.line_number, error_msg)
 
+        if self.duration < self.waveform.tendencies[-1].end:
+            error_msg = (
+                "The repeated tendency has not completed a single repetition.\n"
+                "Perhaps increase the duration of the repeated tendency?\n"
+            )
+            self.annotations.add(self.line_number, error_msg, is_warning=True)
+
         # Link the last tendency to the first tendency in the repeated waveform
         # We must lock the start to 0, otherwise it will take the start value of the
         # previous tendency.