Add timeout to solver options

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/coverage.yml

@@ -0,0 +1,76 @@
+name: coverage
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+      - 144-monitor-test-coverage
+  workflow_dispatch:
+      inputs:
+        slow:
+          type: boolean
+          description: Run with slow tests
+          default: false
+
+jobs:
+  coverage-job:
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.12"]
+
+    env:
+      CONDA_FILE: environment.yml
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get Date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Setup Conda Environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          use-mamba: true
+          activate-environment: cadet-process
+          channels: conda-forge,
+
+      - name: Cache conda
+        uses: actions/cache@v4
+        env:
+          # Increase this value to reset cache if environment.yml has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ${{ env.CONDA }}/envs
+          key: ${{ matrix.os }}-python_${{ matrix.python-version }}-${{ steps.get-date.outputs.today }}-${{ hashFiles(env.CONDA_FILE) }}-${{ env.CACHE_NUMBER }}
+
+      - name: Update environment
+        run: |
+          mamba install "setuptools>=69" "pip>=24"
+          mamba install python=${{ matrix.python-version }}
+          echo "python=${{ matrix.python-version }}.*" > $CONDA_PREFIX/conda-meta/pinned
+          mamba env update -n cadet-process -f ${{ env.CONDA_FILE }}
+        if: steps.cache.outputs.cache-hit != 'true'
+
+      - name: Install
+        run: |
+          pip install -e ./[testing,coverage]
+
+        # Push event doesn't have input context => inputs.notslows is empty => false
+      - name: Coverage Run
+        run: |
+          if [ ${{ github.event.inputs.slow }} ]; then
+            pytest --cov=./CADETProcess --cov=./tests --cov-report term-missing tests
+          else
+            pytest -m "not slow" --cov=./CADETProcess --cov=./tests --cov-report term-missing tests
+          fi

.github/workflows/pipeline.yml

@@ -21,8 +21,8 @@ jobs:
         os: [ubuntu-latest]
         python-version: ["3.10", "3.11", "3.12"]
         include:
-          # - os: windows-latest
-          #   python-version: "3.12"
+          - os: windows-latest
+            python-version: "3.12"
           - os: macos-13
             python-version: "3.12"
 
@@ -41,9 +41,8 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
-          use-mamba: true
           activate-environment: cadet-process
-          channels: conda-forge,
+          channels: conda-forge
 
       - name: Cache conda
         uses: actions/cache@v4
@@ -53,31 +52,32 @@ jobs:
         with:
           path: ${{ env.CONDA }}/envs
           key: ${{ matrix.os }}-python_${{ matrix.python-version }}-${{ steps.get-date.outputs.today }}-${{ hashFiles(env.CONDA_FILE) }}-${{ env.CACHE_NUMBER }}
+        id: cache
 
       - name: Update environment
         run: |
-          mamba install "setuptools>=69" "pip>=24"
-          mamba install python=${{ matrix.python-version }}
+          conda install "setuptools>=69" "pip>=24"
+          conda install python=${{ matrix.python-version }}
           echo "python=${{ matrix.python-version }}.*" > $CONDA_PREFIX/conda-meta/pinned
-          mamba env update -n cadet-process -f ${{ env.CONDA_FILE }}
+          conda env update -n cadet-process -f ${{ env.CONDA_FILE }}
         if: steps.cache.outputs.cache-hit != 'true'
 
       - name: Install
         run: |
-          pip install -e ./[testing]
+          conda run pip install -e ./[testing]
 
       - name: Test
         run: |
-          python -m unittest discover -s tests
+          pytest tests -m "not slow" --durations=0
 
       - name: Install pypa/build
         run: |
-          python -m pip install build --user
+          conda run python -m pip install build --user
 
       - name: Build binary wheel and source tarball
         run: |
-          python -m build --sdist --wheel --outdir dist/ .
+          conda run python -m build --sdist --wheel --outdir dist/ .
 
       - name: Test Wheel install and import
         run: |
-          python -c "import CADETProcess; print(CADETProcess.__version__)"
+          conda run python -c "import CADETProcess; print(CADETProcess.__version__)"

CADETProcess/__init__.py

@@ -22,6 +22,7 @@
 settings = Settings()
 
 from . import sysinfo
+from . import numerics
 from . import dataStructure
 from . import transform
 from . import plotting

CADETProcess/comparison/comparator.py

@@ -13,6 +13,7 @@
 from CADETProcess.dataStructure import get_nested_value
 from CADETProcess.solution import SolutionBase
 from CADETProcess.comparison import DifferenceBase
+from CADETProcess.numerics import round_to_significant_digits
 
 
 class Comparator(Structure):
@@ -319,10 +320,14 @@ def plot_comparison(
                 solution.smooth_data()
             solution_sliced = metric.slice_and_transform(solution)
 
+            y_max = 1.1 * max(
+                np.max(solution_sliced.solution), np.max(metric.reference.solution)
+            )
+
             fig, ax = solution_sliced.plot(
                 ax=ax,
                 show=False,
-                y_max=1.1*np.max(metric.reference.solution)
+                y_max=y_max,
             )
 
             plot_args = {
@@ -338,12 +343,7 @@ def plot_comparison(
             ax.legend(loc=1)
 
             m = metric.evaluate(solution_sliced, slice=False)
-            m = [
-                np.format_float_scientific(
-                    n, precision=2,
-                )
-                for n in m
-            ]
+            m = round_to_significant_digits(m, digits=2)
 
             text = f"{metric}: "
             if metric.n_metrics > 1:
@@ -356,7 +356,7 @@ def plot_comparison(
                 except AttributeError:
                     text += f"{m}"
             else:
-                text += m[0]
+                text += str(m[0])
 
             plotting.add_text(ax, text, fontsize=14)
 

CADETProcess/comparison/difference.py

@@ -1,7 +1,6 @@
 from abc import abstractmethod
 import copy
 from functools import wraps
-from warnings import warn
 
 import numpy as np
 from scipy.integrate import simpson
@@ -29,14 +28,6 @@
 ]
 
 
-def squishify(*args, **kwargs):
-    warn(
-        'This function is deprecated, use sigmoid_distance.',
-        DeprecationWarning, stacklevel=2
-    )
-    return sigmoid_distance(*args, **kwargs)
-
-
 def sigmoid_distance(measurement, target, normalization=1):
     """Calculate the distance between two values using a sigmoid function.
 
@@ -495,8 +486,9 @@ class Shape(DifferenceBase):
     @wraps(DifferenceBase.__init__)
     def __init__(
             self, *args,
-            use_derivative=True, normalize_metrics=True, normalization_factor=None,
-            include_height=True,
+            use_derivative=True,
+            normalize_metrics=True,
+            normalization_factor=None,
             **kwargs):
         """Initialize Shape metric.
 
@@ -514,10 +506,6 @@ def __init__(
         normalization_factor : float, optional
             Normalization factor used by the sigmoid function.
             Default is None, which sets it to 1/10 of the simulation time.
-        include_height : bool, optional
-            If True, also return a metric for the height difference.
-            If `use_derivative` is also true, also return height differences
-            for the derivatives.
         **kwargs : dict
             Keyword arguments passed to the base class constructor.
 
@@ -532,13 +520,6 @@ def __init__(
                     "Shape currently only supports single component."
                 )
 
-        self.include_height = include_height
-        if include_height:
-            warn("Peak height will be removed from the Shape difference metric.", DeprecationWarning)
-            self.peak_height = PeakHeight(
-                *args, normalize=False, normalize_metrics=normalize_metrics, **kwargs
-            )
-
         self.use_derivative = use_derivative
         if use_derivative:
             self.reference_der = self.reference.derivative
@@ -555,17 +536,6 @@ def __init__(
                 coordinates={'time': (self.start, self.end)}
             )
 
-            self.peak_der_min = PeakHeight(
-                self.reference_der, *args[1:], normalize=False,
-                find_minima=True, normalize_metrics=normalize_metrics,
-                **kwargs
-            )
-            self.peak_der_max = PeakHeight(
-                self.reference_der, *args[1:], normalize=False,
-                find_minima=False, normalize_metrics=normalize_metrics,
-                **kwargs
-            )
-
         self.normalize_metrics = normalize_metrics
         if normalization_factor is None:
             normalization_factor = self.reference.time[-1]/10
@@ -575,29 +545,16 @@ def __init__(
     def n_metrics(self):
         n_metrics = 2
 
-        if self.include_height:
-            n_metrics += 1
-
         if self.use_derivative:
             n_metrics += 1
 
-            if self.include_height:
-                n_metrics += 2
-
         return n_metrics
 
     @property
     def labels(self):
         labels = ['Pearson Correleation', 'Time offset']
-        if self.include_height:
-            labels += ["Peak Height"]
         if self.use_derivative:
             labels += ['Pearson Correlation Derivative']
-            if self.include_height:
-                labels += [
-                    'Peak Minimum Derivative',
-                    'Peak Maximum Derivative'
-                ]
         return labels
 
     def _evaluate(self, solution):
@@ -615,9 +572,6 @@ def _evaluate(self, solution):
             solution.solution_interpolated.solutions[0],
         )
 
-        if self.include_height:
-            peak_height = self.peak_height(solution, slice=False)
-
         if self.normalize_metrics:
             offset = sigmoid_distance(
                 offset_original, target=0, normalization=self.normalization_factor
@@ -626,10 +580,7 @@ def _evaluate(self, solution):
             offset = np.abs(offset_original)
 
         if not self.use_derivative:
-            if self.include_height:
-                return np.array([corr, offset, peak_height[0]])
-            elif not self.include_height:
-                return np.array([corr, offset])
+            return np.array([corr, offset])
 
         solution_der = solution.derivative
         solution_der_sliced = self.slice_and_transform(solution_der)
@@ -641,23 +592,12 @@ def _evaluate(self, solution):
             offset_original,
         )
 
-        der_min = self.peak_der_min(solution_der_sliced, slice=False)
-        der_max = self.peak_der_max(solution_der_sliced, slice=False)
-
-        if self.include_height:
-            return np.array(
-                [
-                    corr, offset, peak_height[0],
-                    corr_der, der_min[0], der_max[0]
-                ]
-            )
-        elif not self.include_height:
-            return np.array(
-                [
-                    corr, offset,
-                    corr_der,
-                ]
-            )
+        return np.array(
+            [
+                corr, offset,
+                corr_der,
+            ]
+        )
 
 
 class PeakHeight(DifferenceBase):

CADETProcess/dataStructure/__init__.py

@@ -41,3 +41,4 @@
 from .cache import *
 from .diskcache import *
 from .nested_dict import *
+from .deprecation import *