Change behavior for adding Difference Metrics

.github/workflows/pipeline.yml

@@ -5,49 +5,77 @@ on:
     branches:
       - master
       - dev
+      - test_ci
   pull_request:
 
 jobs:
   test-job:
     runs-on: ${{ matrix.os }}
+
     defaults:
       run:
         shell: bash -l {0}
+
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
-        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+        include:
+          - os: windows-latest
+            python-version: "3.12"
+          - os: macos-latest
+            python-version: "3.12"
+
+    env:
+      CONDA_FILE: environment.yml
+
     steps:
-    - uses: actions/checkout@v3
-    - name: Cache conda
-      uses: actions/cache@v3
-      env:
-        # Increase this value to reset cache if etc/example-environment.yml has not changed
-        CACHE_NUMBER: 2
-      with:
-        path: ~/conda_pkgs_dir
-        key:
-          ${{ matrix.os }}-python_${{ matrix.python-version }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('etc/example-environment.yml') }}
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-        miniforge-variant: Mambaforge
-        use-mamba: true
-        auto-update-conda: true
-        channels: conda-forge,
-    - name: Install dependencies
-      run: |
-        mamba install cadet
-        pip install -e ./[testing]
-    - name: Test
-      run: |
-        python -m unittest discover -s tests
-    - name: Install pypa/build
-      run: |
-        python -m pip install build --user
-    - name: Build binary wheel and source tarball
-      run: |
-        python -m build --sdist --wheel --outdir dist/ .
-    - name: Test Wheel install and import
-      run: |
-        python -c "import CADETProcess; print(CADETProcess.__version__)"
+      - uses: actions/checkout@v4
+
+      - name: Get Date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Setup Conda Environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Mambaforge
+          use-mamba: true
+          activate-environment: cadet-process
+          channels: conda-forge,
+
+      - name: Cache conda
+        uses: actions/cache@v3
+        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) }}-${{ env.CACHE_NUMBER }}
+
+      - name: Update environment
+        run: |
+          mamba install python==${{ matrix.python-version }}
+          mamba env update -n cadet-process -f ${{ env.CONDA_FILE }}
+        if: steps.cache.outputs.cache-hit != 'true'
+
+      - name: Install
+        run: |
+          pip install -e ./[testing]
+
+      - name: Test
+        run: |
+          python -m unittest discover -s tests
+
+      - name: Install pypa/build
+        run: |
+          python -m pip install build --user
+
+      - name: Build binary wheel and source tarball
+        run: |
+          python -m build --sdist --wheel --outdir dist/ .
+
+      - name: Test Wheel install and import
+        run: |
+          python -c "import CADETProcess; print(CADETProcess.__version__)"

CADETProcess/__init__.py

@@ -20,6 +20,7 @@
 from .settings import Settings
 settings = Settings()
 
+from . import sysinfo
 from . import dataStructure
 from . import transform
 from . import plotting

CADETProcess/comparison/comparator.py

@@ -1,6 +1,7 @@
 import copy
 import importlib
 import functools
+import warnings
 
 import numpy as np
 import matplotlib.pyplot as plt
@@ -81,6 +82,11 @@ def metrics(self):
         """list: List of difference metrics."""
         return self._metrics
 
+    @property
+    def n_diffference_metrics(self):
+        """int: Number of difference metrics in the Comparator."""
+        return len(self.metrics)
+
     @property
     def n_metrics(self):
         """int: Number of metrics to be evaluated."""
@@ -116,20 +122,19 @@ def labels(self):
 
         return labels
 
-    @functools.wraps(DifferenceBase.__init__)
     def add_difference_metric(
-            self, difference_metric, reference, solution_path,
+            self, difference_metric, solution_path, reference,
             *args, **kwargs):
         """Add a difference metric to the Comparator.
 
         Parameters
         ----------
-        difference_metric : str
-            Name of the difference metric to be evaluated.
-        reference : str or SolutionBase
-            Name of the reference or reference itself.
+        difference_metric : DifferenceMetricBase
+            Difference metric to be evaluated.
         solution_path : str
             Path to the solution in SimulationResults.
+        reference : str or SolutionBase
+            Name of the reference or reference itself.
         *args, **kwargs
             Additional arguments and keyword arguments to be passed to the
             difference metric constructor.
@@ -139,29 +144,36 @@ def add_difference_metric(
         CADETProcessError
             If the difference metric or reference is unknown.
         """
-        try:
-            module = importlib.import_module(
-                'CADETProcess.comparison.difference'
+        if isinstance(difference_metric, str):
+            warnings.warn(
+                'This method of adding difference metrics is deprecated. '
+                'Instead, pass an instance of the desired metric class.',
+                DeprecationWarning, stacklevel=2
             )
-            cls_ = getattr(module, difference_metric)
-        except KeyError:
-            raise CADETProcessError("Unknown Metric Type.")
+            if isinstance(reference, SolutionBase):
+                reference = reference.name
 
-        if isinstance(reference, SolutionBase):
-            reference = reference.name
+            if reference not in self.references:
+                raise CADETProcessError("Unknown Reference.")
 
-        if reference not in self.references:
-            raise CADETProcessError("Unknown Reference.")
-
-        reference = self.references[reference]
-
-        metric = cls_(reference, *args, **kwargs)
+            reference = self.references[reference]
+            try:
+                module = importlib.import_module(
+                    'CADETProcess.comparison.difference'
+                )
+                cls_ = getattr(module, difference_metric)
+                difference_metric = cls_(reference, *args, **kwargs)
+            except KeyError:
+                raise CADETProcessError("Unknown Difference Metric.")
+        else:
+            if not isinstance(difference_metric, DifferenceBase):
+                raise TypeError("Expected DifferenceBase.")
 
-        self.solution_paths[metric] = solution_path
+        self.solution_paths[difference_metric] = solution_path
 
-        self._metrics.append(metric)
+        self._metrics.append(difference_metric)
 
-        return metric
+        return difference_metric
 
     def extract_solution(self, simulation_results, metric):
         """Extract the solution for a given metric from the SimulationResults object.
@@ -233,22 +245,20 @@ def setup_comparison_figure(self, plot_individual=False):
         tuple
             A tuple of the comparison figure(s) and axes object(s).
         """
-        n = len(self.metrics)
-
-        if n == 0:
+        if self.n_diffference_metrics == 0:
             return (None, None)
 
-        comparison_fig_all, comparison_axs_all = plt.subplots(
-            nrows=n,
-            figsize=(8 + 4 + 2, n*8 + 2),
+        comparison_fig_all, comparison_axs_all = plotting.setup_figure(
+            n_rows=self.n_diffference_metrics,
             squeeze=False
         )
+
         plt.close(comparison_fig_all)
         comparison_axs_all = comparison_axs_all.reshape(-1)
 
         comparison_fig_ind = []
         comparison_axs_ind = []
-        for i in range(n):
+        for i in range(self.n_diffference_metrics):
             fig, axs = plt.subplots()
             comparison_fig_ind.append(fig)
             comparison_axs_ind.append(axs)

CADETProcess/comparison/difference.py

@@ -4,7 +4,7 @@
 from warnings import warn
 
 import numpy as np
-from scipy.integrate import simps
+from scipy.integrate import simpson
 from scipy.special import expit
 
 from CADETProcess import CADETProcessError
@@ -177,7 +177,7 @@ def reference(self, reference):
             self._reference.smooth_data()
         reference = slice_solution(
             self._reference,
-            None,
+            self.components,
             self.use_total_concentration,
             self.use_total_concentration_components,
             coordinates={'time': (self.start, self.end)}
@@ -407,10 +407,10 @@ def _evaluate(self, solution):
             Concentration profile of simulation.
 
         """
-        area_ref = simps(
+        area_ref = simpson(
             self.reference.solution, self.reference.time, axis=0
         )
-        area_sol = simps(solution.solution, solution.time, axis=0)
+        area_sol = simpson(solution.solution, solution.time, axis=0)
 
         return abs(area_ref - area_sol)
 
@@ -427,10 +427,10 @@ def _evaluate(self, solution):
             Concentration profile of simulation.
 
         """
-        area_ref = simps(
-            self.reference.solution, self.reference.time, axis=0
+        area_ref = simpson(
+            self.reference.solution, x=self.reference.time, axis=0
         )
-        area_new = simps(solution.solution, solution.time, axis=0)
+        area_new = simpson(solution.solution, x=solution.time, axis=0)
 
         return abs(area_ref - area_new)/area_ref
 

CADETProcess/dataStructure/parameter.py

@@ -42,7 +42,7 @@ class ParameterBase(Descriptor):
     Tuple
     Float
     String
-    Dict
+    Dictionary
     """
 
     def __init__(
@@ -378,7 +378,7 @@ class Typed(ParameterBase):
     Tuple
     Float
     String
-    Dict
+    Dictionary
     """
 
     def __init__(self, *args, ty=None, **kwargs):
@@ -568,15 +568,8 @@ class List(Typed):
     ty = list
 
 
-class Dict(Typed):
-    """
-    Parameter descriptor constrained to dictionary (`dict`) values.
-
-    Notes
-    -----
-    When integrating with libraries like `addict`, be cautious about potential
-    name collisions with `addict.Dict`.
-    """
+class Dictionary(Typed):
+    """Parameter descriptor constrained to dictionary (`dict`) values."""
 
     ty = dict
 
@@ -1036,10 +1029,10 @@ def check_size(self, instance, value):
             return
 
         size = self.get_size(value)
-        exptected_size = self.get_expected_size(instance)
+        expected_size = self.get_expected_size(instance)
 
-        if size != exptected_size:
-            raise ValueError(f"Expected size {exptected_size}")
+        if size != expected_size:
+            raise ValueError(f"Expected size {expected_size}")
 
     def _prepare(self, instance, value, recursive=False):
         """
@@ -1529,7 +1522,7 @@ def fill_values(self, dims, value):
             raise ValueError("Can only set single entry if n_entries == 1.")
 
         if isinstance(value, np.ndarray) and value.size == 1:
-            value = float(value)
+            value = float(value.squeeze())
 
         if isinstance(value, (int, float)):
             value = n_entries * [value]
@@ -1650,12 +1643,17 @@ def check_mod_value(self, instance, value):
             If the modulo condition of the size does not meet the expected criteria.
         """
         size = self.get_size(value)
-        exptected_size = self.get_expected_size(instance)
+        expected_size = self.get_expected_size(instance)
 
-        size %= exptected_size
+        size %= expected_size
 
         if size != 0:
-            raise ValueError("Size mod exptected size is not 0")
+            raise ValueError(
+                f"The size of the value modulo the expected size is not zero. "
+                f"Size: {size}, Expected Size: {expected_size}"
+            )
+
+    check_size = check_mod_value
 
 
 class DependentlyModulatedUnsignedList(UnsignedList, SizedList, DependentlyModulated):