V0.10.0

.github/PULL_REQUEST_TEMPLATE/release.md

@@ -0,0 +1,16 @@
+## Workflow to release a new version `vX.Y.Z`
+
+- [ ] Create new branch `vX.Y.Z` from `dev`
+- [ ] Bump version in `setup.cfg` and `CADETProcess/__init__.py`
+- [ ] Add release notes
+  - [ ] General description
+  - [ ] Deprecations / other changes
+  - [ ] Closed Issues/PRs
+  - [ ] Add entry in `index.md`
+- [ ] Commit with message `vX.Y.Z`
+- [ ] Add tag (`git tag 'vX.Y.Z'`)
+- [ ] Push and open PR (base onto `master`). Also push tag: `git push origin --tag`
+- [ ] When ready, rebase again onto `dev` (in case changes were made)
+- [ ] Merge into master
+- [ ] Make release on GitHub using tag and release notes.
+- [ ] Check that workflows automatically publish to PyPI and readthedocs

.github/workflows/pipeline.yml

@@ -21,9 +21,9 @@ jobs:
         os: [ubuntu-latest]
         python-version: ["3.10", "3.11", "3.12"]
         include:
-          - os: windows-latest
-            python-version: "3.12"
-          - os: macos-12
+          # - os: windows-latest
+          #   python-version: "3.12"
+          - os: macos-13
             python-version: "3.12"
 
     env:
@@ -40,7 +40,6 @@ jobs:
       - name: Setup Conda Environment
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           miniforge-version: latest
           use-mamba: true
           activate-environment: cadet-process

.zenodo.json

@@ -0,0 +1,46 @@
+{
+    "title": "CADET-Process v0.10.0",
+    "upload_type": "software",
+    "creators": [
+        {
+            "name": "Schmölder, Johannes",
+            "orcid": "0000-0003-0446-7209",
+            "affiliation": "Forschungszentrum Jülich"
+        },
+        {
+            "name": "Jäpel, Ronald",
+            "orcid": "0000-0002-4912-5176",
+            "affiliation": "Forschungszentrum Jülich"
+        },
+        {
+            "name": "Schunck, Florian",
+            "orcid": "0000-0001-7245-953X",
+            "affiliation": "Forschungszentrum Jülich"
+        },
+        {
+            "name": "Klauß, Daniel",
+            "orcid": "0009-0005-2022-7776",
+            "affiliation": "Forschungszentrum Jülich"
+        },
+        {
+            "name": "Lanzrath, Hannah",
+            "orcid": "0000-0002-2675-9002",
+            "affiliation": "Forschungszentrum Jülich"
+        }
+    ],
+    "license": "GPL-3.0",
+    "keywords": [
+        "modeling",
+        "simulation",
+        "biotechnology",
+        "process",
+        "chromatography",
+        "CADET",
+        "general rate model",
+        "Python"
+    ],
+    "version": "0.10.0",
+    "access_right": "open",
+    "communities": [{"identifier": "open-source"}],
+    "doi": "10.5281/zenodo.14202878"
+}

CADETProcess/__init__.py

@@ -10,7 +10,7 @@
 """
 # Version information
 name = "CADET-Process"
-__version__ = "0.9.1"
+__version__ = "0.10.0"
 
 # Imports
 from .CADETProcessError import *

CADETProcess/comparison/comparator.py

@@ -84,7 +84,7 @@ def metrics(self):
         return self._metrics
 
     @property
-    def n_diffference_metrics(self):
+    def n_difference_metrics(self):
         """int: Number of difference metrics in the Comparator."""
         return len(self.metrics)
 
@@ -242,11 +242,11 @@ def setup_comparison_figure(
         tuple
             A tuple of the comparison figure(s) and axes object(s).
         """
-        if self.n_diffference_metrics == 0:
+        if self.n_difference_metrics == 0:
             return (None, None)
 
         comparison_fig_all, comparison_axs_all = plotting.setup_figure(
-            n_rows=self.n_diffference_metrics,
+            n_rows=self.n_difference_metrics,
             squeeze=False
         )
 
@@ -255,7 +255,7 @@ def setup_comparison_figure(
 
         comparison_fig_ind: list[Figure] = []
         comparison_axs_ind: list[Axes] = []
-        for i in range(self.n_diffference_metrics):
+        for i in range(self.n_difference_metrics):
             fig, axs = plt.subplots()
             comparison_fig_ind.append(fig)
             comparison_axs_ind.append(axs)
@@ -271,33 +271,33 @@ def setup_comparison_figure(
 
     def plot_comparison(
             self,
-            simulation_results: list[SimulationResults],
+            simulation_results: SimulationResults,
             axs: Axes | list[Axes] | None = None,
             figs: Figure | list[Figure] | None = None,
             file_name: str | None = None,
             show: bool = True,
             plot_individual: bool = False,
-            use_minutes: bool = True,
+            x_axis_in_minutes: bool = True,
             ) -> tuple[list[Figure], list[Axes]]:
         """
         Plot the comparison of the simulation results with the reference data.
 
         Parameters
         ----------
-        simulation_results : list of SimulationResults
-            List of simulation results to compare to reference data.
-        axs : list of AxesSubplot, optional
+        simulation_results : SimulationResults
+            Simulation results to compare to reference data.
+        axs : list of Axes, optional
             List of subplot axes to use for plotting the metrics.
-        figs : list of Figure, optional
+        figs : list of Figures, optional
             List of figures to use for plotting the metrics.
         file_name : str, optional
             Name of the file to save the figure to.
         show : bool, optional
             If True, displays the figure(s) on the screen.
         plot_individual : bool, optional
             If True, generates a separate figure for each metric.
-        use_minutes : bool, optional
-            Option to use x-aches (time) in minutes, default is set to True.
+        x_axis_in_minutes: bool, optional
+            If True, the x-axis will be plotted using minutes. The default is True.
 
         Returns
         -------
@@ -331,7 +331,7 @@ def plot_comparison(
                 'label': 'reference',
             }
             ref_time = metric.reference.time
-            if use_minutes:
+            if x_axis_in_minutes:
                 ref_time = ref_time / 60
 
             plotting.add_overlay(ax, metric.reference.solution, ref_time, **plot_args)