sbmlsim 0.7.0__tar.gz → 0.7.2__tar.gz

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.7.0"
+current_version = "0.7.2"
 commit = true
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/.github/workflows/ci-cd.yml

@@ -120,6 +120,14 @@ jobs:
     - uses: actions/checkout@v7
       with:
         persist-credentials: false
+    - name: Install the python dev files
+      # the extension of libroadrunner links against libpython, which the
+      # standalone interpreters do not put on the library search path; the
+      # submission below imports roadrunner
+      run: |
+        sudo add-apt-repository -y ppa:deadsnakes/ppa
+        sudo apt-get update
+        sudo apt-get install -y python3.14-dev
     - name: Install uv
       uses: astral-sh/setup-uv@v10.0.1
       with:
@@ -135,7 +143,11 @@ jobs:
         packages-dir: dist
     - name: Run the SBML Test Suite against its newest release
       # the results a submission to the SBML Test Suite Database is made of.
-      # A release submits against the newest suite, not against the pinned one
+      # A release submits against the newest suite, not against the pinned one.
+      # The archive is an attachment of the release and never blocks it: the
+      # package is on PyPI by this point and a failure here would otherwise
+      # leave the release half made, without its notes, as it did for 0.7.0
+      continue-on-error: true
       run: |
         uv sync --extra dev
         uv run python scripts/testsuite.py submission --version latest --output submission
@@ -144,6 +156,8 @@ jobs:
       with:
         body_path: "release-notes/${{ github.ref_name }}.md"
         files: submission/*.zip
+        # the submission above may have been skipped, the notes are the release
+        fail_on_unmatched_files: false
         draft: false
         prerelease: false
 

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/.github/workflows/docs.yml

@@ -56,7 +56,7 @@ jobs:
         # Only a build which can be published pays the three minutes: a pull
         # request builds the site to check that it builds, it does not deploy
         if: github.event_name != 'pull_request'
-        run: uv run python scripts/testsuite.py report --output site/testsuite
+        run: uv run python scripts/testsuite.py report --output site/testsuite/report
       - name: Upload the site
         uses: actions/upload-pages-artifact@v5
         with:

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/.gitignore

@@ -37,3 +37,6 @@ examples/**/_results/
 .vscode/
 *~
 .DS_Store
+
+# personal notes next to the sources, never part of the library
+/src/roadmap.md

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/CITATION.cff

@@ -8,9 +8,9 @@ authors:
     given-names: "Matthias"
     orcid: "https://orcid.org/0000-0003-1725-179X"
     affiliation: "Humboldt-University Berlin, Faculty of Life Science, Institute for Biology, Biology, Berlin; University Lübeck; University Hospital Schleswig-Holstein, Campus Lübeck, First Department of Medicine, Germany"
-version: "0.7.0"
+version: "0.7.2"
 date-released: "2026-02-01"
-doi: "10.5281/zenodo.597149"
+doi: "10.5281/zenodo.3597770"
 license: MIT
 repository-code: "https://github.com/matthiaskoenig/sbmlsim"
 url: "https://matthiaskoenig.github.io/sbmlsim"

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: sbmlsim
-Version: 0.7.0
+Version: 0.7.2
 Summary: sbmlsim are python utilities for the simulation of SBML models.
 Project-URL: Homepage, https://matthiaskoenig.github.io/sbmlsim
 Project-URL: Documentation, https://matthiaskoenig.github.io/sbmlsim
@@ -61,7 +61,7 @@ Description-Content-Type: text/markdown
 [![Version](https://img.shields.io/pypi/v/sbmlsim.svg)](https://pypi.org/project/sbmlsim/)
 [![Python Versions](https://img.shields.io/pypi/pyversions/sbmlsim.svg)](https://pypi.org/project/sbmlsim/)
 [![MIT License](https://img.shields.io/pypi/l/sbmlsim.svg)](https://opensource.org/licenses/MIT)
-[![DOI](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3597770.svg)](https://doi.org/10.5281/zenodo.3597770)
 
 `sbmlsim` is a collection of python utilities for the simulation of models in the [Systems Biology Markup Language](https://sbml.org) (SBML), built on [libroadrunner](https://libroadrunner.org).
 
@@ -78,11 +78,11 @@ The documentation is available at [https://matthiaskoenig.github.io/sbmlsim](htt
 If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/sbmlsim/issues).
 
 ## How to cite
-[![DOI](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3597770.svg)](https://doi.org/10.5281/zenodo.3597770)
 
-If you use `sbmlsim` please cite the archived software on [Zenodo](https://zenodo.org/badge/latestdoi/55952847):
+If you use `sbmlsim` please cite the archived software on [Zenodo](https://doi.org/10.5281/zenodo.3597770):
 
-> König, M. (2026). *sbmlsim: SBML simulation made easy* (Version 0.6.0) [Computer software]. Zenodo. https://zenodo.org/badge/latestdoi/55952847
+> König, M. (2026). *sbmlsim: SBML simulation made easy* (Version 0.6.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.22653603
 
 ```bibtex
 @software{konig_sbmlsim,
@@ -92,7 +92,8 @@ If you use `sbmlsim` please cite the archived software on [Zenodo](https://zenod
   month     = sep,
   version   = {0.6.0},
   publisher = {Zenodo},
-  url       = {https://zenodo.org/badge/latestdoi/55952847},
+  doi       = {10.5281/zenodo.22653603},
+  url       = {https://doi.org/10.5281/zenodo.22653603},
 }
 ```
 

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/README.md

@@ -6,7 +6,7 @@
 [![Version](https://img.shields.io/pypi/v/sbmlsim.svg)](https://pypi.org/project/sbmlsim/)
 [![Python Versions](https://img.shields.io/pypi/pyversions/sbmlsim.svg)](https://pypi.org/project/sbmlsim/)
 [![MIT License](https://img.shields.io/pypi/l/sbmlsim.svg)](https://opensource.org/licenses/MIT)
-[![DOI](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3597770.svg)](https://doi.org/10.5281/zenodo.3597770)
 
 `sbmlsim` is a collection of python utilities for the simulation of models in the [Systems Biology Markup Language](https://sbml.org) (SBML), built on [libroadrunner](https://libroadrunner.org).
 
@@ -23,11 +23,11 @@ The documentation is available at [https://matthiaskoenig.github.io/sbmlsim](htt
 If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/sbmlsim/issues).
 
 ## How to cite
-[![DOI](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3597770.svg)](https://doi.org/10.5281/zenodo.3597770)
 
-If you use `sbmlsim` please cite the archived software on [Zenodo](https://zenodo.org/badge/latestdoi/55952847):
+If you use `sbmlsim` please cite the archived software on [Zenodo](https://doi.org/10.5281/zenodo.3597770):
 
-> König, M. (2026). *sbmlsim: SBML simulation made easy* (Version 0.6.0) [Computer software]. Zenodo. https://zenodo.org/badge/latestdoi/55952847
+> König, M. (2026). *sbmlsim: SBML simulation made easy* (Version 0.6.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.22653603
 
 ```bibtex
 @software{konig_sbmlsim,
@@ -37,7 +37,8 @@ If you use `sbmlsim` please cite the archived software on [Zenodo](https://zenod
   month     = sep,
   version   = {0.6.0},
   publisher = {Zenodo},
-  url       = {https://zenodo.org/badge/latestdoi/55952847},
+  doi       = {10.5281/zenodo.22653603},
+  url       = {https://doi.org/10.5281/zenodo.22653603},
 }
 ```
 

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/docs/index.md

@@ -1,7 +1,7 @@
 ![](images/favicon/sbmlsim-100x100-300dpi.png)
 
 # sbmlsim: SBML simulation made easy
-[![GitHub Actions CI/CD Status](https://github.com/matthiaskoenig/sbmlsim/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/matthiaskoenig/sbmlsim/actions/workflows/ci-cd.yml) [![Documentation](https://img.shields.io/badge/docs-sbmlsim-3f51b5.svg)](https://matthiaskoenig.github.io/sbmlsim) [![Version](https://img.shields.io/pypi/v/sbmlsim.svg)](https://pypi.org/project/sbmlsim/) [![Python Versions](https://img.shields.io/pypi/pyversions/sbmlsim.svg)](https://pypi.org/project/sbmlsim/) [![MIT License](https://img.shields.io/pypi/l/sbmlsim.svg)](https://opensource.org/licenses/MIT) [![DOI](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
+[![GitHub Actions CI/CD Status](https://github.com/matthiaskoenig/sbmlsim/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/matthiaskoenig/sbmlsim/actions/workflows/ci-cd.yml) [![Documentation](https://img.shields.io/badge/docs-sbmlsim-3f51b5.svg)](https://matthiaskoenig.github.io/sbmlsim) [![Version](https://img.shields.io/pypi/v/sbmlsim.svg)](https://pypi.org/project/sbmlsim/) [![Python Versions](https://img.shields.io/pypi/pyversions/sbmlsim.svg)](https://pypi.org/project/sbmlsim/) [![MIT License](https://img.shields.io/pypi/l/sbmlsim.svg)](https://opensource.org/licenses/MIT) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3597770.svg)](https://doi.org/10.5281/zenodo.3597770)
 
 `sbmlsim` is a collection of python utilities for the simulation of models in the [Systems Biology Markup Language](https://sbml.org) (SBML), built on [libroadrunner](https://libroadrunner.org). The source code is available from [https://github.com/matthiaskoenig/sbmlsim](https://github.com/matthiaskoenig/sbmlsim).
 
@@ -51,11 +51,11 @@ Continue with [Installation](installation.md) and the [timecourse simulation gui
 
 ## How to cite
 
-[![DOI](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3597770.svg)](https://doi.org/10.5281/zenodo.3597770)
 
-If you use `sbmlsim` please cite the archived software on [Zenodo](https://zenodo.org/badge/latestdoi/55952847):
+If you use `sbmlsim` please cite the archived software on [Zenodo](https://doi.org/10.5281/zenodo.3597770):
 
-> König, M. (2026). *sbmlsim: SBML simulation made easy* [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.597149
+> König, M. (2026). *sbmlsim: SBML simulation made easy* (Version 0.6.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.22653603
 
 ## License
 

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/docs/plotting.md

@@ -1,6 +1,6 @@
 # Plots and reports
 
-Figures of a simulation experiment are described independent of the plotting backend: a `Figure` holds `Plot` panels, a plot has axes and `Curve` objects, and a curve references `Data` with a `Style`. The description is serialized with the experiment and exported to SED-ML; matplotlib renders it.
+Figures of a simulation experiment are described independent of the plotting backend: a `Figure` holds `Plot` panels, a plot has axes and `Curve` objects, and a curve references `Data` with a `Style`. The description is serialized with the experiment, and the format chooses what renders it: matplotlib draws the static images, plotly the interactive pages.
 
 ## Figures and plots
 
@@ -21,7 +21,7 @@ plots[1].set_xaxis("[X]", unit="dimensionless")
 print(fig, len(plots))
 ```
 
-An `Axis` has a label and a unit, which together form the axis label, a `scale` (`linear` or `log`), `min`, `max`, `grid` and visibility flags. The data plotted on an axis are converted to its unit, see [Units](units.md).
+An `Axis` has a label and a unit, which together form the axis label `name`, a `scale` (`linear` or `log`), `min`, `max`, `grid` and visibility flags. `name` follows both parts, i.e. `axis.unit = "week"` updates the label a figure renders; setting `name` overrides them and setting it to `None` hands the axis back to its label and its unit. The data plotted on an axis are converted to its unit, see [Units](units.md).
 
 ## Curves
 
@@ -76,7 +76,7 @@ plots[0].curve(
 print(style)
 ```
 
-Colors are `ColorType` objects, created from matplotlib color names or hex strings, which are serialized to the `#RRGGBBAA` colors of SED-ML.
+Colors are `ColorType` objects, created from matplotlib color names or hex strings and normalized to `#RRGGBBAA`.
 
 ## Rendering
 

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/docs/testsuite.md

@@ -2,7 +2,7 @@
 
 The [SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite) is the conformance suite of SBML. Every semantic case is a model, a settings file which says how to simulate it and a CSV with the results a correct simulator produces, and the tags of a case say which parts of SBML it exercises. Running it answers what `sbmlsim`, i.e. libroadrunner, supports, and the results are what a submission to the SBML Test Suite Database is made of.
 
-[**The report of the current run**](testsuite/index.html) is generated with the documentation, so it describes the code of the `develop` branch.
+[**The report of the current run**](testsuite/report/index.html) is generated with the documentation, so it describes the code of the `develop` branch.
 
 ## What is run
 
@@ -29,7 +29,7 @@ A case which does not pass does so in one of four ways, and the report separates
 uv run python scripts/testsuite.py download
 
 # run the cases and write the interactive report
-uv run python scripts/testsuite.py report --output site/testsuite
+uv run python scripts/testsuite.py report --output site/testsuite/report
 
 # the archive which is submitted to the SBML Test Suite Database
 uv run python scripts/testsuite.py submission --output dist

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/examples/glucose/experiments/dose_response.py

@@ -3,12 +3,12 @@ from pathlib import Path
 import numpy as np
 import pandas as pd
 import xarray as xr
+from matplotlib import pyplot as plt
 from matplotlib.pyplot import Figure
 
 from sbmlsim.data import Data, DataSet, load_pkdb_dataframe
 from sbmlsim.experiment import SimulationExperiment
 from sbmlsim.model import AbstractModel
-from sbmlsim.plot.serialization_matplotlib import plt
 from sbmlsim.result import XResult
 from sbmlsim.simulation import Dimension, ScanSim, Timecourse, TimecourseSim
 from sbmlsim.task import Task

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/examples/model_change.py

@@ -5,9 +5,9 @@ For instance clamping species to given formulas.
 """
 
 import pandas as pd
+from matplotlib import pyplot as plt
 
 from sbmlsim.model import ModelChange, RoadrunnerSBMLModel
-from sbmlsim.plot.serialization_matplotlib import plt
 from sbmlsim.resources import REPRESSILATOR_SBML
 from sbmlsim.result import XResult
 from sbmlsim.simulation import Timecourse, TimecourseSim

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/examples/model_sensitivity.py

@@ -2,7 +2,8 @@
 Example shows basic model simulations and plotting.
 """
 
-from sbmlsim.plot.serialization_matplotlib import plt
+from matplotlib import pyplot as plt
+
 from sbmlsim.resources import REPRESSILATOR_SBML
 from sbmlsim.result import XResult
 from sbmlsim.simulation import Timecourse, TimecourseSim

sbmlsim-0.7.2/release-notes/0.7.1.md

@@ -0,0 +1,10 @@
+# Release notes for sbmlsim 0.7.1
+![sbmlsim](https://github.com/matthiaskoenig/sbmlsim/raw/develop/docs/images/favicon/sbmlsim-100x100-300dpi.png)
+
+A patch release of the fixes which 0.7.0 surfaced: the page of the SBML Test Suite in the documentation was replaced by the report it links, the release workflow could not build the submission it attaches, and a file which is not part of the library was published with the sources.
+
+## Fixes
+
+- **the documentation of the SBML Test Suite is a page again.** `zensical` renders `docs/testsuite.md` into `site/testsuite/index.html` and the documentation workflow wrote the interactive report to `site/testsuite`, so the report replaced the page which describes it: [SBML Test Suite](https://matthiaskoenig.github.io/sbmlsim/testsuite/) served the report without the theme, without the navigation and without the search of the documentation, and the page itself was unreachable. The report is written to `site/testsuite/report` now and the page links it there, i.e. it is at [SBML Test Suite / report](https://matthiaskoenig.github.io/sbmlsim/testsuite/report/). The link of a page is resolved against its source, which is why it carries the `testsuite/` of the page itself; `tests/testsuite/test_report_path.py` pins the two paths against each other, since a report at the address of its documentation renders perfectly well and only the page is missing
+- **the release workflow builds the submission it attaches.** The extension of libroadrunner links against libpython, which the standalone interpreters do not put on the library search path, so the `test` and the `sbml test suite` jobs install `python<version>-dev` first. The `release` job did not, although the submission it writes imports roadrunner, and it died with `ImportError: libpython3.14.so.1.0` on the tag of 0.7.0, after the package was published and before the GitHub release was created. The archive of the submission is an attachment and is `continue-on-error` now, so a failure to produce it costs the release its attachment and not its notes
+- **`src/roadmap.md` is not part of the repository.** Personal notes next to the sources were committed by accident and are part of the sdist of 0.7.0 on PyPI, which cannot be changed; the wheel never carried them, since it is built from `src/sbmlsim`. The file is out of the repository and `.gitignore` keeps it out

sbmlsim-0.7.2/release-notes/0.7.2.md

@@ -0,0 +1,31 @@
+# Release notes for sbmlsim 0.7.2
+![sbmlsim](https://github.com/matthiaskoenig/sbmlsim/raw/develop/docs/images/favicon/sbmlsim-100x100-300dpi.png)
+
+A patch release of the plotting: the axis labels of a figure, an inspection of the figure model and of its matplotlib rendering, and the citation.
+
+## Fixes
+
+- **the axis label follows the label and the unit** ([#167](https://github.com/matthiaskoenig/sbmlsim/issues/167)). `Axis.name` is the text a figure renders and it was computed once, in the constructor, so `axis.unit = "week"` or `axis.label = "duration"` left the old label on the plot. `label`, `unit` and `name` are properties now and `name` is derived from the other two, so a change of either is reflected; `name` is still the complete axis label and overrides them, and setting it to `None` hands the axis back to its label and its unit. A copied axis keeps that distinction, i.e. a derived label stays derived instead of being pinned to the text it had when it was copied
+- **an axis without a unit is not labelled `[None]`.** `Axis("time")` rendered `time [None]` and `Axis(unit="week")` rendered `None [week]`, since the part which was not given was formatted into the label anyway. A part which is missing is left out now, i.e. `time` and `[week]`, and a `dimensionless` unit is written as `-` as before
+- **copying an axis keeps its `reverse` flag.** `Axis.__copy__` did not pass it, so a plot which was copied, i.e. every plot of `Figure.add_plots` and of `create_plots`, lost the flag which inverts the axis
+- **the spines of a missing axis were the spines of the other one.** A plot without an x axis hid the left and the right spine, i.e. the sides of the y axis, and kept the line of the axis it was hiding; they are also hidden on the panel itself rather than on whatever the styling loop before them had left over
+- **`Axis.reverse` did nothing unless both bounds were set.** It swapped `min` and `max` instead of inverting the axis, so a reversed axis with only a lower bound assigned `None`. The bounds are the bounds and `reverse` is the direction they are drawn in
+- **`Style.resolve_style` rewrote the style it derives from.** It returned the base style itself and assigned onto it, so resolving one derived style changed the base and every other style sharing it; and it looked the inherited attributes up under the camel case names of SED-ML, which no field of `Line`, `Marker` or `Fill` ever had, so the line type, the marker type and its edge, and the second fill colour were never inherited at all
+- `Style.__copy__` dropped `base_style` and `Plot.__copy__` dropped `yaxis_right`
+- **a plot knows its figure.** A plot resolves its data through its figure and only `add_plots` associated the two, so `plot.figure` and `plot.experiment` raised for every plot of `Figure.from_plots` or of `add_subplot`
+- **`:` is the dotted linestyle of matplotlib.** The mapping carried the marker `.` in its place, so the canonical spelling raised a `KeyError`; the aliases matplotlib accepts for a shape the model has are understood, and a shape it cannot express raises a `ValueError` which names what it can
+- **settings which were never rendered.** `Plot.facecolor` was built, defaulted and read by no serializer, and the `capsize` of a curve was defaulted, dropped by `Style.from_mpl_kwargs` and merged from an empty dictionary, so no error bar ever had a cap
+- **code which could not run:** `interp`, `Figure._area_interpolation_points`, and the branches for an axis which is `None`, which the fallback to an empty `Axis` made unreachable together with the `ValueError` about a plot with curves and no axes
+- `yaxis_right` is type checked like the other two axes, the span messages of `Figure.add_subplot` print the number they test, and `Figure.from_plots` takes the optional experiment `Figure.__init__` takes
+- the Zenodo badge and the citation of the README, the documentation index and `CITATION.cff` carried the GitHub repository id and the concept DOI of sbmlutils, so every Zenodo link of sbmlsim resolved to the sbmlutils archive; they use the sbmlsim concept DOI `10.5281/zenodo.3597770` now ([#206](https://github.com/matthiaskoenig/sbmlsim/pull/206))
+
+## Plotting
+
+- **the rendering does not go through the global state of `pyplot`.** `plt.figure()` keeps every figure it creates in a global registry until someone closes it, so a library which renders many leaks them and matplotlib warns from the twentieth on, while a fit report draws about seventy. The serializer creates the figure itself, as the matplotlib documentation asks of a library; showing a figure is the one thing which needs a manager and gets one there
+- **a curve without error data is drawn with `plot`** and not with `errorbar`, which builds the containers of the bars whether or not there are any: 8.13 ms to 7.70 ms for a panel of ten curves, and 0.278 ms to 0.120 ms for the draw call itself, the rest being the resolution of the data and the conversion of its units
+- `ticks_visible` hides the tick labels with `tick_params`, which is correct for any locator and which an empty list of tick labels is not; a spine which is not drawn is hidden rather than painted in the colour of the figure, which only worked while the panel had that colour; a curve kept out of the legend is labelled `_nolegend_`, which is what matplotlib documents; and the grid of the figure comes from `add_gridspec`
+- `legend_position` was read for a plot with one y axis only; a plot with a right y axis puts the curves of both axes into one legend when the legend is outside, since two of them would sit on top of each other
+
+## Documentation
+
+- [Plots and reports](https://matthiaskoenig.github.io/sbmlsim/plotting/) no longer says that a figure is exported to SED-ML, which was removed in 0.7.0, and names both backends rather than matplotlib alone; the axis label and what follows what is described where the axis is

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/scripts/testsuite.py

@@ -9,7 +9,7 @@ the command line around `sbmlsim.testsuite`:
 uv run python scripts/testsuite.py download
 
 # run the cases and write the interactive report
-uv run python scripts/testsuite.py report --output site/testsuite
+uv run python scripts/testsuite.py report --output site/testsuite/report
 
 # refresh the expected outcomes after a change which fixes or breaks cases
 uv run python scripts/testsuite.py baseline
@@ -191,7 +191,7 @@ def main(argv: list[str] | None = None) -> int:
         "-o",
         "--output",
         type=Path,
-        default=Path("site") / "testsuite",
+        default=Path("site") / "testsuite" / "report",
         help="directory of the report or of the submission archive",
     )
     options = parser.parse_args(argv)

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/src/sbmlsim/__init__.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 __author__ = "Matthias Koenig"
-__version__ = "0.7.0"
+__version__ = "0.7.2"
 
 
 BASE_PATH = Path(__file__).parent

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/src/sbmlsim/experiment/experiment.py

@@ -9,6 +9,8 @@ from copy import deepcopy
 from dataclasses import dataclass
 from pathlib import Path
 
+from matplotlib import pyplot as plt
+
 from sbmlsim.data import Data, DataSet
 from sbmlsim.fit import FitMapping
 from sbmlsim.fit.objects import FitDataInitialized
@@ -17,7 +19,6 @@ from sbmlsim.plot import Figure
 from sbmlsim.plot.serialization_matplotlib import (
     FigureMPL,
     MatplotlibFigureSerializer,
-    plt,
 )
 from sbmlsim.result import XResult
 from sbmlsim.serialization import ObjectJSONEncoder
@@ -644,10 +645,22 @@ class SimulationExperiment:
 
     @timeit
     def show_mpl_figures(self, mpl_figures: dict[str, FigureMPL]) -> None:
-        """Show matplotlib figures."""
+        """Show matplotlib figures.
+
+        The figures of the serializer are created without `pyplot`, so that
+        rendering does not fill its global registry; a figure it does not
+        manage cannot show itself. Showing is the one place which needs the
+        state machine, so a figure gets a manager here and only here.
+
+        Args:
+            mpl_figures: the figures to show.
+        """
         for _, fig_mpl in mpl_figures.items():
-            # see https://stackoverflow.com/questions/23141452/difference-between-plt-draw-and-plt-show-in-matplotlib/23141491#23141491
-            # fig_mpl.draw(renderer=)
+            if fig_mpl.canvas.manager is None:
+                manager = plt.figure().canvas.manager
+                if manager is not None:
+                    manager.canvas.figure = fig_mpl
+                    fig_mpl.set_canvas(manager.canvas)
             fig_mpl.show()
 
     @timeit
@@ -703,8 +716,17 @@ class SimulationExperiment:
         return figures_to_html(self, results_path)
 
     @classmethod
-    def close_mpl_figures(cls, mpl_figures: dict[str, FigureMPL]):
-        """Close matplotlib figures."""
+    def close_mpl_figures(cls, mpl_figures: dict[str, FigureMPL]) -> None:
+        """Close matplotlib figures.
+
+        A figure of the serializer is not in the registry of `pyplot` and is
+        released when nothing refers to it any more, for which this is a no-op.
+        A figure of `figures_mpl()` may well come from `pyplot`, and that one
+        is closed here.
+
+        Args:
+            mpl_figures: the figures to close.
+        """
         for _, fig_mpl in mpl_figures.items():
             plt.close(fig_mpl)
 

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/src/sbmlsim/fit/identifiability.py

@@ -105,6 +105,7 @@ from typing import Any
 import numpy as np
 import pandas as pd
 import scipy.optimize
+from matplotlib import pyplot as plt
 from matplotlib.axes import Axes
 from scipy.stats import chi2
 
@@ -113,7 +114,6 @@ from sbmlsim.fit.objects import FitParameter
 from sbmlsim.fit.optimization import FitTimeout, OptimizationProblem
 from sbmlsim.fit.options import FitSettings
 from sbmlsim.fit.parameters import ParameterSet
-from sbmlsim.plot.serialization_matplotlib import plt
 
 logger = logging.getLogger(__name__)
 

{sbmlsim-0.7.0 → sbmlsim-0.7.2}/src/sbmlsim/fit/report.py

@@ -25,6 +25,7 @@ from typing import Any, ClassVar
 import matplotlib
 import numpy as np
 import pandas as pd
+from matplotlib import pyplot as plt
 from matplotlib.axes import Axes
 from matplotlib.figure import Figure
 from matplotlib.lines import Line2D
@@ -40,7 +41,6 @@ from sbmlsim.fit.options import FitSettings
 from sbmlsim.fit.parameter_mapping import has_renamed_targets
 from sbmlsim.fit.parameters import ParameterSet, ParameterSets
 from sbmlsim.fit.result import OptimizationResult, bound_warnings
-from sbmlsim.plot.serialization_matplotlib import plt
 from sbmlsim.report.templates import template_environment
 
 logger = logging.getLogger(__name__)