Prepare Release 0.13.0

.github/workflows/ci.yml

@@ -16,6 +16,9 @@ jobs:
       matrix:
         include:
           # Fast PR matrix
+          - os: ubuntu-latest
+            python: "3.14"
+            toxenv: base
           - os: ubuntu-latest
             python: "3.13"
             toxenv: base
@@ -26,42 +29,42 @@ jobs:
             python: "3.11"
             toxenv: base
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.14"
             toxenv: visualization
 
           # macOS sanity
           - os: macos-latest
-            python: "3.11"
+            python: "3.14"
             toxenv: mac
 
           # Quality
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.14"
             toxenv: quality
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.14"
             toxenv: project
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.14"
             toxenv: doc
           - os: ubuntu-latest
             python: "3.11"
             toxenv: migrate
 
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.14"
             toxenv: external-R
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.14"
             toxenv: external-other-simulators
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.14"
             toxenv: petab
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.14"
             toxenv: base-notebooks
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.14"
             toxenv: external-notebooks
 
     steps:

.gitignore

@@ -69,3 +69,6 @@ dask-worker-space
 *.lock
 *tmp*
 *amici_models*
+
+# macOS
+.DS_Store

CHANGELOG.rst

@@ -4,6 +4,39 @@ Release Notes
 =============
 
 
+0.13 Series
+...........
+
+0.13.0 (2026-07-30)
+-------------------
+
+General:
+
+* Add support for python3.14
+* Add execution time profiling to the ABC-SMC run, reporting pure simulation
+  time, parallel-pipeline setup time, and in-between-iteration time,
+  including population-size calculation and distance-function adaptation.
+  The timings are also returned by ``run_generation``. Resolves #325.
+* Minor bug fixes and improved typesetting.
+
+Visualization:
+
+* ``plot_walltime`` and ``plot_total_walltime`` now report the actual
+  per-generation walltimes and no longer include the idle time that passed
+  between a stored analysis and a later resumed run. Resolves #667.
+
+Storage (breaking):
+
+* Store the per-generation walltime in the database (new ``wall_time`` column,
+  database version 2). Databases created with older pyABC versions must be
+  migrated via ``abc-migrate`` before they can be resumed; for such databases
+  the walltime plots fall back to the previous, end-time-based behavior.
+* Particle weights are now stored using the global normalization (weights sum
+  to 1 across all particles of all models, matching the in-memory
+  ``Population`` representation). This is bundled into database version 2 and
+  handled by ``abc-migrate`` for existing databases. Resolves #47.
+
+
 0.12 Series
 ...........
 

README.md

@@ -26,4 +26,5 @@
 - 📄 **Cite**: [https://pyabc.rtfd.io/en/latest/cite.html](https://pyabc.rtfd.io/en/latest/cite.html)
 
 #### Related Projects
-- 🧠 **Neural Posterior Estimation**: [BayesFlow](https://bayesflow.org/main/_examples/From_ABC_to_BayesFlow.html)
+- **Parameter Estimation with Likelihoods**: [pyPESTO](https://github.com/ICB-DCM/pyPESTO)
+- **Neural Posterior Estimation**: [BayesFlow](https://bayesflow.org/main/_examples/From_ABC_to_BayesFlow.html)

doc/conf.py

@@ -13,6 +13,7 @@
 # serve to show the default.
 
 import os
+import subprocess
 import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -32,18 +33,20 @@
     'sphinx.ext.autodoc',
     # generate autodoc summaries
     'sphinx.ext.autosummary',
-    # use mathjax for latex formulas
-    'sphinx.ext.mathjax',
-    # link to code
-    'sphinx.ext.viewcode',
+    # test snippets in the documentation
+    'sphinx.ext.doctest',
+    # link to external urls
+    'sphinx.ext.extlinks',
     # link to other projects' docs
     'sphinx.ext.intersphinx',
+    # use mathjax for latex formulas
+    'sphinx.ext.mathjax',
     # support numpy and google style docstrings
     'sphinx.ext.napoleon',
     # support todo items
     'sphinx.ext.todo',
-    # test snippets in the documentation
-    'sphinx.ext.doctest',
+    # link to code
+    'sphinx.ext.viewcode',
     # source parser for jupyter notebook files
     'nbsphinx',
     # code highlighting in jupyter cells
@@ -68,7 +71,7 @@
     'numpy': ('https://numpy.org/devdocs/', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/dev', None),
-    'petab': ('https://petab.readthedocs.io/en/stable/', None),
+    'petab': ('https://petab.readthedocs.io/en/latest/', None),
     'amici': ('https://amici.readthedocs.io/en/latest/', None),
     'sklearn': ('https://scikit-learn.org/stable/', None),
 }
@@ -99,6 +102,30 @@
 #
 # The short X.Y version.
 
+
+# Resolve the current branch name
+def get_branch():
+    # Read the Docs sets this automatically ("latest", "stable", branch name...)
+    rtd_version = os.environ.get('READTHEDOCS_VERSION')
+    if rtd_version and rtd_version not in ('latest', 'stable'):
+        return rtd_version
+    try:
+        return subprocess.check_output(
+            ['git', 'rev-parse', '--abbrev-ref', 'HEAD'], text=True
+        ).strip()
+    except Exception:
+        return 'main'
+
+
+# Set up links that resolve to the branch of the documentation
+branch = get_branch()
+extlinks = {
+    'repository': (
+        f'https://github.com/ICB-DCM/pyABC/blob/{branch}/%s',
+        '%s',
+    ),
+}
+
 import pyabc  # noqa: E402
 
 version = pyabc.__version__

doc/index.rst

@@ -11,8 +11,8 @@ pyABC - distributed, likelihood-free inference
    :target: https://badge.fury.io/py/pyabc
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3257587.svg
    :target: https://doi.org/10.5281/zenodo.3257587
-.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
-   :target: https://github.com/psf/black
+.. image:: https://img.shields.io/badge/code%20style-ruff-41B5BE.svg
+   :target: https://github.com/astral-sh/ruff
 
 :Release: |version|
 :Source code: https://github.com/icb-dcm/pyabc

doc/installation.rst

@@ -6,7 +6,7 @@ Install
 Preparation
 -----------
 
-This package requires Python 3.8 or later.
+This package requires Python 3.11 or later.
 The package is continuously tested on Linux, and in parts on iOS,
 via GitHub Actions.
 
@@ -77,20 +77,11 @@ home directory with
 
 .. _anacondaCluster:
 
-Installing Anaconda on a Cluster environment
---------------------------------------------
-
-To install `Anaconda <https://anaconda.com/products/distribution>`_, run::
-
-   wget https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh
-   bash Anaconda3-2021.11-Linux-x86_64.sh
-
-and follow the installation guide.
-Replace the "2021.11" by the most recent version of Anaconda, see
-https://repo.anaconda.com/archive.
+Installing Miniconda on a Cluster environment
+---------------------------------------------
 
 `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_
-provides an alternative, minimal installer for conda, including
+provides a minimal installer for conda, including
 only conda, Python, and some core and useful packages. Install the latest
 version via::
 
@@ -102,7 +93,7 @@ version via::
 Optional dependencies
 ---------------------
 
-pyABC has various optional dependencies, see `setup.cfg`.
+pyABC has various optional dependencies, see :repository:`pyproject.toml`.
 
 In particular, pyABC has optional interfaces to the :ref:`R <api_external_r>`
 and :ref:`Julia <api_external_julia>` languages, see the API documentation

pyabc/acceptor/acceptor.py

@@ -347,9 +347,9 @@ class StochasticAcceptor(Acceptor):
 
     def __init__(
         self,
-        pdf_norm_method: Callable = None,
+        pdf_norm_method: Callable | None = None,
         apply_importance_weighting: bool = True,
-        log_file: str = None,
+        log_file: str | None = None,
     ):
         """
         Parameters
@@ -429,7 +429,7 @@ def _update(
         self,
         t: int,
         get_weighted_distances: Callable[[], pd.DataFrame],
-        prev_temp: float = None,
+        prev_temp: float | None = None,
         acceptance_rate: float = 1.0,
     ):
         """

pyabc/acceptor/pdf_norm.py

@@ -32,7 +32,10 @@ def pdf_norm_max_found(
         prev_pdf_norm = -np.inf
 
     # take maximum over all normalizations
-    pdf_norm = max(prev_pdf_norm, *pdfs)
+    if len(pdfs) == 0:
+        pdf_norm = prev_pdf_norm
+    else:
+        pdf_norm = max(prev_pdf_norm, float(pdfs.max()))
 
     return pdf_norm
 

pyabc/copasi/model.py

@@ -34,16 +34,16 @@ class BasicoModel(Model):
     def __init__(
         self,
         sbml_file: str,
-        changes: dict[str, float] = None,
+        changes: dict[str, float] | None = None,
         change_unit: bool = True,
         method: str = 'stochastic',
-        t0: float = None,
-        duration: float = None,
-        num_steps: int = None,
+        t0: float | None = None,
+        duration: float | None = None,
+        num_steps: int | None = None,
         automatic: bool = True,
         use_numbers: bool = False,
-        output: list[str] = None,
-        model_name: str = None,
+        output: list[str] | None = None,
+        model_name: str | None = None,
     ):
         """
         Parameters

pyabc/distance/aggregate.py

@@ -26,8 +26,8 @@ class AggregatedDistance(Distance):
     def __init__(
         self,
         distances: list[Distance | Callable],
-        weights: list | dict = None,
-        factors: list | dict = None,
+        weights: list | dict | None = None,
+        factors: list | dict | None = None,
     ):
         """
         Parameters
@@ -126,8 +126,8 @@ def __call__(
         self,
         x: dict,
         x_0: dict,
-        t: int = None,
-        par: dict = None,
+        t: int | None = None,
+        par: dict | None = None,
     ) -> float:
         """
         Applies all distance functions and computes the weighted sum of all
@@ -221,21 +221,21 @@ class AdaptiveAggregatedDistance(AggregatedDistance):
     def __init__(
         self,
         distances: list[Distance],
-        initial_weights: list = None,
-        factors: list | dict = None,
+        initial_weights: list | None = None,
+        factors: list | dict | None = None,
         adaptive: bool = True,
-        scale_function: Callable = None,
-        log_file: str = None,
+        scale_function: Callable | None = None,
+        log_file: str | None = None,
     ):
         super().__init__(distances=distances)
-        self.initial_weights: list = initial_weights
-        self.factors: list | dict = factors
+        self.initial_weights: list | None = initial_weights
+        self.factors: list | dict | None = factors
         self.adaptive: bool = adaptive
         self.x_0: dict | None = None
         if scale_function is None:
             scale_function = span
         self.scale_function: Callable = scale_function
-        self.log_file: str = log_file
+        self.log_file: str | None = log_file
 
     def requires_calibration(self) -> bool:
         return self.initial_weights is None or any(