Merge pull request #639 from ICB-DCM/develop

Minor bug fixes, new release

Author: arrjon

.flake8

@@ -13,6 +13,8 @@ extend-ignore =
   E501
   # Empty method in an abstract base class
   B027
+  # Disable black would make changes warning
+  BLK100
 
 per-file-ignores =
   # Imported but unused

.github/workflows/ci.yml

@@ -7,23 +7,23 @@ on:
     - main
   pull_request:
   schedule:
-    # run Monday and Thursday at 03:18 UTC
-    - cron: '18 15 * * MON,THU'
+    # run Monday at 03:18 UTC
+    - cron: '18 15 * * MON'
 
 jobs:
 
   base:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.9']
+        python-version: ['3.12', '3.11', '3.10']
 
     steps:
     - name: Check out repository
       uses: actions/checkout@v2
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -54,14 +54,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.9']
+        python-version: ['3.12']
 
     steps:
     - name: Check out repository
       uses: actions/checkout@v2
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -100,7 +100,7 @@ jobs:
       uses: actions/checkout@v2
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -127,14 +127,14 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.9']
+        python-version: ['3.12']
 
     steps:
       - name: Check out repository
         uses: actions/checkout@v2
 
       - name: Prepare python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -161,14 +161,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - name: Check out repository
       uses: actions/checkout@v2
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -189,14 +189,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - name: Check out repository
       uses: actions/checkout@v2
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -224,7 +224,7 @@ jobs:
       uses: actions/checkout@v2
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/deploy.yml

@@ -3,21 +3,21 @@ name: Deploy
 on:
   release:
     types: [created]
-   
+
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.12]
 
     steps:
     - name: Check out repository
       uses: actions/checkout@v2
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 

CHANGELOG.rst

@@ -7,6 +7,18 @@ Release Notes
 0.12 Series
 ...........
 
+0.12.15 (2024-10-29)
+--------------------
+
+General:
+
+* Minor improvements in the documentation
+* Minor bug fixes in dependencies
+* Minor bug fixed in general
+* Dropping support of python 3.9
+* Adding support for python 3.12
+
+
 0.12.14 (2023-11-10)
 --------------------
 
@@ -24,7 +36,7 @@ General:
 
 Fixes (#615):
 
-* Fix for wrong assets path in abc-server-dash 
+* Fix for wrong assets path in abc-server-dash
 
 General
 

doc/conf.py

@@ -155,7 +155,7 @@
 
 # Add notebooks prolog to Google Colab and nbviewer
 nbsphinx_prolog = r"""
-{% set docname = 'github/icb-dcm/pyabc/blob/main/doc/' + env.doc2path(env.docname, base=None) %}
+{% set docname = 'github/icb-dcm/pyabc/blob/main/doc/' + env.doc2path(env.docname, base=None) | string %}
 .. raw:: html
 
     <div class="note">

pyabc/acceptor/__init__.py

@@ -5,7 +5,6 @@
 Acceptors handle the acceptance step.
 """
 
-
 from .acceptor import (
     Acceptor,
     AcceptorResult,

pyabc/model/model.py

@@ -47,7 +47,7 @@ class Model:
     .. note::
 
         Most likely you do not want to use this class directly, but the
-        :class:`SimpleModel` instead, or even just pass a plain function
+        :class:`FunctionModel` instead, or even just pass a plain function
         as model.
 
     Parameters
@@ -216,7 +216,7 @@ class FunctionModel(Model):
     A model which is initialized with a function which generates the samples.
     For most cases this class will be adequate.
     Note that you can also pass a plain function to the ABCSMC class, which
-    then gets automatically converted to a SimpleModel.
+    then gets automatically converted to a FunctionModel.
 
     Parameters
     ----------
@@ -252,7 +252,7 @@ def to_model(maybe_model: Union[Callable, Model]) -> Model:
         Parameters
         ----------
         maybe_model:
-            Constructs a SimpleModel instance if a function is passed.
+            Constructs a FunctionModel instance if a function is passed.
             If a Model instance is passed, the Model instance itself is
             returned.
 

pyabc/petab/__init__.py

@@ -4,5 +4,16 @@
 
 Problem definitions in the PEtab format (https://petab.rtfd.io).
 """
+import warnings
 
 from .amici import AmiciPetabImporter
+
+try:
+    import petab
+except ImportError:
+    warnings.warn(
+        "PEtab import requires an installation of petab "
+        "(https://github.com/PEtab-dev/PEtab). "
+        "Install via `pip3 install petab`.",
+        stacklevel=1,
+    )

pyabc/petab/amici.py

@@ -14,8 +14,8 @@
 logger = logging.getLogger("ABC.PEtab")
 
 try:
-    import petab
-    import petab.C as C
+    import petab.v1 as petab
+    import petab.v1.C as C
 except ImportError:
     petab = C = None
     logger.error(
@@ -82,8 +82,8 @@ def __call__(self, par: Union[Sequence, Mapping]) -> Mapping:
         for key in self.prior_scales.keys():
             par[key] = rescale(
                 val=par[key],
-                origin_scale=self.prior_scales,
-                target_scale=self.scaled_scales,
+                origin_scale=self.prior_scales[key],
+                target_scale=self.scaled_scales[key],
             )
 
         # simulate model

pyabc/petab/base.py

@@ -14,8 +14,8 @@
 logger = logging.getLogger("ABC.PEtab")
 
 try:
-    import petab
-    import petab.C as C
+    import petab.v1 as petab
+    import petab.v1.C as C
 except ImportError:
     petab = C = None
     logger.error(

pyabc/transition/local_transition.py

@@ -136,7 +136,10 @@ def _cov_and_inv(self, n, indices):
         while det <= 0:
             cov += np.identity(cov.shape[0]) * self.EPS
             det = la.det(cov)
-        inv_cov = la.inv(cov)
+        try:
+            inv_cov = la.inv(cov)
+        except np.linalg.LinAlgError:
+            inv_cov = np.linalg.pinv(cov)  # Use pseudo-inverse as a fallback
         return cov, inv_cov, det
 
     def _cov(self, indices, n):

pyabc/version.py

@@ -1 +1 @@
-__version__ = '0.12.14'
+__version__ = '0.12.15'

pyabc/weighted_statistics/weighted_statistics.py

@@ -129,7 +129,10 @@ def resample(points, weights, n):
     """
     weights = np.asarray(weights)
     weights /= np.sum(weights)
-    resampled = np.random.choice(points, size=n, p=weights)
+    indices = np.random.choice(
+        points.shape[0], size=n, p=weights
+    )  # sample index from multi-dimensional sample
+    resampled = points[indices]
     return resampled
 
 

setup.cfg

@@ -33,9 +33,9 @@ classifiers =
     License :: OSI Approved :: BSD License
     Operating System :: OS Independent
     Programming Language :: Python
+    Programming Language :: Python :: 3.12
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.10
-    Programming Language :: Python :: 3.9
 keywords =
     likelihood-free
     inference
@@ -51,7 +51,7 @@ requires =
 
 [options]
 install_requires =
-    numpy >= 1.19.1
+    numpy >= 1.23.5
     scipy >= 1.5.2
     pandas >= 2.0.1
     cloudpickle >= 1.5.0
@@ -60,11 +60,11 @@ install_requires =
     redis >= 2.10.6
     distributed >= 2022.10.2
     matplotlib >= 3.3.0
-    sqlalchemy >= 2.0.12
+    sqlalchemy
     jabbar >= 0.0.10
     gitpython >= 3.1.7
 
-python_requires = >=3.9
+python_requires = >=3.10
 
 # not zip safe b/c of Flask templates
 zip_safe = False
@@ -74,11 +74,11 @@ include_package_data = True
 packages = find:
 
 [options.extras_require]
-webserver_flask =
+webserver-flask =
     flask-bootstrap >= 3.3.7.1
     flask >= 1.1.2
     bokeh >= 3.0.1
-webserver_dash =
+webserver-dash =
     dash >= 2.11.1
     dash-bootstrap-components >= 1.4.2
 pyarrow =
@@ -111,9 +111,9 @@ autograd =
 examples =
     notebook >= 6.1.4
 doc =
-    sphinx >= 6.2.1
-    nbsphinx >= 0.8.9
-    nbconvert >= 6.5.0
+    sphinx >= 8.1.3
+    nbsphinx >= 0.9.5
+    nbconvert >= 7.16.4
     sphinx-rtd-theme >= 1.2.0
     sphinx-autodoc-typehints >= 1.18.3
     ipython >= 8.4.0

test/migrate/create_test_db.py

@@ -31,7 +31,13 @@ def model(p):
 
 distance = pyabc.PNormDistance(p=2)
 
-abc = pyabc.ABCSMC(model, prior, distance, population_size=10)
+abc = pyabc.ABCSMC(
+    model,
+    prior,
+    distance,
+    population_size=10,
+    sampler=pyabc.SingleCoreSampler(),
+)
 db_file = os.path.join(tempfile.gettempdir(), 'pyabc_test_migrate.db')
 abc.new("sqlite:///" + db_file, observation)
 abc.run(minimum_epsilon=0.1, max_nr_populations=3)

test/petab/test_petab.py

@@ -8,8 +8,8 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-import petab
-import petab.C as C
+import petab.v1 as petab
+import petab.v1.C as C
 import pytest
 import scipy.stats
 
@@ -18,9 +18,7 @@
 
 
 @pytest.fixture(
-    params=itertools.product(
-        [petab.C.LIN, petab.C.LOG, petab.C.LOG10], [*petab.C.PRIOR_TYPES, None]
-    )
+    params=itertools.product([C.LIN, C.LOG, C.LOG10], [*C.PRIOR_TYPES, None])
 )
 def prior_specs(request):
     """A one-line parameter df for a given prior type."""