Test with pandas 3

.github/workflows/pipeline.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.14"]
         pymc-version: ["without", "'pymc>=5.0.0'"]
     defaults:
       run:
@@ -36,25 +36,24 @@ jobs:
     - name: Test without PyMC
       if: matrix.pymc-version == 'without'
       run: |
-        pytest --cov=./murefi --cov-append --cov-report xml --cov-report term-missing murefi/tests.py
+        pytest -v --cov=./murefi --cov-append --cov-report xml --cov-report term-missing murefi/test_core.py
     - name: Install and test with PyMC
       if: matrix.pymc-version != 'without'
       run: |
         pip install ${{ matrix.pymc-version }}
-        pytest --cov=./murefi --cov-append --cov-report xml --cov-report term-missing murefi/tests.py
+        pytest -v --cov=./murefi --cov-append --cov-report xml --cov-report term-missing murefi/test_core.py
     - name: Install and test with sunode
       if: matrix.pymc-version != 'without'
       run : |
         mamba install "sunode>=0.5.0"
-        pytest --cov=./murefi --cov-append --cov-report xml --cov-report term-missing murefi/tests.py
+        pytest -v --cov=./murefi --cov-append --cov-report xml --cov-report term-missing murefi/test_core.py
     - name: Upload coverage
       uses: codecov/codecov-action@v5
-      if: matrix.python-version == 3.11
       with:
         file: ./coverage.xml
     - name: Test Wheel install and import
       run: |
-        python setup.py bdist_wheel
+        python -m build
         cd dist
         pip install murefi*.whl
         python -c "import murefi; print(murefi.__version__)"

.github/workflows/release.yml

@@ -18,17 +18,17 @@ jobs:
       with:
         environment-file: environment-dev.yml
         create-args: >-
-          python=3.11
+          python=3.13
     - name: Install dependencies
       run: |
         conda activate murefi-env
         pip install -e .
     - name: Test without PyMC
       run: |
-        pytest --cov=./murefi --cov-append --cov-report xml --cov-report term-missing murefi/tests.py
+        pytest -v --cov=./murefi --cov-append --cov-report xml --cov-report term-missing murefi/test_core.py
     - name: Build package
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
     - name: Check version number match
       run: |
         echo "GITHUB_REF: ${GITHUB_REF}"

.gitignore

@@ -17,3 +17,4 @@ murefi/examples/Sandbox.ipynb
 *.h5
 /docs/build*
 /notebooks/*.png
+dist/*

.readthedocs.yml

@@ -7,7 +7,7 @@ version: 2
 
 # Set the OS, Python version and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
     python: "3.12"
 
@@ -19,6 +19,5 @@ sphinx:
 python:
   install:
     - requirements: docs/requirements.txt
-    - requirements: requirements.txt
     - method: pip
       path: .

environment-dev.yml

@@ -1,12 +1,12 @@
 name: murefi-env
 channels:
-- conda-forge
+  - conda-forge
 dependencies:
-- codecov
-- flake8
-- pytest
-- pytest-cov
-- twine
-- wheel
-- pip:
-  - -r requirements.txt
+  - codecov
+  - flake8
+  - pandas>=3.0.0
+  - pytest
+  - pytest-cov
+  - twine
+  - pip:
+    - build

murefi/__init__.py

@@ -1,3 +1,22 @@
+# murefi
+# Copyright (C) 2019  Forschungszentrum Jülich GmbH
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published
+# by the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# For more information contact the maintainers of https://github.com/JuBiotech.
+
+import importlib.metadata
+
 from . import objectives
 from .core import ParameterMapping
 from .datastructures import (
@@ -11,4 +30,4 @@
 )
 from .ode import BaseODEModel
 
-__version__ = "5.3.0"
+__version__ = importlib.metadata.version(__package__ or __name__)

murefi/objectives.py

@@ -51,7 +51,7 @@ def negative_loglikelihood_dataset(theta):
             for (cm, observed_ts) in em_ts_list:
                 predicted_ts = predicted_replicate[cm.dependent_key]
                 ll = cm.loglikelihood(
-                    y=observed_ts.y, x=predicted_ts.y, replicate_id=rid, dependent_key=cm.dependent_key
+                    y=observed_ts.y, x=predicted_ts.y, name=f"{rid}.{cm.dependent_key}"
                 ).sum()
                 L.append(ll)
 

pyproject.toml

@@ -1,11 +1,56 @@
-# inspired by https://hynek.me/articles/sharing-your-labor-of-love-pypi-quick-and-dirty/
-
 [build-system]
-requires = ["setuptools", "wheel"]
+requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "murefi"
+version = "5.3.0"
+description = "Toolbox for multiple replicate fitting and Bayesian modeling."
+readme = "README.md"
+requires-python = ">=3.11"
+license = "AGPL-3.0-or-later"
+authors = [
+    {name = "Michael Osthege", email = "m.osthege@fz-juelich.de"},
+    {name = "Laura Helleckes", email = "l.helleckes@fz-juelich.de"},
+]
+classifiers = [
+    "Programming Language :: Python",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+]
+dependencies = [
+    "calibr8>=7.0.0",
+    "h5py",
+    "numpy",
+    "pandas",
+    "scipy",
+    "typing_extensions",
+]
+
+[project.urls]
+Homepage = "https://github.com/jubiotech/murefi"
+Documentation = "https://murefi.readthedocs.io/en/latest/"
+Download = "https://pypi.org/project/murefi/"
+
+[tool.setuptools]
+package-dir = {"murefi" = "murefi"}
+
+[tool.setuptools.package-data]
+"murefi" = ["py.typed"]
+
 [tool.black]
 line-length = 110
 
 [tool.isort]
 profile = "black"
+
+[tool.mypy]
+ignore_missing_imports = true
+exclude = [
+    'test_.*?\.py$',
+]