diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml index c877f66..ed8381a 100644 --- a/.github/workflows/pipeline.yml +++ b/.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__)" diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 2047654..f9a4225 100644 --- a/.github/workflows/release.yml +++ b/.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}" diff --git a/.gitignore b/.gitignore index 7d6b9a1..3df214f 100644 --- a/.gitignore +++ b/.gitignore @@ -17,3 +17,4 @@ murefi/examples/Sandbox.ipynb *.h5 /docs/build* /notebooks/*.png +dist/* diff --git a/.readthedocs.yml b/.readthedocs.yml index a527416..4e8177d 100644 --- a/.readthedocs.yml +++ b/.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: . diff --git a/environment-dev.yml b/environment-dev.yml index 4cbdd5c..f5a72f8 100644 --- a/environment-dev.yml +++ b/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 diff --git a/murefi/__init__.py b/murefi/__init__.py index 8f8b823..0a18418 100644 --- a/murefi/__init__.py +++ b/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 . +# 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__) diff --git a/murefi/objectives.py b/murefi/objectives.py index 2b09267..8731b27 100644 --- a/murefi/objectives.py +++ b/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) diff --git a/murefi/tests.py b/murefi/test_core.py similarity index 100% rename from murefi/tests.py rename to murefi/test_core.py diff --git a/pyproject.toml b/pyproject.toml index 9046bc1..43efbf1 100644 --- a/pyproject.toml +++ b/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$', +] diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 2a6a399..0000000 --- a/requirements.txt +++ /dev/null @@ -1,7 +0,0 @@ -calibr8>=7.0.0 -h5py -numpy -pandas -scipy -setuptools -typing_extensions diff --git a/setup.py b/setup.py deleted file mode 100644 index 2acaf5b..0000000 --- a/setup.py +++ /dev/null @@ -1,62 +0,0 @@ -# Copyright 2020 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 . - -import pathlib - -import setuptools - -__packagename__ = "murefi" -ROOT = pathlib.Path(__file__).parent - - -def get_version(): - import pathlib - import re - - VERSIONFILE = pathlib.Path(pathlib.Path(__file__).parent, __packagename__, "__init__.py") - initfile_lines = open(VERSIONFILE, "rt").readlines() - VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]" - for line in initfile_lines: - mo = re.search(VSRE, line, re.M) - if mo: - return mo.group(1) - raise RuntimeError("Unable to find version string in %s." % (VERSIONFILE,)) - - -__version__ = get_version() - - -setuptools.setup( - name=__packagename__, - packages=setuptools.find_packages(), # this must be the same as the name above - version=__version__, - description="Package for multiple replicate fitting and Bayesian modeling.", - url="https://github.com/JuBiotech/murefi", - author="Laura Marie Helleckes, Michael Osthege", - author_email="l.helleckes@fz-juelich.de, m.osthege@fz-juelich.de", - license="GNU Affero General Public License v3", - classifiers=[ - "Programming Language :: Python", - "Operating System :: OS Independent", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "License :: OSI Approved :: GNU Affero General Public License v3", - "Intended Audience :: Science/Research", - "Topic :: Scientific/Engineering", - "Topic :: Scientific/Engineering :: Mathematics", - ], - install_requires=[open(pathlib.Path(ROOT, "requirements.txt")).readlines()], -)