setup.py -> pyproject.toml

Author: dweindl

.github/workflows/ci.yml

@@ -98,7 +98,9 @@ jobs:
 
       # install package
       - name: Install the package
-        run: python -m pip install .[all]
+        run: |
+          python -m pip install .[all]
+          python -m pip install amici
 
       #############################################
       ## Lint
@@ -120,7 +122,7 @@ jobs:
           if [[ "${TAG}" =~ ^refs/tags/ ]]; then
             version="${TAG/refs\/tags\//}"
           else
-            version=$(python -c "import glob; import importlib.util; version_filename = glob.glob('**/_version.py', recursive=True)[0]; spec = importlib.util.spec_from_file_location('module.name', version_filename); module = importlib.util.module_from_spec(spec); spec.loader.exec_module(module); print(module.__version__)")
+            version=$(python -c "from biosimulators_amici import __version__; print(__version__)")
           fi
 
           echo "version=$version" >> $GITHUB_OUTPUT
@@ -180,7 +182,7 @@ jobs:
       ## Compile documentation
       #############################################
       - name: Install the requirements for compiling the documentation
-        run: python -m pip install -r docs-src/requirements.txt
+        run: python -m pip install .[doc]
 
       - name: Compile the documentation
         run: |

CONTRIBUTING.md

@@ -13,10 +13,6 @@ The repository follows standard Python conventions:
 * `README.md`: Overview of the repository
 * `biosimulators_amici/`: Python code for a BioSimulators-compliant command-line interface to AMICI
 * `tests/`: unit tests for the command-line interface
-* `setup.py`: installation script for the command-line interface
-* `setup.cfg`: configuration for the installation of the command-line interface
-* `requirements.txt`: dependencies for the command-line interface
-* `requirements.optional.txt`: optional dependencies for the command-line interface
 * `MANIFEST.in`: a list of files to include in the package for the command-line interface
 * `LICENSE`: License
 * `CONTRIBUTING.md`: Guide to contributing to BioSimulators-AMICI (this document)
@@ -54,7 +50,7 @@ coverage html
 BioSimulators-AMICI is documented using [reStructuredText](https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html) and the [napoleon Sphinx plugin](https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html). The documentation can be compiled by running the following commands:
 
 ```
-python -m pip install -r docs-src/requirements.txt
+python -m pip install .[doc]
 sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
 sphinx-build docs-src docs
 ```
@@ -71,16 +67,12 @@ Below are instructions for releasing a new version:
 
 1. Make the required changes to the repository.
   * To update the version of the underyling simulator, update its version numbers in the following files:
-    * `requirements.txt`
     * `Dockerfile`
     * `biosimulators.json`
 2. Commit the changes to this repository.
-3. Increment the `__version__` variable in `biosimulators_amici/_version.py`.
-4. Commit this change to `biosimulators_amici/_version.py`.
-5. Add a tag for the new version by running `git tag { version }`. `version` should be equal to the value of the
-   `__version__` variable in `biosimulators_amici/_version.py`.
-6. Push these commits and the new tag to GitHub by running `git push && git push --tags`.
-7. This push will trigger a GitHub action which will execute the following tasks:
+3. Add a tag for the new version by running `git tag { version }`.
+4. Push these commits and the new tag to GitHub by running `git push && git push --tags`.
+5. This push will trigger a GitHub action which will execute the following tasks:
    * Create a GitHub release for the version.
    * Push the release to PyPI.
    * Compile the documentation and push the compiled documentation to the repository so that the new documentation is viewable at github.io.

Dockerfile

@@ -32,6 +32,7 @@ LABEL \
 # Install requirements
 RUN apt-get update -y \
     && apt-get install -y --no-install-recommends \
+        git \
         g++ \
         libexpat1 \
         libatlas-base-dev \
@@ -47,7 +48,7 @@ RUN apt-get update -y \
 # Copy code for command-line interface into image and install it
 COPY . /root/Biosimulators_AMICI
 RUN pip install pip==23.0.1
-RUN pip install sympy /root/Biosimulators_AMICI \
+RUN SETUPTOOLS_SCM_PRETEND_VERSION_FOR_BIOSIMULATORS_AMICI=${VERSION} pip install sympy /root/Biosimulators_AMICI \
     && rm -rf /root/Biosimulators_AMICI
 #RUN pip install sympy /root/Biosimulators_AMICI amici==${SIMULATOR_VERSION} \
 #    && rm -rf /root/Biosimulators_AMICI

MANIFEST.in

@@ -3,7 +3,3 @@ include README.rst
 
 # license
 include LICENSE
-
-# requirements
-include requirements.txt
-include requirements.optional.txt

biosimulators_amici/__init__.py

@@ -1,7 +1,12 @@
 import amici
 
-from ._version import __version__  # noqa: F401
-# :obj:`str`: version
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("biosimulators-amici")
+except PackageNotFoundError:
+    # package is not installed
+    pass
 
 from .core import exec_sed_task, preprocess_sed_task, exec_sed_doc, exec_sedml_docs_in_combine_archive  # noqa: F401
 

biosimulators_amici/__main__.py

@@ -7,7 +7,7 @@
 """
 
 from . import get_simulator_version
-from ._version import __version__
+from . import __version__
 from .core import exec_sedml_docs_in_combine_archive
 from biosimulators_utils.simulator.cli import build_cli
 

biosimulators_amici/_version.py

@@ -4,10 +4,10 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-import re
 import datetime
 import os
 import sys
+import biosimulators_amici
 
 # -- Path setup --------------------------------------------------------------
 
@@ -23,15 +23,10 @@
 copyright = '{}, BioSimulators Team'.format(datetime.datetime.now().year)
 author = 'BioSimulators Team'
 
-# The short X.Y version
-filename = os.path.join(source_dir, '_version.py')
-verstrline = open(filename, 'rt').read()
-VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
-mo = re.search(VSRE, verstrline, re.M)
-version = mo.group(1)
-
 # The full version, including alpha/beta/rc tags
-release = '.'.join(version.split('.')[0:3])
+release = biosimulators_amici.__version__
+# The short X.Y version
+version = '.'.join(release.split('.')[0:2])
 
 # -- General configuration ---------------------------------------------------
 

docs-src/conf.py

@@ -0,0 +1,67 @@
+[build-system]
+requires = ["setuptools>=80", "setuptools-scm[simple]>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "biosimulators_amici"
+dynamic = ["version"]
+
+description = "BioSimulators-compliant command-line interface to the AMICI simulation program <https://github.com/AMICI-dev/amici>."
+readme = "README.md"
+authors = [
+  { name = "Center for Reproducible Biomedical Modeling", email = "[email protected]" }
+]
+license = { text = "MIT" }
+keywords = [
+  "BioSimulators",
+  "systems biology",
+  "computational biology",
+  "mathematical model",
+  "kinetic model",
+  "simulation",
+  "SBML",
+  "SED-ML",
+  "COMBINE",
+  "OMEX",
+]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = [
+    "biosimulators-utils[logging] >= 0.1.180",
+    "amici >= 0.11.17",
+    "kisao >= 2.33",
+    "lxml",
+    "numpy",
+]
+
+[project.optional-dependencies]
+tests = [
+    "biosimulators_utils[containers]",
+    "python_dateutil",
+]
+doc = [
+    "pydata-sphinx-theme",
+    "sphinx >= 1.8",
+]
+all = [
+    "biosimulators_utils[containers]",
+    "python_dateutil",
+    "pydata-sphinx-theme",
+    "sphinx >= 1.8",
+]
+
+[project.urls]
+Homepage = "https://github.com/biosimulators/Biosimulators_AMICI"
+Download = "https://github.com/biosimulators/Biosimulators_AMICI"
+
+[project.scripts]
+biosimulators-amici = "biosimulators_amici.__main__:main"
+
+[tool.setuptools.packages.find]
+where = ["."]
+exclude = ["tests", "tests.*"]