emulsim 0.5.0__tar.gz

emulsim-0.5.0/.github/workflows/continous_integration.yml

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+name: "CI"
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    types: [opened, reopened, synchronize, ready_for_review]
+
+jobs:
+  tests:
+    name: ${{ matrix.os }}, python ${{ matrix.python-version }}, ${{ matrix.uv-resolution }} dependencies
+    if: github.event_name == 'push' || github.event.pull_request.draft == false
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.10", "3.13"]
+        uv-resolution:
+          - "lowest"
+          - "highest"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          resolution-strategy: ${{ matrix.uv-resolution }}
+
+      - name: Install dependencies
+        # install all requirements. Note that the full requirements are installed separately
+        # so the job does not fail if one of the packages cannot be installed. This allows
+        # testing the package for newer python version even when some of the optional
+        # packages are not yet available.
+        run: |
+          python -m pip install --upgrade pip
+          uv pip install -r requirements.txt --system
+          cat tests/requirements_full.txt | sed -e '/^\s*#.*$/d' -e '/^\s*$/d' | xargs -I % sh -c "uv pip install % --system || true"
+          uv pip install -r tests/requirements.txt --system
+
+      - name: Test with pytest
+        env:
+          NUMBA_WARNINGS: 1
+          MPLBACKEND: agg
+        run: |
+          uv pip install pytest --system
+          cd scripts
+          python run_tests.py --unit --parallel
+
+      - name: Test types with mypy
+        continue-on-error: true
+        run: |
+          python -m mypy --config-file pyproject.toml --pretty --package emulsim

emulsim-0.5.0/.github/workflows/docs.yml

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+name: "Build documentation"
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    types: [opened, reopened, synchronize, ready_for_review]
+
+jobs:
+  docs:
+    if: github.event_name == 'push' || github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: ammaraskar/sphinx-action@master
+        with:
+          docs-folder: "docs/"

emulsim-0.5.0/.github/workflows/release_pip.yml

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+name: Upload Python Package
+
+on:
+  release:
+    types: [released]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # https://github.com/pypa/setuptools_scm/issues/480
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Prepare build
+        run: |
+          python -m build 2>&1 | tee build.log
+          # exit `fgrep -i warning build.log | wc -l`
+
+      - name: Check the package
+        run: twine check --strict dist/*
+
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: python -m twine upload dist/*

emulsim-0.5.0/.gitignore

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+# project specific folders
+docs/source/packages
+docs/source/examples
+docs/source/examples_gallery
+docs/source/snippets
+tests/coverage/
+.DS_Store
+.settings
+debug/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# LaTeX
+*.aux
+*.bbl
+*.blg
+*.bgl
+*.out
+*.synctex.gz
+*.toc
+*Notes.bib
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+/.project
+/.pydevproject
+.vscode/settings.json
+docs/source/sg_execution_times.rst
+docs/methods/effective_droplet_model

emulsim-0.5.0/.readthedocs.yaml

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+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+formats:
+   - epub
+   - pdf
+
+python:
+   install:
+   - requirements: docs/requirements.txt

emulsim-0.5.0/LICENSE

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+MIT License
+
+Copyright (c) 2019 David Zwicker
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

emulsim-0.5.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: emulsim
+Version: 0.5.0
+Summary: Python framework for simulating physical systems consisting of multiple, interacting droplets.
+Author-email: David Zwicker <david.zwicker@ds.mpg.de>
+License-Expression: MIT
+Project-URL: homepage, https://github.com/zwicker-group/emulsim
+Project-URL: documentation, http://emulsim.readthedocs.io
+Project-URL: repository, https://github.com/zwicker-group/emulsim
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: <3.14,>=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib>=3.1
+Requires-Dist: networkx>=2
+Requires-Dist: numba>=0.59
+Requires-Dist: numpy>=1.22
+Requires-Dist: py-droplets>=0.23
+Requires-Dist: py-modelrunner<0.20,>=0.18
+Requires-Dist: py-pde>=0.38
+Requires-Dist: scipy>=1.4
+Requires-Dist: sympy>=1.5
+Requires-Dist: zarr<3,>=2.16
+Dynamic: license-file
+
+# emulsim
+
+Framework for simulating physical systems consisting of multiple, interacting entities.
+The current focus of the package lies on simulating interacting droplets in a common
+environment, but the framework is extensible and flexible.
+
+
+## Main idea
+
+The main idea is that the physical system consists of multiple `elements`, which
+together describe the state of the system. The dynamical rules are encoded in `actors`,
+which either act on individual elements, encoding their autonomous dynamics, or on
+multiple elements, introducing couplings.
+
+
+## Installation
+
+The package is not yet available on `pip` and must thus be cloned from Github. The
+necessary python packages can be installed using `pip`. To install the package together
+with the requirements, the following commands can be used:
+
+```bash
+git clone https://github.com/david-zwicker/emulsim.git
+pip install -r emulsim/requirements.txt
+```
+
+## Documentation
+
+The [documentation for this package is available online](https://emulsim.readthedocs.io/)
+
+
+## Running tests
+
+The package comes with automated tests that reside in `tests` directory. The purpose of
+these tests is to ensure some basic functionality of the package. Consequently, it is
+good practice to run the tests and fix problems before committing to the repository. To
+run tests, first install the the necessary python modules:
+
+```bash
+pip install -r tests/requirements.txt
+```
+
+The tests can be run using pytest or using the convenient scripts collected in the
+`scripts` directory:
+
+* `tests_run.sh` runs all tests in sequential order. The script takes an
+  optional argument that selects which tests are run: Only test files or methods
+  that match the argument will be run.
+* `tests_parallel.sh` runs all tests in parallel. Also takes a pattern argument.
+* `tests_coverage.sh` checks how much of the code is covered by tests.
+* `tests_types.sh` tests the type annotations in the python files. Type annotations are
+  optional in python, but they can be helpful to spot subtle programming problems. 
+* `format_code.sh` enforces the code style on all files.

emulsim-0.5.0/README.md

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+# emulsim
+
+Framework for simulating physical systems consisting of multiple, interacting entities.
+The current focus of the package lies on simulating interacting droplets in a common
+environment, but the framework is extensible and flexible.
+
+
+## Main idea
+
+The main idea is that the physical system consists of multiple `elements`, which
+together describe the state of the system. The dynamical rules are encoded in `actors`,
+which either act on individual elements, encoding their autonomous dynamics, or on
+multiple elements, introducing couplings.
+
+
+## Installation
+
+The package is not yet available on `pip` and must thus be cloned from Github. The
+necessary python packages can be installed using `pip`. To install the package together
+with the requirements, the following commands can be used:
+
+```bash
+git clone https://github.com/david-zwicker/emulsim.git
+pip install -r emulsim/requirements.txt
+```
+
+## Documentation
+
+The [documentation for this package is available online](https://emulsim.readthedocs.io/)
+
+
+## Running tests
+
+The package comes with automated tests that reside in `tests` directory. The purpose of
+these tests is to ensure some basic functionality of the package. Consequently, it is
+good practice to run the tests and fix problems before committing to the repository. To
+run tests, first install the the necessary python modules:
+
+```bash
+pip install -r tests/requirements.txt
+```
+
+The tests can be run using pytest or using the convenient scripts collected in the
+`scripts` directory:
+
+* `tests_run.sh` runs all tests in sequential order. The script takes an
+  optional argument that selects which tests are run: Only test files or methods
+  that match the argument will be run.
+* `tests_parallel.sh` runs all tests in parallel. Also takes a pattern argument.
+* `tests_coverage.sh` checks how much of the code is covered by tests.
+* `tests_types.sh` tests the type annotations in the python files. Type annotations are
+  optional in python, but they can be helpful to spot subtle programming problems. 
+* `format_code.sh` enforces the code style on all files.

emulsim-0.5.0/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

emulsim-0.5.0/docs/build_all.sh

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+#!/bin/sh
+
+make html
+make latexpdf
+make linkcheck