sindy-exp 0.2.0__tar.gz

sindy_exp-0.2.0/.github/workflows/main.yaml

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+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  Linting:
+    name: Linting
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: "Set up Python"
+      uses: actions/setup-python@v3
+      with:
+          python-version: "3.10"
+    - name: run pre-commit
+      run: |
+        pip install pre-commit
+        pre-commit run --all-files
+
+  Typing:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: "Set up Python"
+      uses: actions/setup-python@v3
+      with:
+          python-version: "3.10"
+    - name: install dependencies
+      run: |
+        pip install -e .[dev,jax]
+    - name: run mypy
+      run: |
+        mypy
+
+
+  Tests:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      max-parallel: 4
+      matrix:
+          python-version: ["3.10", "3.11", "3.12"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+          python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+          pip install --upgrade pip
+          pip install .[dev,jax]
+    - name: Test with pytest
+      run: |
+          coverage run --source=src/sindy_exp -m pytest tests  && coverage xml
+    - uses: actions/cache@v3
+      with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-dev.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-

sindy_exp-0.2.0/.github/workflows/release.yml

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+name: Release
+on:
+  push:
+    tags:
+      - '**'
+
+jobs:
+  print-context:
+    runs-on: ubuntu-latest
+    steps:
+      - name: print-gh-context
+        env:
+          GITHUB_CONTEXT: ${{ toJson(github) }}
+        run: echo "$GITHUB_CONTEXT"
+
+  pypi-publish:
+    name: Deploy release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/sindy-exp
+    permissions:
+      id-token: write
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v6
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.10"
+      - name: Install Build
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build .
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.13.0

sindy_exp-0.2.0/.gitignore

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+commit-msg
+todo
+scratch/
+*.png
+debugme*.py
+trials/*
+
+# IDE files
+.vscode
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# 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/

sindy_exp-0.2.0/.pre-commit-config.yaml

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+fail_fast: false
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+    - id: check-added-large-files
+      args: ["--maxkb=775"]
+    - id: check-merge-conflict
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+        exclude: > # multiline regex pattern
+          (?x)^(
+            scratch/.*
+          )
+- repo: https://github.com/psf/black
+  rev: 24.8.0
+  hooks:
+    - id: black
+- repo: https://github.com/PyCQA/flake8
+  rev: 7.0.0
+  hooks:
+    - id: flake8
+      exclude: > # multiline regex pattern
+        (?x)^(
+          scratch/.*
+        )
+      additional_dependencies: [flake8-comprehensions]
+      args: ["--config=setup.cfg"]
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+        types: [text]  # overwrite types: [rst]
+        types_or: [python, rst]
+      - id: rst-inline-touching-normal
+        types: [text]  # overwrite types: [rst]
+        types_or: [python, rst]
+-   repo: https://github.com/sphinx-contrib/sphinx-lint
+    rev: v0.9.1
+    hooks:
+    - id: sphinx-lint
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+    -   id: codespell
+        exclude: > # multiline regex pattern
+          (?x)^(
+            scratch/.*
+          )
+        types_or: [python, rst, markdown]
+        additional_dependencies: [tomli]
+        args: ["--toml=pyproject.toml"]
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+    -   id: end-of-file-fixer
+        exclude: (.txt|^docs/JOSS1|^docs/JOSS2|^examples/data/)
+        stages: [commit, merge-commit, push, prepare-commit-msg, commit-msg, post-checkout, post-commit, post-merge, post-rewrite]
+    -   id: trailing-whitespace
+        stages: [commit, merge-commit, push, prepare-commit-msg, commit-msg, post-checkout, post-commit, post-merge, post-rewrite]
+        exclude: (.txt|^docs/JOSS1|^docs/JOSS2|^examples/data/)

sindy_exp-0.2.0/CITATION.cff

@@ -0,0 +1,33 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: pysindy-experiments
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Jacob
+    family-names: Stevens-Haas
+    email: jacob.stevens.haas@gmail.com
+    affiliation: University of Washington
+    orcid: 'https://orcid.org/0000-0003-4142-5550'
+  - given-names: Yash
+    family-names: Bhangale
+    email: yash6599@uw.edu
+    affiliation: University of Washington
+repository-code: 'https://github.com/Jacob-Stevens-Haas/gen-experiments'
+abstract: >-
+  A package for forming pysindy experiments to be run in
+  mitosis.
+keywords:
+  - reproducibility
+  - experiments
+  - pysindy
+  - SINDy
+  - dynamical systems
+license: MIT
+commit: 31383318ae86fe3c662d683e0d4a9caf9a2def51
+version: 0.1.1
+date-released: '2024-04-28'

sindy_exp-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 Jacob Stevens-Haas
+
+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.

sindy_exp-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: sindy-exp
+Version: 0.2.0
+Summary: A basic library for constructing dynamics experiments
+Author-email: Jake Stevens-Haas <jacob.stevens.haas@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2022 Jacob Stevens-Haas
+        
+        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.
+        
+Project-URL: homepage, https://github.com/Jake-Stevens-Haas/gen-experiments
+Keywords: Machine Learning,Science,Mathematics,Experiments
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python
+Classifier: Framework :: Jupyter
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX :: Linux
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: seaborn
+Requires-Dist: scipy
+Requires-Dist: sympy
+Requires-Dist: dysts
+Provides-Extra: jax
+Requires-Dist: jax[cuda12]; extra == "jax"
+Requires-Dist: diffrax; extra == "jax"
+Requires-Dist: sympy2jax; extra == "jax"
+Requires-Dist: typing_extensions; extra == "jax"
+Provides-Extra: dev
+Requires-Dist: ipykernel; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pytest>=6.0.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: flake8-comprehensions>=3.1.0; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: codecov; extra == "dev"
+Requires-Dist: tomli; extra == "dev"
+Requires-Dist: pysindy>=2.1.0; extra == "dev"
+Dynamic: license-file
+
+# Dynamics Experiments
+
+A library for constructing dynamics experiments.
+This includes data generation and plotting/evaluation.
+
+## Getting started
+
+It's not yet on PyPI, so install it with `pip install sindy_exp @ git+https://github.com/Jacob-Stevens-Haas/sindy-experiments`
+
+Generate data
+
+    data = sindy_exp.data.gen_data("lorenz", num_trajectories=5, t_end=10.0, dt=0.01)["data]
+
+Evaluate your SINDy-like model with:
+
+    sindy_exp.odes.fit_eval(model, data)
+
+![Coefficient plots](images/coeff.png)
+
+A list of available ODE systems can be found in `ODE_CLASSES`, which includes most
+of the systems from the [dysts package](https://pypi.org/project/dysts/) as well as some non-chaotic systems.
+
+## ODE representation
+
+We deal primarily with autonomous ODE systems of the form:
+
+    dx/dt = sum_i f_i(x)
+
+Thus, we represent ODE systems as a list of right-hand side expressions.
+Each element is a dictionary mapping a term (Sympy expression) to its coefficient.
+
+## Other useful imports, compatibility, and extensions
+
+This is built to be compatible with dynamics learning models that follow the
+pysindy _BaseSINDy interface.
+The experiments are also built to be compatible with the `mitosis` tool,
+an experiment runner.
+To integrate your own experiments or data generation in a way that is compatible,
+see the `ProbData` and `DynamicsTrialData` classes.
+For plotting tools, see `plot_coefficients`, `compare_coefficient_plots_from_dicts`,
+`plot_test_trajectory`, `plot_training_data`, and `COLOR`.
+For metrics, see `coeff_metrics`, `pred_metrics`, and `integration_metrics`.
+
+![3d plot](images/composite.png)
+![1d plot](images/1d.png)

sindy_exp-0.2.0/README.md

@@ -0,0 +1,45 @@
+# Dynamics Experiments
+
+A library for constructing dynamics experiments.
+This includes data generation and plotting/evaluation.
+
+## Getting started
+
+It's not yet on PyPI, so install it with `pip install sindy_exp @ git+https://github.com/Jacob-Stevens-Haas/sindy-experiments`
+
+Generate data
+
+    data = sindy_exp.data.gen_data("lorenz", num_trajectories=5, t_end=10.0, dt=0.01)["data]
+
+Evaluate your SINDy-like model with:
+
+    sindy_exp.odes.fit_eval(model, data)
+
+![Coefficient plots](images/coeff.png)
+
+A list of available ODE systems can be found in `ODE_CLASSES`, which includes most
+of the systems from the [dysts package](https://pypi.org/project/dysts/) as well as some non-chaotic systems.
+
+## ODE representation
+
+We deal primarily with autonomous ODE systems of the form:
+
+    dx/dt = sum_i f_i(x)
+
+Thus, we represent ODE systems as a list of right-hand side expressions.
+Each element is a dictionary mapping a term (Sympy expression) to its coefficient.
+
+## Other useful imports, compatibility, and extensions
+
+This is built to be compatible with dynamics learning models that follow the
+pysindy _BaseSINDy interface.
+The experiments are also built to be compatible with the `mitosis` tool,
+an experiment runner.
+To integrate your own experiments or data generation in a way that is compatible,
+see the `ProbData` and `DynamicsTrialData` classes.
+For plotting tools, see `plot_coefficients`, `compare_coefficient_plots_from_dicts`,
+`plot_test_trajectory`, `plot_training_data`, and `COLOR`.
+For metrics, see `coeff_metrics`, `pred_metrics`, and `integration_metrics`.
+
+![3d plot](images/composite.png)
+![1d plot](images/1d.png)

sindy_exp-0.2.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=62", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sindy-exp"
+dynamic = ["version"]
+description = "A basic library for constructing dynamics experiments"
+readme = "README.md"
+requires-python = ">=3.10"
+license = {file = "LICENSE"}
+keywords = ["Machine Learning", "Science", "Mathematics", "Experiments"]
+authors = [
+  {email = "jacob.stevens.haas@gmail.com", name = "Jake Stevens-Haas"}
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Programming Language :: Python",
+  "Framework :: Jupyter",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Natural Language :: English",
+  "Operating System :: POSIX :: Linux",
+]
+dependencies = [
+  "matplotlib",
+  "numpy >= 2.0.0",
+  "seaborn",
+  "scipy",
+  "sympy",
+  "dysts",
+]
+
+[project.optional-dependencies]
+jax = [
+  "jax[cuda12]",
+  "diffrax",
+  "sympy2jax",
+  "typing_extensions"
+]
+dev = [
+  "ipykernel",
+  "mypy",
+  "pytest >= 6.0.0",
+  "pytest-cov",
+  "flake8",
+  "flake8-comprehensions>=3.1.0",
+  "black",
+  "coverage",
+  "isort",
+  "pre-commit",
+  "codecov",
+  "tomli",
+  "pysindy>=2.1.0",
+]
+
+[project.urls]
+homepage = "https://github.com/Jake-Stevens-Haas/gen-experiments"
+
+[tool.setuptools_scm]
+
+[tool.black]
+line-length = 88
+extend-exclude = '''
+/(
+    \.git
+  | \.mypy_cache
+  | \.venv
+  | .vscode
+  | version.py
+  | build
+  | dist
+  | scratch
+  | env
+)/
+'''
+preview = true
+
+[tool.codespell]
+skip = '*.html,./env,./scratch/*,todo'
+ignore-words-list = "nd, aks, ser"
+
+[tool.isort]
+profile = "black"
+src_paths = ["src/sindy_exp", "tests"]
+
+[tool.pytest.ini_options]
+filterwarnings = [
+  "ignore::RuntimeWarning",
+  "ignore::UserWarning",]
+addopts = '-m "not slow"'
+markers = ["slow"]
+
+[tool.mypy]
+files = [
+  "src/sindy_exp/__init__.py",
+  "src/sindy_exp/_utils.py",
+  "tests/test_all.py",
+]
+
+[[tool.mypy.overrides]]
+module="sklearn.*"
+ignore_missing_imports=true
+
+[[tool.mypy.overrides]]
+module="pysindy.*"
+ignore_missing_imports=true
+
+[[tool.mypy.overrides]]
+module="sympy.*"
+ignore_missing_imports=true
+
+[[tool.mypy.overrides]]
+module="scipy.*"
+ignore_missing_imports=true

sindy_exp-0.2.0/setup.cfg

@@ -0,0 +1,26 @@
+[flake8]
+exclude = 
+	.git,
+	env,
+	dist,
+	build,
+	site-packages,
+	bin,
+	scratch,
+	debug*,
+	composite_plots*,
+	__pycache__
+ignore = 
+	W503
+	E704
+	E203
+max-line-length = 88
+import-order-style = smarkets
+statistics = True
+count = True
+verbose = 1
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

sindy_exp-0.2.0/src/sindy_exp/__init__.py

@@ -0,0 +1,28 @@
+from ._data import ODE_CLASSES, gen_data
+from ._odes import fit_eval, plot_ode_panel
+from ._plotting import (
+    COLOR,
+    compare_coefficient_plots_from_dicts,
+    plot_coefficients,
+    plot_test_trajectory,
+    plot_training_data,
+)
+from ._typing import DynamicsTrialData, ProbData
+from ._utils import coeff_metrics, integration_metrics, pred_metrics
+
+__all__ = [
+    "gen_data",
+    "fit_eval",
+    "ProbData",
+    "DynamicsTrialData",
+    "coeff_metrics",
+    "pred_metrics",
+    "integration_metrics",
+    "ODE_CLASSES",
+    "plot_ode_panel",
+    "plot_coefficients",
+    "compare_coefficient_plots_from_dicts",
+    "plot_test_trajectory",
+    "plot_training_data",
+    "COLOR",
+]