gotranx 0.1.0__tar.gz

gotranx-0.1.0/PKG-INFO

@@ -0,0 +1,276 @@
+Metadata-Version: 2.1
+Name: gotranx
+Version: 0.1.0
+Summary: Sync local directories with dropbox
+Author-email: Henrik Finsberg <henriknf@simula.no>
+License: MIT
+Project-URL: Homepage, https://github.com/finsberg/gotranx
+Keywords: parser,lark,gotran,ode
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: attrs
+Requires-Dist: clang-format-docs
+Requires-Dist: black
+Requires-Dist: lark
+Requires-Dist: pint
+Requires-Dist: rich-click
+Requires-Dist: structlog
+Requires-Dist: sympy
+Requires-Dist: typer
+Requires-Dist: graphlib-backport; python_version < "3.9"
+Requires-Dist: typing_extensions; python_version < "3.9"
+Provides-Extra: dev
+Requires-Dist: bump-my-version; extra == "dev"
+Requires-Dist: ipython; extra == "dev"
+Requires-Dist: pdbpp; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: wheel; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs; extra == "docs"
+Requires-Dist: mkdocs-material; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pre-commit; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+
+[![pre-commit](https://github.com/finsberg/gotranx/actions/workflows/pre-commit.yml/badge.svg)](https://github.com/finsberg/gotranx/actions/workflows/pre-commit.yml)
+[![CI](https://github.com/finsberg/gotranx/actions/workflows/main.yml/badge.svg)](https://github.com/finsberg/gotranx/actions/workflows/main.yml)
+[![github pages](https://github.com/finsberg/gotranx/actions/workflows/pages.yml/badge.svg)](https://finsberg.github.io/gotranx)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+# gotranx
+
+`gotranx` is the next generation General ODE translator and is an attempt to a full rewrite of [gotran](https://github.com/ComputationalPhysiology/gotran).
+
+The general idea is that you write your ODE in a high level markup language and use `gotranx` to generate code for solving the ODE in different programming languages.
+
+`gotranx` uses [`sympy`](https://www.sympy.org/en/index.html) to generate the numerical schemes.
+
+**Note: `gotranx` is still under active development, so do not expect it to be complete.**
+
+## Install
+Install with pip
+```
+python3 -m pip install gotranx
+```
+or for the development version
+```
+python3 -m pip install git+https://github.com/finsberg/gotranx
+```
+
+## Quick start
+Define you ode in an `.ode` file, for example for the Lorentz attractor you can write the following file (called `lorentz.ode`)
+```
+parameters(
+sigma=12.0,
+rho=21.0,
+beta=2.4
+)
+
+states(x=1.0, y=2.0,z=3.05)
+
+dx_dt = sigma * (y - x)
+dy_dt = x * (rho - z) - y
+dz_dt = x * y - beta * z
+```
+which defines the parameters and states with default initial conditions. For each state-variable we also define the derivatives using `dx_dt` for the state with name `x`.
+
+Now we can generate code that can be used to solve the equation, e.g
+```
+python3 -m gotranx lorentz.ode --to .py --scheme forward_explicit_euler
+```
+which will generate a python file `lorentz.py` containing the following functions
+```python
+import numpy
+
+def parameter_index(name: str) -> float:
+    """Return the index of the parameter with the given name
+
+    Arguments
+    ---------
+    name : str
+        The name of the parameter
+
+    Returns
+    -------
+    float
+        The index of the parameter
+
+    Raises
+    ------
+    KeyError
+        If the name is not a valid parameter
+    """
+
+    data = {"beta": 0, "rho": 1, "sigma": 2}
+    return data[name]
+
+
+def state_index(name: str) -> float:
+    """Return the index of the state with the given name
+
+    Arguments
+    ---------
+    name : str
+        The name of the state
+
+    Returns
+    -------
+    float
+        The index of the state
+
+    Raises
+    ------
+    KeyError
+        If the name is not a valid state
+    """
+
+    data = {"x": 0, "y": 1, "z": 2}
+    return data[name]
+
+
+def init_parameter_values(**values):
+    """Initialize parameter values"""
+    # beta=2.4, rho=21.0, sigma=12.0
+
+    parameters = numpy.array([2.4, 21.0, 12.0])
+
+    for key, value in values.items():
+        parameters[parameter_index(key)] = value
+
+    return parameters
+
+
+def init_state_values(**values):
+    """Initialize state values"""
+    # x=1.0, y=2.0, z=3.05
+
+    states = numpy.array([1.0, 2.0, 3.05])
+
+    for key, value in values.items():
+        states[state_index(key)] = value
+
+    return states
+
+
+def rhs(t, states, parameters):
+    # Assign states
+    x = states[0]
+    y = states[1]
+    z = states[2]
+
+    # Assign parameters
+    beta = parameters[0]
+    rho = parameters[1]
+    sigma = parameters[2]
+
+    # Assign expressions
+    values = numpy.zeros(3)
+    values[0] = sigma * (-x + y)
+    values[1] = x * (rho - z) - y
+    values[2] = -beta * z + x * y
+
+    return values
+
+
+def forward_explicit_euler(states, t, dt, parameters):
+    # Assign states
+    x = states[0]
+    y = states[1]
+    z = states[2]
+
+    # Assign parameters
+    beta = parameters[0]
+    rho = parameters[1]
+    sigma = parameters[2]
+
+    # Assign expressions
+    values = numpy.zeros(3)
+    dx_dt = sigma * (-x + y)
+    values[0] = dt * dx_dt + x
+    dy_dt = x * (rho - z) - y
+    values[1] = dt * dy_dt + y
+    dz_dt = -beta * z + x * y
+    values[2] = dt * dz_dt + z
+
+    return values
+
+```
+
+Similarly, you can use the following command
+```
+python3 -m gotranx lorentz.ode --to .h --scheme forward_explicit_euler
+```
+to generate a C-header file with the following content
+```C
+#include <math.h>
+
+void init_parameter_values(double *parameters)
+{
+    /*
+    beta=2.4, rho=21.0, sigma=12.0
+    */
+    parameters[0] = 2.4;
+    parameters[1] = 21.0;
+    parameters[2] = 12.0;
+}
+
+void init_state_values(double *states)
+{
+    /*
+    x=1.0, y=2.0, z=3.05
+    */
+    states[0] = 1.0;
+    states[1] = 2.0;
+    states[2] = 3.05;
+}
+
+void rhs(const double t, const double *__restrict states, const double *__restrict parameters, double *values)
+{
+
+    // Assign states
+    const double x = states[0];
+    const double y = states[1];
+    const double z = states[2];
+
+    // Assign parameters
+    const double beta = parameters[0];
+    const double rho = parameters[1];
+    const double sigma = parameters[2];
+
+    // Assign expressions
+    values[0] = sigma * (-x + y);
+    values[1] = x * (rho - z) - y;
+    values[2] = -beta * z + x * y;
+}
+
+void forward_explicit_euler(const double *__restrict states, const double t, const double dt,
+                            const double *__restrict parameters, double *values)
+{
+
+    // Assign states
+    const double x = states[0];
+    const double y = states[1];
+    const double z = states[2];
+
+    // Assign parameters
+    const double beta = parameters[0];
+    const double rho = parameters[1];
+    const double sigma = parameters[2];
+
+    // Assign expressions
+    const double dx_dt = sigma * (-x + y);
+    values[0] = dt * dx_dt + x;
+    const double dy_dt = x * (rho - z) - y;
+    values[1] = dt * dy_dt + y;
+    const double dz_dt = -beta * z + x * y;
+    values[2] = dt * dz_dt + z;
+}
+```

gotranx-0.1.0/README.md

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+[![pre-commit](https://github.com/finsberg/gotranx/actions/workflows/pre-commit.yml/badge.svg)](https://github.com/finsberg/gotranx/actions/workflows/pre-commit.yml)
+[![CI](https://github.com/finsberg/gotranx/actions/workflows/main.yml/badge.svg)](https://github.com/finsberg/gotranx/actions/workflows/main.yml)
+[![github pages](https://github.com/finsberg/gotranx/actions/workflows/pages.yml/badge.svg)](https://finsberg.github.io/gotranx)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+# gotranx
+
+`gotranx` is the next generation General ODE translator and is an attempt to a full rewrite of [gotran](https://github.com/ComputationalPhysiology/gotran).
+
+The general idea is that you write your ODE in a high level markup language and use `gotranx` to generate code for solving the ODE in different programming languages.
+
+`gotranx` uses [`sympy`](https://www.sympy.org/en/index.html) to generate the numerical schemes.
+
+**Note: `gotranx` is still under active development, so do not expect it to be complete.**
+
+## Install
+Install with pip
+```
+python3 -m pip install gotranx
+```
+or for the development version
+```
+python3 -m pip install git+https://github.com/finsberg/gotranx
+```
+
+## Quick start
+Define you ode in an `.ode` file, for example for the Lorentz attractor you can write the following file (called `lorentz.ode`)
+```
+parameters(
+sigma=12.0,
+rho=21.0,
+beta=2.4
+)
+
+states(x=1.0, y=2.0,z=3.05)
+
+dx_dt = sigma * (y - x)
+dy_dt = x * (rho - z) - y
+dz_dt = x * y - beta * z
+```
+which defines the parameters and states with default initial conditions. For each state-variable we also define the derivatives using `dx_dt` for the state with name `x`.
+
+Now we can generate code that can be used to solve the equation, e.g
+```
+python3 -m gotranx lorentz.ode --to .py --scheme forward_explicit_euler
+```
+which will generate a python file `lorentz.py` containing the following functions
+```python
+import numpy
+
+def parameter_index(name: str) -> float:
+    """Return the index of the parameter with the given name
+
+    Arguments
+    ---------
+    name : str
+        The name of the parameter
+
+    Returns
+    -------
+    float
+        The index of the parameter
+
+    Raises
+    ------
+    KeyError
+        If the name is not a valid parameter
+    """
+
+    data = {"beta": 0, "rho": 1, "sigma": 2}
+    return data[name]
+
+
+def state_index(name: str) -> float:
+    """Return the index of the state with the given name
+
+    Arguments
+    ---------
+    name : str
+        The name of the state
+
+    Returns
+    -------
+    float
+        The index of the state
+
+    Raises
+    ------
+    KeyError
+        If the name is not a valid state
+    """
+
+    data = {"x": 0, "y": 1, "z": 2}
+    return data[name]
+
+
+def init_parameter_values(**values):
+    """Initialize parameter values"""
+    # beta=2.4, rho=21.0, sigma=12.0
+
+    parameters = numpy.array([2.4, 21.0, 12.0])
+
+    for key, value in values.items():
+        parameters[parameter_index(key)] = value
+
+    return parameters
+
+
+def init_state_values(**values):
+    """Initialize state values"""
+    # x=1.0, y=2.0, z=3.05
+
+    states = numpy.array([1.0, 2.0, 3.05])
+
+    for key, value in values.items():
+        states[state_index(key)] = value
+
+    return states
+
+
+def rhs(t, states, parameters):
+    # Assign states
+    x = states[0]
+    y = states[1]
+    z = states[2]
+
+    # Assign parameters
+    beta = parameters[0]
+    rho = parameters[1]
+    sigma = parameters[2]
+
+    # Assign expressions
+    values = numpy.zeros(3)
+    values[0] = sigma * (-x + y)
+    values[1] = x * (rho - z) - y
+    values[2] = -beta * z + x * y
+
+    return values
+
+
+def forward_explicit_euler(states, t, dt, parameters):
+    # Assign states
+    x = states[0]
+    y = states[1]
+    z = states[2]
+
+    # Assign parameters
+    beta = parameters[0]
+    rho = parameters[1]
+    sigma = parameters[2]
+
+    # Assign expressions
+    values = numpy.zeros(3)
+    dx_dt = sigma * (-x + y)
+    values[0] = dt * dx_dt + x
+    dy_dt = x * (rho - z) - y
+    values[1] = dt * dy_dt + y
+    dz_dt = -beta * z + x * y
+    values[2] = dt * dz_dt + z
+
+    return values
+
+```
+
+Similarly, you can use the following command
+```
+python3 -m gotranx lorentz.ode --to .h --scheme forward_explicit_euler
+```
+to generate a C-header file with the following content
+```C
+#include <math.h>
+
+void init_parameter_values(double *parameters)
+{
+    /*
+    beta=2.4, rho=21.0, sigma=12.0
+    */
+    parameters[0] = 2.4;
+    parameters[1] = 21.0;
+    parameters[2] = 12.0;
+}
+
+void init_state_values(double *states)
+{
+    /*
+    x=1.0, y=2.0, z=3.05
+    */
+    states[0] = 1.0;
+    states[1] = 2.0;
+    states[2] = 3.05;
+}
+
+void rhs(const double t, const double *__restrict states, const double *__restrict parameters, double *values)
+{
+
+    // Assign states
+    const double x = states[0];
+    const double y = states[1];
+    const double z = states[2];
+
+    // Assign parameters
+    const double beta = parameters[0];
+    const double rho = parameters[1];
+    const double sigma = parameters[2];
+
+    // Assign expressions
+    values[0] = sigma * (-x + y);
+    values[1] = x * (rho - z) - y;
+    values[2] = -beta * z + x * y;
+}
+
+void forward_explicit_euler(const double *__restrict states, const double t, const double dt,
+                            const double *__restrict parameters, double *values)
+{
+
+    // Assign states
+    const double x = states[0];
+    const double y = states[1];
+    const double z = states[2];
+
+    // Assign parameters
+    const double beta = parameters[0];
+    const double rho = parameters[1];
+    const double sigma = parameters[2];
+
+    // Assign expressions
+    const double dx_dt = sigma * (-x + y);
+    values[0] = dt * dx_dt + x;
+    const double dy_dt = x * (rho - z) - y;
+    values[1] = dt * dy_dt + y;
+    const double dz_dt = -beta * z + x * y;
+    values[2] = dt * dz_dt + z;
+}
+```

gotranx-0.1.0/pyproject.toml

@@ -0,0 +1,154 @@
+[build-system]
+requires = ["setuptools>=61.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "gotranx"
+version = "0.1.0"
+description = "Sync local directories with dropbox"
+authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
+license = {text = "MIT"}
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+]
+keywords = ["parser", "lark", "gotran", "ode"]
+urls = {Homepage = "https://github.com/finsberg/gotranx"}
+requires-python = ">=3.8"
+dependencies = [
+    "attrs",
+    "clang-format-docs",
+    "black",
+    "lark",
+    "pint",
+    "rich-click",
+    "structlog",
+    "sympy",
+    "typer",
+    'graphlib-backport;python_version < "3.9"',
+    'typing_extensions;python_version < "3.9"',
+]
+
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
+
+[project.optional-dependencies]
+dev = [
+    "bump-my-version",
+    "ipython",
+    "pdbpp",
+    "pre-commit",
+    "twine",
+    "wheel",
+]
+docs = [
+    "mkdocs",
+    "mkdocs-material",
+]
+test = [
+    "pre-commit",
+    "pytest",
+    "pytest-cov",
+]
+
+[project.scripts]
+gotranx = "gotranx.cli:app"
+
+[tool.setuptools]
+include-package-data = true
+package-dir = {"" = "src"}
+zip-safe = false
+
+[tool.setuptools.packages.find]
+where = ["src"]
+namespaces = false
+
+[tool.setuptools.package-data]
+"*" = ["*.lark"]
+
+[tool.aliases]
+test = "pytest"
+
+[tool.pytest.ini_options]
+addopts = "--cov=gotranx --cov-report html --cov-report xml --cov-report term-missing -v"
+testpaths = ["tests"]
+
+[tool.isort]
+profile = "black"
+
+[tool.mypy]
+files = ["src/gotranx", "tests"]
+ignore_missing_imports = true
+exclude = "docs"
+
+[tool.coverage.run]
+omit = ["src/gotranx/__main__.py", "src/gotranx/templates/__init__.py"]
+
+
+[tool.ruff]
+# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
+select = ["E", "F"]
+ignore = ["E402", "E741", "E743", "E731"]
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+fixable = ["A", "B", "C", "D", "E", "F"]
+unfixable = []
+
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".hg",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+]
+
+# Same as Black.
+line-length = 100
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+# Assume Python 3.10.
+target-version = "py310"
+
+[tool.ruff.mccabe]
+# Unlike Flake8, default to a complexity level of 10.
+max-complexity = 10
+
+
+[tool.bumpversion]
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+current_version = "0.1.0"
+
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'

gotranx-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

gotranx-0.1.0/src/gotranx/__init__.py

@@ -0,0 +1,51 @@
+from importlib.metadata import metadata
+
+from . import cli
+from . import codecomponent
+from . import exceptions
+from . import load
+from . import ode
+from . import ode_component
+from . import parser
+from . import codegen
+from . import transformer
+from . import units
+from . import sympytools
+from . import schemes
+from . import templates
+from . import cellml
+from .load import load_ode
+from .ode import ODE
+from .ode_component import Component
+from .parser import Parser
+from .transformer import TreeToODE
+
+
+meta = metadata("gotranx")
+__version__ = meta["Version"]
+__author__ = meta["Author"]
+__license__ = meta["License"]
+__email__ = meta["Author-email"]
+__program_name__ = meta["Name"]
+
+__all__ = [
+    "cli",
+    "parser",
+    "Parser",
+    "codegen",
+    "transformer",
+    "TreeToODE",
+    "exceptions",
+    "load",
+    "load_ode",
+    "ode_component",
+    "Component",
+    "ode",
+    "ODE",
+    "units",
+    "codecomponent",
+    "sympytools",
+    "schemes",
+    "templates",
+    "cellml",
+]