finitewave-model-courtemanche 0.2.0__tar.gz

finitewave_model_courtemanche-0.2.0/.gitignore

@@ -0,0 +1,207 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/

finitewave_model_courtemanche-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Finitewave
+
+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.

finitewave_model_courtemanche-0.2.0/PKG-INFO

@@ -0,0 +1,117 @@
+Metadata-Version: 2.4
+Name: finitewave-model-courtemanche
+Version: 0.2.0
+Summary: Courtemanche model.
+License: MIT
+License-File: LICENSE
+Keywords: cardiac,electrophysiology,finitewave,model
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+
+## Courtemanche finitewave model
+
+This model describes the ionic currents and action potential dynamics of human atrial myocytes. It includes detailed formulations for major ionic currents (fast sodium current, L-type calcium current, inward rectifier potassium current, transient outward potassium current, rapid and slow delayed rectifier potassium currents, and Na⁺/Ca²⁺ exchanger), as well as calcium handling mechanisms.
+
+The Courtemanche model is widely used as a reference atrial electrophysiology model. It has served as the basis for many subsequent atrial modeling studies, including investigations of atrial fibrillation and drug effects.
+
+### Reference
+Courtemanche M, Ramirez RJ, Nattel S. Ionic mechanisms underlying human atrial action potential properties: insights from a mathematical model. Am J Physiol. 1998 Jul;275(1):H301-21. 
+
+DOI: 10.1152/ajpheart.1998.275.1.H301
+
+### How to use (quickstart)
+```bash
+python -m examples.courtemanche_example
+```
+
+### How to test
+```bash
+python -m pytest -q
+```
+
+### Repository structure
+```text
+.
+├── courtemanche/                    # equations package (ops.py)
+│   ├── __init__.py
+│   └── ops.py                       # model equations (pure functions)
+├── implementation/                  # 0D model implementation
+│   ├── __init__.py
+│   └── courtemanche_0d.py
+├── example/
+│   └── courtemanche_example.py      # minimal script to run a short trace
+├── tests/
+│   └── test.py                      # smoke test; reproducibility checks
+├── .gitignore
+├── LICENSE                          # MIT
+├── pyproject.toml                   # configuration file
+└── README.md                        # this file
+```
+
+### Variables
+- `u = -84.5` - Membrane potential (mV)
+- `nai = 11.2` - intracellular Na⁺ concentration (mM)
+- `ki = 139` - intracellular K⁺ concentration (mM)
+- `cai = 0.000102` - intracellular Ca²⁺ concentration (mM)
+- `caup = 1.6` - Ca²⁺ concentration in uptake compartment (mM)
+- `carel = 1.1` - Ca²⁺ concentration in release compartment (mM)
+- `m = 0.00291 ` - activation gate of fast Na⁺ current
+- `h = 0.965` - fast inactivation gate of I_Na
+- `j = 0.978` - slow inactivation gate of I_Na
+- `d = 0.000137` - activation gate of L-type Ca²⁺ current
+- `f = 0.999837` - inactivation gate of I_CaL
+- `oa = 0.000592` - activation gate of transient outward K⁺ current
+- `oi = 0.9992` - inactivation gate of I_to
+- `ua = 0.003519` - activation gate of ultra-rapid K⁺ current
+- `ui = 0.9987` - inactivation gate of I_Kur
+- `xs = 0.0187` - activation gate of slow delayed rectifier K⁺ current
+- `xr = 0.0000329` - activation gate of rapid delayed rectifier K⁺ current
+- `fca = 0.775` - Ca²⁺-dependent inactivation gate of I_CaL
+- `irel  = 0` - Ca²⁺ release current from SR
+- `vrel  = 1` - SR release flux variable (voltage-dependent)
+- `urel  = 0` - SR release gate variable
+- `wrel  = 0.9` - SR recovery variable
+
+
+### Parameters
+- `gna = 7.8` - maximum conductance of fast sodium current (mS/cm²)
+- `gnab = 0.000674` - maximum conductance of background sodium current (mS/cm²)
+- `gk1 = 0.09` - maximum conductance of inward rectifier potassium current (mS/cm²)
+- `gkr = 0.0294` - maximum conductance of rapid delayed rectifier potassium current (mS/cm²)
+- `gks = 0.129` - maximum conductance of slow delayed rectifier potassium current (mS/cm²)
+- `gto = 0.1652` - maximum conductance of transient outward potassium current (mS/cm²)
+- `gcal = 0.1238` - maximum conductance of L-type calcium current (mS/cm²)
+- `gcab = 0.00113` - maximum conductance of background calcium current (mS/cm²)
+- `Vc = 20100` - cell volume (µL)
+- `Vj = Vc * 0.68` - junction volume (µL)
+- `Vup = Vj * 0.06 * 0.92` - uptake compartment volume (µL)
+- `Vrel = Vj * 0.06 * 0.08` - release compartment volume (µL)
+- `ibk = 0.0` - background current (µA/cm²)
+- `cao = 1.8` - extracellular Ca²⁺ concentration (mM)
+- `nao = 140` - extracellular Na⁺ concentration (mM)
+- `ko = 5.4` - extracellular K⁺ concentration (mM)
+- `caupmax = 15` - maximum Ca²⁺ uptake rate (mM/ms)
+- `kup = 0.00092` - uptake rate constant (mM)
+- `kmnai = 10` - Michaelis-Menten constant for Na⁺ (mM)
+- `kmko = 1.5` - Michaelis-Menten constant for K⁺ (mM)
+- `kmnancx = 87.5` - Michaelis-Menten constant for Na⁺/Ca²⁺ exchanger (mM)
+- `kmcancx = 1.38` - Michaelis-Menten constant for Ca²⁺/Na⁺ exchanger (mM)
+- `ksatncx = 0.1` - saturation constant for Na⁺/Ca²⁺ exchanger
+- `kmcmdn = 0.00238` - Michaelis-Menten constant for calmodulin (mM)
+- `kmtrpn = 0.0005` - Michaelis-Menten constant for troponin (mM)
+- `kmcsqn = 0.8` - Michaelis-Menten constant for calsequestrin (mM)
+- `trpnmax = 0.07` - maximum troponin concentration (mM)
+- `cmdnmax = 0.05` - maximum calmodulin concentration (mM)
+- `csqnmax = 10.0` - maximum calsequestrin concentration (mM)
+- `inacamax = 1600` - maximum Na⁺ current (µA/cm²)
+- `inakmax = 0.6` - maximum Na⁺/K⁺ pump current (µA/cm²)
+- `ipcamax = 0.275` - maximum Ca²⁺ pump current (µA/cm²)
+- `krel = 30` - release rate constant
+- `iupmax = 0.005` - maximum uptake current (µA/cm²)
+- `kq10 = 3` - temperature sensitivity coefficient
+

finitewave_model_courtemanche-0.2.0/README.md

@@ -0,0 +1,102 @@
+## Courtemanche finitewave model
+
+This model describes the ionic currents and action potential dynamics of human atrial myocytes. It includes detailed formulations for major ionic currents (fast sodium current, L-type calcium current, inward rectifier potassium current, transient outward potassium current, rapid and slow delayed rectifier potassium currents, and Na⁺/Ca²⁺ exchanger), as well as calcium handling mechanisms.
+
+The Courtemanche model is widely used as a reference atrial electrophysiology model. It has served as the basis for many subsequent atrial modeling studies, including investigations of atrial fibrillation and drug effects.
+
+### Reference
+Courtemanche M, Ramirez RJ, Nattel S. Ionic mechanisms underlying human atrial action potential properties: insights from a mathematical model. Am J Physiol. 1998 Jul;275(1):H301-21. 
+
+DOI: 10.1152/ajpheart.1998.275.1.H301
+
+### How to use (quickstart)
+```bash
+python -m examples.courtemanche_example
+```
+
+### How to test
+```bash
+python -m pytest -q
+```
+
+### Repository structure
+```text
+.
+├── courtemanche/                    # equations package (ops.py)
+│   ├── __init__.py
+│   └── ops.py                       # model equations (pure functions)
+├── implementation/                  # 0D model implementation
+│   ├── __init__.py
+│   └── courtemanche_0d.py
+├── example/
+│   └── courtemanche_example.py      # minimal script to run a short trace
+├── tests/
+│   └── test.py                      # smoke test; reproducibility checks
+├── .gitignore
+├── LICENSE                          # MIT
+├── pyproject.toml                   # configuration file
+└── README.md                        # this file
+```
+
+### Variables
+- `u = -84.5` - Membrane potential (mV)
+- `nai = 11.2` - intracellular Na⁺ concentration (mM)
+- `ki = 139` - intracellular K⁺ concentration (mM)
+- `cai = 0.000102` - intracellular Ca²⁺ concentration (mM)
+- `caup = 1.6` - Ca²⁺ concentration in uptake compartment (mM)
+- `carel = 1.1` - Ca²⁺ concentration in release compartment (mM)
+- `m = 0.00291 ` - activation gate of fast Na⁺ current
+- `h = 0.965` - fast inactivation gate of I_Na
+- `j = 0.978` - slow inactivation gate of I_Na
+- `d = 0.000137` - activation gate of L-type Ca²⁺ current
+- `f = 0.999837` - inactivation gate of I_CaL
+- `oa = 0.000592` - activation gate of transient outward K⁺ current
+- `oi = 0.9992` - inactivation gate of I_to
+- `ua = 0.003519` - activation gate of ultra-rapid K⁺ current
+- `ui = 0.9987` - inactivation gate of I_Kur
+- `xs = 0.0187` - activation gate of slow delayed rectifier K⁺ current
+- `xr = 0.0000329` - activation gate of rapid delayed rectifier K⁺ current
+- `fca = 0.775` - Ca²⁺-dependent inactivation gate of I_CaL
+- `irel  = 0` - Ca²⁺ release current from SR
+- `vrel  = 1` - SR release flux variable (voltage-dependent)
+- `urel  = 0` - SR release gate variable
+- `wrel  = 0.9` - SR recovery variable
+
+
+### Parameters
+- `gna = 7.8` - maximum conductance of fast sodium current (mS/cm²)
+- `gnab = 0.000674` - maximum conductance of background sodium current (mS/cm²)
+- `gk1 = 0.09` - maximum conductance of inward rectifier potassium current (mS/cm²)
+- `gkr = 0.0294` - maximum conductance of rapid delayed rectifier potassium current (mS/cm²)
+- `gks = 0.129` - maximum conductance of slow delayed rectifier potassium current (mS/cm²)
+- `gto = 0.1652` - maximum conductance of transient outward potassium current (mS/cm²)
+- `gcal = 0.1238` - maximum conductance of L-type calcium current (mS/cm²)
+- `gcab = 0.00113` - maximum conductance of background calcium current (mS/cm²)
+- `Vc = 20100` - cell volume (µL)
+- `Vj = Vc * 0.68` - junction volume (µL)
+- `Vup = Vj * 0.06 * 0.92` - uptake compartment volume (µL)
+- `Vrel = Vj * 0.06 * 0.08` - release compartment volume (µL)
+- `ibk = 0.0` - background current (µA/cm²)
+- `cao = 1.8` - extracellular Ca²⁺ concentration (mM)
+- `nao = 140` - extracellular Na⁺ concentration (mM)
+- `ko = 5.4` - extracellular K⁺ concentration (mM)
+- `caupmax = 15` - maximum Ca²⁺ uptake rate (mM/ms)
+- `kup = 0.00092` - uptake rate constant (mM)
+- `kmnai = 10` - Michaelis-Menten constant for Na⁺ (mM)
+- `kmko = 1.5` - Michaelis-Menten constant for K⁺ (mM)
+- `kmnancx = 87.5` - Michaelis-Menten constant for Na⁺/Ca²⁺ exchanger (mM)
+- `kmcancx = 1.38` - Michaelis-Menten constant for Ca²⁺/Na⁺ exchanger (mM)
+- `ksatncx = 0.1` - saturation constant for Na⁺/Ca²⁺ exchanger
+- `kmcmdn = 0.00238` - Michaelis-Menten constant for calmodulin (mM)
+- `kmtrpn = 0.0005` - Michaelis-Menten constant for troponin (mM)
+- `kmcsqn = 0.8` - Michaelis-Menten constant for calsequestrin (mM)
+- `trpnmax = 0.07` - maximum troponin concentration (mM)
+- `cmdnmax = 0.05` - maximum calmodulin concentration (mM)
+- `csqnmax = 10.0` - maximum calsequestrin concentration (mM)
+- `inacamax = 1600` - maximum Na⁺ current (µA/cm²)
+- `inakmax = 0.6` - maximum Na⁺/K⁺ pump current (µA/cm²)
+- `ipcamax = 0.275` - maximum Ca²⁺ pump current (µA/cm²)
+- `krel = 30` - release rate constant
+- `iupmax = 0.005` - maximum uptake current (µA/cm²)
+- `kq10 = 3` - temperature sensitivity coefficient
+

finitewave_model_courtemanche-0.2.0/courtemanche/__init__.py

@@ -0,0 +1 @@
+from . import ops