libcuflynx 0.4.0__tar.gz

libcuflynx-0.4.0/LICENSE

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+Copyright 2024–2026 Finbar J. Argus
+
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libcuflynx-0.4.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: libcuflynx
+Version: 0.4.0
+Summary: Generation and calibration of CellML circulatory system models from module/vessel arrays
+Author: Finbar J. Argus
+License: Apache-2.0
+Keywords: cellml,circulatory,modeling,parameter-identification
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.19.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: pyyaml>=5.4.0
+Requires-Dist: libcellml<0.7.0,>=0.6.3
+Requires-Dist: myokit>=1.39.1
+Requires-Dist: matplotlib>=3.3.0
+Requires-Dist: seaborn>=0.11.0
+Requires-Dist: SALib==1.5.1
+Requires-Dist: rdflib>=5.0.0
+Requires-Dist: emcee>=3.0.0
+Requires-Dist: corner>=2.2.0
+Requires-Dist: pint>=0.18
+Requires-Dist: numdifftools>=0.9.0
+Requires-Dist: scikit-learn
+Requires-Dist: tqdm>=4.62.0
+Requires-Dist: nevergrad>=1.0.12
+Requires-Dist: statsmodels>=0.12.0
+Provides-Extra: mpi
+Requires-Dist: mpi4py>=3.0.0; extra == "mpi"
+Requires-Dist: schwimmbad>=0.3.0; extra == "mpi"
+Provides-Extra: casadi
+Requires-Dist: casadi>=3.7.2; extra == "casadi"
+Provides-Extra: uq
+Requires-Dist: pymc>=5.0; extra == "uq"
+Requires-Dist: arviz>=0.15; extra == "uq"
+Provides-Extra: emulation
+Requires-Dist: autoemulate<3,>=2.1; extra == "emulation"
+Provides-Extra: cpp
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=3.0.0; extra == "dev"
+Requires-Dist: pytest-mpi>=0.6.0; extra == "dev"
+Requires-Dist: pytest-xdist>=2.5.0; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: flake8>=4.0.0; extra == "dev"
+Requires-Dist: mypy>=0.950; extra == "dev"
+Requires-Dist: tomli; python_version < "3.11" and extra == "dev"
+Requires-Dist: libcuflynx[mpi]; extra == "dev"
+Requires-Dist: libcuflynx[casadi]; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.0; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.24; extra == "docs"
+Requires-Dist: black>=22.0.0; extra == "docs"
+Provides-Extra: all
+Requires-Dist: libcuflynx[mpi]; extra == "all"
+Requires-Dist: libcuflynx[casadi]; extra == "all"
+Requires-Dist: libcuflynx[uq]; extra == "all"
+Requires-Dist: libcuflynx[emulation]; extra == "all"
+Requires-Dist: libcuflynx[cpp]; extra == "all"
+Dynamic: license-file
+
+# Overview
+
+[![Tests](https://github.com/physiomelinks/circulatory_autogen/actions/workflows/tests.yml/badge.svg?branch=master&event=push)](https://github.com/physiomelinks/circulatory_autogen/actions/workflows/tests.yml)
+
+This project allows the generation and calibration of cellml (and soon to be more) circulatory system models from an array of module/vessel names and connections.
+
+**The repository is `circulatory_autogen`; the package it installs is `libcuflynx`.** They are the
+same project under two names: papers, issues and this repository say *circulatory_autogen*, while
+PyPI, `pip install` and every `import` say *libcuflynx*. Searching for either name should find you
+this page.
+
+> **Note:** Test results and pass percentage are displayed in the [GitHub Actions workflow summary](https://github.com/physiomelinks/circulatory_autogen/actions/workflows/tests.yml). The badge above shows the overall test status (passing/failing) for `master` of this repository, which is where pull requests are merged. 
+
+# Installing, and what each extra costs
+
+The package is `libcuflynx`. A plain install gives you generation, simulation, calibration,
+sensitivity analysis and the built-in (emcee) MCMC:
+
+```
+pip install libcuflynx
+```
+
+Everything beyond that is an extra, because the optional parts are not small. These are
+installed sizes on disk, not wheel sizes — measured by installing into a fresh venv on Linux
+and taking `du` of `site-packages`, so they include the shared libraries that show up as
+companion directories (`scipy.libs`, `numpy.libs`) and every transitive dependency:
+
+| install | on disk | what it buys |
+|---|---|---|
+| `libcuflynx` | **≈ 540 MB** | generation, simulation, calibration, Sobol SA, emcee MCMC, Laplace identifiability |
+| `libcuflynx[mpi]` | **+5 MB**, and a system MPI toolchain | multi-rank runs under `mpiexec` |
+| `libcuflynx[casadi]` | **+221 MB** | `model_type: casadi_python`, `solver: casadi_integrator`, symbolic AD gradients |
+| `libcuflynx[uq]` | **+65 MB** | the pyMC sampler (`UQ_options: library: pymc`) |
+| `libcuflynx[emulation]` | **+750 MB or more** | training and using surrogate models (`do_emulation` / `use_emulator`) |
+| `libcuflynx[cpp]` | +0 MB | `model_type: cpp` — needs a C++ toolchain, which pip cannot install |
+| `libcuflynx[all]` | **≈ 1.6 GB** | all of the above |
+
+`[emulation]` is the one to think about before typing: `autoemulate` pulls in **torch**, which
+is 734 MB on its own — more than the whole default install — and requires Python >=3.10,<3.13.
+On Linux, pip's default torch wheel also drags in the bundled NVIDIA CUDA libraries, which can
+take it past 2 GB; install a CPU-only torch first if you do not want them. Because `[all]`
+includes `[emulation]`, `[all]` inherits that Python range too.
+
+The per-package numbers below do not add up to the total: the long tail of small transitive
+dependencies (packaging, dateutil, six, typing-extensions, cycler, joblib, threadpoolctl, ...)
+accounts for the rest.
+
+What makes up the default install: scipy 109 (+27 in `scipy.libs`), pandas 65, statsmodels 49,
+scikit-learn 46, numpy 41 (+27 in `numpy.libs`), matplotlib 28 with fontTools 25 / pillow 21,
+myokit 13, lxml 12, libcellml 8, kiwisolver 7, nevergrad 5, SALib 5, rdflib 5, libcuflynx
+itself 4, pint 3, seaborn 3, and emcee / corner / tqdm / numdifftools at about 1 MB each.
+
+The two that are larger than they look are **statsmodels (49 MB)** and **scikit-learn (46 MB)**.
+Neither is optional today: statsmodels supplies the Geweke diagnostic run after every emcee
+MCMC chain, and scikit-learn fits the quadratic used by the Laplace identifiability analysis.
+Both are on paths a plain install is expected to reach.
+
+**`[mpi]` is an extra, and that is the deliberate part.** `mpi4py` itself is only 5 MB, but it
+compiles against a system MPI toolchain (`libopenmpi-dev`, `mpich`) at install time, and that
+is the commonest `pip install` failure on macOS and Windows. A serial calibration needs none of
+it: `libcuflynx.utilities.mpi_utils` answers rank/size and supplies the one-rank collectives
+without ever importing `mpi4py`. Install the toolchain first, then the extra:
+
+```
+sudo apt install libopenmpi-dev          # or: brew install open-mpi
+pip install "libcuflynx[mpi]"
+```
+
+Ask for a model type, solver or analysis whose extra is missing and the error names the extra
+to install rather than reporting a bare missing module.
+
+Developing on a checkout instead: `pip install -e ".[dev]"`, which adds the test and lint
+tooling plus `mpi4py` (`tests/conftest.py` imports it at module scope, so the suite will not
+even collect without it) and `casadi` (whose tests otherwise `importorskip` themselves into
+silence).
+
+# Quickstart
+
+```
+pip install libcuflynx
+```
+
+No import path setup and no checkout are required — the package is importable, and its
+commands runnable, from any directory:
+
+```python
+from libcuflynx.utilities.utility_funcs import get_default_inp_data_dict
+from libcuflynx.scripts.script_generate_with_new_architecture import generate_with_new_architecture
+from libcuflynx.solver_wrappers import get_simulation_helper_from_inp_data_dict
+from libcuflynx.param_id.paramID import CVS0DParamID
+
+inp = get_default_inp_data_dict(file_prefix, input_param_file, resources_dir)
+generate_with_new_architecture(inp_data_dict=inp)     # CSV arrays -> CellML
+sim = get_simulation_helper_from_inp_data_dict(inp)   # simulate it
+sim.run()
+pid = CVS0DParamID.init_from_dict(inp)                # calibrate it
+```
+
+Each pipeline stage also has a console command, all configured from
+`user_run_files/user_inputs.yaml` and all taking `--help`:
+
+| Command | Stage |
+|---|---|
+| `cuflynx-generate` | generate a model from the CSV arrays |
+| `cuflynx-param-id` | generate + calibrate (`mpiexec -n N` for parallel) |
+| `cuflynx-sequential-param-id` | staged calibration — declared, not yet implemented |
+| `cuflynx-sensitivity` | Sobol sensitivity analysis |
+| `cuflynx-identifiability` | Laplace / profile-likelihood identifiability |
+| `cuflynx-train-emulator` | train a surrogate of the obs features |
+| `cuflynx-plot` | plot calibration results |
+
+### `CUFLYNX_USER_DIR` — where an installed libcuflynx reads and writes
+
+Every stage needs a directory holding `user_run_files/user_inputs.yaml`, and (unless the
+config overrides them) `resources/`, `module_config_user/`, `funcs_user/`,
+`generated_models/` and `param_id_output/`. It is `$CUFLYNX_USER_DIR` if set; otherwise the
+circulatory_autogen checkout being run from, if this is one — so a clone or a
+`pip install -e .` needs no configuration; otherwise the current working directory.
+
+After a plain `pip install libcuflynx` there is no checkout, so either run from your working
+directory or point the variable at it:
+
+```bash
+export CUFLYNX_USER_DIR=/path/to/my_study
+cuflynx-param-id
+```
+
+Nothing is ever written inside the installed package.
+
+**Imports without the `libcuflynx.` prefix are deprecated.** `from param_id.paramID import
+CVS0DParamID` still works in 0.4.0 and emits a `DeprecationWarning`; the shims are **removed in
+0.5.0**. See `CHANGELOG.md` for the migration, including the one for anyone who edited
+`funcs_user/*_funcs_user.py` in place.
+
+# Tutorial
+
+Follow the instructions in the tutorial to run the project: https://physiomelinks.github.io/circulatory_autogen/
+
+# AI-generated interactive tutorial
+
+BETA MODE: This AI-generated tutorial can be used to further understand the code base: https://deepwiki.com/FinbarArgus/circulatory_autogen/1-overview
+
+# The `CVODE_opencor` solver requires OpenCOR
+
+Every solver works from a plain install **except** `CVODE_opencor`. That backend needs the
+`opencor` Python module, which is supplied by an [OpenCOR](https://opencor.ws) installation
+and is not published on PyPI — so it cannot be shipped in a wheel and no `pip install` can
+provide it. Asking for it without OpenCOR raises an error naming the alternative rather than
+a bare `ModuleNotFoundError`.
+
+- **Use `solver: CVODE_myokit` instead.** It is a drop-in replacement: the same CellML model,
+  integrated by CVODE, with no OpenCOR involved. It is what `user_inputs.yaml` ships with,
+  and nothing else in the project needs OpenCOR.
+- **Or run inside OpenCOR**, whose bundled interpreter provides `opencor`. That route is
+  deprecated — see
+  [Deprecated: OpenCOR-based setup](https://physiomelinks.github.io/circulatory_autogen/getting-started/#deprecated-opencor-based-setup).
+
+This is expected to be replaced by a plain `pip install libopencor` once
+[libOpenCOR](https://opencor.ws/libopencor/) reaches PyPI; the bundled-interpreter route and
+the scripts that support it will be removed then.
+
+The handful of tests that exercise this backend are marked `need_opencor`. They have **no
+auto-skip**, so without OpenCOR they fail rather than skip — deselect them with
+`-m "not need_opencor"`, which is what CI does.
+
+# Releasing
+
+Releases are cut from a `v*` tag and published to PyPI by
+[`.github/workflows/release.yml`](.github/workflows/release.yml) using trusted publishing
+(OIDC) — no API token is stored anywhere. The procedure, the release-notes checklist, and the
+rules that cannot be undone (the tag must match `version` in `pyproject.toml`; a PyPI version
+can never be re-uploaded) are in [CONTRIBUTING.md](CONTRIBUTING.md#making-a-release).
+
+# Citing this work
+
+Cite the project as **circulatory_autogen** — that is the name used by the publications, the
+repository and any archived DOI. The PyPI distribution `libcuflynx` is the *same* software under
+its packaging name, so a paper citing circulatory_autogen and an environment listing
+`libcuflynx==0.4.0` refer to one artifact, not two. When it helps reproducibility, record both:
+the citation for the project and the exact package version installed, e.g.
+"circulatory_autogen (PyPI package `libcuflynx`, version 0.4.0)".
+
+# License
+circulatory_autogen is fully open source and distributed under the very permissive Apache License 2.0. See LICENSE for more information.
+
+## Optional third-party backends (not part of circulatory_autogen)
+
+circulatory_autogen is complete and fully open source on its own. Every feature works
+without installing any proprietary software.
+
+Separately, the project ships optional *adapters* that let users who already hold a licence
+for certain third-party products plug them in. Those products are **not part of
+circulatory_autogen**, are **not bundled or installed with it**, are **not covered by the
+Apache-2.0 licence above**, and are **not required by any feature**.
+
+- See [Optional third-party backends](https://physiomelinks.github.io/circulatory_autogen/getting-started/) in the tutorial for more info.

libcuflynx-0.4.0/README.md

@@ -0,0 +1,196 @@
+# Overview
+
+[![Tests](https://github.com/physiomelinks/circulatory_autogen/actions/workflows/tests.yml/badge.svg?branch=master&event=push)](https://github.com/physiomelinks/circulatory_autogen/actions/workflows/tests.yml)
+
+This project allows the generation and calibration of cellml (and soon to be more) circulatory system models from an array of module/vessel names and connections.
+
+**The repository is `circulatory_autogen`; the package it installs is `libcuflynx`.** They are the
+same project under two names: papers, issues and this repository say *circulatory_autogen*, while
+PyPI, `pip install` and every `import` say *libcuflynx*. Searching for either name should find you
+this page.
+
+> **Note:** Test results and pass percentage are displayed in the [GitHub Actions workflow summary](https://github.com/physiomelinks/circulatory_autogen/actions/workflows/tests.yml). The badge above shows the overall test status (passing/failing) for `master` of this repository, which is where pull requests are merged. 
+
+# Installing, and what each extra costs
+
+The package is `libcuflynx`. A plain install gives you generation, simulation, calibration,
+sensitivity analysis and the built-in (emcee) MCMC:
+
+```
+pip install libcuflynx
+```
+
+Everything beyond that is an extra, because the optional parts are not small. These are
+installed sizes on disk, not wheel sizes — measured by installing into a fresh venv on Linux
+and taking `du` of `site-packages`, so they include the shared libraries that show up as
+companion directories (`scipy.libs`, `numpy.libs`) and every transitive dependency:
+
+| install | on disk | what it buys |
+|---|---|---|
+| `libcuflynx` | **≈ 540 MB** | generation, simulation, calibration, Sobol SA, emcee MCMC, Laplace identifiability |
+| `libcuflynx[mpi]` | **+5 MB**, and a system MPI toolchain | multi-rank runs under `mpiexec` |
+| `libcuflynx[casadi]` | **+221 MB** | `model_type: casadi_python`, `solver: casadi_integrator`, symbolic AD gradients |
+| `libcuflynx[uq]` | **+65 MB** | the pyMC sampler (`UQ_options: library: pymc`) |
+| `libcuflynx[emulation]` | **+750 MB or more** | training and using surrogate models (`do_emulation` / `use_emulator`) |
+| `libcuflynx[cpp]` | +0 MB | `model_type: cpp` — needs a C++ toolchain, which pip cannot install |
+| `libcuflynx[all]` | **≈ 1.6 GB** | all of the above |
+
+`[emulation]` is the one to think about before typing: `autoemulate` pulls in **torch**, which
+is 734 MB on its own — more than the whole default install — and requires Python >=3.10,<3.13.
+On Linux, pip's default torch wheel also drags in the bundled NVIDIA CUDA libraries, which can
+take it past 2 GB; install a CPU-only torch first if you do not want them. Because `[all]`
+includes `[emulation]`, `[all]` inherits that Python range too.
+
+The per-package numbers below do not add up to the total: the long tail of small transitive
+dependencies (packaging, dateutil, six, typing-extensions, cycler, joblib, threadpoolctl, ...)
+accounts for the rest.
+
+What makes up the default install: scipy 109 (+27 in `scipy.libs`), pandas 65, statsmodels 49,
+scikit-learn 46, numpy 41 (+27 in `numpy.libs`), matplotlib 28 with fontTools 25 / pillow 21,
+myokit 13, lxml 12, libcellml 8, kiwisolver 7, nevergrad 5, SALib 5, rdflib 5, libcuflynx
+itself 4, pint 3, seaborn 3, and emcee / corner / tqdm / numdifftools at about 1 MB each.
+
+The two that are larger than they look are **statsmodels (49 MB)** and **scikit-learn (46 MB)**.
+Neither is optional today: statsmodels supplies the Geweke diagnostic run after every emcee
+MCMC chain, and scikit-learn fits the quadratic used by the Laplace identifiability analysis.
+Both are on paths a plain install is expected to reach.
+
+**`[mpi]` is an extra, and that is the deliberate part.** `mpi4py` itself is only 5 MB, but it
+compiles against a system MPI toolchain (`libopenmpi-dev`, `mpich`) at install time, and that
+is the commonest `pip install` failure on macOS and Windows. A serial calibration needs none of
+it: `libcuflynx.utilities.mpi_utils` answers rank/size and supplies the one-rank collectives
+without ever importing `mpi4py`. Install the toolchain first, then the extra:
+
+```
+sudo apt install libopenmpi-dev          # or: brew install open-mpi
+pip install "libcuflynx[mpi]"
+```
+
+Ask for a model type, solver or analysis whose extra is missing and the error names the extra
+to install rather than reporting a bare missing module.
+
+Developing on a checkout instead: `pip install -e ".[dev]"`, which adds the test and lint
+tooling plus `mpi4py` (`tests/conftest.py` imports it at module scope, so the suite will not
+even collect without it) and `casadi` (whose tests otherwise `importorskip` themselves into
+silence).
+
+# Quickstart
+
+```
+pip install libcuflynx
+```
+
+No import path setup and no checkout are required — the package is importable, and its
+commands runnable, from any directory:
+
+```python
+from libcuflynx.utilities.utility_funcs import get_default_inp_data_dict
+from libcuflynx.scripts.script_generate_with_new_architecture import generate_with_new_architecture
+from libcuflynx.solver_wrappers import get_simulation_helper_from_inp_data_dict
+from libcuflynx.param_id.paramID import CVS0DParamID
+
+inp = get_default_inp_data_dict(file_prefix, input_param_file, resources_dir)
+generate_with_new_architecture(inp_data_dict=inp)     # CSV arrays -> CellML
+sim = get_simulation_helper_from_inp_data_dict(inp)   # simulate it
+sim.run()
+pid = CVS0DParamID.init_from_dict(inp)                # calibrate it
+```
+
+Each pipeline stage also has a console command, all configured from
+`user_run_files/user_inputs.yaml` and all taking `--help`:
+
+| Command | Stage |
+|---|---|
+| `cuflynx-generate` | generate a model from the CSV arrays |
+| `cuflynx-param-id` | generate + calibrate (`mpiexec -n N` for parallel) |
+| `cuflynx-sequential-param-id` | staged calibration — declared, not yet implemented |
+| `cuflynx-sensitivity` | Sobol sensitivity analysis |
+| `cuflynx-identifiability` | Laplace / profile-likelihood identifiability |
+| `cuflynx-train-emulator` | train a surrogate of the obs features |
+| `cuflynx-plot` | plot calibration results |
+
+### `CUFLYNX_USER_DIR` — where an installed libcuflynx reads and writes
+
+Every stage needs a directory holding `user_run_files/user_inputs.yaml`, and (unless the
+config overrides them) `resources/`, `module_config_user/`, `funcs_user/`,
+`generated_models/` and `param_id_output/`. It is `$CUFLYNX_USER_DIR` if set; otherwise the
+circulatory_autogen checkout being run from, if this is one — so a clone or a
+`pip install -e .` needs no configuration; otherwise the current working directory.
+
+After a plain `pip install libcuflynx` there is no checkout, so either run from your working
+directory or point the variable at it:
+
+```bash
+export CUFLYNX_USER_DIR=/path/to/my_study
+cuflynx-param-id
+```
+
+Nothing is ever written inside the installed package.
+
+**Imports without the `libcuflynx.` prefix are deprecated.** `from param_id.paramID import
+CVS0DParamID` still works in 0.4.0 and emits a `DeprecationWarning`; the shims are **removed in
+0.5.0**. See `CHANGELOG.md` for the migration, including the one for anyone who edited
+`funcs_user/*_funcs_user.py` in place.
+
+# Tutorial
+
+Follow the instructions in the tutorial to run the project: https://physiomelinks.github.io/circulatory_autogen/
+
+# AI-generated interactive tutorial
+
+BETA MODE: This AI-generated tutorial can be used to further understand the code base: https://deepwiki.com/FinbarArgus/circulatory_autogen/1-overview
+
+# The `CVODE_opencor` solver requires OpenCOR
+
+Every solver works from a plain install **except** `CVODE_opencor`. That backend needs the
+`opencor` Python module, which is supplied by an [OpenCOR](https://opencor.ws) installation
+and is not published on PyPI — so it cannot be shipped in a wheel and no `pip install` can
+provide it. Asking for it without OpenCOR raises an error naming the alternative rather than
+a bare `ModuleNotFoundError`.
+
+- **Use `solver: CVODE_myokit` instead.** It is a drop-in replacement: the same CellML model,
+  integrated by CVODE, with no OpenCOR involved. It is what `user_inputs.yaml` ships with,
+  and nothing else in the project needs OpenCOR.
+- **Or run inside OpenCOR**, whose bundled interpreter provides `opencor`. That route is
+  deprecated — see
+  [Deprecated: OpenCOR-based setup](https://physiomelinks.github.io/circulatory_autogen/getting-started/#deprecated-opencor-based-setup).
+
+This is expected to be replaced by a plain `pip install libopencor` once
+[libOpenCOR](https://opencor.ws/libopencor/) reaches PyPI; the bundled-interpreter route and
+the scripts that support it will be removed then.
+
+The handful of tests that exercise this backend are marked `need_opencor`. They have **no
+auto-skip**, so without OpenCOR they fail rather than skip — deselect them with
+`-m "not need_opencor"`, which is what CI does.
+
+# Releasing
+
+Releases are cut from a `v*` tag and published to PyPI by
+[`.github/workflows/release.yml`](.github/workflows/release.yml) using trusted publishing
+(OIDC) — no API token is stored anywhere. The procedure, the release-notes checklist, and the
+rules that cannot be undone (the tag must match `version` in `pyproject.toml`; a PyPI version
+can never be re-uploaded) are in [CONTRIBUTING.md](CONTRIBUTING.md#making-a-release).
+
+# Citing this work
+
+Cite the project as **circulatory_autogen** — that is the name used by the publications, the
+repository and any archived DOI. The PyPI distribution `libcuflynx` is the *same* software under
+its packaging name, so a paper citing circulatory_autogen and an environment listing
+`libcuflynx==0.4.0` refer to one artifact, not two. When it helps reproducibility, record both:
+the citation for the project and the exact package version installed, e.g.
+"circulatory_autogen (PyPI package `libcuflynx`, version 0.4.0)".
+
+# License
+circulatory_autogen is fully open source and distributed under the very permissive Apache License 2.0. See LICENSE for more information.
+
+## Optional third-party backends (not part of circulatory_autogen)
+
+circulatory_autogen is complete and fully open source on its own. Every feature works
+without installing any proprietary software.
+
+Separately, the project ships optional *adapters* that let users who already hold a licence
+for certain third-party products plug them in. Those products are **not part of
+circulatory_autogen**, are **not bundled or installed with it**, are **not covered by the
+Apache-2.0 licence above**, and are **not required by any feature**.
+
+- See [Optional third-party backends](https://physiomelinks.github.io/circulatory_autogen/getting-started/) in the tutorial for more info.