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Remove ODES solver (pybamm-team#3932)
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* Remove ODES

* Remove some additional ODES files

* More ODES removals

* Update .github/workflows/run_periodic_tests.yml

* Change versions and fix comments

* Remove some unneeded comments

* Change log and docker

* Apply suggestions from code review

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

* Docker fix and bumping version in a test

* Revert test version

* Replace skipped test

* Update change log

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
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2 people authored and js1tr3 committed Aug 12, 2024
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2 changes: 0 additions & 2 deletions .github/codecov.yml
Original file line number Diff line number Diff line change
@@ -1,2 +0,0 @@
ignore:
- pybamm/install_odes.py
64 changes: 0 additions & 64 deletions .github/workflows/run_periodic_tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -149,19 +149,12 @@ jobs:
- name: Install build-time dependencies & run unit tests for M-series macOS runner
shell: bash
env:
# Point scikits.odes to the correct SUNDIALS installation
SUNDIALS_INST: $HOME/.local/lib
# Homebrew environment variables
HOMEBREW_NO_INSTALL_CLEANUP: 1
NONINTERACTIVE: 1
run: |
eval "$(pyenv init -)"
pyenv activate pybamm-${{ matrix.python-version }}
python -m pip install --upgrade pip nox
# Don't use Homebrew to install SUNDIALS because scikits.odes looks for
# in Homebrew folders instead, which we don't want
brew uninstall sundials --force
pip cache remove scikits.odes
python -m nox -s pybamm-requires -- --force
python -m nox -s unit
Expand All @@ -178,60 +171,3 @@ jobs:
eval "$(pyenv init -)"
pyenv activate pybamm-${{ matrix.python-version }}
pyenv uninstall -f $( python --version )
test_install_odes:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest, macos-12]
python-version: ["3.8", "3.9", "3.10", "3.11"]
# Include macOS M1 runners
include:
- os: macos-14
python-version: "3.10"
- os: macos-14
python-version: "3.11"
# scikits.odes is not available on Python 3.12 yet
# See https://github.com/bmcage/odes/issues/162
# - os: macos-14
# python-version: "3.12"
fail-fast: false
name: Test pybamm_install_odes (${{ matrix.os }} / Python ${{ matrix.python-version }})

steps:
- name: Check out PyBaMM repository
uses: actions/checkout@v4

- name: Install Linux system dependencies
if: matrix.os == 'ubuntu-latest'
run: |
sudo apt-get update
sudo apt-get install gfortran gcc libopenblas-dev
- name: Install macOS system dependencies
if: matrix.os == 'macos-12' || matrix.os == 'macos-14'
env:
# Homebrew environment variables
HOMEBREW_NO_INSTALL_CLEANUP: 1
HOMEBREW_NO_AUTO_UPDATE: 1
HOMEBREW_NO_COLOR: 1
# Speed up CI
NONINTERACTIVE: 1
run: |
brew analytics off
brew install openblas
brew reinstall gcc gfortran
- name: Set up Python ${{ matrix.python-version }}
id: setup-python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- name: Install PyBaMM
run: python -m pip install -e .

- name: Test pybamm_install_odes on ${{ matrix.os }}
run: |
python -m pip cache purge
python -m pip install wget cmake
pybamm_install_odes
32 changes: 9 additions & 23 deletions .github/workflows/test_on_push.yml
Original file line number Diff line number Diff line change
Expand Up @@ -38,11 +38,10 @@ jobs:
matrix:
os: [ubuntu-latest, macos-12, windows-latest]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
# We check coverage on Ubuntu with Python 3.11, so we skip unit tests for it here
# TODO: check coverage with Python 3.12 when [odes] supports it
# We check coverage on Ubuntu with Python 3.12, so we skip unit tests for it here
exclude:
- os: ubuntu-latest
python-version: "3.11"
python-version: "3.12"
# Include macOS M1 runners
include:
- os: macos-14
Expand All @@ -57,7 +56,6 @@ jobs:
- name: Check out PyBaMM repository
uses: actions/checkout@v4

# Install and cache apt packages
- name: Install Linux system dependencies
uses: awalsh128/cache-apt-pkgs-action@v1.4.2
if: matrix.os == 'ubuntu-latest'
Expand All @@ -76,7 +74,6 @@ jobs:
- name: Install macOS system dependencies
if: matrix.os == 'macos-12' || matrix.os == 'macos-14'
env:
# Homebrew environment variables
HOMEBREW_NO_INSTALL_CLEANUP: 1
HOMEBREW_NO_AUTO_UPDATE: 1
HOMEBREW_NO_COLOR: 1
Expand Down Expand Up @@ -121,20 +118,17 @@ jobs:
- name: Run unit tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
run: python -m nox -s unit

# Runs only on Ubuntu with Python 3.11
# TODO: check coverage with Python 3.12 when [odes] supports it
check_coverage:
needs: style
runs-on: ubuntu-latest
strategy:
fail-fast: false
name: Coverage tests (ubuntu-latest / Python 3.11)
name: Coverage tests (ubuntu-latest / Python 3.12)

steps:
- name: Check out PyBaMM repository
uses: actions/checkout@v4

# Install and cache apt packages
- name: Install Linux system dependencies
uses: awalsh128/cache-apt-pkgs-action@v1.4.2
with:
Expand All @@ -148,11 +142,11 @@ jobs:
sudo dot -c
sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
- name: Set up Python 3.11
- name: Set up Python 3.12
id: setup-python
uses: actions/setup-python@v5
with:
python-version: 3.11
python-version: 3.12
cache: 'pip'

- name: Install nox
Expand Down Expand Up @@ -204,7 +198,6 @@ jobs:
- name: Check out PyBaMM repository
uses: actions/checkout@v4

# Install and cache apt packages
- name: Install Linux system dependencies
uses: awalsh128/cache-apt-pkgs-action@v1.4.2
if: matrix.os == 'ubuntu-latest'
Expand All @@ -223,7 +216,6 @@ jobs:
- name: Install macOS system dependencies
if: matrix.os == 'macos-12' || matrix.os == 'macos-14'
env:
# Homebrew environment variables
HOMEBREW_NO_INSTALL_CLEANUP: 1
HOMEBREW_NO_AUTO_UPDATE: 1
HOMEBREW_NO_COLOR: 1
Expand Down Expand Up @@ -268,8 +260,7 @@ jobs:
- name: Run integration tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
run: python -m nox -s integration

# Runs only on Ubuntu with Python 3.12. Skips IDAKLU module compilation
# for speedups, which is already tested in other jobs.
# Skips IDAKLU module compilation for speedups, which is already tested in other jobs.
run_doctests:
needs: style
runs-on: ubuntu-latest
Expand All @@ -283,7 +274,6 @@ jobs:
with:
fetch-depth: 0

# Install and cache apt packages
- name: Install Linux system dependencies
uses: awalsh128/cache-apt-pkgs-action@v1.4.2
with:
Expand All @@ -297,7 +287,7 @@ jobs:
sudo dot -c
sudo apt-get install texlive-latex-extra dvipng
- name: Set up Python 3.11
- name: Set up Python
id: setup-python
uses: actions/setup-python@v5
with:
Expand All @@ -308,13 +298,12 @@ jobs:
run: |
pip install --upgrade pip wheel setuptools nox
- name: Install docs dependencies and run doctests for GNU/Linux with Python 3.11
- name: Install docs dependencies and run doctests for GNU/Linux
run: python -m nox -s doctests

- name: Check if the documentation can be built for GNU/Linux with Python 3.11
- name: Check if the documentation can be built for GNU/Linux
run: python -m nox -s docs

# Runs only on Ubuntu with Python 3.12
run_example_tests:
needs: style
runs-on: ubuntu-latest
Expand All @@ -326,7 +315,6 @@ jobs:
- name: Check out PyBaMM repository
uses: actions/checkout@v4

# Install and cache apt packages
- name: Install Linux system dependencies
uses: awalsh128/cache-apt-pkgs-action@v1.4.2
with:
Expand Down Expand Up @@ -369,7 +357,6 @@ jobs:
- name: Install dev dependencies and run example tests for GNU/Linux with Python 3.11
run: python -m nox -s examples

# Runs only on Ubuntu with Python 3.12
run_scripts_tests:
needs: style
runs-on: ubuntu-latest
Expand All @@ -381,7 +368,6 @@ jobs:
- name: Check out PyBaMM repository
uses: actions/checkout@v4

# Install and cache apt packages
- name: Install Linux system dependencies
uses: awalsh128/cache-apt-pkgs-action@v1.4.2
with:
Expand Down
3 changes: 0 additions & 3 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -107,9 +107,6 @@ KLU_module_deps
# setup
setup.log

# odes setup
scikits_odes_setup.log

# test
test.c
test.json
Expand Down
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@

## Breaking changes

- The ODES solver was removed due to compatability issues. Users should use IDAKULU, Casadi, or JAX instead. ([#3932](https://github.com/pybamm-team/PyBaMM/pull/3932))
- Integrated the `[pandas]` extra into the core PyBaMM package, deprecating the `pybamm[pandas]` optional dependency. Pandas is now a required dependency and will be installed upon installing PyBaMM ([#3892](https://github.com/pybamm-team/PyBaMM/pull/3892))
- Renamed "have_optional_dependency" to "import_optional_dependency" ([#3866](https://github.com/pybamm-team/PyBaMM/pull/3866))
- Integrated the `[latexify]` extra into the core PyBaMM package, deprecating the `pybamm[latexify]` set of optional dependencies. SymPy is now a required dependency and will be installed upon installing PyBaMM ([#3848](https://github.com/pybamm-team/PyBaMM/pull/3848))
Expand Down
3 changes: 1 addition & 2 deletions README.md
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Expand Up @@ -128,9 +128,8 @@ conda install -c conda-forge pybamm

### Optional solvers

Following GNU/Linux and macOS solvers are optionally available:
The following solvers are optionally available:

- [scikits.odes](https://scikits-odes.readthedocs.io/en/latest/)-based solver, see [the documentation](https://docs.pybamm.org/en/latest/source/user_guide/installation/gnu-linux-mac.html#optional-scikits-odes-solver).
- [jax](https://jax.readthedocs.io/en/latest/notebooks/quickstart.html)-based solver, see [the documentation](https://docs.pybamm.org/en/latest/source/user_guide/installation/gnu-linux-mac.html#optional-jaxsolver).

## 📖 Citing PyBaMM
Expand Down
1 change: 0 additions & 1 deletion docs/source/api/solvers/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@ Solvers
jax_solver
idaklu_solver
idaklu_jax
scikits_solvers
casadi_solver
algebraic_solvers
solution
Expand Down
8 changes: 0 additions & 8 deletions docs/source/api/solvers/scikits_solvers.rst

This file was deleted.

56 changes: 0 additions & 56 deletions docs/source/user_guide/installation/gnu-linux-mac.rst
Original file line number Diff line number Diff line change
Expand Up @@ -89,62 +89,6 @@ installed automatically when you install PyBaMM using ``pip``.
For an introduction to virtual environments, see
(https://realpython.com/python-virtual-environments-a-primer/).

.. _scikits.odes-label:

Optional - scikits.odes solver
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Users can install `scikits.odes <https://github.com/bmcage/odes>`__ to utilize its interfaced SUNDIALS ODE and DAE `solvers <https://docs.pybamm.org/en/latest/source/api/solvers/scikits_solvers.html>`__ wrapped in PyBaMM.

.. note::

Currently, only GNU/Linux and macOS are supported.

.. note::

The ``scikits.odes`` solver is not supported on Python 3.12 yet. Please refer to https://github.com/bmcage/odes/issues/162.
There is support for Python 3.8, 3.9, 3.10, and 3.11.

.. tab:: Debian/Ubuntu

In a terminal, run the following commands:

.. code:: bash
sudo apt-get install libopenblas-dev cmake
pybamm_install_odes
This will compile and install SUNDIALS for the system (under ``~/.local``), before installing ``scikits.odes``. (Alternatively, one can install SUNDIALS without this script and run ``pip install pybamm[odes]`` to install ``pybamm`` with ``scikits.odes``.)

.. tab:: macOS

In a terminal, run the following command:

.. code:: bash
brew install openblas gcc gfortran cmake
pybamm_install_odes
The ``pybamm_install_odes`` command, installed with PyBaMM, automatically downloads and installs the SUNDIALS library on your
system (under ``~/.local``), before installing `scikits.odes <https://scikits-odes.readthedocs.io/en/stable/installation.html>`__ . (Alternatively, one can install SUNDIALS without this script and run ``pip install pybamm[odes]`` to install ``pybamm`` with `scikits.odes <https://scikits-odes.readthedocs.io/en/stable/installation.html>`__)

To avoid installation failures when using ``pip install pybamm[odes]``, make sure to set the ``SUNDIALS_INST`` environment variable. If you have installed SUNDIALS using Homebrew, set the variable to the appropriate location. For example:

.. code:: bash
export SUNDIALS_INST=$(brew --prefix sundials)
Ensure that the path matches the installation location on your system. You can verify the installation location by running:

.. code:: bash
brew info sundials
Look for the installation path, and use that path to set the ``SUNDIALS_INST`` variable.

Note: The location where Homebrew installs SUNDIALS might vary based on the system architecture (ARM or Intel). Adjust the path in the ``export SUNDIALS_INST`` command accordingly.

To avoid manual setup of path the ``pybamm_install_odes`` is recommended for a smoother installation process, as it takes care of automatically downloading and installing the SUNDIALS library on your system.

Optional - JaxSolver
~~~~~~~~~~~~~~~~~~~~
Expand Down
20 changes: 1 addition & 19 deletions docs/source/user_guide/installation/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,8 @@ It can be installed using ``pip`` or ``conda``, or from source.
Optional solvers
----------------

Following GNU/Linux and macOS solvers are optionally available:
The following solvers are optionally available:

* `scikits.odes <https://scikits-odes.readthedocs.io/en/latest/>`_ -based solver, see `Optional - scikits.odes solver <https://docs.pybamm.org/en/latest/source/user_guide/installation/gnu-linux-mac.html#optional-scikits-odes-solver>`_.
* `jax <https://jax.readthedocs.io/en/latest/notebooks/quickstart.html>`_ -based solver, see `Optional - JaxSolver <https://docs.pybamm.org/en/latest/source/user_guide/installation/gnu-linux-mac.html#optional-jaxsolver>`_.

Dependencies
Expand Down Expand Up @@ -204,23 +203,6 @@ Dependency Minimu
`jaxlib <https://pypi.org/project/jaxlib/>`__ 0.4.20 jax Support library for JAX
========================================================================= ================== ================== =======================

.. _install.odes_dependencies:

odes dependencies
^^^^^^^^^^^^^^^^^

Installable with ``pip install "pybamm[odes]"``

======================================================================================================================================= ================== ================== =============================
Dependency Minimum Version pip extra Notes
======================================================================================================================================= ================== ================== =============================
`scikits.odes <https://docs.pybamm.org/en/latest/source/user_guide/installation/gnu-linux-mac.html#optional-scikits-odes-solver>`__ \- odes For scikits ODE & DAE solvers
======================================================================================================================================= ================== ================== =============================

.. note::

Before running ``pip install "pybamm[odes]"``, make sure to install ``scikits.odes`` build-time requirements as described `here <https://docs.pybamm.org/en/latest/source/user_guide/installation/gnu-linux-mac.html#optional-scikits-odes-solver>`_ .

Full installation guide
-----------------------

Expand Down
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