Remove ODES solver (pybamm-team#3932)

* 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 <[email protected]> * Docker fix and bumping version in a test * Revert test version * Replace skipped test * Update change log --------- Co-authored-by: Agriya Khetarpal <[email protected]>
cringeyburger · Mar 29, 2024 · 60ba076 · 60ba076
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diff --git a/.github/codecov.yml b/.github/codecov.yml
@@ -1,2 +0,0 @@
-ignore:
-  - pybamm/install_odes.py

diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml
@@ -150,19 +150,12 @@ 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
 
@@ -179,60 +172,3 @@ 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
diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
@@ -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
@@ -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/[email protected]
         if: matrix.os == 'ubuntu-latest'
@@ -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
@@ -123,20 +120,17 @@ 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/[email protected]
         with:
@@ -150,11 +144,11 @@ 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
@@ -206,7 +200,6 @@ jobs:
       - name: Check out PyBaMM repository
         uses: actions/checkout@v4
 
-      # Install and cache apt packages
       - name: Install Linux system dependencies
         uses: awalsh128/[email protected]
         if: matrix.os == 'ubuntu-latest'
@@ -225,7 +218,6 @@ 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
@@ -272,8 +264,7 @@ 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
@@ -287,7 +278,6 @@ jobs:
         with:
           fetch-depth: 0
 
-      # Install and cache apt packages
       - name: Install Linux system dependencies
         uses: awalsh128/[email protected]
         with:
@@ -301,7 +291,7 @@ 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:
@@ -311,13 +301,12 @@ jobs:
       - name: Install nox
         run: python -m pip install 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
@@ -329,7 +318,6 @@ jobs:
       - name: Check out PyBaMM repository
         uses: actions/checkout@v4
 
-      # Install and cache apt packages
       - name: Install Linux system dependencies
         uses: awalsh128/[email protected]
         with:
@@ -372,7 +360,6 @@ jobs:
       - name: Run example notebooks tests for GNU/Linux with Python 3.12
         run: python -m nox -s examples
 
-  # Runs only on Ubuntu with Python 3.12
   run_scripts_tests:
     needs: style
     runs-on: ubuntu-latest
@@ -384,7 +371,6 @@ jobs:
       - name: Check out PyBaMM repository
         uses: actions/checkout@v4
 
-      # Install and cache apt packages
       - name: Install Linux system dependencies
         uses: awalsh128/[email protected]
         with:

diff --git a/.gitignore b/.gitignore
@@ -107,9 +107,6 @@ KLU_module_deps
 # setup
 setup.log
 
-# odes setup
-scikits_odes_setup.log
-
 # test
 test.c
 test.json

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -28,6 +28,7 @@
 
 ## 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))

diff --git a/README.md b/README.md
@@ -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

diff --git a/docs/source/api/solvers/index.rst b/docs/source/api/solvers/index.rst
@@ -9,7 +9,6 @@ Solvers
   jax_solver
   idaklu_solver
   idaklu_jax
-  scikits_solvers
   casadi_solver
   algebraic_solvers
   solution

diff --git a/docs/source/api/solvers/scikits_solvers.rst b/docs/source/api/solvers/scikits_solvers.rst
diff --git a/docs/source/user_guide/installation/gnu-linux-mac.rst b/docs/source/user_guide/installation/gnu-linux-mac.rst
@@ -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
 ~~~~~~~~~~~~~~~~~~~~

diff --git a/docs/source/user_guide/installation/index.rst b/docs/source/user_guide/installation/index.rst
@@ -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
@@ -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
 -----------------------