From 2414375a2c3acfb467acac6fb224e69948e98491 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 3 Aug 2023 23:34:59 +0530
Subject: [PATCH 01/17] Add caches for `pip` and restore keys for `nox`

---
 .github/workflows/test_on_push.yml | 38 +++++++++++++++++++++++++-----
 1 file changed, 32 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index 3a1142c939..8907a6444a 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -111,18 +111,40 @@ jobs:
             ${{ env.HOME }}/.local/lib/
             ${{ env.HOME }}/.local/include/
             ${{ env.HOME }}/.local/examples/
-          key: nox-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/install_KLU_Sundials.py') }}
+          key: nox-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         if: matrix.os == 'ubuntu-latest'
         run: nox -s pybamm-requires
 
+      - name: Restore pip cache on GNU/Linux
+        uses: actions/cache@v3
+        if: matrix.os == 'ubuntu-latest'
+        with:
+          path: ${{ env.HOME }}/.cache/pip
+          key: pip-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
+
+      - name: Restore pip cache on macOS
+        uses: actions/cache@v3
+        if: matrix.os == 'macos-latest'
+        with:
+          path: ${{ env.HOME }}/Library/Caches/pip
+          key: pip-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
+
+      - name: Restore pip cache on Windows
+        uses: actions/cache@v3
+        if: matrix.os == 'windows-latest'
+        with:
+          path: ${{ env.HOME }}\AppData\Local\pip\Cache
+          key: pip-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
+
       - name: Cache unit tests nox environment for GNU/Linux with Python 3.8, 3.9, and 3.10, and for macOS and Windows with all Python versions
         uses: actions/cache@v3
         if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
         with:
           path: ${{ github.workspace }}/.nox/unit/
-          key: ${{ runner.os }}-nox-unit-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/setup.py') }}
+          key: ${{ runner.os }}-nox-unit-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
+          restore-keys: ${{ runner.os }}-nox-unit-${{ steps.setup-python.outputs.python-version }}-
 
       - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10 and for macOS and Windows with all Python versions
         if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
@@ -133,7 +155,8 @@ jobs:
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         with:
           path: ${{ github.workspace }}/.nox/coverage/
-          key: ${{ runner.os }}-nox-coverage-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/setup.py', '**/.coveragerc') }}
+          key: ${{ runner.os }}-nox-coverage-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
+          restore-keys: ${{ runner.os }}-nox-coverage-${{ steps.setup-python.outputs.python-version }}-
 
       - name: Run unit tests for GNU/Linux with Python 3.11 and generate coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
@@ -148,7 +171,8 @@ jobs:
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         with:
           path: ${{ github.workspace }}/.nox/integration/
-          key: ${{ runner.os }}-nox-integration-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/setup.py') }}
+          key: ${{ runner.os }}-nox-integration-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
+          restore-keys: ${{ runner.os }}-nox-integration-${{ steps.setup-python.outputs.python-version }}-
 
       - name: Run integration tests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
@@ -159,7 +183,8 @@ jobs:
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         with:
           path: ${{ github.workspace }}/.nox/doctests/
-          key: ${{ runner.os }}-nox-doctests-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/setup.py', '**/docs/requirements.txt') }}
+          key: ${{ runner.os }}-nox-doctests-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
+          restore-keys: ${{ runner.os }}-nox-doctests-${{ steps.setup-python.outputs.python-version }}-
 
       - name: Install docs dependencies and run doctests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
@@ -170,7 +195,8 @@ jobs:
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         with:
           path: ${{ github.workspace }}/.nox/examples/
-          key: ${{ runner.os }}-nox-examples-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/setup.py') }}
+          key: ${{ runner.os }}-nox-examples-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
+          restore-keys: ${{ runner.os }}-nox-examples-${{ steps.setup-python.outputs.python-version }}-
 
       - name: Install dev dependencies and run example tests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11

From 153608047a9666c7bc29741eebb9dcf79c816795 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Fri, 4 Aug 2023 00:01:24 +0530
Subject: [PATCH 02/17] Update `pip` cache keys, test `nox` keys

---
 .github/workflows/test_on_push.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index 8907a6444a..b198fc58aa 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -76,8 +76,6 @@ jobs:
         env:
           # Homebrew environment variables
           HOMEBREW_NO_INSTALL_CLEANUP: 1
-          HOMEBREW_NO_ANALYTICS: 1
-          HOMEBREW_NO_GOOGLE_ANALYTICS: 1
           HOMEBREW_NO_AUTO_UPDATE: 1
           # Speed up CI
           NONINTERACTIVE: 1
@@ -86,6 +84,7 @@ jobs:
           rm -f /usr/local/bin/idle3*
           rm -f /usr/local/bin/pydoc3*
           rm -f /usr/local/bin/python3*
+          brew analytics off
           brew update
           brew install graphviz openblas
 
@@ -121,21 +120,21 @@ jobs:
         uses: actions/cache@v3
         if: matrix.os == 'ubuntu-latest'
         with:
-          path: ${{ env.HOME }}/.cache/pip
+          path: ~/.cache/pip
           key: pip-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
 
       - name: Restore pip cache on macOS
         uses: actions/cache@v3
         if: matrix.os == 'macos-latest'
         with:
-          path: ${{ env.HOME }}/Library/Caches/pip
+          path: ~/Library/Caches/pip
           key: pip-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
 
       - name: Restore pip cache on Windows
         uses: actions/cache@v3
         if: matrix.os == 'windows-latest'
         with:
-          path: ${{ env.HOME }}\AppData\Local\pip\Cache
+          path: ~\AppData\Local\pip\Cache
           key: pip-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
 
       - name: Cache unit tests nox environment for GNU/Linux with Python 3.8, 3.9, and 3.10, and for macOS and Windows with all Python versions

From 98a42fb0371cd764bb0111325645c1bae61f80a7 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Fri, 4 Aug 2023 00:22:47 +0530
Subject: [PATCH 03/17] Remove `pip` cache and `requirements.txt`

---
 .github/workflows/test_on_push.yml | 21 ---------------------
 requirements.txt                   | 19 -------------------
 2 files changed, 40 deletions(-)
 delete mode 100644 requirements.txt

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index b198fc58aa..4c0aa76c77 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -116,27 +116,6 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: nox -s pybamm-requires
 
-      - name: Restore pip cache on GNU/Linux
-        uses: actions/cache@v3
-        if: matrix.os == 'ubuntu-latest'
-        with:
-          path: ~/.cache/pip
-          key: pip-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
-
-      - name: Restore pip cache on macOS
-        uses: actions/cache@v3
-        if: matrix.os == 'macos-latest'
-        with:
-          path: ~/Library/Caches/pip
-          key: pip-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
-
-      - name: Restore pip cache on Windows
-        uses: actions/cache@v3
-        if: matrix.os == 'windows-latest'
-        with:
-          path: ~\AppData\Local\pip\Cache
-          key: pip-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
-
       - name: Cache unit tests nox environment for GNU/Linux with Python 3.8, 3.9, and 3.10, and for macOS and Windows with all Python versions
         uses: actions/cache@v3
         if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index d33b212a2e..0000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,19 +0,0 @@
-numpy >= 1.16
-scipy >= 1.3
-pandas >= 0.24
-anytree >= 2.4.3
-autograd >= 1.2
-scikit-fem >= 0.2.0
-casadi >= 3.6.0
-imageio>=2.9.0
-pybtex>=0.24.0
-sympy >= 1.8
-xarray
-bpx
-tqdm
-# Note: Matplotlib is loaded for debug plots but to ensure pybamm runs
-# on systems without an attached display it should never be imported
-# outside of plot() methods.
-# Should not be imported
-matplotlib >= 2.0
-#

From c6a77570b5dc8d6a866e7ded5a41774e289c7411 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 11:43:36 +0530
Subject: [PATCH 04/17] Cache `pip` with `setup-python`

---
 .github/workflows/test_on_push.yml | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index 4c0aa76c77..c2f2f91127 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -45,12 +45,10 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
-      - id: setup-python
-        name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v3
         with:
-          python-version: ${{ matrix.python-version }}
+          fetch-depth: 0
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
@@ -92,10 +90,16 @@ jobs:
         if: matrix.os == 'windows-latest'
         run: choco install graphviz --version=8.0.5
 
-      - name: Install standard Python dependencies
-        run: |
-          python -m pip install --upgrade pip wheel setuptools
-          python -m pip install nox
+      - name: Set up Python ${{ matrix.python-version }} and install standard Python dependencies
+        id: setup-python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: setup.py
+      - run: |
+          pip install --upgrade pip wheel setuptools nox
+          pip install -e .'[all,docs]'
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3

From 0fe74804111e18dc029cc5ba131b4f3e220f5c3c Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 12:05:06 +0530
Subject: [PATCH 05/17] Use `session.run_always` instead of `session.install`

---
 noxfile.py | 34 +++++++++++++++++++---------------
 1 file changed, 19 insertions(+), 15 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index 0c4cea7e2c..6ab24c34b4 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -19,6 +19,10 @@
 # Do not stdout ANSI colours on GitHub Actions
 if os.getenv("CI") == "true":
     os.environ["NO_COLOR"] = "1"
+    # The setup-python action installs and caches dependencies by default, so we skip
+    # installing them again in nox environments. The dev and docs sessions will still
+    # require a virtual environment, but we don't run them in the CI
+    nox.options.default_venv_backend = "none"
 
 
 def set_environment_variables(env_dict, session):
@@ -42,7 +46,7 @@ def run_pybamm_requires(session):
     """Download, compile, and install the build-time requirements for Linux and macOS: the SuiteSparse and SUNDIALS libraries."""  # noqa: E501
     set_environment_variables(PYBAMM_ENV, session=session)
     if sys.platform != "win32":
-        session.install("wget", "cmake")
+        session.run_always("pip", "install", "wget", "cmake")
         session.run("python", "scripts/install_KLU_Sundials.py")
         if not os.path.exists("./pybind11"):
             session.run(
@@ -60,11 +64,11 @@ def run_pybamm_requires(session):
 def run_coverage(session):
     """Run the coverage tests and generate an XML report."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    session.install("coverage")
-    session.install("-e", ".[all]")
+    session.run_always("pip", "install", "coverage")
+    session.run_always("pip", "install", "-e", ".[all]")
     if sys.platform != "win32":
-        session.install("-e", ".[odes]")
-        session.install("-e", ".[jax]")
+        session.run_always("pip", "install", "-e", ".[odes]")
+        session.run_always("pip", "install", "-e", ".[jax]")
     session.run("coverage", "run", "--rcfile=.coveragerc", "run-tests.py", "--nosub")
     session.run("coverage", "combine")
     session.run("coverage", "xml")
@@ -74,16 +78,16 @@ def run_coverage(session):
 def run_integration(session):
     """Run the integration tests."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    session.install("-e", ".[all]")
+    session.run_always("pip", "install", "-e", ".[all]")
     if sys.platform == "linux":
-        session.install("-e", ".[odes]")
+        session.run_always("pip", "install", "-e", ".[odes]")
     session.run("python", "run-tests.py", "--integration")
 
 
 @nox.session(name="doctests")
 def run_doctests(session):
     """Run the doctests and generate the output(s) in the docs/build/ directory."""
-    session.install("-e", ".[all,docs]")
+    session.run_always("pip", "install", "-e", ".[all,docs]")
     session.run("python", "run-tests.py", "--doctest")
 
 
@@ -91,17 +95,17 @@ def run_doctests(session):
 def run_unit(session):
     """Run the unit tests."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    session.install("-e", ".[all]")
+    session.run_always("pip", "install", "-e", ".[all]")
     if sys.platform == "linux":
-        session.install("-e", ".[odes]")
-        session.install("-e", ".[jax]")
+        session.run_always("pip", "install", "-e", ".[odes]")
+        session.run_always("pip", "install", "-e", ".[jax]")
     session.run("python", "run-tests.py", "--unit")
 
 
 @nox.session(name="examples")
 def run_examples(session):
     """Run the examples tests for Jupyter notebooks and Python scripts."""
-    session.install("-e", ".[all]")
+    session.run_always("pip", "install", "-e", ".[all]")
     session.run("python", "run-tests.py", "--examples")
 
 
@@ -127,10 +131,10 @@ def set_dev(session):
 def run_tests(session):
     """Run the unit tests and integration tests sequentially."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    session.install("-e", ".[all]")
+    session.run_always("pip", "install", "-e", ".[all]")
     if sys.platform == "linux" or sys.platform == "darwin":
-        session.install("-e", ".[odes]")
-        session.install("-e", ".[jax]")
+        session.run_always("pip", "install", "-e", ".[odes]")
+        session.run_always("pip", "install", "-e", ".[jax]")
     session.run("python", "run-tests.py", "--all")
 
 

From d361902ace405bc75b37b18f0aaa58c6c83022a8 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 12:10:02 +0530
Subject: [PATCH 06/17] Remove old `brew` Python symlink fixes

Not needed anymore after the issue was resolved
---
 .github/workflows/test_on_push.yml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index c2f2f91127..6a7e774752 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -66,22 +66,16 @@ jobs:
           sudo dot -c
           sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
 
-      # Added fixes to homebrew installs:
-      # rm -f /usr/local/bin/2to3
-      # (see https://github.com/actions/virtual-environments/issues/2322)
       - name: Install macOS system dependencies
         if: matrix.os == 'macos-latest'
         env:
           # Homebrew environment variables
           HOMEBREW_NO_INSTALL_CLEANUP: 1
           HOMEBREW_NO_AUTO_UPDATE: 1
+          HOMEBREW_NO_COLOR: 1
           # Speed up CI
           NONINTERACTIVE: 1
         run: |
-          rm -f /usr/local/bin/2to3*
-          rm -f /usr/local/bin/idle3*
-          rm -f /usr/local/bin/pydoc3*
-          rm -f /usr/local/bin/python3*
           brew analytics off
           brew update
           brew install graphviz openblas

From 9e1fc784881512f4f2b8305b31fff38a593f9d28 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 12:24:50 +0530
Subject: [PATCH 07/17] Fix Windows build error and add separate job

---
 .github/workflows/test_on_push.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index 6a7e774752..15dda8ba29 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -84,16 +84,18 @@ jobs:
         if: matrix.os == 'windows-latest'
         run: choco install graphviz --version=8.0.5
 
-      - name: Set up Python ${{ matrix.python-version }} and install standard Python dependencies
+      - name: Set up Python ${{ matrix.python-version }}
         id: setup-python
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
           cache-dependency-path: setup.py
+      
+      - name: Install PyBaMM dependencies
       - run: |
           pip install --upgrade pip wheel setuptools nox
-          pip install -e .'[all,docs]'
+          pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3

From a6b3c080bb047185e03c53d0ccadd948ebd76d00 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 12:26:03 +0530
Subject: [PATCH 08/17] Lint

---
 .github/workflows/test_on_push.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index 15dda8ba29..b79994c833 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -91,7 +91,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
           cache-dependency-path: setup.py
-      
+
       - name: Install PyBaMM dependencies
       - run: |
           pip install --upgrade pip wheel setuptools nox

From e30c34d948d852fad6248557b1dac309ace6c504 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 13:01:45 +0530
Subject: [PATCH 09/17] Remove inessential `nox` environment caches

---
 .github/workflows/test_on_push.yml | 42 +-----------------------------
 1 file changed, 1 insertion(+), 41 deletions(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index b79994c833..be461711dd 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -93,7 +93,7 @@ jobs:
           cache-dependency-path: setup.py
 
       - name: Install PyBaMM dependencies
-      - run: |
+        run: |
           pip install --upgrade pip wheel setuptools nox
           pip install -e .[all,docs]
 
@@ -116,26 +116,10 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: nox -s pybamm-requires
 
-      - name: Cache unit tests nox environment for GNU/Linux with Python 3.8, 3.9, and 3.10, and for macOS and Windows with all Python versions
-        uses: actions/cache@v3
-        if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
-        with:
-          path: ${{ github.workspace }}/.nox/unit/
-          key: ${{ runner.os }}-nox-unit-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
-          restore-keys: ${{ runner.os }}-nox-unit-${{ steps.setup-python.outputs.python-version }}-
-
       - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10 and for macOS and Windows with all Python versions
         if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
         run: nox -s unit
 
-      - name: Cache coverage nox environment for GNU/Linux with Python 3.11
-        uses: actions/cache@v3
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        with:
-          path: ${{ github.workspace }}/.nox/coverage/
-          key: ${{ runner.os }}-nox-coverage-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
-          restore-keys: ${{ runner.os }}-nox-coverage-${{ steps.setup-python.outputs.python-version }}-
-
       - name: Run unit tests for GNU/Linux with Python 3.11 and generate coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         run: nox -s coverage
@@ -144,38 +128,14 @@ jobs:
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         uses: codecov/codecov-action@v2.1.0
 
-      - name: Cache integration tests nox environment for GNU/Linux with Python 3.11
-        uses: actions/cache@v3
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        with:
-          path: ${{ github.workspace }}/.nox/integration/
-          key: ${{ runner.os }}-nox-integration-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
-          restore-keys: ${{ runner.os }}-nox-integration-${{ steps.setup-python.outputs.python-version }}-
-
       - name: Run integration tests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         run: nox -s integration
 
-      - name: Cache doctests nox environment for GNU/Linux with Python 3.11
-        uses: actions/cache@v3
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        with:
-          path: ${{ github.workspace }}/.nox/doctests/
-          key: ${{ runner.os }}-nox-doctests-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
-          restore-keys: ${{ runner.os }}-nox-doctests-${{ steps.setup-python.outputs.python-version }}-
-
       - name: Install docs dependencies and run doctests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         run: nox -s doctests
 
-      - name: Cache examples nox environment for GNU/Linux with Python 3.11
-        uses: actions/cache@v3
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        with:
-          path: ${{ github.workspace }}/.nox/examples/
-          key: ${{ runner.os }}-nox-examples-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/setup.py') }}
-          restore-keys: ${{ runner.os }}-nox-examples-${{ steps.setup-python.outputs.python-version }}-
-
       - name: Install dev dependencies and run example tests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         run: nox -s examples

From 23af9f0d22e5ed1bc8d54db91c5b757aadc40bc8 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 13:42:33 +0530
Subject: [PATCH 10/17] Update `pybamm-requires` cache

---
 .github/workflows/test_on_push.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index be461711dd..fcd29d6273 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -103,7 +103,6 @@ jobs:
         with:
           path: |
             # Repository files
-            ${{ github.workspace }}/.nox/pybamm-requires/
             ${{ github.workspace }}/pybind11/
             ${{ github.workspace }}/install_KLU_Sundials/
             # Headers and dynamic library files for SuiteSparse and SUNDIALS

From 2194023171545ccc4dfae7d607d34e3cba28e5b5 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 17:10:14 +0530
Subject: [PATCH 11/17] Try installing `scikits.odes` with other extras

---
 .github/workflows/test_on_push.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index fcd29d6273..cf696f5cbf 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -95,7 +95,7 @@ jobs:
       - name: Install PyBaMM dependencies
         run: |
           pip install --upgrade pip wheel setuptools nox
-          pip install -e .[all,docs]
+          pip install -e .[all,docs,odes]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3

From a8ea890e9a78f270529753bac67612817d047db6 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 17:14:55 +0530
Subject: [PATCH 12/17] Move Python dependencies step below `pybamm-requires`

---
 .github/workflows/test_on_push.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index cf696f5cbf..8d3ec4f6e0 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -92,11 +92,6 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
-        run: |
-          pip install --upgrade pip wheel setuptools nox
-          pip install -e .[all,docs,odes]
-
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
         if: matrix.os == 'ubuntu-latest'
@@ -115,6 +110,11 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: nox -s pybamm-requires
 
+      - name: Install PyBaMM dependencies
+        run: |
+          pip install --upgrade pip wheel setuptools nox
+          pip install -e .[all,docs,odes]
+
       - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10 and for macOS and Windows with all Python versions
         if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
         run: nox -s unit

From e283248cf37a9e4d329dec6ef890df66fcc0ce13 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 17:16:18 +0530
Subject: [PATCH 13/17] Remove `odes` extra

---
 .github/workflows/test_on_push.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index 8d3ec4f6e0..329f83b9c0 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -113,7 +113,7 @@ jobs:
       - name: Install PyBaMM dependencies
         run: |
           pip install --upgrade pip wheel setuptools nox
-          pip install -e .[all,docs,odes]
+          pip install -e .[all,docs]
 
       - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10 and for macOS and Windows with all Python versions
         if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')

From a7bd94bb87f7237c500d5d77315d6bb7b412d187 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 17:21:17 +0530
Subject: [PATCH 14/17] Revert Python dependencies step

---
 .github/workflows/test_on_push.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index 329f83b9c0..cf696f5cbf 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -92,6 +92,11 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
+      - name: Install PyBaMM dependencies
+        run: |
+          pip install --upgrade pip wheel setuptools nox
+          pip install -e .[all,docs,odes]
+
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
         if: matrix.os == 'ubuntu-latest'
@@ -110,11 +115,6 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: nox -s pybamm-requires
 
-      - name: Install PyBaMM dependencies
-        run: |
-          pip install --upgrade pip wheel setuptools nox
-          pip install -e .[all,docs]
-
       - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10 and for macOS and Windows with all Python versions
         if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
         run: nox -s unit

From 4235fa8102abb8b486aa0faa26c0f94d8fe71eb3 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 17:28:01 +0530
Subject: [PATCH 15/17] Remove `odes` extra again

---
 .github/workflows/test_on_push.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index cf696f5cbf..fcd29d6273 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -95,7 +95,7 @@ jobs:
       - name: Install PyBaMM dependencies
         run: |
           pip install --upgrade pip wheel setuptools nox
-          pip install -e .[all,docs,odes]
+          pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3

From 22615ffc6c8d1bf13ccdab6013087e079466b7a1 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 19:20:06 +0530
Subject: [PATCH 16/17] Set environment variables in the `examples` session

---
 noxfile.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/noxfile.py b/noxfile.py
index 6ab24c34b4..2a08865037 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -105,6 +105,7 @@ def run_unit(session):
 @nox.session(name="examples")
 def run_examples(session):
     """Run the examples tests for Jupyter notebooks and Python scripts."""
+    set_environment_variables(PYBAMM_ENV, session=session)
     session.run_always("pip", "install", "-e", ".[all]")
     session.run("python", "run-tests.py", "--examples")
 

From 72038ec72fc7cd0e0ed24df80131909f2058f0f3 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Sat, 5 Aug 2023 23:33:02 +0530
Subject: [PATCH 17/17] Remove `fetch-depth` value

---
 .github/workflows/test_on_push.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index fcd29d6273..8fb1aae588 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -47,8 +47,6 @@ jobs:
     steps:
       - name: Check out PyBaMM repository
         uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
 
       # Install and cache apt packages
       - name: Install Linux system dependencies