Add basic tests

.github/workflows/build_docs.yml

@@ -0,0 +1,32 @@
+name: Build documentation
+
+on:
+  pull_request:
+    branches:
+      - "main"
+
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  html:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          pip install -e ".[dev]"
+      - name: Build documentation
+        run: |
+          cd docs
+          make html SPHINXOPTS="-W --keep-going"

.github/workflows/pre-commit.yml

@@ -0,0 +1,17 @@
+name: Static analysis
+
+on:
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+      - uses: pre-commit/[email protected]

.github/workflows/unit_tests.yml

@@ -0,0 +1,52 @@
+name: Unit tests
+
+on:
+  pull_request:
+    branches:
+      - "main"
+    paths:
+      - '**.py'
+
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          pip install -e ".[dev]"
+      - name: Test with pytest
+        run: |
+          pytest
+
+  pytest-windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          pip install -e ".[dev]"
+      - name: Test with pytest
+        run: |
+          pytest

.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - dev
+
+sphinx:
+  configuration: docs/conf.py

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

docs/source/api/numerical_methods.rst

@@ -1,10 +1,6 @@
 Numerical Methods
 =================
 
-.. autofunction:: conjugate_gradient
+.. autofunction:: pbeis.bicgstab
 
-.. autofunction:: bicgstab
-
-.. autofunction:: prebicgstab
-
-.. autofunction:: matrix_rescale
+.. autofunction:: pbeis.prebicgstab

examples/compare_methods.py

@@ -54,7 +54,7 @@ def current_function(t):
 print("Time domain method: ", time_elapsed, "s")
 
 # Frequency domain
-methods = ["direct"]
+methods = ["direct", "bicgstab", "prebicgstab"]
 impedances_freqs = []
 for method in methods:
     start_time = timer.time()

pbeis/__init__.py

@@ -1,4 +1,6 @@
+from pbeis.version import __version__
+
 from .eis_simulation import EISSimulation
-from .numerical_methods import bicgstab, conjugate_gradient, prebicgstab
+from .numerical_methods import bicgstab, prebicgstab
 from .plotting import nyquist_plot
 from .utils import SymbolReplacer

pbeis/eis_simulation.py

@@ -86,7 +86,7 @@ def set_up_model_for_eis(self, model):
         model : :class:`pybamm.BaseModel`
             Model to set up for EIS.
         """
-        pybamm.logger.info("Start setting up {} for EIS".format(self.model_name))
+        pybamm.logger.info(f"Start setting up {self.model_name} for EIS")
 
         # Make a new copy of the model
         new_model = model.new_copy()
@@ -132,7 +132,7 @@ def set_up_model_for_eis(self, model):
         new_model.algebraic[I_var] = I_ - I_applied
         new_model.initial_conditions[I_var] = 0
 
-        pybamm.logger.info("Finish setting up {} for EIS".format(self.model_name))
+        pybamm.logger.info(f"Finish setting up {self.model_name} for EIS")
 
         return new_model
 
@@ -179,9 +179,9 @@ def solve(self, frequencies, method="direct", inputs=None):
         Compute the impedance at the given frequencies by solving problem
 
         .. math::
-            i \omega \tau M x = J x + b
+            i \\omega \tau M x = J x + b
 
-        where i is the imagianary unit, \omega is the frequency, \tau is the model
+        where i is the imagianary unit, \\omega is the frequency, \tau is the model
         timescale, M is the mass matrix, J is the Jacobian, x is the state vector,
         and b gives a periodic forcing in the current.
 
@@ -191,7 +191,7 @@ def solve(self, frequencies, method="direct", inputs=None):
             The frequencies at which to compute the impedance.
         method : str, optional
             The method used to calculate the impedance. Can be 'direct', 'prebicgstab',
-            'bicgstab' or 'cg'. Default is 'direct'.
+            or 'bicgstab'. Default is 'direct'.
         inputs : dict, optional
             Any input parameters to pass to the model when solving
 
@@ -216,11 +216,11 @@ def solve(self, frequencies, method="direct", inputs=None):
                 # entry and the current density variable is the final entry
                 z = -x[-2][0] / x[-1][0]
                 zs.append(z)
-        elif method in ["prebicgstab", "bicgstab", "cg"]:
+        elif method in ["prebicgstab", "bicgstab"]:
             zs = self.iterative_method(frequencies, method=method)
         else:
-            raise NotImplementedError(
-                "'method' must be 'direct', 'prebicgstab', 'bicgstab' or 'cg', ",
+            raise ValueError(
+                "'method' must be 'direct', 'prebicgstab' or 'bicgstab', ",
                 f"but is '{method}'",
             )
 
@@ -238,9 +238,9 @@ def iterative_method(self, frequencies, method="prebicgstab"):
         Compute the impedance at the given frequencies by solving problem
 
         .. math::
-            i \omega \tau M x = J x + b
+            i \\omega \tau M x = J x + b
 
-        using an iterative method, where i is the imagianary unit, \omega
+        using an iterative method, where i is the imagianary unit, \\omega
         is the frequency, \tau is the model timescale, M is the mass matrix,
         J is the Jacobian, x is the state vector, and b gives a periodic
         forcing in the current.
@@ -251,7 +251,6 @@ def iterative_method(self, frequencies, method="prebicgstab"):
             The frequencies at which to compute the impedance.
         method : str, optional
             The method used to calculate the impedance. Can be:
-            'cg' - conjugate gradient - only use for Hermitian matrices
             'bicgstab' - use bicgstab with no preconditioner
             'prebicgstab' - use bicgstab with a preconditioner, this is
             the default.
@@ -303,10 +302,8 @@ def callback(xk):
                 )
                 solve_time = time.process_time() - solve_start_time
 
-            elif method == "cg":
-                sol = pbeis.conjugate_gradient(
-                    A, self.b, start_point=sol, callback=callback
-                )
+            else:
+                raise ValueError
 
             # Store number of iterations at this frequency
             iters_per_frequency.append(num_iters)
@@ -316,7 +313,7 @@ def callback(xk):
             z = -sol[-2][0] / sol[-1][0]
             zs.append(z)
 
-        return self.zs
+        return zs
 
     def nyquist_plot(self, **kwargs):
         """