Other platform tests (#1113)

* blind attempt mac

* brew installs

* try python 3.11 numba

* try windows

* fix cache

* stuff

* stuff

* stuff

* stuff

* minimal test

* add basic workflow test

* Update .github/workflows/ci.yml

Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>

* close figures

---------

Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>

.github/workflows/ci.yml

@@ -17,8 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # update to 3.11 when numba allows (needed in umap)
-        python-version: ['3.9', '3.10']
+        python-version: ['3.9', '3.11']
 
     steps:
     - name: Check out repository
@@ -48,6 +47,65 @@ jobs:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
 
+  mac:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v3
+
+    - name: Prepare python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci
+
+    - name: Install dependencies
+      run: .github/workflows/install_deps.sh amici
+
+    - name: Run tests
+      timeout-minutes: 30
+      run: tox -e base
+
+    - name: Coverage
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
+
+  windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v3
+
+    - name: Prepare python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        pip install tox
+
+    - name: Run tests
+      shell: bash
+      timeout-minutes: 10
+      run: tox -e windows
+
   petab:
     runs-on: ubuntu-latest
     strategy:

.github/workflows/install_deps.sh

@@ -9,8 +9,14 @@ pip install wheel setuptools
 # Used to create local test environments
 pip install tox
 
-# Update apt
-sudo apt-get update
+# Update package lists
+if [ "$(uname)" == "Darwin" ]; then
+  # MacOS
+  brew update
+else
+  # Linux
+  sudo apt-get update
+fi
 
 # Check arguments
 for par in "$@"; do
@@ -22,8 +28,12 @@ for par in "$@"; do
 
     amici)
       # for amici
-      sudo apt-get install \
-        swig libatlas-base-dev libhdf5-serial-dev
+      if [ "$(uname)" == "Darwin" ]; then
+        brew install swig hdf5 libomp
+      else
+        sudo apt-get install \
+          swig libatlas-base-dev libhdf5-serial-dev
+      fi
     ;;
 
     ipopt)

test/base/test_workflow.py

@@ -0,0 +1,142 @@
+"""Test a basic workflow, with minimum dependencies.
+
+These tests are not for correctness, but for basic functionality.
+"""
+
+from functools import wraps
+
+import matplotlib.pyplot as plt
+
+import pypesto
+import pypesto.optimize as optimize
+import pypesto.profile as profile
+import pypesto.sample as sample
+import pypesto.visualize as visualize
+
+from ..util import CRProblem
+
+
+def close_fig(fun):
+    """Close figure."""
+
+    @wraps(fun)
+    def wrapped_fun(*args, **kwargs):
+        ret = fun(*args, **kwargs)
+        plt.close('all')
+        return ret
+
+    return wrapped_fun
+
+
+def test_objective():
+    """Test a simple objective function."""
+    crproblem = CRProblem()
+    obj = crproblem.get_objective()
+    p = crproblem.p_true
+
+    assert obj(p) == crproblem.get_fnllh()(p)
+    assert obj(p, sensi_orders=(0,)) == crproblem.get_fnllh()(p)
+    assert (obj(p, sensi_orders=(1,)) == crproblem.get_fsnllh()(p)).all()
+    assert (obj(p, sensi_orders=(2,)) == crproblem.get_fs2nllh()(p)).all()
+    fval, grad = obj(p, sensi_orders=(0, 1))
+    assert fval == crproblem.get_fnllh()(p)
+    assert (grad == crproblem.get_fsnllh()(p)).all()
+
+
+@close_fig
+def test_optimize():
+    """Test a simple multi-start optimization."""
+    crproblem = CRProblem()
+    problem = pypesto.Problem(
+        objective=crproblem.get_objective(),
+        lb=crproblem.lb,
+        ub=crproblem.ub,
+    )
+    optimizer = optimize.ScipyOptimizer()
+    n_start = 20
+    result = optimize.minimize(
+        problem=problem,
+        optimizer=optimizer,
+        n_starts=n_start,
+    )
+
+    # check basic sanity
+    assert len(result.optimize_result.list) == n_start
+    assert len(result.optimize_result.fval) == n_start
+    assert len(result.optimize_result.x) == n_start
+
+    # check that the results are sorted
+    fvals = result.optimize_result.fval
+    assert fvals == sorted(fvals)
+
+    # check that optimization was successful
+    assert fvals[0] < crproblem.get_fnllh()(crproblem.p_true)
+
+    # visualize the results
+    visualize.waterfall(result)
+
+
+@close_fig
+def test_profile():
+    """Test a simple profile calculation."""
+    crproblem = CRProblem()
+    problem = pypesto.Problem(
+        objective=crproblem.get_objective(),
+        lb=crproblem.lb,
+        ub=crproblem.ub,
+    )
+    optimizer = optimize.ScipyOptimizer()
+    n_starts = 5
+    result = optimize.minimize(
+        problem=problem,
+        optimizer=optimizer,
+        n_starts=n_starts,
+    )
+    profile_result = profile.parameter_profile(
+        problem=problem,
+        result=result,
+        optimizer=optimizer,
+        profile_index=[0],
+    )
+
+    # check basic sanity
+    assert len(profile_result.profile_result.list) == 1
+
+    # visualize the results
+    visualize.profiles(profile_result)
+
+
+@close_fig
+def test_sample():
+    """Test a simple sampling."""
+    crproblem = CRProblem()
+    problem = pypesto.Problem(
+        objective=crproblem.get_objective(),
+        lb=crproblem.lb,
+        ub=crproblem.ub,
+    )
+    optimizer = optimize.ScipyOptimizer()
+    n_start = 5
+    result = optimize.minimize(
+        problem=problem,
+        optimizer=optimizer,
+        n_starts=n_start,
+    )
+    sampler = sample.AdaptiveMetropolisSampler()
+    n_samples = 500
+    sample_result = sample.sample(
+        problem=problem,
+        result=result,
+        sampler=sampler,
+        n_samples=n_samples,
+    )
+
+    # check basic sanity
+    assert sample_result.sample_result.trace_x.shape == (
+        1,
+        n_samples + 1,
+        len(crproblem.p_true),
+    )
+
+    # visualize the results
+    visualize.sampling_1d_marginals(sample_result)

tox.ini

@@ -61,6 +61,16 @@ commands =
 description =
     Test basic functionality
 
+[testenv:windows]
+extras = test
+commands =
+    pytest \
+        test/base/test_prior.py \
+        test/base/test_problem.py \
+        test/base/test_workflow.py
+description =
+    Test basic functionality on Windows
+
 [testenv:petab]
 extras = test,amici,petab,pyswarm
 deps =