Move trapping_extended towards master

.github/workflows/main.yml

@@ -1,17 +1,23 @@
 name: Tests
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
 
 jobs:
   Linting:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v1
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v3
         with:
-          python-version: 3.7
+          python-version: "3.9"
       - name: Linting
         run: |
           pip install pre-commit
@@ -23,39 +29,36 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.9", "3.11"]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        pip install -r requirements-dev.txt
-        pip install sympy # needed for notebook 9, but not required for pysindy
+        pip install --upgrade pip
+        pip install .[dev,miosr,cvxpy,sbr]
     - name: Build the docs
       # Not exactly how RTD does it, but close.
       run: |
+        sudo apt-get update -y
         sudo apt-get install pandoc
+        pip install .[docs]
         cd docs
         python -m sphinx -T -E -W -b html -d _build/doctrees . _build/html
         cd ..
     - name: Test with pytest
       run: |
-        pytest test --cov=pysindy --cov-report=xml
+        coverage run --source=pysindy -m pytest test -m "not slow"  && coverage xml
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
-    - name: Execute feature notebook with papermill
-      run: |
-        pip install papermill
-        cd examples
-        papermill --report-mode 1_feature_overview.ipynb out.json
-    - uses: actions/cache@v1
+    - uses: actions/cache@v3
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-dev.txt') }}

test/conftest.py

@@ -69,7 +69,7 @@ def data_lorenz():
 
 
 @pytest.fixture
-def data_multiple_trajctories():
+def data_multiple_trajectories():
 
     n_points = [100, 200, 500]
     initial_conditions = [

test/test_pysindy.py

@@ -343,8 +343,8 @@ def test_score_pde(data_1d_random_pde):
     assert model.score(u, t) <= 1
 
 
-def test_fit_multiple_trajectories(data_multiple_trajctories):
-    x, t = data_multiple_trajctories
+def test_fit_multiple_trajectories(data_multiple_trajectories):
+    x, t = data_multiple_trajectories
     model = SINDy()
 
     # Should fail if multiple_trajectories flag is not set
@@ -371,8 +371,8 @@ def test_fit_multiple_trajectories(data_multiple_trajctories):
         model.fit(x, t=t, multiple_trajectories=True)
 
 
-def test_predict_multiple_trajectories(data_multiple_trajctories):
-    x, t = data_multiple_trajctories
+def test_predict_multiple_trajectories(data_multiple_trajectories):
+    x, t = data_multiple_trajectories
     model = SINDy()
     model.fit(x, t=t, multiple_trajectories=True)
 
@@ -384,8 +384,8 @@ def test_predict_multiple_trajectories(data_multiple_trajctories):
     assert len(p) == len(x)
 
 
-def test_score_multiple_trajectories(data_multiple_trajctories):
-    x, t = data_multiple_trajctories
+def test_score_multiple_trajectories(data_multiple_trajectories):
+    x, t = data_multiple_trajectories
     model = SINDy()
     model.fit(x, t=t, multiple_trajectories=True)
 
@@ -547,13 +547,13 @@ def test_print_discrete_time_multiple_trajectories(
     assert len(out) > 1
 
 
-def test_differentiate(data_lorenz, data_multiple_trajctories):
+def test_differentiate(data_lorenz, data_multiple_trajectories):
     x, t = data_lorenz
 
     model = SINDy()
     model.differentiate(x, t)
 
-    x, t = data_multiple_trajctories
+    x, t = data_multiple_trajectories
     model.differentiate(x, t, multiple_trajectories=True)
 
     model = SINDy(discrete_time=True)

test/test_sindyc.py

@@ -235,8 +235,8 @@ def test_score(data):
     assert model.score(x, u=u, t=t, x_dot=x) <= 1
 
 
-def test_fit_multiple_trajectores(data_multiple_trajctories):
-    x, t = data_multiple_trajctories
+def test_fit_multiple_trajectories(data_multiple_trajectories):
+    x, t = data_multiple_trajectories
     u = [np.ones((xi.shape[0], 2)) for xi in x]
 
     model = SINDy()
@@ -271,8 +271,8 @@ def test_fit_multiple_trajectores(data_multiple_trajctories):
     check_is_fitted(model)
 
 
-def test_predict_multiple_trajectories(data_multiple_trajctories):
-    x, t = data_multiple_trajctories
+def test_predict_multiple_trajectories(data_multiple_trajectories):
+    x, t = data_multiple_trajectories
     u = [np.ones((xi.shape[0], 2)) for xi in x]
 
     model = SINDy()
@@ -286,8 +286,8 @@ def test_predict_multiple_trajectories(data_multiple_trajctories):
     assert len(p) == len(x)
 
 
-def test_score_multiple_trajectories(data_multiple_trajctories):
-    x, t = data_multiple_trajctories
+def test_score_multiple_trajectories(data_multiple_trajectories):
+    x, t = data_multiple_trajectories
     u = [np.ones((xi.shape[0], 2)) for xi in x]
 
     model = SINDy()