Promote weak form SINDy from a feature library to a sibling SINDy class.

.flake8

@@ -8,8 +8,10 @@ exclude =
     bin,
     __pycache__
 ignore =
-    W503         # Line break before binary operator - Conflicts black
-    E203         # Whitespace before ':' - Conflicts black
+    # Line break before binary operator - Conflicts black
+    W503
+    # Whitespace before ':' - Conflicts black
+    E203
 per-file-ignores =
     __init__.py:F401,F403
     examples/**:E402,E501

.github/workflows/main.yml

@@ -19,11 +19,8 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
-      - name: Linting
-        run: |
-          pip install pre-commit
-          pre-commit run --all-files
+          python-version: "3.12"
+      - uses: pre-commit/action@v3.0.1
 
   build:
     name: Build
@@ -34,7 +31,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: "3.10"
+        python-version: "3.12"
     - name: build
       run: pip install .
     - name: test import
@@ -51,7 +48,7 @@ jobs:
     - name: "Set up Python"
       uses: actions/setup-python@v4
       with:
-          python-version: "3.11"
+          python-version: "3.12"
     - name: Install doc dependencies
       run: |
         sudo apt-get update -y
@@ -72,13 +69,12 @@ jobs:
 
   tests:
     name: Tests
-    needs: linting
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       max-parallel: 4
       matrix:
-        python-version: ["3.10", "3.12"]
+        python-version: ["3.12", "3.13", "3.14"]
 
     steps:
     - uses: actions/checkout@v4
@@ -131,15 +127,18 @@ jobs:
       contents: write   # gh-pages publishing
 
     steps:
+    # checkout code
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0  # ASV history
 
+    # Get Python
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
+    # Restore environment if it's cached
     - name: Cache pip
       uses: actions/cache@v4
       with:
@@ -148,12 +147,14 @@ jobs:
         restore-keys: |
           ${{ runner.os }}-pip-
 
+    # Otherwise, restore environment
     - name: Install dependencies
       run: |
         pip install --upgrade pip
         pip install .[dev]
         pip install asv
 
+    # Restore any cached ASV environments
     - name: Cache ASV environments
       uses: actions/cache@v4
       with:
@@ -162,28 +163,57 @@ jobs:
         restore-keys: |
           asv-${{ runner.os }}-py${{ matrix.python-version }}-
 
+    # Detect machine information for benchmarks
     - name: Setup ASV machine
       run: |
         cd asv_bench
         asv machine --yes
 
+    # Check regressions of any benchmarks
     - name: Check regression
       if: github.event_name == 'pull_request'
       run: |
         cd asv_bench
         git fetch origin $GITHUB_BASE_REF:base $GITHUB_REF:pr
         asv continuous base pr -e
 
+    # This whole second section should be a separate workflow, triggered by
+    # commit to main, not PRs
+    # Checkout gh-pages into a side folder (if it exists)
+    - uses: actions/checkout@v4
+      continue-on-error: true
+      with:
+        ref: gh-pages
+        path: gh-pages
+
+    # Restore historical ASV results into workspace
+    - name: Restore ASV history
+      run: |
+        mkdir -p asv_bench/.asv/results
+        if [ -d gh-pages/.asv/results ]; then
+          rsync -a gh-pages/.asv/results/ asv_bench/.asv/results/
+        fi
+
+    # Generate website benchmark results for new commits
     - name: Run benchmarks on main
       if: github.event_name == 'push' && github.ref == 'refs/heads/main'
       run: |
         cd asv_bench
-        asv run
+        asv run --skip-existing-successful
         asv publish
+
+    # Stage site payload: html + updated results
+    - name: Prepare Pages payload
+      run: |
+        rm -rf pages && mkdir -p pages/.asv
+        rsync -a asv_bench/.asv/html/ pages/
+        rsync -a asv_bench/.asv/results/ pages/.asv/results/
+
+    # Deploy
     - name: Deploy ASV dashboard to gh-pages
       if: github.event_name == 'push' && github.ref == 'refs/heads/main'
       uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: asv_bench/.asv/html
-        force_orphan: true
+        force_orphan: false

.github/workflows/notebooks.yml

@@ -30,7 +30,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - name: Install dependencies
         run: |
           pip install .[cvxpy,miosr] sympy nbconvert jupyter matplotlib seaborn pandas dysts

.github/workflows/release.yml

@@ -14,7 +14,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - name: Install Build
         run: |
           python -m pip install --upgrade pip

.pre-commit-config.yaml

@@ -11,11 +11,11 @@ repos:
   hooks:
     - id: reorder-python-imports
 - repo: https://github.com/ambv/black
-  rev: 22.3.0
+  rev: 23.12.1
   hooks:
     - id: black
 - repo: https://github.com/PyCQA/flake8
-  rev: 5.0.4
+  rev: 7.3.0
   hooks:
     - id: flake8
       args: ["--config=.flake8"]

asv_bench/asv.conf.json

@@ -9,6 +9,9 @@
     "results_dir": ".asv/results",
     "html_dir": ".asv/html",
     "show_commit_url": "https://github.com/$OWNER/$REPO/commit/",
+    "install_command": [
+        "in-dir={env_dir} python -m pip install {wheel_file}[dev,miosr,cvxpy,sbr]"
+    ],
     "build_command": [
         "python -m build --outdir {build_cache_dir} {build_dir}"
     ]

asv_bench/benchmarks/defaults.py

@@ -0,0 +1,90 @@
+from abc import ABC
+from abc import abstractmethod
+
+import sindy_exp
+from asv_runner.benchmarks.mark import SkipNotImplemented
+
+import pysindy as ps
+
+
+class LorenzMixin:
+    def make_data(self):
+        trajectories, terms = sindy_exp.gen_data(
+            "lorenz", 4, noise_abs=0.1, dt=0.03, t_end=10
+        )["data"]
+        traj = trajectories[0]
+        self.true_eqns = terms
+        self.x = traj.x_train
+        self.x_dot_true = traj.x_train_true_dot
+        self.t = traj.t_train
+
+
+class DefaultBM(ABC):
+    @abstractmethod
+    def make_data(self) -> None:
+        ...
+
+    @abstractmethod
+    def make_model(self) -> None:
+        ...
+
+    def setup(self):
+        self.make_data()
+        self.make_model()
+
+    def time_fit(self):
+        self.model.fit([self.x], [self.t])
+
+    def peakmem_fit(self):
+        self.model.fit([self.x], [self.t])
+
+    def track_score_fit(self):
+        self.model.fit([self.x], [self.t])
+        if not hasattr(self.model, "feature_names_"):
+            raise SkipNotImplemented
+        true_ode_align, est_ode_align = sindy_exp._utils.unionize_coeff_dicts(
+            self.model, self.true_eqns
+        )
+        metrics = sindy_exp.coeff_metrics(est_ode_align, true_ode_align)
+        return metrics["coeff_mae"]
+
+    def time_fit_predict(self):
+        self.model.fit([self.x], [self.t])
+        self.model.predict(self.x)
+
+    def peakmem_fit_predict(self):
+        self.model.fit([self.x], [self.t])
+        self.model.predict(self.x)
+
+    def track_score_fit_predict(self):
+        self.model.fit([self.x], [self.t])
+        self.model.predict(self.x)
+        metrics = sindy_exp.pred_metrics(
+            self.model, self.x, self.x_dot_true  # type: ignore
+        )
+        return metrics["pred_l2_fro"]
+
+
+class SINDyMixin:
+    def make_model(self):
+        self.model = ps.SINDy()
+
+
+class SINDyLorenz(LorenzMixin, SINDyMixin, DefaultBM):
+    pass
+
+
+class WeakMixin:
+    def make_model(self):
+        if not hasattr(ps, "WeakSINDy"):
+            raise SkipNotImplemented
+        self.model = ps.WeakSINDy()
+
+
+class WeakLorenz(LorenzMixin, WeakMixin, DefaultBM):
+    pass
+
+
+# class WeakHeat:
+
+# class WeakBurgers: