From 964e5589815e41de6a28a6c17d92edaadb380616 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 9 Nov 2025 06:46:00 +0000
Subject: [PATCH 1/3] Initial plan


From 420673af25e723da7702a026601ca3da4fbdddb3 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 9 Nov 2025 07:01:23 +0000
Subject: [PATCH 2/3] Fix Python 3.8/3.9 compatibility: replace PEP 604 type
 hints and pin CI actions

Co-authored-by: edithatogo <15080672+edithatogo@users.noreply.github.com>
---
 .github/workflows/ci.yml | 20 ++++++++++----------
 pymars/_forward.py       | 15 ++++++++-------
 pymars/_pruning.py       | 13 +++++++------
 pymars/_record.py        | 13 +++++++------
 pymars/earth.py          |  3 ++-
 5 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 00f97d3..365f441 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,9 +14,9 @@ jobs:
         python-version: [3.8, 3.9, '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -29,9 +29,9 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v4
       with:
         python-version: '3.11'
     - name: Install dependencies
@@ -44,9 +44,9 @@ jobs:
   type-check:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v4
       with:
         python-version: '3.11'
     - name: Install dependencies
@@ -59,9 +59,9 @@ jobs:
   coverage:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v4
       with:
         python-version: '3.11'
     - name: Install dependencies
@@ -80,9 +80,9 @@ jobs:
   format:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v4
       with:
         python-version: '3.11'
     - name: Install dependencies
diff --git a/pymars/_forward.py b/pymars/_forward.py
index 7ada1e0..cf9806a 100644
--- a/pymars/_forward.py
+++ b/pymars/_forward.py
@@ -7,6 +7,7 @@
 """
 
 import logging
+from typing import List, Optional, Tuple
 
 import numpy as np
 
@@ -39,7 +40,7 @@ def __init__(self, earth_model: Earth):
         self.y_train = None
         self.n_samples = 0
         self.n_features = 0
-        self.current_basis_functions: list[BasisFunction] = []
+        self.current_basis_functions: List[BasisFunction] = []
         self.current_B_matrix = None
         self.current_coefficients = None
         self.current_rss = np.inf
@@ -53,7 +54,7 @@ def __init__(self, earth_model: Earth):
 
     def _calculate_rss_and_coeffs(
         self, B_matrix: np.ndarray, y: np.ndarray, *, drop_nan_rows: bool = True
-    ) -> tuple[float, np.ndarray | None, int]:
+    ) -> Tuple[float, Optional[np.ndarray], int]:
         if B_matrix is None or B_matrix.shape[1] == 0:
             mean_y = np.mean(y)
             rss = np.sum((y - mean_y)**2)
@@ -93,7 +94,7 @@ def _calculate_rss_and_coeffs(
         except np.linalg.LinAlgError:
             return np.inf, None, num_valid_rows
 
-    def _build_basis_matrix(self, X_processed: np.ndarray, basis_functions: list[BasisFunction]) -> np.ndarray:
+    def _build_basis_matrix(self, X_processed: np.ndarray, basis_functions: List[BasisFunction]) -> np.ndarray:
         if not basis_functions:
             return np.empty((X_processed.shape[0], 0))
 
@@ -108,7 +109,7 @@ def _build_basis_matrix(self, X_processed: np.ndarray, basis_functions: list[Bas
         return B_matrix
 
     def run(self, X_fit_processed: np.ndarray, y_fit: np.ndarray,
-            missing_mask: np.ndarray, X_fit_original: np.ndarray) -> tuple[list[BasisFunction], np.ndarray]:
+            missing_mask: np.ndarray, X_fit_original: np.ndarray) -> Tuple[List[BasisFunction], np.ndarray]:
         self.X_train = X_fit_processed
         self.y_train = y_fit
         self.missing_mask = missing_mask
@@ -225,7 +226,7 @@ def run(self, X_fit_processed: np.ndarray, y_fit: np.ndarray,
 
         return self.current_basis_functions, self.current_coefficients
 
-    def _calculate_gcv_for_basis_set(self, basis_functions: list[BasisFunction]) -> tuple[float | None, np.ndarray | None]:
+    def _calculate_gcv_for_basis_set(self, basis_functions: List[BasisFunction]) -> Tuple[Optional[float], Optional[np.ndarray]]:
         if not basis_functions:
             # This implies an intercept-only model for GCV calculation purposes
             rss_intercept_only = np.sum((self.y_train - np.mean(self.y_train))**2)
@@ -348,8 +349,8 @@ def _get_allowable_knot_values(self, X_col_original_for_var: np.ndarray, parent_
             minspan_countdown = max(0, minspan_abs - 1)
         return np.array(final_allowable_knots)
 
-    def _generate_candidates(self) -> list[tuple[BasisFunction, BasisFunction | None]]:
-        candidate_additions: list[tuple[BasisFunction, BasisFunction | None]] = []
+    def _generate_candidates(self) -> List[Tuple[BasisFunction, Optional[BasisFunction]]]:
+        candidate_additions: List[Tuple[BasisFunction, Optional[BasisFunction]]] = []
         for parent_bf in self.current_basis_functions:
             if parent_bf.degree() + 1 > self.model.max_degree: continue
             parent_involved_vars = parent_bf.get_involved_variables()
diff --git a/pymars/_pruning.py b/pymars/_pruning.py
index 07bb477..1ae4711 100644
--- a/pymars/_pruning.py
+++ b/pymars/_pruning.py
@@ -8,6 +8,7 @@
 """
 
 import logging
+from typing import List, Optional, Tuple
 
 import numpy as np
 
@@ -35,10 +36,10 @@ def __init__(self, earth_model: Earth):
         self.X_fit_original = None
 
         self.best_gcv_so_far = np.inf
-        self.best_basis_functions_so_far: list[BasisFunction] = []
+        self.best_basis_functions_so_far: List[BasisFunction] = []
         self.best_coeffs_so_far: np.ndarray = None
 
-    def _calculate_rss_and_coeffs(self, B_matrix: np.ndarray, y_data: np.ndarray) -> tuple[float, np.ndarray | None, int]:
+    def _calculate_rss_and_coeffs(self, B_matrix: np.ndarray, y_data: np.ndarray) -> Tuple[float, Optional[np.ndarray], int]:
         """
         Calculates RSS, coefficients, and num_valid_rows, considering NaNs in B_matrix.
         y_data is assumed finite.
@@ -78,7 +79,7 @@ def _calculate_rss_and_coeffs(self, B_matrix: np.ndarray, y_data: np.ndarray) ->
             )
             return np.inf, None, num_valid_rows
 
-    def _build_basis_matrix(self, X_data: np.ndarray, basis_functions: list[BasisFunction],
+    def _build_basis_matrix(self, X_data: np.ndarray, basis_functions: List[BasisFunction],
                             missing_mask: np.ndarray) -> np.ndarray:
         """
         Constructs the basis matrix B from X_data (which is X_processed)
@@ -97,7 +98,7 @@ def _build_basis_matrix(self, X_data: np.ndarray, basis_functions: list[BasisFun
 
     def _compute_gcv_for_subset(self, X_fit_processed: np.ndarray, y_fit: np.ndarray,
                                 missing_mask: np.ndarray, X_fit_original: np.ndarray,
-                                basis_subset: list[BasisFunction]) -> tuple[float | None, float | None, np.ndarray | None]:
+                                basis_subset: List[BasisFunction]) -> Tuple[Optional[float], Optional[float], Optional[np.ndarray]]:
         """
         Computes GCV, RSS, and coefficients for a given subset of basis functions.
         Returns (gcv, rss, coeffs).
@@ -155,8 +156,8 @@ def _compute_gcv_for_subset(self, X_fit_processed: np.ndarray, y_fit: np.ndarray
 
     def run(self, X_fit_processed: np.ndarray, y_fit: np.ndarray,
             missing_mask: np.ndarray, X_fit_original: np.ndarray,
-            initial_basis_functions: list[BasisFunction],
-            initial_coefficients: np.ndarray) -> tuple[list[BasisFunction], np.ndarray, float]:
+            initial_basis_functions: List[BasisFunction],
+            initial_coefficients: np.ndarray) -> Tuple[List[BasisFunction], np.ndarray, float]:
 
         self.X_train = X_fit_processed
         self.y_train = y_fit.ravel()
diff --git a/pymars/_record.py b/pymars/_record.py
index eea572a..37809fd 100644
--- a/pymars/_record.py
+++ b/pymars/_record.py
@@ -7,6 +7,7 @@
 """
 
 import logging
+from typing import List
 
 import numpy as np
 
@@ -29,13 +30,13 @@ def __init__(self, X, y, earth_model_instance):
         # Pruning pass tracking
         # These will store the sequence of models considered during pruning.
         # Each element corresponds to a model of a certain size.
-        self.pruning_trace_basis_functions_: list[list[BasisFunction]] = []
-        self.pruning_trace_coeffs_: list[np.ndarray] = []
-        self.pruning_trace_gcv_: list[float] = []
-        self.pruning_trace_rss_: list[float] = []
+        self.pruning_trace_basis_functions_: List[List[BasisFunction]] = []
+        self.pruning_trace_coeffs_: List[np.ndarray] = []
+        self.pruning_trace_gcv_: List[float] = []
+        self.pruning_trace_rss_: List[float] = []
 
         # Final selected model details (can be set after pruning)
-        self.final_basis_: list[BasisFunction] = None
+        self.final_basis_: List[BasisFunction] = None
         self.final_coeffs_ = None
         self.final_gcv_ = None
         self.final_rss_ = None
@@ -47,7 +48,7 @@ def log_forward_pass_step(self, basis_functions, coefficients, rss):
         self.fwd_coeffs_.append(np.copy(coefficients))
         self.fwd_rss_.append(rss)
 
-    def log_pruning_step(self, basis_functions: list['BasisFunction'],
+    def log_pruning_step(self, basis_functions: List['BasisFunction'],
                          coefficients: np.ndarray, gcv: float, rss: float): # Renamed
         """
         Log a model state (basis functions, coefficients, GCV, RSS) encountered
diff --git a/pymars/earth.py b/pymars/earth.py
index 0fbb091..433f4fe 100644
--- a/pymars/earth.py
+++ b/pymars/earth.py
@@ -3,6 +3,7 @@
 The main Earth class, coordinating the model fitting process.
 """
 import logging
+from typing import List, Optional
 
 import numpy as np
 from sklearn.base import BaseEstimator, RegressorMixin
@@ -127,7 +128,7 @@ def __init__(self, max_degree: int = 1, penalty: float = 3.0, max_terms: int = N
                  allow_linear: bool = True,
                  allow_missing: bool = False, # New parameter
                  feature_importance_type: str = None,
-                 categorical_features: list[int] = None
+                 categorical_features: Optional[List[int]] = None
                  # TODO: Consider other py-earth params
                  ):
         super().__init__()

From a49b00979b927be1def5acbc043ed64544f8d0bc Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 9 Nov 2025 07:02:41 +0000
Subject: [PATCH 3/3] Pin all GitHub Actions workflows to v4 for consistency

---
 .github/workflows/benchmarks.yml   | 4 ++--
 .github/workflows/code-quality.yml | 4 ++--
 .github/workflows/docs.yml         | 4 ++--
 .github/workflows/release.yml      | 6 +++---
 .github/workflows/security.yml     | 4 ++--
 5 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 697327b..3248455 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -10,9 +10,9 @@ jobs:
   benchmark:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v4
       with:
         python-version: '3.11'
 
diff --git a/.github/workflows/code-quality.yml b/.github/workflows/code-quality.yml
index ee9934d..ad56236 100644
--- a/.github/workflows/code-quality.yml
+++ b/.github/workflows/code-quality.yml
@@ -10,9 +10,9 @@ jobs:
   code-quality:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v4
       with:
         python-version: '3.11'
 
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 2428c5f..5938355 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -12,12 +12,12 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
       with:
         ref: docs  # Always check out the docs branch
         
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v4
       with:
         python-version: '3.11'
 
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index f8b82c6..87660f7 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -13,9 +13,9 @@ jobs:
       contents: write
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v4
       with:
         python-version: '3.11'
 
@@ -34,7 +34,7 @@ jobs:
     needs: release
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0  # Fetch all history for all tags and branches
     - name: Generate release notes
diff --git a/.github/workflows/security.yml b/.github/workflows/security.yml
index de9e1c6..9c37df4 100644
--- a/.github/workflows/security.yml
+++ b/.github/workflows/security.yml
@@ -12,9 +12,9 @@ jobs:
   security:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v4
       with:
         python-version: '3.11'