MNT add py39 support (#196)

Author: MatthewSZhang

.github/workflows/asv.yml

@@ -27,7 +27,7 @@ jobs:
         run: |
           git branch main origin/main
 
-      - uses: prefix-dev/[email protected].0
+      - uses: prefix-dev/[email protected].3
         with:
           environments: dev
           cache: true
@@ -93,7 +93,7 @@ jobs:
             cp -r "$d"/* "asv_benchmarks/results/"
           done
 
-      - uses: prefix-dev/[email protected].0
+      - uses: prefix-dev/[email protected].3
         with:
           environments: dev
           cache: true

.github/workflows/static.yml

@@ -9,7 +9,7 @@ jobs:
 
     steps:
       - uses: actions/checkout@v5
-      - uses: prefix-dev/[email protected].0
+      - uses: prefix-dev/[email protected].3
         with:
           environments: static
           cache: true

.github/workflows/test.yml

@@ -16,23 +16,26 @@ jobs:
 
     steps:
       - uses: actions/checkout@v5
-      - uses: prefix-dev/[email protected].0
+      - uses: prefix-dev/[email protected].3
         with:
           environments: >-
             dev
             docs
             nogil
+            py39
           cache: true
 
       - name: Re-install local
         run: |
           pixi reinstall -e dev --frozen fastcan
           pixi reinstall -e docs --frozen fastcan
           pixi reinstall -e nogil --frozen fastcan
+          pixi reinstall -e py39 --frozen fastcan
 
       - name: Test with pytest
         run: |
           pixi run -e dev test
+          pixi run -e py39 test
       - name: Test with doctest
         if: matrix.os == 'ubuntu-latest'
         run: |

.github/workflows/wheel.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
-      - uses: prefix-dev/[email protected].0
+      - uses: prefix-dev/[email protected].3
         with:
           environments: dev
           cache: true
@@ -36,7 +36,7 @@ jobs:
         uses: pypa/[email protected]
         env:
           CIBW_SKIP: "*_i686 *_ppc64le *_s390x *_universal2 *-musllinux_* cp314t*"
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.10"
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
           CIBW_ARCHS_LINUX: auto
           CIBW_ARCHS_MACOS: x86_64 arm64
           CIBW_ARCHS_WINDOWS: AMD64

fastcan/_beam.py

@@ -13,7 +13,7 @@ def _beam_search(
     X, V, n_features_to_select, beam_width, indices_include, mask_exclude, tol, verbose
 ):
     """
-    Perform beam search to find the best subset of features.
+    Beam search with SSC.
 
     Parameters:
     X : np.ndarray
@@ -48,12 +48,16 @@ def _beam_search(
             X_support, X_selected = _prepare_candidates(
                 X, mask_exclude, indices_include
             )
+            if X_selected.shape[1] == 0:
+                beams_scores = np.sum((X.T @ V) ** 2, axis=1)
+                beams_scores[~X_support] = 0
+            else:
+                W_selected = orth(X_selected)
+                selected_score = np.sum((W_selected.T @ V) ** 2)
+                beams_scores = _gram_schmidt(
+                    X, X_support, X_selected, selected_score, V, tol
+                )
             beams_selected_ids = [indices_include for _ in range(beam_width)]
-            W_selected = orth(X_selected)
-            selected_score = np.sum((W_selected.T @ V) ** 2)
-            beams_scores = _gram_schmidt(
-                X, X_support, X_selected, selected_score, V, tol
-            )
             beams_selected_ids, top_k_scores = _select_top_k(
                 beams_scores[None, :],
                 beams_selected_ids,
@@ -123,11 +127,9 @@ def _select_top_k(
     return new_ids_selected, top_k_scores
 
 
-def _gram_schmidt(X, X_support, X_selected, selected_score, V, tol, modified=True):
+def _gram_schmidt(X, X_support, X_selected, selected_score, V, tol):
     X = np.copy(X)
-    if modified:
-        # Change to Modified Gram-Schmidt
-        W_selected = orth(X_selected)
+    W_selected = orth(X_selected) # Change to Modified Gram-Schmidt
     scores = np.zeros(X.shape[1])
     for i, support in enumerate(X_support):
         if not support:

pixi.lock

@@ -3,10 +3,10 @@ channels = ["conda-forge"]
 platforms = ["win-64", "linux-64", "osx-64", "osx-arm64", "linux-aarch64"]
 
 [dependencies]
-python = ">=3.10"
-scikit-learn = ">=1.7.0,!=1.7.1"
-cython = ">=3.1.0" # build dependencies
-meson-python = ">=0.18.0" # build dependencies
+python = ">=3.9"
+scikit-learn = ">=1.6.0"
+cython = ">=3.0.10" # build dependencies
+meson-python = ">=0.16.0" # build dependencies
 
 [target.osx-64.dependencies]
 compilers = "*" # build dependencies
@@ -74,12 +74,13 @@ python-build = "*"
 pip = "*"
 
 [feature.nogil.dependencies]
+python = "<3.14"
 python-freethreading = "*"
 cython = ">=3.1.0" # build dependencies
 meson-python = ">=0.18.0" # build dependencies
 
 [feature.nogil.pypi-dependencies]
-scikit-learn = ">=1.7.0,!=1.7.1"
+scikit-learn = ">=1.6.0"
 fastcan = { path = ".", editable = true }
 
 [tasks]
@@ -138,9 +139,16 @@ pyodide-build-recipe = { cmd = "rm -rf dist && bash -c 'source emsdk/emsdk_env.s
 pyodide-download = '''bash -c "[ -d pyodide ] || (LATEST_TAG=$(curl -s https://api.github.com/repos/pyodide/pyodide/releases/latest | grep \"tag_name\" | cut -d \" -f4) && curl -L https://github.com/pyodide/pyodide/releases/download/${LATEST_TAG}/pyodide-${LATEST_TAG}.tar.bz2 | tar -xjf -)"'''
 pyodide-test-recipe = { cmd = "mv ../dist/* . && python -m http.server --directory .", cwd = "pyodide", depends-on = ["pyodide-download", "pyodide-build-recipe"] }
 
+[feature.py39.dependencies]
+python = "==3.9.0"
+scikit-learn = "==1.6.0"
+meson-python = "==0.16.0"
+cython = "==3.0.10"
+
 [environments]
 dev = ["test", "build", "jupyter", "asv"]
 docs = ["docs"]
 static = { features = ["static"], no-default-feature = true }
 nogil = { features = ["nogil"], no-default-feature = true }
-wasm = { features = ["wasm"], no-default-feature = true }
+wasm = { features = ["wasm"], no-default-feature = true }
+py39 = { features = ["py39", "test"] }

pixi.toml

@@ -5,11 +5,11 @@ description = "A fast canonical-correlation-based greedy search algorithm"
 authors = [
     { name = "Matthew Sikai Zhang", email = "[email protected]" },
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.9"
 readme = "README.rst"
 license = { file = "LICENSE" }
 
-dependencies = ["scikit-learn>=1.7.0,!=1.7.1"]
+dependencies = ["scikit-learn>=1.6.0"]
 
 classifiers = [
     "Development Status :: 4 - Beta",
@@ -19,6 +19,7 @@ classifiers = [
     "Operating System :: Unix",
     "Operating System :: MacOS",
     "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -33,7 +34,13 @@ download = "https://pypi.org/project/fastcan/#files"
 tracker = "https://github.com/scikit-learn-contrib/fastcan/issues"
 
 [build-system]
-requires = ["meson-python>=0.18.0", "Cython>=3.1.0", "scikit-learn>=1.7.0"]
+requires = [
+    "scikit-learn>=1.6.0",
+    "meson-python>=0.18.0; python_version > '3.9'",
+    "Cython>=3.1.0; python_version > '3.9'",
+    "meson-python==0.16.0; python_version == '3.9'",
+    "Cython==3.0.10; python_version == '3.9'",
+]
 build-backend = "mesonpy"
 
 # Needed on Windows CI to compile with Visual Studio compiler