Merge branch 'devel' into switch-to-poetry

.github/workflows/test-and-deploy.yml

@@ -28,7 +28,7 @@ jobs:
         with:
           python-version: ${{ matrix.python }}
 
-      - name: Install dependencies
+      - name: Install build dependencies
         run: |
           pip install poetry
       
@@ -36,7 +36,11 @@ jobs:
         run: |
           poetry install
 
-      - name: pytest
+      - name: Install lib
+        run: |
+          python setup.py develop
+      
+       - name: pytest
         run: |
           poetry run pytest
 
@@ -55,7 +59,7 @@ jobs:
         with:
           python-version: ${{ matrix.python }}
 
-      - name: Install dependencies
+      - name: Install build dependencies
         run: |
           pip install poetry
       
@@ -66,6 +70,7 @@ jobs:
       - name: pytest
         run: |
           poetry run pytest
+
   test-macos:
     strategy:
       matrix:
@@ -159,12 +164,11 @@ jobs:
         matrix:
           python: ['cp39-cp39', 'cp310-cp310', 'cp311-cp311', 'cp312-cp312']
     runs-on: ubuntu-latest
-    container:
-      image: quay.io/pypa/manylinux2014_x86_64
+    container: quay.io/pypa/manylinux2014_x86_64
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v1
 
       - name: Install poetry
         run: |
@@ -201,11 +205,15 @@ jobs:
       - name: List contents of dist
         run: ls -R dist
 
+      - name: Get the name of the wheel file
+        id: get-wheel-name
+        run: echo "::set-output name=wheel-name::$(ls dist/*.whl)"
+
       - name: Archive build artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v1
         with:
           name: dist-artifacts-manylinux-${{ matrix.python }}
-          path: dist/*
+          path: ${{ steps.get-wheel-name.outputs.wheel-name }}
 
   deploy:
     runs-on: ubuntu-latest

CHANGELOG.md

@@ -2,6 +2,11 @@
 
 ## Unreleased
 
+## v1.13.2 (2024-07-21)
+* update string checks in initialization method for latent variable and put `empirical_samples` init-method on a deprecation path
+
+* update dependencies to `numpy>=1.7.0,<2.0.0`
+
 * update import in `.plotting.matplot_dep.defaults` due to change in matplotlib
 
 * Correct dl_dm term in student t inference #1065

GPy/__version__.py

@@ -1 +1 @@
-__version__ = "1.13.1"
+__version__ = "1.13.2"

GPy/util/initialization.py

@@ -1,31 +1,59 @@
-'''
+"""
 Created on 24 Feb 2014
 
 @author: maxz
-'''
+"""
 
 import numpy as np
+import warnings
 from ..util.pca import PCA
 
+
 def initialize_latent(init, input_dim, Y):
+    """
+    :param init: initialization method for the latent space, 'PCA' or 'random'
+    """
     Xr = np.asfortranarray(np.random.normal(0, 1, (Y.shape[0], input_dim)))
-    if 'PCA' in init:
+    if "PCA" == init:
         p = PCA(Y)
         PC = p.project(Y, min(input_dim, Y.shape[1]))
-        Xr[:PC.shape[0], :PC.shape[1]] = PC
-        var = .1*p.fracs[:input_dim]
-    elif init in 'empirical_samples':
+        Xr[: PC.shape[0], : PC.shape[1]] = PC
+        var = 0.1 * p.fracs[:input_dim]
+    elif init == "empirical_samples":
+        # dealing with depcrecated initialization method
+        # should be remove along the next major release
+        warnings.warn(
+            "Deprecated initialization method 'empirical_samples'. "
+            "Use 'random' instead.",
+            DeprecationWarning,
+        )
+
         from ..util.linalg import tdot
         from ..util import diag
+
         YYT = tdot(Y)
         diag.add(YYT, 1e-6)
-        EMP = np.asfortranarray(np.random.multivariate_normal(np.zeros(Y.shape[0]), YYT, min(input_dim, Y.shape[1])).T)
-        Xr[:EMP.shape[0], :EMP.shape[1]] = EMP
+        EMP = np.asfortranarray(
+            np.random.multivariate_normal(
+                np.zeros(Y.shape[0]), YYT, min(input_dim, Y.shape[1])
+            ).T
+        )
+        Xr[: EMP.shape[0], : EMP.shape[1]] = EMP
         var = np.random.uniform(0.5, 1.5, input_dim)
-    else:
+    elif init == "random":
         var = Xr.var(0)
+    else:
+        # dealing with depcrecated initialization method
+        # should be remove along the next major release
+        warnings.warn(
+            f"{init} is not a valid initialization method."
+            "Supoprt for anything else than 'PCA' or 'random' will be removed in the next major release.",
+            DeprecationWarning,
+        )
+        var = Xr.var(0)
+        
 
     Xr -= Xr.mean(0)
     Xr /= Xr.std(0)
 
-    return Xr, var/var.max()
+    return Xr, var / var.max()

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.13.1
+current_version = 1.13.2
 tag = True
 commit = True
 

setup.py

@@ -140,7 +140,7 @@ except ModuleNotFoundError:
     ext_mods = []
 
 install_requirements = [
-    "numpy>=1.7",
+    "numpy>=1.7,<2.0.0",
     "six",
     "paramz>=0.9.6",
     "cython>=0.29",
@@ -197,7 +197,7 @@ setup(
     include_package_data=True,
     py_modules=["GPy.__init__"],
     test_suite="GPy.testing",
-    setup_requires=["numpy>=1.7"],
+    setup_requires=["numpy>=1.7,<2.0.0"],
     install_requires=install_requirements,
     extras_require={
         "docs": ["sphinx"],