Updated comparison between std and 0 to have a machine epsilon margin. (

#1)

* Updated comparison between std and 0 to have a machine epsilon margin. Also separated some GitHub Actions workflows and updated README badges accordingly.

* Updated max line length in build action flake8 to be 88.

.github/actions/build/action.yml

@@ -23,8 +23,8 @@ runs:
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        # exit-zero treats all errors as warnings.
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=88 --statistics
       shell: bash
 
     - name: Install CVMatrix dependencies

.github/workflows/package_workflow.yml

@@ -0,0 +1,27 @@
+name: Python Package
+
+on:
+    workflow_run:
+        workflows: ["Tests"]
+        types:
+            - completed
+
+jobs:
+    build_package:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - uses: ./.github/actions/build
+
+    publish_package:
+        needs: build_package
+        runs-on: ubuntu-latest
+        if: ${{ github.event.workflow_run.conclusion == 'success' }}
+        steps:  
+            - uses: actions/checkout@v4
+            - uses: ./.github/actions/publish
+        permissions:
+            id-token: write
+        environment:
+            name: pypi
+            url: https://pypi.org/p/ikpls

.github/workflows/pull_request_package_workflow.yml

@@ -0,0 +1,18 @@
+name: Pull Request Python Package
+
+on:
+    pull_request:
+        branches: [ "main" ]
+        paths:
+            - 'cvmatrix/**'
+            - 'tests/**'
+            - '.github/**'
+            - 'pyproject.toml'
+            - 'poetry.lock'
+
+jobs:
+    build_package:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - uses: ./.github/actions/build

.github/workflows/pull_request_test_workflow.yml

@@ -0,0 +1,25 @@
+name: Pull Request Tests
+
+on:
+  pull_request:
+    branches: [ "main" ]
+    paths:
+      - 'cvmatrix/**'
+      - 'tests/**'
+      - '.github/**'
+      - 'pyproject.toml'
+      - 'poetry.lock'
+
+jobs:
+  test_package:
+    runs-on: ${{ matrix.os }}
+    strategy:  
+      fail-fast: false  
+      matrix:  
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/test
+        with:
+          PYTHON_VERSION: ${{ matrix.python-version }}

.github/workflows/test_workflow.yml

@@ -0,0 +1,25 @@
+name: Tests
+
+on:
+    push:
+        branches: [ "main" ]
+        paths:
+            - 'cvmatrix/**'
+            - 'tests/**'
+            - '.github/**'
+            - 'pyproject.toml'
+            - 'poetry.lock'
+
+jobs:
+    test_package:
+        runs-on: ${{ matrix.os }}  
+        strategy:  
+            fail-fast: false  
+            matrix:  
+                os: [ubuntu-latest, windows-latest, macos-latest]
+                python-version: ["3.9", "3.10", "3.11", "3.12"]
+        steps:
+            - uses: actions/checkout@v4
+            - uses: ./.github/actions/test
+              with:
+                    PYTHON_VERSION: ${{ matrix.python-version }}

README.md

@@ -10,7 +10,9 @@
 
 [![Documentation Status](https://readthedocs.org/projects/cvmatrix/badge/?version=latest)](https://cvmatrix.readthedocs.io/en/latest/?badge=latest)
 
-[![Build Status](https://github.com/Sm00thix/CVMatrix/actions/workflows/workflow.yml/badge.svg)](https://github.com/Sm00thix/CVMatrix/actions/workflows/workflow.yml)
+[![Tests Status](https://github.com/Sm00thix/CVMatrix/actions/workflows/test_workflow.yml/badge.svg)](https://github.com/Sm00thix/CVMatrix/actions/workflows/test_workflow.yml)
+
+[![Package Status](https://github.com/Sm00thix/CVMatrix/actions/workflows/package_workflow.yml/badge.svg)](https://github.com/Sm00thix/CVMatrix/actions/workflows/package_workflow.yml)
 
 The [`cvmatrix`](https://pypi.org/project/cvmatrix/) package implements the fast algorithms by Engstrøm [[1]](#references) for computation of training set $\mathbf{X}^{\mathbf{T}}\mathbf{X}$ and $\mathbf{X}^{\mathbf{T}}\mathbf{Y}$ in a cross-validation setting. In addition to correctly handling arbitrary row-wise pre-processing, the algorithms allow for and efficiently and correctly handle any combination of column-wise centering and scaling of `X` and `Y` based on training set statistics.
 

cvmatrix/__init__.py

@@ -1 +1 @@
-__version__ = '1.0.1'
+__version__ = '1.0.2'

cvmatrix/cvmatrix.py

@@ -85,6 +85,7 @@ def __init__(
         self.scale_Y = scale_Y
         self.dtype = dtype
         self.copy = copy
+        self.eps = np.finfo(dtype).eps
         self.X_total = None
         self.Y_total = None
         self.N = None
@@ -533,7 +534,7 @@ def _compute_training_mat_std(
                 + train_sum_sq_mat
             )
         )
-        mat_train_std[mat_train_std == 0] = 1
+        mat_train_std[np.abs(mat_train_std) <= self.eps] = 1
         return mat_train_std
 
     def _init_mat(self, mat: np.ndarray) -> np.ndarray:

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cvmatrix"
-version = "1.0.1"
+version = "1.0.2"
 description = "Fast computation of possibly centered/scaled training set kernel matrices in a cross-validation setting."
 authors = ["Sm00thix <[email protected]>"]
 maintainers = ["Sm00thix <[email protected]>"]