Development - Updating dependencies

.pylintrc

@@ -3,7 +3,8 @@
 # A comma-separated list of package or module names from where C extensions may
 # be loaded. Extensions are loading into the active Python interpreter and may
 # run arbitrary code.
-extension-pkg-whitelist=numpy,scipy
+extension-pkg-whitelist=numpy
+ignored-modules=scipy,scipy.special
 
 [MESSAGES CONTROL]
 
@@ -26,4 +27,6 @@ disable=no-name-in-module
 # (useful for modules/projects where namespaces are manipulated during runtime
 # and thus existing member attributes cannot be deduced by static analysis. It
 # supports qualified module names, as well as Unix pattern matching.
-ignored-modules=scipy
+ignored-modules=scipy, scipy.special
+ignored-classes=scipy,scipy.special
+generated-members=scipy.*

GitVersion.yml

@@ -1,10 +1,19 @@
-mode: Mainline
+mode: ContinuousDelivery
+
 major-version-bump-message: '\+semver:\s?(breaking|major)'
 minor-version-bump-message: '\+semver:\s?(feature|minor)'
 patch-version-bump-message: '\+semver:\s?(fix|patch)'
+
 commit-message-incrementing: Enabled
-branches: {}
+
+branches:
+  main:
+    is-mainline: true
+    regex: ^main$
+    is-main-branch: true
+    increment: Patch
+
 ignore:
   sha: []
-merge-message-formats: {}
 
+merge-message-formats: {}

README.rst

@@ -99,10 +99,8 @@ Clone your fork of the UQpy repo from your GitHub account to your local disk (to
 
                         git clone https://github.com/SURGroup/UQpy.git
                         cd UQpy/
-                        python setup.py {version} install  (user installation)
-                        python setup.py {version} develop (developer installation)
-
-You will need to replace {version} with the latest version.
+                        pip install .        (user installation)
+                        pip install -e .     (developer installation)
 
 Referencing UQpy
 =================

VERSION

@@ -0,0 +1 @@
+4.2.1

azure-pipelines.yml

@@ -5,11 +5,11 @@
 
 
 variables:
-  pythonVersion: 3.9
+  pythonVersion: 3.12
   srcDirectory: src
 
 trigger:
-  - master
+  - main
   - Development
   - feature/*
   - bugfix/*
@@ -18,7 +18,7 @@ trigger:
 pr:
   branches:
     include:
-    - master
+    - main
     - Development
 
 jobs:
@@ -28,28 +28,31 @@ jobs:
     vmImage: "macOS-latest"
 
   steps:
+    - checkout: self
+      fetchDepth: 0
+
     - task: UsePythonVersion@0
       displayName: "Use Python $(pythonVersion)"
       inputs:
         versionSpec: "$(pythonVersion)"
 
-    - task: gitversion/setup@0
+    - task: gitversion-setup@4
       displayName: Setup GitVersion
       inputs:
-        versionSpec: '5.x'
+        versionSpec: '6.x'
 
-    - task: gitversion/execute@0
+    - task: gitversion-execute@4
       displayName: Calculate GitVersion
       inputs:
         useConfigFile: true
         configFilePath: 'GitVersion.yml'
 
     - powershell: |
-        echo "Current version: $(GitVersion.SemVer)"
+        echo "Current version: $env:GITVERSION_SEMVER"
       displayName: Shows currently compiling version
 
-    - task: SonarCloudPrepare@1
-      condition: or(eq(variables['Build.SourceBranch'], 'refs/heads/master'), eq(variables['System.PullRequest.TargetBranch'], 'master'))
+    - task: SonarCloudPrepare@3
+      condition: or(eq(variables['Build.SourceBranch'], 'refs/heads/main'), eq(variables['System.PullRequest.TargetBranch'], 'main'))
       inputs:
         SonarCloud: 'SonarCloud.UQpy'
         organization: 'jhusurg'
@@ -68,7 +71,7 @@ jobs:
 
     - script: |
         pip install pylint
-        pylint --ignored-modules=numpy,scipy,matplotlib,sklearn,torch --disable=E0202,E1136,E1120,E0401,E0213,E1102 --disable=R,C,W  src/UQpy
+        pylint --ignored-modules=numpy,scipy,scipy.*,matplotlib,sklearn,torch --disable=E0202,E1136,E1120,E0401,E0213,E1102,E0606 --disable=R,C,W  src/UQpy
       displayName: "Running Pylint"
 
     - script: |
@@ -83,47 +86,49 @@ jobs:
         testResultsFiles: '**/test-*.xml'
         testRunTitle: 'Publish test results for Python $(python.version)'
 
-    - task: PublishCodeCoverageResults@1
+    - task: PublishCodeCoverageResults@2
       inputs:
-        codeCoverageTool: Cobertura
         summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
-        reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov'
-        additionalCodeCoverageFiles: '$(System.DefaultWorkingDirectory)/ **'
 
-    - task: SonarCloudAnalyze@1
-      condition: or(eq(variables['Build.SourceBranch'], 'refs/heads/master'), eq(variables['System.PullRequest.TargetBranch'], 'master'))
+    - task: SonarCloudAnalyze@3
+      condition: or(eq(variables['Build.SourceBranch'], 'refs/heads/main'), eq(variables['System.PullRequest.TargetBranch'], 'main'))
 
-    - task: SonarCloudPublish@1
-      condition: or(eq(variables['Build.SourceBranch'], 'refs/heads/master'), eq(variables['System.PullRequest.TargetBranch'], 'master'))
+    - task: SonarCloudPublish@3
+      condition: or(eq(variables['Build.SourceBranch'], 'refs/heads/main'), eq(variables['System.PullRequest.TargetBranch'], 'main'))
       inputs:
         pollingTimeoutSec: '300'
 
     - script: |
-        python setup.py $(GitVersion.SemVer) sdist bdist_wheel
+        pip install build
+        echo "$(GitVersion.SemVer)" > VERSION
+        python -m build
       displayName: Artifact creation
-      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/main')
 
     - task: CopyFiles@2
-      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/main')
       inputs:
         SourceFolder: 'dist'
         Contents: '**'
         TargetFolder: '$(Build.ArtifactStagingDirectory)'
 
-    - task: PublishBuildArtifacts@1
-      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+    - task: PublishPipelineArtifact@1
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/main')
       inputs:
         PathtoPublish: '$(Build.ArtifactStagingDirectory)'
         ArtifactName: 'dist'
         publishLocation: 'Container'
 
     - script: |
-        twine upload --repository-url https://upload.pypi.org/legacy/ dist/* --username "$(TESTPYPIU)" --password "$(TESTPYPIP)"
+        twine upload --non-interactive dist/*
       displayName: Upload to PyPi
-      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/main')
+      env:
+        TWINE_USERNAME: $(TESTPYPIU)
+        TWINE_PASSWORD: $(TESTPYPIP)
 
     - task: GitHubRelease@1
-      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/main')
       inputs:
         gitHubConnection: 'GitHub_OAuth'
         repositoryName: '$(Build.Repository.Name)'
@@ -139,34 +144,37 @@ jobs:
   pool:
      vmImage: "ubuntu-latest"
   steps:
-    - task: gitversion/setup@0
+    - checkout: self
+      fetchDepth: 0 
+
+    - task: gitversion-setup@4
       displayName: Setup GitVersion
-      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/main')
       inputs:
-        versionSpec: '5.x'
+        versionSpec: '6.x'
 
-    - task: gitversion/execute@0
+    - task: gitversion-execute@4
       displayName: Calculate GitVersion
-      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/main')
       inputs:
         useConfigFile: true
         configFilePath: 'GitVersion.yml'
 
     - task: Docker@2
       displayName: Login to Dockerhub
-      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/main')
       inputs:
         containerRegistry: 'docker_registry_surg'
         command: 'login'
 
     - powershell: |
           echo "Current version: $(GitVersion.SemVer)"
       displayName: Shows currently compiling version
-      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/main')
 
     - task: Docker@2
       displayName: Build and push packages to Dockerhub
-      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/main')
       inputs:
         containerRegistry: 'docker_registry_surg'
         command: 'buildAndPush'
@@ -176,7 +184,7 @@ jobs:
 
     - task: Docker@2
       displayName: Logout from Dockerhub
-      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/main')
       inputs:
         containerRegistry: 'docker_registry_surg'
         command: 'logout'

docs/code/reliability/sorm/local_model4.py

@@ -1,3 +1,9 @@
+"""
+
+Auxiliary file
+==============================================
+
+"""
 import numpy as np
 
 

docs/code/sampling/tempering/local_reliability_funcs.py

@@ -1,3 +1,9 @@
+"""
+
+Auxiliary file
+==============================================
+
+"""
 import numpy as np
 
 

docs/code/scientific_machine_learning/deep_operator_network/local_integral_data.py

@@ -1,3 +1,9 @@
+"""
+
+Auxiliary file
+==============================================
+
+"""
 import torch
 import numpy as np
 from UQpy.stochastic_process import SpectralRepresentation

docs/code/surrogates/gpr/local_python_model_1Dfunction.py

@@ -1,3 +1,9 @@
+"""
+
+Auxiliary file
+==============================================
+
+"""
 def y_func(z):
     import numpy as np
     return np.sin(z)

docs/code/surrogates/gpr/local_python_model_function.py

@@ -1,3 +1,9 @@
+"""
+
+Auxiliary file
+==============================================
+
+"""
 def y_func(z):
     return 1/(6.2727*(abs(0.3-z[:, 0]**2-z[:, 1]**2)+0.01))
 

docs/source/index.rst

@@ -68,7 +68,7 @@ From GitHub: Clone your fork of the :py:mod:`UQpy` repo from your GitHub account
 
     git clone https://github.com/SURGroup/UQpy.git
     cd UQpy
-    python setup.py {version} install
+    pip install .
 
 ------------
 
@@ -77,7 +77,7 @@ Development
 
 :py:mod:`UQpy` is designed to serve as a platform for developing new UQ methodologies and algorithms. To install :py:mod:`UQpy` as a developer, run::
 
-    python setup.py {version} develop
+    pip install -e .
 
 
 ------------

pyproject.toml

@@ -0,0 +1,68 @@
+[build-system]
+requires = ["setuptools>=77", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "UQpy"
+dynamic = ["version"]
+description = "UQpy is a general purpose toolbox for Uncertainty Quantification"
+readme = "README.rst"
+requires-python = ">3.9.0"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [
+    { name = "Michael D. Shields" },
+    { name = "Dimitris G. Giovanis" },
+    { name = "Audrey Olivier" },
+    { name = "Aakash Bangalore-Satish" },
+    { name = "Mohit Chauhan" },
+    { name = "Lohit Vandanapu" },
+    { name = "Ketson R.M. dos Santos" },
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Mathematics",
+    "Natural Language :: English",
+]
+dependencies = [
+    "numpy>=2.0.0",
+    "scipy>=1.13.0",
+    "matplotlib>=3.9.0",
+    "scikit-learn>=1.5.0",
+    "fire>=0.6.0",
+    "beartype>=0.18.5",
+    "torch >= 2.2.2",
+    "torchinfo >= 1.8.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest == 8.2.0",
+    "pytest-cov == 5.0.0",
+    "pylint >= 3.2.0",
+    "pytest-azurepipelines == 1.0.5",
+    "wheel == 0.43.0",
+    "twine == 5.0.0",
+    "sphinx_autodoc_typehints == 1.23.0",
+    "sphinx_rtd_theme == 1.2.0",
+    "sphinx_gallery == 0.13.0",
+    "sphinxcontrib_bibtex == 2.5.0",
+    "Sphinx==6.1.3",
+    "hypothesis>=6.0.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/SURGroup/UQpy"
+
+[tool.setuptools]
+platforms = ["OSX", "Windows", "Linux"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"*" = ["*.pdf"]
+
+[tool.setuptools.dynamic]
+version = { file = "VERSION" }