Merge remote-tracking branch 'origin/feature/version4' into feature/v…

…ersion4

# Conflicts:
#	tests/unit_tests/surrogates/test_gpr.py

.readthedocs.yaml

@@ -6,7 +6,7 @@ sphinx:
 build:
   image: latest
 python:
-  version: 3.7
+  version: 3.9
   install:
     - requirements: docs/requirements.txt
   system_packages: true

Dockerfile

@@ -0,0 +1,9 @@
+#RUN curl -fsSL https://get.docker.com -o get-docker.sh
+#RUN chmod +x get-docker.sh
+#RUN sh get-docker.sh
+
+# Build the image based on the official Python version 3.9 image
+FROM python:3.9
+
+# Use RUN to install Python packages (numpy and scipy) via pip, Python's package manager
+RUN pip3 install UQpy

azure-pipelines.yml

@@ -21,159 +21,193 @@ pr:
     - master
     - Development
 
-pool:
-  vmImage: "macOS-latest"
-
-steps:
-  - task: UsePythonVersion@0
-    displayName: "Use Python $(pythonVersion)"
-    inputs:
-      versionSpec: "$(pythonVersion)"
-
-  - task: gitversion/setup@0
-    # condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-    displayName: Setup GitVersion
-    inputs:
-      versionSpec: '5.x'
-
-  - task: gitversion/execute@0
-    # condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-    displayName: Calculate GitVersion
-    inputs:
-      useConfigFile: true
-      configFilePath: 'GitVersion.yml'
-
-  - powershell: |
-      echo "Current version: $(GitVersion.SemVer)"
-    displayName: Shows currently compiling version
-    # condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-
-  - task: SonarCloudPrepare@1
-    condition: or(eq(variables['Build.SourceBranch'], 'refs/heads/master'),eq(variables['Build.Reason'], 'PullRequest'))
-    inputs:
-      SonarCloud: 'SonarCloud.UQpy'
-      organization: 'jhusurg'
-      scannerMode: 'CLI'
-      configMode: 'manual'
-      cliProjectKey: 'SURGroup_UQpy'
-      cliProjectName: 'UQpy'
-      cliSources: '.'
-      extraProperties: |
-        sonar.exclusions=**/example/**, **/tests/**, **/docs/**
-        sonar.python.coverage.reportPaths=./coverage.xml
-
-#  - task: Cache@2
+jobs:
+- job: "Build_UQpy_and_run_tests"
+  pool:
+    vmImage: "macOS-latest"
+
+  steps:
+    - task: UsePythonVersion@0
+      displayName: "Use Python $(pythonVersion)"
+      inputs:
+        versionSpec: "$(pythonVersion)"
+
+    - task: gitversion/setup@0
+      displayName: Setup GitVersion
+      inputs:
+        versionSpec: '5.x'
+
+    - task: gitversion/execute@0
+      displayName: Calculate GitVersion
+      inputs:
+        useConfigFile: true
+        configFilePath: 'GitVersion.yml'
+
+    - powershell: |
+        echo "Current version: $(GitVersion.SemVer)"
+      displayName: Shows currently compiling version
+
+    - task: SonarCloudPrepare@1
+      condition: or(eq(variables['Build.SourceBranch'], 'refs/heads/master'),eq(variables['Build.Reason'], 'PullRequest'))
+      inputs:
+        SonarCloud: 'SonarCloud.UQpy'
+        organization: 'jhusurg'
+        scannerMode: 'CLI'
+        configMode: 'manual'
+        cliProjectKey: 'SURGroup_UQpy'
+        cliProjectName: 'UQpy'
+        cliSources: '.'
+        extraProperties: |
+          sonar.exclusions=**/example/**, **/tests/**, **/docs/**
+          sonar.python.coverage.reportPaths=./coverage.xml
+
+    - script: |
+        pip install -r requirements.txt
+      displayName: Install project dependencies
+
+    - script: |
+        pip install pylint
+        pylint --ignored-modules=numpy,scipy,matplotlib,sklearn --disable=E0202,E1136,E1120,E0401,E0213 --disable=R,C,W  src/UQpy
+      displayName: "Running Pylint"
+
+    - script: |
+        pip install pytest pytest-cov
+        PYTHONPATH=src pytest --cov=src tests/ --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html
+  #      PYTHONPATH=src pytest tests/unit_test/*.py --cov=src tests/ --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html
+      workingDirectory: $(Build.SourcesDirectory)
+      displayName: 'Test with pytest'
+
+    - task: PublishTestResults@2
+      condition: succeededOrFailed()
+      inputs:
+        testResultsFiles: '**/test-*.xml'
+        testRunTitle: 'Publish test results for Python $(python.version)'
+
+    - task: PublishCodeCoverageResults@1
+      inputs:
+        codeCoverageTool: Cobertura
+        summaryFileLocation: '$(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['Build.Reason'], 'PullRequest'))
+
+    - task: SonarCloudPublish@1
+      condition: or(eq(variables['Build.SourceBranch'], 'refs/heads/master'),eq(variables['Build.Reason'], 'PullRequest'))
+      inputs:
+        pollingTimeoutSec: '300'
+
+    - script: |
+        python setup.py $(GitVersion.SemVer) sdist bdist_wheel
+      displayName: Artifact creation
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+
+    - task: CopyFiles@2
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      inputs:
+        SourceFolder: 'dist'
+        Contents: '**'
+        TargetFolder: '$(Build.ArtifactStagingDirectory)'
+
+    - task: PublishBuildArtifacts@1
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      inputs:
+        PathtoPublish: '$(Build.ArtifactStagingDirectory)'
+        ArtifactName: 'dist'
+        publishLocation: 'Container'
+
+    - script: |
+        twine upload --repository-url https://upload.pypi.org/legacy/ dist/* --username "$(TESTPYPIU)" --password "$(TESTPYPIP)"
+      displayName: Upload to PyPi
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+
+    - task: GitHubRelease@1
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+      inputs:
+        gitHubConnection: 'GitHub_OAuth'
+        repositoryName: '$(Build.Repository.Name)'
+        action: 'create'
+        target: '$(Build.SourceVersion)'
+        tagSource: 'userSpecifiedTag'
+        tag: 'v$(GitVersion.SemVer)'
+        changeLogCompareToRelease: 'lastFullRelease'
+        changeLogType: 'commitBased'
+
+    - bash: echo "##vso[task.prependpath]$CONDA/bin"
+      displayName: Add conda to PATH
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+
+    - bash: sudo chown -R $USER $CONDA
+      displayName: Take ownership of conda installation
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+
+    - bash: conda create --yes --quiet --name myEnvironment
+      displayName: Create Anaconda environment
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+
+    - bash: |
+        source activate myEnvironment
+        conda install --yes --quiet --name myEnvironment python=$(pythonVersion) conda-build anaconda-client
+      displayName: Install Anaconda packages
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+
+    - bash: |
+        source activate myEnvironment
+        conda build . recipe --variants "{'version': ['$(GitVersion.SemVer)']}"
+      displayName: Build Noarch conda packages
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+
+    - bash: |
+        source activate myEnvironment
+        anaconda login --username $(ANACONDAUSER) --password $(ANACONDAPW)
+        anaconda upload /usr/local/miniconda/envs/myEnvironment/conda-bld/noarch/*.tar.bz2
+      displayName: Upload conda packages
+      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+
+#- job: "Create_Docker_images"
+#  dependsOn: Build_UQpy_and_run_tests
+#  pool:
+#     vmImage: "ubuntu-latest"
+#  steps:
+#    - task: gitversion/setup@0
+#      displayName: Setup GitVersion
+#      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
 #      inputs:
-#        key: 'python | "$(Agent.OS)" | requirements.txt'
-#        restoreKeys: |
-#          python | "$(Agent.OS)"
-#          python
-#        path: $(PIP_CACHE_DIR)
-#      displayName: Cache pip packages
-
-  - script: |
-      pip install -r requirements.txt
-    displayName: Install project dependencies
-
-  - script: |
-      pip install pylint
-      pylint --ignored-modules=numpy,scipy,matplotlib,sklearn --disable=E0202,E1136,E1120,E0401 --disable=R,C,W  src/UQpy
-    displayName: "Running Pylint"
-
-  - script: |
-      pip install pytest pytest-cov
-      PYTHONPATH=src pytest --cov=src tests/ --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html
-#      PYTHONPATH=src pytest tests/unit_test/*.py --cov=src tests/ --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html
-    workingDirectory: $(Build.SourcesDirectory)
-    displayName: 'Test with pytest'
-
-  - task: PublishTestResults@2
-    condition: succeededOrFailed()
-    inputs:
-      testResultsFiles: '**/test-*.xml'
-      testRunTitle: 'Publish test results for Python $(python.version)'
-
-  - task: PublishCodeCoverageResults@1
-    inputs:
-      codeCoverageTool: Cobertura
-      summaryFileLocation: '$(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['Build.Reason'], 'PullRequest'))
-
-  - task: SonarCloudPublish@1
-    condition: or(eq(variables['Build.SourceBranch'], 'refs/heads/master'),eq(variables['Build.Reason'], 'PullRequest'))
-    inputs:
-      pollingTimeoutSec: '300'
-
-  - script: |
-      python setup.py $(GitVersion.SemVer) sdist bdist_wheel
-    displayName: Artifact creation
-    condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-  
-  - task: CopyFiles@2
-    condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-    inputs:
-      SourceFolder: 'dist'
-      Contents: '**'
-      TargetFolder: '$(Build.ArtifactStagingDirectory)'
-
-  - task: PublishBuildArtifacts@1
-    condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-    inputs:
-      PathtoPublish: '$(Build.ArtifactStagingDirectory)'
-      ArtifactName: 'dist'
-      publishLocation: 'Container'
-
-  - script: |
-      twine upload --repository-url https://upload.pypi.org/legacy/ dist/* --username "$(TESTPYPIU)" --password "$(TESTPYPIP)"
-    displayName: Upload to PyPi
-    condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-
-  - task: GitHubRelease@1
-    condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-    inputs:
-      gitHubConnection: 'GitHub_OAuth'
-      repositoryName: '$(Build.Repository.Name)'
-      action: 'create'
-      target: '$(Build.SourceVersion)'
-      tagSource: 'userSpecifiedTag'
-      tag: 'v$(GitVersion.SemVer)'
-      changeLogCompareToRelease: 'lastFullRelease'
-      changeLogType: 'commitBased'
-
-  - bash: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
-    condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-
-  - bash: sudo chown -R $USER $CONDA
-    displayName: Take ownership of conda installation
-    condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-
-  - bash: conda create --yes --quiet --name myEnvironment
-    displayName: Create Anaconda environment
-    condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-
-  - bash: |
-      source activate myEnvironment
-      conda install --yes --quiet --name myEnvironment python=$(pythonVersion) conda-build anaconda-client
-    displayName: Install Anaconda packages
-    condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-
-  - bash: |
-      source activate myEnvironment
-      conda build . recipe --variants "{'version': ['$(GitVersion.SemVer)']}"
-    displayName: Build Noarch conda packages
-    condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-
-  - bash: |
-      source activate myEnvironment
-      anaconda login --username $(ANACONDAUSER) --password $(ANACONDAPW)
-      anaconda upload /usr/local/miniconda/envs/myEnvironment/conda-bld/noarch/*.tar.bz2
-    displayName: Upload conda packages
-    condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
-
-
-
+#        versionSpec: '5.x'
+#
+#    - task: gitversion/execute@0
+#      displayName: Calculate GitVersion
+#      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+#      inputs:
+#        useConfigFile: true
+#        configFilePath: 'GitVersion.yml'
+#
+#    - task: Docker@2
+#      displayName: Login to Dockerhub
+#      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+#      inputs:
+#        containerRegistry: 'docker_registry_uqpy'
+#        command: 'login'
+#
+#    - powershell: |
+#          echo "Current version: $(GitVersion.SemVer)"
+#      displayName: Shows currently compiling version
+#      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+#
+#    - task: Docker@2
+#      displayName: Build and push packages to Dockerhub
+#      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+#      inputs:
+#        containerRegistry: 'docker_registry_uqpy'
+#        command: 'buildAndPush'
+#        repository: 'surgroup/uqpy'
+#        Dockerfile: 'Dockerfile'
+#        tags: '$(GitVersion.SemVer)'
+#
+#    - task: Docker@2
+#      displayName: Logout from Dockerhub
+#      condition: eq(variables['Build.SourceBranch'], 'refs/heads/master')
+#      inputs:
+#        containerRegistry: 'docker_registry_uqpy'
+#        command: 'logout'

docs/code/RunModel/abaqus_example.py

@@ -15,7 +15,7 @@
 import time
 
 from UQpy.distributions import Normal, Uniform
-from UQpy.run_model.RunModel import *
+from UQpy.run_model.RunModel_New import *
 from UQpy.sampling import MonteCarloSampling
 
 calling_directory = os.getcwd()

docs/code/RunModel/ls_dyna_example_multijob.py

@@ -11,7 +11,7 @@
 
 # %%
 from UQpy.distributions import Uniform
-from UQpy.run_model.RunModel import RunModel
+from UQpy.run_model.RunModel_New import RunModel_New
 from UQpy.sampling import MonteCarloSampling
 
 # %% md

docs/code/RunModel/ls_dyna_example_singlejob.py

@@ -11,7 +11,7 @@
 
 # %%
 from UQpy.distributions import Uniform
-from UQpy.run_model.RunModel import RunModel
+from UQpy.run_model.RunModel_New import RunModel_New
 from UQpy.sampling import MonteCarloSampling
 
 # %% md