Merge pull request #28 from 1313e/dev

Mark release of v1.2.0

.appveyor.yml

@@ -1,46 +1,46 @@
 environment:
-    matrix:
-        - PYTHON: "C:\\Python35"
-          PYTHON_VERSION: "3.5.x"
-          PYTHON_ARCH: "32"
+  matrix:
+    - PYTHON: "C:\\Python35"
+      PYTHON_VERSION: "3.5.x"
+      PYTHON_ARCH: "32"
 
-        - PYTHON: "C:\\Python35-x64"
-          PYTHON_VERSION: "3.5.x"
-          PYTHON_ARCH: "64"
+    - PYTHON: "C:\\Python35-x64"
+      PYTHON_VERSION: "3.5.x"
+      PYTHON_ARCH: "64"
 
-        - PYTHON: "C:\\Python36"
-          PYTHON_VERSION: "3.6.x"
-          PYTHON_ARCH: "32"
+    - PYTHON: "C:\\Python36"
+      PYTHON_VERSION: "3.6.x"
+      PYTHON_ARCH: "32"
 
-        - PYTHON: "C:\\Python36-x64"
-          PYTHON_VERSION: "3.6.x"
-          PYTHON_ARCH: "64"
+    - PYTHON: "C:\\Python36-x64"
+      PYTHON_VERSION: "3.6.x"
+      PYTHON_ARCH: "64"
 
-        - PYTHON: "C:\\Python37"
-          PYTHON_VERSION: "3.7.x"
-          PYTHON_ARCH: "32"
+    - PYTHON: "C:\\Python37"
+      PYTHON_VERSION: "3.7.x"
+      PYTHON_ARCH: "32"
 
-        - PYTHON: "C:\\Python37-x64"
-          PYTHON_VERSION: "3.7.x"
-          PYTHON_ARCH: "64"
+    - PYTHON: "C:\\Python37-x64"
+      PYTHON_VERSION: "3.7.x"
+      PYTHON_ARCH: "64"
 
 install:
-    # Prepend newly installed Python to the PATH of this build (this cannot be
-    # done from inside the powershell script as it would require to restart
-    # the parent CMD process).
-    - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
+  # Prepend newly installed Python to the PATH of this build (this cannot be
+  # done from inside the powershell script as it would require to restart
+  # the parent CMD process).
+  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
 
-    # Upgrade pip
-    - "python -m pip install --user --upgrade pip setuptools wheel"
+  # Upgrade pip
+  - "python -m pip install --upgrade pip setuptools wheel"
 
-    # Install PRISM
-    - "pip install -r requirements_dev.txt"
-    - "check-manifest"
-    - "python setup.py sdist bdist_wheel"
-    - "twine check dist/*"
-    - "python -c \"import prism; prism.get_info()\""
+  # Install PRISM
+  - "pip install -r requirements_dev.txt"
+  - "check-manifest"
+  - "python setup.py sdist bdist_wheel"
+  - "twine check dist/*"
+  - "python -c \"import prism; prism.get_info()\""
 
 build: false
 
 test_script:
-    - "pytest"
+  - "pytest --cov --cov-config=setup.cfg --cov-report=term-missing"

.azure-pipelines.yml

@@ -5,6 +5,7 @@
 
 variables:
   python.arch: 'x64'
+  upload_coverage: false
 
 schedules:
 - cron: "0 0 * * 0"
@@ -25,9 +26,11 @@ strategy:
     linux-python37:
       imageName: 'ubuntu-16.04'
       python.version: '3.7'
+      upload_coverage: true
     mac-python37:
       imageName: 'macos-10.13'
       python.version: '3.7'
+      upload_coverage: true
     windows-x86-python35:
       imageName: 'windows-2019'
       python.version: '3.5'
@@ -40,18 +43,17 @@ strategy:
       imageName: 'windows-2019'
       python.version: '3.7'
       python.arch: 'x86'
+      upload_coverage: true
     windows-x64-python35:
       imageName: 'windows-2019'
       python.version: '3.5'
-      python.arch: 'x64'
     windows-x64-python36:
       imageName: 'windows-2019'
       python.version: '3.6'
-      python.arch: 'x64'
     windows-x64-python37:
       imageName: 'windows-2019'
       python.version: '3.7'
-      python.arch: 'x64'
+      upload_coverage: true
   maxParallel: 10
 
 pool:
@@ -65,6 +67,13 @@ steps:
     addToPath: true
   displayName: Use Python $(python.version) $(python.arch)
 
+# Install missing libraries on Linux
+- bash: |
+    sudo apt-get install -y xvfb libdbus-1-3 libxkbcommon-x11-0
+    echo "##vso[task.setvariable variable=QT_QPA_PLATFORM]offscreen"
+  condition: eq(variables['Agent.OS'], 'Linux')
+  displayName: Install missing libraries required for Qt on Linux
+
 # Install dependencies and PRISM
 - script: |
     python -m pip install --upgrade pip setuptools wheel
@@ -84,43 +93,37 @@ steps:
     coverage run --rcfile=setup.cfg -m pytest
   displayName: Test package in serial
 
-# Install MPI, mpi4py and run MPI tests
+# Install MPI
 # Linux
 - bash: |
     sudo apt-get install -y -q openmpi-bin libopenmpi-dev
-    pip install --no-cache-dir mpi4py
-    mpiexec -n 2 coverage run --rcfile=setup.cfg -m mpi4py -m pytest
   condition: eq(variables['Agent.OS'], 'Linux')
-  displayName: Install MPI distribution on Linux and run in MPI
+  displayName: Install MPI distribution on Linux
 # Mac OS-X
 - bash: |
     brew install openmpi
-    pip install --no-cache-dir mpi4py
-    mpiexec -n 2 coverage run --rcfile=setup.cfg -m mpi4py -m pytest
   condition: eq(variables['Agent.OS'], 'Darwin')
-  displayName: Install MPI distribution on Mac OS-X and run in MPI
+  displayName: Install MPI distribution on Mac OS-X
 # Windows
 - powershell: |
     iwr -outf ..\MSMpiSDK.msi https://download.microsoft.com/download/A/E/0/AE002626-9D9D-448D-8197-1EA510E297CE/MSMpiSDK.msi
     Start-Process ..\MSMpiSDK.msi -ArgumentList "/quiet /qn" -Wait
     iwr -outf ..\MSMpiSetup.exe https://download.microsoft.com/download/A/E/0/AE002626-9D9D-448D-8197-1EA510E297CE/MSMpiSetup.exe
     Start-Process ..\MSMpiSetup.exe -ArgumentList "-unattend -force -verbose" -Wait
-    $Env:MSMPI_BIN = "C:\Program Files\Microsoft MPI\Bin"
-    $Env:Path += ";C:\Program Files\Microsoft MPI\Bin"
-    pip install --no-cache-dir mpi4py
-    cmd \c mpiexec -n 2 coverage run --rcfile=setup.cfg -m mpi4py -m pytest
+    echo "##vso[task.setvariable variable=MSMPI_BIN]C:\Program Files\Microsoft MPI\Bin"
+    echo "##vso[task.setvariable variable=Path]$Env:Path;C:\Program Files\Microsoft MPI\Bin"
   condition: eq(variables['Agent.OS'], 'Windows_NT')
-  displayName: Install MPI distribution on Windows and run in MPI
+  displayName: Install MPI distribution on Windows
 
 # Install mpi4py
-#- script: |
-#    pip install --no-cache-dir mpi4py
-#  displayName: Install mpi4py
+- script: |
+    pip install --no-cache-dir mpi4py
+  displayName: Install mpi4py
 
 # Test package in MPI
-#- script: |
-#    mpiexec -n 2 coverage run --rcfile=setup.cfg -m mpi4py -m pytest
-#  displayName: Test package in MPI
+- script: |
+    mpiexec -n 2 coverage run --rcfile=setup.cfg -m mpi4py -m pytest
+  displayName: Test package in MPI
 
 # Report coverage
 - script: |
@@ -129,6 +132,7 @@ steps:
   displayName: Coverage report
 
 # Upload covarage report to CodeCov
-- script: |
-    codecov
-  displayName: Upload coverage report
+- bash: |
+    curl -s https://codecov.io/bash | bash
+  condition: and(succeeded(), eq(variables['upload_coverage'], true))
+  displayName: Upload coverage report if requested

.codecov.yml

@@ -1,7 +1,5 @@
 codecov:
     token: 6a194e41-c88d-4b7e-af10-29d9f54f8d84
-    notify:
-        require_ci_to_pass: yes
 
 coverage:
     range: 90..100

.travis.yml

@@ -3,82 +3,66 @@ os: linux
 dist: xenial
 sudo: true
 
-matrix:
-    include:
-        - os: osx
-          language: generic
-          env: RUN_COVERAGE=0 PY=3
-          python: 3
-        - python: 3.5
-          env: RUN_COVERAGE=1
-        - python: 3.5-dev
-          env: RUN_COVERAGE=0
-        - python: 3.6
-          env: RUN_COVERAGE=0
-        - python: 3.6-dev
-          env: RUN_COVERAGE=0
-        - python: 3.7
-          env: RUN_COVERAGE=0
-        - python: 3.7-dev
-          env: RUN_COVERAGE=0
+jobs:
+  include:
+    - os: osx
+      python: 3
+      language: generic
+      env: PY=3
+    - python: 3.5
+    - python: 3.5-dev
+    - python: 3.6
+    - python: 3.6-dev
+    - python: 3.7
+    - python: 3.7-dev
+    - python: 3.8-dev
+  allow_failures:
+    - python: 3.8-dev
 
 before_install:
-    - |
-      if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-          sudo apt-get update -q
-      else
-          brew update
-          brew cask uninstall oclint
-          brew upgrade python
-      fi
-    - python$PY -m pip install --upgrade pip setuptools wheel
-    - python$PY -m pip install -r requirements_dev.txt
+  - |
+    if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+      sudo apt-get update -q
+      sudo apt-get install -y xvfb libdbus-1-3 libxkbcommon-x11-0
+      export QT_QPA_PLATFORM=offscreen
+    else
+      brew update
+      brew cleanup
+    fi
+  - python$PY -m pip install --upgrade pip setuptools wheel
+  - pip$PY install -r requirements_dev.txt
 install:
-    - check-manifest
-    - python$PY setup.py sdist bdist_wheel
-    - twine check dist/*
-    - python$PY -c "import prism; prism.get_info()"
+  - check-manifest
+  - python$PY setup.py sdist bdist_wheel
+  - twine check dist/*
+  - python$PY -c "import prism; prism.get_info()"
 script:
-    - |
-      if [[ "$RUN_COVERAGE" == "1" ]]; then
-          coverage run --rcfile=setup.cfg -m pytest
-      else
-          pytest
-      fi
-    - |
-      if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-          sudo apt-get install -y -q openmpi-bin libopenmpi-dev
-      else
-          brew install openmpi
-      fi
-    - python$PY -m pip --no-cache-dir install mpi4py
-    - |
-      if [[ "$RUN_COVERAGE" == "1" ]]; then
-          mpiexec -n 2 coverage run --rcfile=setup.cfg -m mpi4py -m pytest
-          coverage combine
-          coverage report -m
-      else
-          mpiexec -n 2 pytest
-      fi
-after_success:
-    - |
-      if [[ "$RUN_COVERAGE" == "1" ]]; then
-          codecov
-      fi
+  - coverage run --rcfile=setup.cfg -m pytest
+  - |
+    if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+      sudo apt-get install -y -q openmpi-bin libopenmpi-dev
+    else
+      brew install openmpi
+    fi
+  - pip$PY --no-cache-dir install mpi4py
+  - |
+    mpiexec -n 2 coverage run --rcfile=setup.cfg -m mpi4py -m pytest
+    coverage combine
+    coverage report -m
 before_deploy:
-    - rm -r dist
-    - rm -r build
+  - rm -r dist
+  - rm -r build
 deploy:
-    provider: pypi
-    user: 1313e
-    password:
-        secure: "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"
-    distributions: "sdist bdist_wheel"
-    skip_existing: true
-    on:
-        branch: master
-        condition: $TRAVIS_OS_NAME == linux
-        tags: true
+  provider: pypi
+  user: 1313e
+  password:
+    secure: "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"
+  distributions: "sdist bdist_wheel"
+  skip_existing: true
+  on:
+    branch: master
+    condition: $TRAVIS_OS_NAME == linux
+    tags: true
 
 notifications:
   webhooks:

MANIFEST.in

@@ -2,6 +2,7 @@ include LICENSE
 include README.rst
 include MANIFEST.in
 include requirements*.txt
+include conftest.py
 recursive-include prism data/*
 
 exclude docs joss_paper logo prism_trash tutorials .github

README.rst

@@ -93,7 +93,7 @@ The `online docs`_ and `the tutorials`_ have several examples explaining the dif
 .. _repository: https://github.com/1313e/PRISM
 .. _PyPI: https://pypi.org/project/prism
 .. _online docs: https://prism-tool.readthedocs.io
-.. _the tutorials: ./tutorials
+.. _the tutorials: https://github.com/1313e/PRISM/tree/master/tutorials
 
 
 Running tests