Merge branch 'master' into dependabot/pip/jupyter-server-2.7.2

.github/workflows/failure_workflow.yaml

@@ -0,0 +1,24 @@
+---
+name: Failure on Workflow
+
+on:
+  workflow_run:
+    workflows: 
+      - "Windows Test"
+      - "test and make pages"
+    types:
+      - completed
+
+jobs:
+  on-failure:
+    runs-on: ubuntu-latest
+    if: ${{ github.event.workflow_run.conclusion == 'failure' }}
+    steps:
+    - uses: ravsamhq/notify-slack-action@v2
+      with:
+        status: ${{ github.event.workflow_run.conclusion }}
+        notification_title: " ${{github.event.workflow_run.name}} - ${{github.event.workflow_run.conclusion}} on ${{github.event.workflow_run.head_branch}} - <${{github.server_url}}/${{github.repository}}/actions/runs/${{github.event.workflow_run.id}}|View Failure>"
+        message_format: ":fire: *${{github.event.workflow_run.name}}* ${{github.event.workflow_run.conclusion}} in <${{github.server_url}}/${{github.repository}}/${{github.event.workflow_run.head_branch}}|${{github.repository}}>"
+        footer: "Linked Repo <${{github.server_url}}/${{github.repository}}|${{github.repository}}> | <${{github.server_url}}/${{github.repository}}/actions/runs/${{github.event.workflow_run.id}}|View Failure>"
+      env:
+        SLACK_WEBHOOK_URL: ${{ secrets.MONITORING_SLACK }}

.github/workflows/test_deploy.yaml

@@ -2,40 +2,45 @@ name: test and make pages
 
 on:
   push:
-    branches: [ master ]
+    branches: [ test ]
   pull_request:
     branches: [ master ]
   schedule:
     - cron: "0 2 * * *"
+  workflow_dispatch:
 
 jobs:
-
   test:
     name: hazard test
     runs-on: ubuntu-latest
     env:
       MPLBACKEND: 'Agg'
-
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: "3.10"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest
         git clone --depth=1 https://github.com/gem/oq-engine.git
-        pip -q install -r oq-engine/requirements-py38-linux64.txt 
-        pip -q install -e oq-engine
+        cd oq-engine
+        python3 install.py devel
+        cd ..
+        source ~/openquake/bin/activate
+        pip list
         pip install -e .
+        pip install pytest
     - name: Run test with pytest
       run: |
+        source ~/openquake/bin/activate
+        oq engine --upgrade-db
+        oq --version
+        sleep 3
         cd openquake
-        oq dbserver start
-        pytest -vsx cat ghm man mbt sub wkf smt
-
+        export MPLBACKEND=Agg
+        pytest -vsx --color=yes cat ghm man mbt sub wkf smt
   pages:
     name: pages
     runs-on: ubuntu-latest
@@ -44,23 +49,26 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.8
+    - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
-    - name: Install dependencies
+        python-version: "3.10"
+    - name: Install OpenQuake dependencies
       run: |
         sudo apt-get install pandoc
         python -m pip install --upgrade pip
         git clone --depth=1 https://github.com/gem/oq-engine.git
-        pip -q install -r oq-engine/requirements-py38-linux64.txt
-        pip -q install -e oq-engine
+        cd oq-engine
+        python3 install.py devel
+        sleep 3
+        source ~/openquake/bin/activate
         pip install sphinx
         pip install recommonmark
         pip install sphinx_rtd_theme
         pip install nbsphinx
     - name: Make html pages
       run: |
+        source ~/openquake/bin/activate
         cd docsrc ; sphinx-apidoc -o contents/ ../openquake ; make html
         touch _build/html/.nojekyll
 

.github/workflows/test_win64.yaml

@@ -1,34 +1,67 @@
-name: Installation and test on Windows
-
+---
+name: Windows Test
 on:
   push:
     branches:
-      - 'ae-310action'
+      - test
+  pull_request:
+    branches: [ master ]
   schedule:
     - cron: "0 4 * * *"
   workflow_dispatch:
 jobs:
-
   test:
     name: Windows Installation
-    runs-on: windows-latest
-
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [windows-2022, windows-2019]
     steps:
-    - name: Extract branch name
-      shell: bash
-      run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
-      id: extract_branch
-    - uses: actions/checkout@v3
-    - name: Run scripts to install on windows
-      run: |
-        Write-Host "Git branch for Run action "${Env:GIT_BRANCH}
-        #
-        $curDir = Get-Location
-        Write-Host "Current Working Directory: $curDir"
-        Get-ChildItem -Path .\windows –recurse
-        .\windows\install_oqmbtk.ps1
-        cd $env:USERPROFILE
-        cd mbtk
-        dir
-        cd oq-mbtk\openquake
-        pytest -vs cat ghm man mbt sub wkf smt 
+      - uses: actions/checkout@v4
+      - name: Installation of GMT from standalone
+        run: |
+          Invoke-WebRequest -Uri "https://github.com/GenericMappingTools/gmt/releases/download/6.4.0/gmt-6.4.0-win64.exe" -OutFile $HOME\gmt.exe
+          cd $HOME
+          $Install = Get-ChildItem -Filter gmt*.exe
+          Start-Process -FilePath $Install.Fullname -ArgumentList "/S" -Wait
+          $Env:PATH += ";C:\programs\gmt6\bin"
+          Write-Host ${env:PATH}
+      - name: Run scripts to install on windows
+        run: |
+          Write-Host "Set LIBRARY PATH for GMT"
+          $Env:GMT_LIBRARY_PATH="C:\programs\gmt6\bin"
+          Write-Host "Git branch for Run action "${Env:GIT_BRANCH}
+          #
+          $curDir = Get-Location
+          Write-Host "Current Working Directory: $curDir"
+          Get-ChildItem -Path .\windows –recurse
+          Write-Host "Install oqmbtk on branch ${{ github.ref_name }}"
+          .\windows\install_oqmbtk.ps1 -mbtk_branch ${{ github.ref_name }}
+          $MYPATH = $HOME + "\mbtk"
+          Write-Host "Print USERPROFILE folder: $env:USERPROFILE"
+          Write-Host "Print MYPATH folder: $MYPATH"
+          $Env:PATH += ";$MYPATH"
+          $Env:PATH += ";$MYPATH\python3\Scripts"
+          $Env:PYTHONUTF8=1
+          #Added to disable TCL
+          $Env:MPLBACKEND="AGG"
+          $Env:PY_PIP=$MYPATH += '\Scripts'
+          $Env:PY_PIP=$MYPATH += '\python3\Scripts'
+          $Env:PY_HOME=$MYPATH
+          $Env:PY_LIBS="$MYPATH\python3\Lib;$MYPATH\python3\Lib\site-package"
+          Write-Host "MYPATH Directory: $MYPATH"
+          Start-Job -ScriptBlock{& 'oq.exe' engine --upgrade-db}
+          oq.exe --version
+          Write-Host "Print all environments variables to check"
+          dir env:
+          Write-Host "Print all pypip packages"
+          pip list
+          $MBTK = $HOME + "\mbtk"
+          Write-Host "MBTK Directory: $MBTK"
+          Set-Location -Path $MBTK
+          $curDir = Get-Location
+          Write-Host "Current Working Directory: $curDir"
+          cd oq-mbtk\openquake
+          Write-Host "Install pytest and run tests"
+          pip install pytest==8.1.2
+          pytest -vs --color=yes --durations=10 cat ghm man mbt sub wkf smt

.gitignore

@@ -1,3 +1,4 @@
+_dev_notebooks/
 
 
 # Byte-compiled / optimized / DLL files

README.md

@@ -1,6 +1,6 @@
 [![test and make pages](https://github.com/GEMScienceTools/oq-mbtk/actions/workflows/test_deploy.yaml/badge.svg)](https://github.com/GEMScienceTools/oq-mbtk/actions/workflows/test_deploy.yaml)
 
 # OpenQuake Model Building Toolkit
-The OpenQuake Model Building Toolkit (OQ-MBTK) is a container for various packages each one with specific modelling or analyses capabilities. The project started with the `mbt` package which provides tools for the construction of components of a PSHA earthquake occurrence model. 
+The OpenQuake Model Building Toolkit (OQ-MBTK) is a container for various packages each one with specific modelling or analysis capabilities. The project started with the `mbt` package which provides tools for the construction of components of a PSHA earthquake occurrence model. The repo now contains a module for processing catalogues (`cat`), one supports workflows creating an earthquake occurrence model for the OQ Engine (`mbt` and `wkf`), one for the construction of the ground-motion characterisation (`smt`), one for the modelling of subduction sources and the classification of an earthquake catalogue by tectonic region (`sub`) and FERMI, a tool for the construction of occurrence models for fault systems (`fnm`).
 
 Documentation accessible at [https://gemsciencetools.github.io/oq-mbtk/index.html](https://gemsciencetools.github.io/oq-mbtk/index.html)