Merge branch 'gwastro:master' into kkacanja-patch-1

.github/workflows/basic-tests.yml

@@ -2,25 +2,29 @@ name: basic tests
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ${{ matrix.os }}
     strategy:
       max-parallel: 60
       matrix:
         os: [ubuntu-20.04]
-        python-version: [3.7, 3.8, 3.9, '3.10']
-        test-type: [help, unittest, search, inference, docs]
+        python-version: [3.8, 3.9, '3.10', '3.11']
+        test-type: [unittest, search, docs]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: installing system packages
       run: |
-        sudo apt-get update
-        sudo apt-get install *fftw3* mpi intel-mkl* git-lfs graphviz
+        sudo apt-get -o Acquire::Retries=3 update
+        sudo apt-get -o Acquire::Retries=3 install *fftw3* mpi intel-mkl* git-lfs graphviz
         pip install "tox<4.0.0" pip setuptools --upgrade
     - name: installing auxiliary data files
       run: |
@@ -35,6 +39,16 @@ jobs:
       run: |
         export LAL_DATA_PATH=$PWD
         tox -e py-${{matrix.test-type}}
+    - name: check help messages work
+      if: matrix.test-type == 'unittest'
+      run: |
+        export LAL_DATA_PATH=$PWD
+        tox -e py-help
+    - name: run inference tests
+      if: matrix.test-type == 'search'
+      run: |
+        export LAL_DATA_PATH=$PWD
+        tox -e py-inference
     - name: store documentation page
       if: matrix.test-type == 'docs' && matrix.python-version == '3.8'
       uses: actions/upload-artifact@v2

.github/workflows/build_venv.yml

@@ -2,6 +2,10 @@ name: build the LVK virtualenv
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-20.04
@@ -10,7 +14,7 @@ jobs:
         uses: actions/checkout@v1
       -
         name: "Set up Python"
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
       -

.github/workflows/distribution.yml

@@ -2,6 +2,10 @@ name: Build Wheels
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build_wheels:
     name: Build wheels on ${{ matrix.os }}
@@ -11,17 +15,18 @@ jobs:
         os: [ubuntu-20.04, macos-latest]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel==2.3.1
-
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_BUILD: cp37-* cp38-* cp39-* cp310-*
+          CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
           CIBW_SKIP: "*musllinux*"
           CIBW_ARCHS_MACOS: x86_64 arm64
       - uses: actions/upload-artifact@v2
@@ -32,13 +37,13 @@ jobs:
     runs-on: ubuntu-20.04
     needs: build_wheels
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: 3.8
     - uses: actions/download-artifact@v2
       with:
         path: ./

.github/workflows/docker-build.yml

@@ -2,6 +2,10 @@ name: docker build
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-20.04
@@ -10,7 +14,7 @@ jobs:
         uses: actions/checkout@v1
       -
         name: "Set up Python"
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
       -

.github/workflows/inference-workflow.yml

@@ -8,25 +8,25 @@ jobs:
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -
         echo "deb http://research.cs.wisc.edu/htcondor/ubuntu/8.9/focal focal contrib" | sudo tee -a /etc/apt/sources.list
         echo "deb-src http://research.cs.wisc.edu/htcondor/ubuntu/8.9/focal focal contrib" | sudo tee -a /etc/apt/sources.list
-        sudo apt-get update
-        sudo apt-get install minihtcondor
+        sudo apt-get -o Acquire::Retries=3 update
+        sudo apt-get -o Acquire::Retries=3 install minihtcondor
         sudo systemctl start condor
         sudo systemctl enable condor
     - name: install pegasus
       run: |
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
-        sudo apt-get update
-        sudo apt-get install pegasus
-    - run: sudo apt-get install *fftw3* intel-mkl*
+        sudo apt-get -o Acquire::Retries=3 update
+        sudo apt-get -o Acquire::Retries=3 install pegasus
+    - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
         python -m pip install --upgrade 'pip<22.0' setuptools

.github/workflows/mac-test.yml

@@ -2,22 +2,26 @@ name: macos basic tests
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ${{ matrix.os }}
     strategy:
       max-parallel: 4
       matrix:
         os: [macos-latest]
-        python-version: [3.7, 3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', '3.11']
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - run: |
-        brew install fftw openssl
+        brew install fftw openssl gsl
         pip install --upgrade pip setuptools "tox<4.0.0"
     - name: run basic pycbc test suite
       run: |

.github/workflows/search-workflow.yml

@@ -2,31 +2,36 @@ name: run small search using pegasus + condor
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-20.04
+    timeout-minutes: 90
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -
         echo "deb http://research.cs.wisc.edu/htcondor/ubuntu/8.9/focal focal contrib" | sudo tee -a /etc/apt/sources.list
         echo "deb-src http://research.cs.wisc.edu/htcondor/ubuntu/8.9/focal focal contrib" | sudo tee -a /etc/apt/sources.list
-        sudo apt-get update
-        sudo apt-get install minihtcondor
+        sudo apt-get -o Acquire::Retries=3 update
+        sudo apt-get -o Acquire::Retries=3 install minihtcondor
         sudo systemctl start condor
         sudo systemctl enable condor
     - name: install pegasus
       run: |
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
-        sudo apt-get update
-        sudo apt-get install pegasus
-    - run: sudo apt-get install *fftw3* intel-mkl*
+        sudo apt-get -o Acquire::Retries=3 update
+        sudo apt-get -o Acquire::Retries=3 install pegasus
+    - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
         python -m pip install --upgrade 'pip<22.0' setuptools

.github/workflows/tmpltbank-workflow.yml

@@ -2,31 +2,35 @@ name: run small template bank generation using pegasus + condor
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-20.04
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -
         echo "deb http://research.cs.wisc.edu/htcondor/ubuntu/8.9/focal focal contrib" | sudo tee -a /etc/apt/sources.list
         echo "deb-src http://research.cs.wisc.edu/htcondor/ubuntu/8.9/focal focal contrib" | sudo tee -a /etc/apt/sources.list
-        sudo apt-get update
-        sudo apt-get install minihtcondor
+        sudo apt-get -o Acquire::Retries=3 update
+        sudo apt-get -o Acquire::Retries=3 install minihtcondor
         sudo systemctl start condor
         sudo systemctl enable condor
     - name: install pegasus
       run: |
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
-        sudo apt-get update
-        sudo apt-get install pegasus
-    - run: sudo apt-get install *fftw3* intel-mkl*
+        sudo apt-get -o Acquire::Retries=3 update
+        sudo apt-get -o Acquire::Retries=3 install pegasus
+    - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
         python -m pip install --upgrade 'pip<22.0' setuptools

.github/workflows/tut-test.yml

@@ -2,24 +2,28 @@ name: tutorial tests
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ${{ matrix.os }}
     strategy:
       max-parallel: 60
       matrix:
         os: [ubuntu-20.04]
-        python-version: [3.7, 3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', '3.11']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: installing packages
       run: |
-        sudo apt-get update
-        sudo apt-get install *fftw3* mpi intel-mkl*
+        sudo apt-get -o Acquire::Retries=3 update
+        sudo apt-get -o Acquire::Retries=3 install *fftw3* mpi intel-mkl*
         pip install tox pip setuptools notebook --upgrade
         pip install .
     - name: retrieving pycbc tutorials

.github/workflows/workflow-tests.yml

@@ -2,6 +2,10 @@ name: run generic example workflow tests
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ${{ matrix.os }}
@@ -13,25 +17,25 @@ jobs:
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -
         echo "deb http://research.cs.wisc.edu/htcondor/ubuntu/8.9/focal focal contrib" | sudo tee -a /etc/apt/sources.list
         echo "deb-src http://research.cs.wisc.edu/htcondor/ubuntu/8.9/focal focal contrib" | sudo tee -a /etc/apt/sources.list
-        sudo apt-get update
-        sudo apt-get install minihtcondor
+        sudo apt-get -o Acquire::Retries=3 update
+        sudo apt-get -o Acquire::Retries=3 install minihtcondor
         sudo systemctl start condor
         sudo systemctl enable condor
     - name: install pegasus
       run: |
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
-        sudo apt-get update
-        sudo apt-get install pegasus
-    - run: sudo apt-get install *fftw3* intel-mkl*
+        sudo apt-get -o Acquire::Retries=3 update
+        sudo apt-get -o Acquire::Retries=3 install pegasus
+    - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
         python -m pip install --upgrade 'pip<22.0' setuptools