Try to deal with flaky failures when apt-getting (gwastro#4384)

.github/workflows/basic-tests.yml

@@ -23,8 +23,8 @@ jobs:
         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: |

.github/workflows/inference-workflow.yml

@@ -16,17 +16,17 @@ jobs:
         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=5.0.3-1+ubuntu18
-    - 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=5.0.3-1+ubuntu18
+    - 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/search-workflow.yml

@@ -20,17 +20,17 @@ jobs:
         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=5.0.3-1+ubuntu18
-    - 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=5.0.3-1+ubuntu18
+    - 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

@@ -20,17 +20,17 @@ jobs:
         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=5.0.3-1+ubuntu18
-    - 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=5.0.3-1+ubuntu18
+    - 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

@@ -22,8 +22,8 @@ jobs:
         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

@@ -25,17 +25,17 @@ jobs:
         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=5.0.3-1+ubuntu18
-    - 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=5.0.3-1+ubuntu18
+    - 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

tools/einsteinathome/pycbc_etch64_compile-usr-local.sh

@@ -5,17 +5,17 @@ set -e
 # update apt
 grep '^deb http://archive.debian.org/debian/' /etc/apt/sources.list ||
   echo 'deb http://archive.debian.org/debian/ etch main' >>/etc/apt/sources.list
-apt-get -y update || true
-apt-get -y install debian-keyring debian-archive-keyring
-apt-get -y update
+apt-get -o Acquire::Retries=3 -y update || true
+apt-get -o Acquire::Retries=3 -y install debian-keyring debian-archive-keyring
+apt-get -o Acquire::Retries=3 -y update
 # tools for pycbc
-apt-get -y install git-core gcc g++ gfortran automake autoconf make libtool pkg-config bzip2
+apt-get -o Acquire::Retries=3 -y install git-core gcc g++ gfortran automake autoconf make libtool pkg-config bzip2
 # libraries for pycbc
-apt-get -y install libpcre3-dev libfreetype6-dev libjpeg-dev libpng-dev libmysqlclient-dev libpq-dev libssl-dev libsqlite3-dev libdb4.4-dev
+apt-get -o Acquire::Retries=3 -y install libpcre3-dev libfreetype6-dev libjpeg-dev libpng-dev libmysqlclient-dev libpq-dev libssl-dev libsqlite3-dev libdb4.4-dev
 # make sure these libraries aren't on the system
-apt-get -y remove lapack3-dev atlas3-base atlas3-headers refblas3
+apt-get -o Acquire::Retries=3 -y remove lapack3-dev atlas3-base atlas3-headers refblas3
 # further necessary / useful tools
-apt-get -y install openssh-server ntpdate zip gettext curl libcurl3-openssl-dev wget bzip2 libbz2-dev screen emacs
+apt-get -o Acquire::Retries=3 -y install openssh-server ntpdate zip gettext curl libcurl3-openssl-dev wget bzip2 libbz2-dev screen emacs
 
 test ".$PREFIX" = "." &&
   PREFIX=/usr/local

tools/install_travis.sh

@@ -7,7 +7,7 @@ set -e
 # We should ask pegasus to update their requirement to psycopg2 2.7 which fixes
 # this bug
 echo -e "Trying to get rid of pg_config"
-sudo apt-get -y purge libpq-dev
+sudo apt-get -o Acquire::Retries=3 -y purge libpq-dev
 echo -e "Making sure it is really gone..."
 if [ -n "`which pg_config`" ]
 then