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azure-template-tox-job.yml
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# File: azure-template-tox-job.yml
# Date: 8-Jul-2019 jdw split out from original pipeline
# Supports: fixtures=mysql,mongodb,mmseq2 (linux)
#
# Updates:
# 6-Aug-2019 jdw build source and binary wheels by default.
# 13-Aug-2019 jdw export config support token prior to launching tox runner
# 20-Jun-2021 jdw add mmseq2 fixture
#
##
parameters:
tox: ""
python: ""
os: "linux"
fixtures: ""
jobs:
- job: ${{ format('build_test_{0}_{1}', parameters.tox, parameters.os) }}
timeoutInMinutes: 0
pool:
${{ if eq(parameters.os, 'macos') }}:
vmImage: "macOS-latest"
${{ if eq(parameters.os, 'linux') }}:
vmImage: "ubuntu-latest"
variables:
- group: py-shared-variables
steps:
#
# ensure the required Python versions are available
- task: UsePythonVersion@0
inputs:
versionSpec: ${{ parameters.python }}
addToPath: true
displayName: setup python
#
- checkout: self
submodules: true
#
- ${{ if startsWith(parameters.os, 'macos') }}:
- bash: |
set -e
ls -la /Applications/Xcode*
sudo xcode-select --switch /Applications/Xcode_16.app/Contents/Developer
which g++
c++ --version
displayName: "setup Xcode"
#
- script: which brew
displayName: "Check package manager"
- script: brew install flex
displayName: "Install flex"
- script: which flex
displayName: "Check flex"
- script: brew install bison
displayName: "Install bison"
- script: which bison
displayName: "Check bison"
#
#
- script: brew install mmseqs2
displayName: "Install mmseqs2"
- script: which mmseqs
displayName: "Check mmseqs2"
#
- script: brew install mariadb
displayName: "Install mariadb"
# ----------------------------------------------
- ${{ if startsWith(parameters.os, 'linux') }}:
- script: lsb_release -a
displayName: "Ubuntu kernal version"
- script: which apt
displayName: "Installing OS dependencies"
- script: apt-cache policy | grep http | awk '{print $2 $3}' | sort -u
displayName: "Checking for repos"
#
- script: sudo apt-get update
displayName: "update apt"
#- script: sudo apt-get upgrade
# displayName: 'upgrade apt'
#- script: sudo apt-get update
# displayName: 'update apt'
- script: sudo apt-get install flex
displayName: "Install flex"
- script: sudo apt-get install bison
displayName: "Install bison"
#
- ? ${{ if and(contains(parameters.fixtures, 'mmseqs2'), startsWith(parameters.os, 'linux')) }}
: - bash: |
[ $(uname -m) = "x86_64" ] && echo "64bit: Yes" || echo "64bit: No"
grep -q sse4_1 /proc/cpuinfo && echo "SSE4.1: Yes" || echo "SSE4.1: No"
grep -q avx2 /proc/cpuinfo && echo "AVX2: Yes" || echo "AVX2: No"
displayName: "Check architecture"
- bash: |
echo "Downloading latest MMseqs2 static build"
attempt=1
while [[ $attempt -le 5 ]]; do
wget https://mmseqs.com/latest/mmseqs-linux-avx2.tar.gz
if [[ $? -eq 0 ]]; then
echo "Download successful."
break
else
echo "Download failed. Retrying in 5 seconds..."
sleep 5
attempt=$((attempt + 1))
fi
done
tar xvzf mmseqs-linux-avx2.tar.gz
sudo cp mmseqs/bin/mmseqs /usr/local/bin/mmseqs
displayName: "Install mmseqs2 binary"
#
- ? ${{ if and(contains(parameters.fixtures, 'mysql'), startsWith(parameters.os, 'linux')) }}
: - bash: |
sudo apt-get install python3-dev mysql-server
sudo apt-get install default-libmysqlclient-dev
sudo apt-get install python-mysqldb
sudo apt list --installed | grep -i mysql
displayName: "Install mysql development libraries"
- bash: |
echo "Retarting mysql service"
sudo systemctl restart mysql.service
mysql -V
mysql --user=root --password=root -e "use mysql; select * from user;"
#
echo "Try resetting password"
mysqladmin --user=root --password=root password 'ChangeMeSoon'
#
# mysql -u root -p root -e "SET PASSWORD FOR root@'localhost' = PASSWORD(‘ChangeMeSoon’);"
# mysql -u root -p root -e "FLUSH PRIVILEGES; update mysql.user set password=password('ChangeMeSoon') where user='root'; FLUSH PRIVILEGES;"
# UPDATE mysql.user SET Password=PASSWORD('ChangeMeSoon') WHERE User='root';
echo "Running preliminary mysql setup"
mysql --user=root --password=ChangeMeSoon <<_EOF_
DELETE FROM mysql.user WHERE User='';
DELETE FROM mysql.user WHERE User='root' AND Host NOT IN ('localhost', '127.0.0.1', '::1');
DROP DATABASE IF EXISTS test;
DELETE FROM mysql.db WHERE Db='test' OR Db='test\\_%';
FLUSH PRIVILEGES;
_EOF_
ps -ef | grep -i my
mysql --user=root --password=ChangeMeSoon -e "show databases;"
#
displayName: "Start and configure mysql ..."
# -----
- ? ${{ if and(contains(parameters.fixtures, 'mongodb'), startsWith(parameters.os, 'linux')) }}
: # Mongo install
- script: |
sudo apt-get install gnupg wget
wget -qO - https://www.mongodb.org/static/pgp/server-4.2.asc | sudo apt-key add -
# sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 9DA31620334BD75D9DCB49F368818C72E52529D4
sudo apt list --installed | grep mongodb
echo "deb [ arch=amd64,arm64 ] https://repo.mongodb.org/apt/ubuntu bionic/mongodb-org/4.2 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-4.2.list
# echo "deb [ arch=amd64,arm64 ] https://repo.mongodb.org/apt/ubuntu xenial/mongodb-org/4.2 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-4.2.list
sudo apt-get update
sudo apt-get install -y mongodb-org
sudo apt list --installed | grep mongo
displayName: "Installing mongodb"
#
- script: |
sudo service mongod start
sudo ss -tulpn
displayName: "Start Mongo service"
#
#
- script: 'python -c "import sys; print(sys.version); print(sys.executable)"'
displayName: show python information
#
- script: python -m pip install --upgrade pip tox
displayName: "Install tools"
#
- script: pip install -r requirements.txt
displayName: "Install dependencies"
#
#
- task: DownloadSecureFile@1
name: oelicense
displayName: "Download OE license file"
inputs:
secureFile: "oe_license.txt"
- ${{ if startsWith(parameters.tox, 'py') }}:
- script: |
export OE_LICENSE=$(oelicense.secureFilePath)
export CONFIG_SUPPORT_TOKEN_ENV=$(VAR_CONFIG_SUPPORT_TOKEN_ENV)
${{ format('python -m tox -e {0}', parameters.tox) }}
displayName: "Running tox task"
- ? ${{ if and(not(startsWith(parameters.tox, 'py')), startsWith(parameters.python, '3.10')) }}
: - script: |
export OE_LICENSE=$(oelicense.secureFilePath)
export CONFIG_SUPPORT_TOKEN_ENV=$(VAR_CONFIG_SUPPORT_TOKEN_ENV)
${{ format('python -m tox -e {0}-py310', parameters.tox) }}
displayName: "Running tox task"
- ? ${{ if and(not(startsWith(parameters.tox, 'py')), startsWith(parameters.python, '3.9')) }}
: - script: |
export OE_LICENSE=$(oelicense.secureFilePath)
export CONFIG_SUPPORT_TOKEN_ENV=$(VAR_CONFIG_SUPPORT_TOKEN_ENV)
${{ format('python -m tox -e {0}-py39', parameters.tox) }}
displayName: "Running tox task"
#
# Build artifacts if this is a test target (i.e. labeled as py##)
#
- ${{ if startsWith(parameters.tox, 'py') }}:
- script: pip install --upgrade pip twine setuptools wheel
displayName: "Acquire build tools"
- script: python setup.py sdist --dist-dir "$(System.DefaultWorkingDirectory)/dist"
displayName: "Build source dist"
- script: python setup.py bdist_wheel --dist-dir "$(System.DefaultWorkingDirectory)/dist"
displayName: "Build wheel"
#
- script: python setup.py sdist --dist-dir "$(System.DefaultWorkingDirectory)/udist"
displayName: "Build source dist"
#
# Check the install artifacts
- script: ls -lR "$(System.DefaultWorkingDirectory)/dist" "$(System.DefaultWorkingDirectory)/udist"
displayName: "Listing of installed software"
#
- publish: $(System.DefaultWorkingDirectory)/dist
artifact: ${{ format('sw_{0}_{1}', parameters.tox, parameters.os) }}
#
- publish: $(System.DefaultWorkingDirectory)/udist
artifact: ${{ format('sw_u_{0}_{1}', parameters.tox, parameters.os) }}
#