diff --git a/.azure-pipelines/azure-pipelines.yml b/.azure-pipelines/azure-pipelines.yml index 2402cfce..ff912a11 100644 --- a/.azure-pipelines/azure-pipelines.yml +++ b/.azure-pipelines/azure-pipelines.yml @@ -1,5 +1,9 @@ variables: - DATABASE_SCHEMA: 1.28.0 + DATABASE_SCHEMA: 4.1.0 # released 2024-03-26 + # Installs from GitHub + # Versions: https://github.com/DiamondLightSource/ispyb-database/tags + # Previous version(s): + # 1.28.0 # released 2021-11-23 trigger: branches: @@ -12,7 +16,11 @@ trigger: resources: containers: - container: mariadb - image: mariadb:10.8 + image: mariadb:11.3.2 # released 2024-05-06 + # Pulls image from DockerHub + # Docker images: https://hub.docker.com/_/mariadb + # Previous version(s): + # 10.8 # released 2023-06-02 # https://hub.docker.com/layers/library/mariadb/10.8/images/sha256-2c79abca2711c7e7fe4ae21864a29544a8404dfb519973fa6f4caebd5445f66b?context=explore env: MYSQL_DATABASE: ispybtest MYSQL_ROOT_PASSWORD: mysql_root_pwd diff --git a/.azure-pipelines/ci.yml b/.azure-pipelines/ci.yml index d0c18dc1..5552dd52 100644 --- a/.azure-pipelines/ci.yml +++ b/.azure-pipelines/ci.yml @@ -1,3 +1,5 @@ +# Contains tasks to be repeated when testing for the different Python versions listed +# in the "Run unit tests" stage in .azure-pipelines/azure-pipelines.yml steps: - checkout: none @@ -6,7 +8,7 @@ steps: mkdir rabbitmq-docker && cd rabbitmq-docker cat <rabbitmq.conf - # allowing remote connections for default user is highly discouraged + # Allowing remote connections for default user is highly discouraged # as it dramatically decreases the security of the system. Delete the user # instead and create a new one with generated secure credentials. loopback_users = none @@ -44,7 +46,7 @@ steps: - script: | set -eux - pip install --disable-pip-version-check -e "$(Pipeline.Workspace)/src"[cicd,clem,client,server,developer] + pip install --disable-pip-version-check -e "$(Pipeline.Workspace)/src"[cicd,client,server,developer] displayName: Install package - script: | diff --git a/pyproject.toml b/pyproject.toml index ad80a6bf..948da577 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,11 +39,6 @@ dependencies = [ cicd = [ "pytest-cov", # Used by Azure Pipelines for PyTest coverage reports ] -clem = [ - # "matplotlib", # For visual statistical analysis of images - "readlif", # cryo-CLEM; open LIF files - "tifffile", # cryo-CLEM; for saving to to TIFF files -] client = [ "procrunner", "textual==0.42.0", @@ -57,17 +52,19 @@ developer = [ "pytest", # Test code functionality ] server = [ + # "matplotlib", # For visual statistical analysis of images "cryptography", "fastapi", - "ispyb", + "ispyb", # Responsible for setting requirements for SQLAlchemy and mysql-connector-python; v10.0.0: sqlalchemy <2, mysql-connector-python >=8.0.32 "jinja2", - "mysql-connector-python<=8.0.29", # ispyb 8.0.0 requires ==8.0.29 "numpy", "packaging", "pillow", "prometheus_client", + "readlif", # Specific to cryo-CLEM workflow "sqlmodel", "stomp-py<=8.1.0", # 8.1.1 (released 2024-04-06) doesn't work with our project + "tifffile", # Specific to cryo-CLEM workflow "uvicorn[standard]", "zocalo", ]