This is alpha quality software and should not be used for production workloads

freenome-build

Packaging, build, and development tools.

freenome-build test-db

Manage a test postgres DB in a Docker container. This also runs a DB setup script and DB migrations. The structure of the setup and migrations scripts is described in more detail in the README

freenome-build test-db start

Start a test DB.

freenome-build test-db start

Stop a test DB.

freenome-build test-db connect

Connect to a running test DB.

freenome-build develop

Setup a conda development environment for the current repo.

Running freenome-build develop $REPO_PATH sets up a development environment for the github repo in $REPO_PATH. Specifically, this command:

1. builds a conda package
   • if a meta.taml file exists in $REPO_PATH/meta.yaml then use that as the package specification
   • if not, use python setup.py bdist_conda to build the conda package
2. install the built packages' dependencies by running conda install $PACKAGE --only-deps
3. install the package in python's develop mode by running python $REPO_PATH/setup.py develop

freenome-build deploy -p $REPO_PATH

Build the package in $REPO_PATH and upload to anaconda cloud.

Caveats, gotchas, and TODO's

The package name is inferred from:

1. the github repo name

TODO Allow the package name to be specified as an argument

The package version is inferred from:

1. a version file at $REPO_PATH/VERSION
2. a __version__ string in $REPO_PATH/$MODULE_NAME that amtches the pattern ^__version__\s*=\s*[\'"]([^\'"]*)[\'"]

TODO Allow version to be specified as an argument

Bootstrapping requires scripts/conda_build.sh

Each repo must clone the freenome-build repo during a travis build so that it can call scripts/conda_build.sh. This requires that that repo on travis has a github access token generated locally using the ruby travis script. For example for LIMS-API I ran the following

travis endpoint --pro --set-default
travis login
travis sshkey --generate -r freenome/LIMS-API     --debug

In order to clone from freenome's conda channel in a .travis.yml you need an anaconda token to be securely encrypted

travis endpoint --pro --set-default
travis login
travis encrypt ANACONDA_TOKEN=[ANACONDA_TOKEN] --add