Installation

To create a standalone installation, in you favorite conda or venv, clone the repository and pip install:

git clone git@github.com:znamlab/flexiznam.git
cd flexiznam
pip install -r requirements.txt
pip install -e .

Don’t forget to use the -e flag when installing flexiznam if you want to be able to edit the code.

To check that the install is successful you can type flexiznam --help in a terminal. You can also start python and import flexiznam.

If you want to install flexiznam to use it in another repository, then run the following with the corresponding virtual environment active:

pip install git+ssh://git@github.com/znamlab/flexiznam.git

You can also install the develop branch:

pip install git+ssh://git@github.com/znamlab/flexiznam.git@dev

Once flexiznam is installed, you can also use pip to keep the package updated:

pip install --upgrade git+ssh://git@github.com/znamlab/flexiznam.git

This will update the package as long as the version of the repository is higher than the one you have installed.

Configuration

The default configuration settings can be created simply by running: flexiznam config. This will create a ~/.flexiznam directory with a config.yml file.

To add newly defined configuration field and set them to their default value, you can run flexiznam config --update. This will not change any existing field or remove any obsolete fields.

The configuration file can be edited manually or using flexiznam.config.update_config. The option should be self explaining but in doubt, see the comments in flexiznam.config.default_config.py.

Password management

To simplify the interaction with MCSM and flexilims, you can store a copy of you passwords in ~/.flexiznam/secret_password.yml. This file can be created and edited manually. It needs to be a yml file formatted like the template in flexiznam.config. Alternatively on can use the CLI:

flexiznam add-password --app mcms --username myname --password uniquepassword