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