Getting started with GoFigr
===========================

Account registration
********************

Before you begin, create an account at https://app.gofigr.io/register

Client setup
*************

First, install the ``gofigr`` client library:

.. code:: bash

    $ pip install gofigr

.. _gfconfig:

Once installed, configure it with ``gfconfig``. The tool will prompt you for a
username and password, and a default workspace.

.. code::

    $ gfconfig
    ------------------------------
    GoFigr configuration
    ------------------------------
    Username: alyssa
    Password:
    Verifying connection...
      => Authenticated successfully
    API key (leave blank to generate a new key):
    Key name: Alyssa's Macbook
      => Your new API key will be saved to /Users/alyssa/.gofigr
      => Connected successfully

    Please select a default workspace:
      [ 1] - Scratchpad - alyssa's personal workspace  - API ID: c6ecd353-321d-4089-b5aa-d94bf0ecb09a
    Selection [1]: 1

    Configuration saved to /Users/alyssa/.gofigr. Happy analysis!

``gfconfig`` only configures the defaults. You will be able to customize
any of the options on a per-notebook basis.

Advanced configuration
----------------------

Optionally, you can call ``gfconfig --advanced`` and customize some additional options:

API URL:
     This is the API URL that the client will connect to. We use it for development, but you can just accept the default.
Auto-publish:
     Whether to automatically capture and publish all figures generated by Jupyter, even without
     an explicit call to ``publish``. Auto-publish is on by default, but you can disable it here.
Default revision metadata:
     JSON that we will automatically store with each figure revision. This is completely up to you. You can leave it
     empty or include details relevant to your team or organization.

.. code::

    $ gfconfig --advanced
    ------------------------------
    GoFigr configuration
    ------------------------------
    Username: mpacula
    Password:
    API URL [https://api.gofigr.io]:
    Verifying connection...
      => Connected successfully
    Auto-publish all figures [Y/n]: y
    Default revision metadata (JSON): {"study": "First in Human trial"}

    Please select a default workspace:
      [ 1] - Primary Workspace              - mpacula's primary workspace    - API ID: c6ecd353-321d-4089-b5aa-d94bf0ecb09a
    Selection [1]: 1

    Configuration saved to /Users/maciej/.gofigr. Happy analysis!


Environment variables
----------------------
By default, GoFigr reads configuration from the file ``.gofigr`` in the user's home directory. However, you
can also use environment variables:

* `GF_USERNAME`
* `GF_PASSWORD`
* `GF_API_KEY`
* `GF_WORKSPACE`: must be an API ID (look it up in the Web App)
* `GF_ANALYSIS`: must be an API ID (look it up in the Web App)
* `GF_URL`: API URL
* `GF_AUTO_PUBLISH`: true or false

.. _jupyter_setup:

Jupyter setup
*************
GoFigr works with both Jupyter Notebook and Jupyter Lab. To use it, simply
load the extension and call :func:`gofigr.jupyter.configure`:

.. code:: python

    %load_ext gofigr

    from gofigr.jupyter import *

    configure(analysis=FindByName("My Analysis", create=True))

This will set your current analysis to ``My Analysis`` under the default workspace (selected through ``gfconfig``),
creating it if it doesn't already exist.

You can also specify a custom workspace, override ``auto_publish``, or supply
default revision metadata:

.. code:: python

    %load_ext gofigr

    from gofigr.jupyter import *

    configure(auto_publish=False,
              workspace=FindByName("Primary Workspace", create=False),
              analysis=FindByName("My Analysis", create=True),
              default_metadata={'requested_by': "Alyssa",
                                'study': 'Pivotal Trial 1'})

.. _specifying_names:

Specifying names & IDs
-----------------------
Instead of using ``FindByName``, you can avoid ambiguity and specify API IDs directly. You
can find the API IDs for workspaces and analyses in the web app. Mixing and matching
is supported as well:

.. code:: python

    %load_ext gofigr

    from gofigr.jupyter import *

    configure(workspace=ApiId("59da9bdb-2095-47a9-b414-c029f8a00e0e"),
              analysis=FindByName("My Analysis", create=True))

Publishing your first figure
*****************************

To publish your first figure, simply call ``publish`` (if you have auto-publish turned on,
the figure will be published automatically without this call). For example, here we publish
a scatter plot:

.. code:: python

    from datetime import datetime
    def test_figure(figsize=(7, 7)):
        df = pd.DataFrame(
             {"x1": npr.normal(size=100),
              "y1": npr.normal(size=100),

              "x2": npr.normal(size=100) + 2,
              "y2": npr.normal(size=100) + 3,

              "x3": npr.normal(size=100) + 3,
              "y3": npr.normal(size=100) - 2})

        fig = plt.figure(figsize=figsize)
        plt.scatter(x=df['x1'], y=df['y1'])
        plt.scatter(x=df['x2'], y=df['y2'])
        plt.scatter(x=df['x3'], y=df['y3'])

        plt.title(f"Example scatter\n{datetime.now()}")
        return plt.gcf(), df

    _ = test_figure()

    publish(fig=plt.gcf(), target=FindByName("My first figure!", create=True))

You will get a barcoded image with a QR code and a unique revision ID:

.. image:: images/scatter_example.png
  :alt: Example published figure

You can now scan the barcode or manually navigate to the figure in the Web App
at https://app.gofigr.io .

.. image:: images/webapp.png
  :alt: Figure displayed in the Web App

Publishing new revisions
-------------------------

Feel free to run the above code multiple times. GoFigr will automatically capture the different revisions:

.. image:: images/revisions_example.png
  :alt: Figure revisions in the Web App