Add api key docs blurb

vanvalenlab · Aug 10, 2023 · 5f8bdf4 · 5f8bdf4
1 parent 55260e3
commit 5f8bdf4
Show file tree

Hide file tree

Showing 5 changed files with 42 additions and 18 deletions.
diff --git a/docs/source/API-key.rst b/docs/source/API-key.rst
@@ -0,0 +1,26 @@
+DeepCell API Key
+================
+
+DeepCell models and training datasets are licensed under a `modified Apache license <http://www.github.com/vanvalenlab/deepcell-tf/blob/master/LICENSE>`_ for non-commercial academic use only. An API key for accessing datasets and models can be obtained at https://users.deepcell.org/login/.
+
+For more information about datasets published through DeepCell, please see :doc:`/data-gallery/index`.
+
+API Key Usage
+-------------
+
+The token that is issued by users.deepcell.org should be added as an environment variable through one of the following methods:
+
+1. Save the token in your shell config script (e.g. `.bashrc`, `.zshrc`, `.bash_profile`, etc.)
+
+.. code-block:: bash
+
+    export DEEPCELL_ACCESS_TOKEN=<token-from-users.deepcell.org>
+
+2. Save the token as an environment variable during a python session. Please be careful to avoid commiting your token to any public repositories.
+
+.. code-block:: python
+
+    import os
+
+    os.environ.update({"DEEPCELL_ACCESS_TOKEN": "<token-from-users.deepcell.org>"})
+
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -20,6 +20,9 @@
 sys.path.insert(0, os.path.abspath('../..'))
 # sys.path.insert(0, os.path.abspath('.'))
 
+# Suppress the warnings that show up as a result of sphinx gallery generating multiple files
+warnings.filterwarnings("default", module="sphinx")
+
 # -- Project information -----------------------------------------------------
 
 project = 'DeepCell'
@@ -231,7 +234,8 @@
     'cython',
     'deepcell_tracking',
     'deepcell_toolbox',
-    'matplotlib'
+    'matplotlib',
+    'tqdm'
 ]
 
 sys.modules['deepcell.utils.compute_overlap'] = mock.Mock()
@@ -298,6 +302,3 @@
      'gallery_dirs': 'data-gallery',  # path to where to save gallery generated output
      'remove_config_comments': True,
 }
-
-# Suppress the warnings that show up as a result of sphinx gallery generating multiple files
-warnings.filterwarnings("default", module="sphinx")
diff --git a/docs/source/datasets/dynamicnuclearnet.py b/docs/source/datasets/dynamicnuclearnet.py
@@ -10,11 +10,13 @@
 Schwartz et al. 2023. The dataset is made up of two subsets, one for tracking and one for
 segmentation.
 
-This dataset is licensed under a `modified Apache license <http://www.github.com/vanvalenlab/deepcell-tf/blob/master/LICENSE>`_ for non-commercial academic use only
+This dataset is licensed under a `modified Apache license
+<http://www.github.com/vanvalenlab/deepcell-tf/blob/master/LICENSE>`_ for non-commercial
+academic use only
 
 The dataset can be accessed using `deepcell.datasets` with a DeepCell API key.
 
-TODO add api key info
+For more information about using a DeepCell API key, please see :doc:`/API-key`
 
 Tracking
 ^^^^^^^^
@@ -23,7 +25,8 @@
 
 * X: raw fluorescent nuclear data
 * y: nuclear segmentation masks
-* lineages: lineage records including the cell id, frames present and division links from parent to daughter cells
+* lineages: lineage records including the cell id, frames present and division links from
+  parent to daughter cells
 
 """
 

diff --git a/docs/source/datasets/tissuenet.py b/docs/source/datasets/tissuenet.py
@@ -33,12 +33,13 @@
 * TissueNet 1.1 (April 2022): This version of TissueNet has gone through an additional
   round of manual QC to ensure consistency in labeling across the entire dataset.
 
-This dataset is licensed under a modified Apache license for non-commercial academic use only
-http://www.github.com/vanvalenlab/deepcell-tf/LICENSE
+This dataset is licensed under a `modified Apache license
+<http://www.github.com/vanvalenlab/deepcell-tf/blob/master/LICENSE>`_ for non-commercial
+academic use only
 
 The dataset can be accessed using `deepcell.datasets` with a DeepCell API key.
 
-TODO add api key info
+For more information about using a DeepCell API key, please see :doc:`/API-key`
 """
 
 from deepcell.datasets.tissue_net import TissueNet

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -3,23 +3,16 @@
 .. toctree::
    :maxdepth: 1
    :hidden:
-   :caption: Start Here:
 
    notebooks/Training-Segmentation
    notebooks/Training-Tracking
 
 .. toctree::
    :maxdepth: 2
    :hidden:
-   :caption: Deepcell API:
 
    API/deepcell
-
-.. toctree::
-   :maxdepth: 2
-   :hidden:
-   :caption: Deepcell Datasets
-
+   API-key.rst
    data-gallery/index.rst
 
 .. mdinclude:: ../../README.md