spacetx · shanaxel42 · Jul 17, 2019 · Jul 2, 2019 · Jul 2, 2019 · Jul 2, 2019
diff --git a/.travis.yml b/.travis.yml
@@ -57,9 +57,6 @@ jobs:
     - name: 3D smFISH data processing example
       if: type = push and branch =~ /^(master|merge)/
       script: make install-dev 3d_smFISH.py
-    - name: iss_cli.sh data processing example
-      if: type = push and branch =~ /^(master|merge)/
-      script: make install-dev iss_cli.sh
     - name: iss_pipeline.py data processing example
       if: type = push and branch =~ /^(master|merge)/
       script: make TESTING=1 install-dev iss_pipeline.py

diff --git a/docs/source/_static/data_processing_examples/iss_cli.sh b/docs/source/_static/data_processing_examples/iss_cli.sh
diff --git a/docs/source/_static/tutorials/exec_running_a_pipeline.py b/docs/source/_static/tutorials/exec_running_a_pipeline.py
diff --git a/docs/source/api/data_structures/index.rst b/docs/source/api/data_structures/index.rst
@@ -56,6 +56,3 @@ serialization for use in single-cell analysis environments such as Seurat_ and S
 
 .. toctree::
    intensity_table.rst
-
-.. toctree::
-   pipeline_component.rst
diff --git a/docs/source/api/data_structures/pipeline_component.rst b/docs/source/api/data_structures/pipeline_component.rst
diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst
@@ -18,9 +18,6 @@ API
 .. toctree::
    spots/index.rst
 
-.. toctree::
-   recipe/index.rst
-
 .. toctree::
    types/index.rst
 

diff --git a/docs/source/api/recipe/index.rst b/docs/source/api/recipe/index.rst
diff --git a/docs/source/creating_an_image_processing_pipeline/index.rst b/docs/source/creating_an_image_processing_pipeline/index.rst
@@ -75,20 +75,6 @@ origin. At this point, it's trivial to create a cell x gene matrix.
 
     tutorials/exec_feature_identification_and_annotation.rst
 
-Putting Together a Pipeline Recipe and Running it
--------------------------------------------------
-
-Pipeline recipes should describe the computational steps to get from the input files to the output files.  Pipeline
-recipes should manage file input and output through the injected ``file_inputs`` and ``file_outputs`` variables.  When a
-recipe is executed, the user should provide a list of file paths or URLs, which are loaded as starfish objects (i.e.,
-:ref:`ImageStack`, :ref:`Codebook`, :ref:`IntensityTable`, or :ref:`ExpressionMatrix`), and provided to the recipe in
-the ``file_inputs`` array.  Correspondingly, any results saved to the ``file_outputs`` array will be written to the
-file paths users provide.
-
-.. toctree::
-    :maxdepth: 1
-
-    tutorials/exec_running_a_pipeline.rst
 
 Old Content not to be deleted yet.
 ----------------------------------

diff --git a/docs/source/getting_started/example_workflow/index.rst b/docs/source/getting_started/example_workflow/index.rst
@@ -40,13 +40,3 @@ The above steps can be recapitulated using starfish as follows:
 
 .. literalinclude:: ../../_static/data_processing_examples/iss_pipeline.py
 
-Using the CLI
--------------
-
-Starfish has a fully-featured CLI that mimics the API such that one does not need to write python
-code to use starfish. Running the commands below will re-produce the notebook_ results using
-starfish's CLI:
-
-.. _notebook: ../../_static/data_processing_examples/iss_pipeline.py
-
-.. literalinclude:: ../../_static/data_processing_examples/iss_cli.sh
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -30,7 +30,7 @@ see the :ref:`Getting Started <getting started>` section.
 
 Starfish's documentation also contains instructions on :ref:`creating image-based transcriptomics
 processing pipelines <creating_an_image_processing_pipeline>`, tutorials on running
-starfish using the CLI, API, and workflow runner, and a worked example of contributing code to
+starfish using the API, and a worked example of contributing code to
 starfish. Finally, advanced users can examine the :ref:`Data Structures <data structures>` and
 :ref:`Help & Reference <help and reference>` sections to learn more details about _starfish_ and its
 object models.
@@ -66,7 +66,6 @@ To see the code or report a bug, please visit the `github repository
 * Spot-Finding: :ref:`API <detection>`
 * Decoding: :ref:`API <decoding>`
 * Segmenting: :ref:`API <segmentation>`
-* Pipelining: :ref:`API <pipeline_component>`
 
 .. raw:: html
 

diff --git a/docs/source/usage/fov-builder/fov-builder.rst b/docs/source/usage/fov-builder/fov-builder.rst
diff --git a/docs/source/usage/index.rst b/docs/source/usage/index.rst
@@ -182,29 +182,15 @@ analysis with *starfish*. Background subtraction, for example, is
 handled by Starfish. If there is confusion about what types of image
 pre-processing should be applied, please open an issue.
 
-
-Getting started with the CLI
-----------------------------
-
-The simplest way to get started with starfish for most users will be to try out the
-command-line interface (CLI). After following the :ref:`installation <installation>`
-instructions, a ``starfish`` command will be available. Running ``starfish --help``
-will print out the subcommands that are available.
-
-.. program-output:: env MPLBACKEND=Agg starfish --help
-
-.. toctree::
-   :maxdepth: 3
-   :caption: CLI:
-
-.. toctree::
-   fov-builder/fov-builder.rst
-
+Configuration
+--------------
 .. toctree::
-   validation/index.rst
+     configuration/index.rst
 
+Validation
+-----------
 .. toctree::
-   configuration/index.rst
+     validation/index.rst
 
 
 Data Formatting Examples