Remove builder until template variation better understood (#90)

MANIFEST.in

@@ -1,8 +1,6 @@
 include LICENSE.txt
 include README.md
 include notebooks/*.ipynb
-include src/seismometer/builder/resources/*.ipynb
-include src/seismometer/builder/resources/*.y*ml
 include src/seismometer/report/*.y*ml 
 include src/seismometer/plot/mpl/ux.mplstyle
 include src/seismometer/html/resources/*

changelog/90.bugfix.rst

@@ -0,0 +1 @@
+Temporarily remove CLI - variation in templates is not stable enough to ensure robustness.

docs/conf.py

@@ -37,7 +37,6 @@
     "sphinxarg.ext",
 ]
 
-templates_path = ["_templates"]
 exclude_patterns = []
 napoleon_google_docstring = False
 napoleon_numpy_docstring = True

docs/getting_started/index.rst

@@ -17,13 +17,13 @@ performance (including inputs and outputs).
 What is in Seismometer
 ======================
 
-Jupyter Notebook templates
+Jupyter Notebook examples
 --------------------------
 
 Open-source Python libraries and Jupyter Notebooks allow data scientists
-to quickly generate a notebook to evaluate model performance.
+to quickly create a notebook to evaluate model performance.
 
-We expect these templates to continually evolve as new validation and
+We expect these examples to continually expand and evolve as new validation and
 analysis techniques and approaches are created.
 
 Data Schemas
@@ -34,8 +34,7 @@ Standardized data schemas to incorporate data from single or multiple source sys
 Notebook configuration definitions
 ----------------------------------
 
-A config file provides instructions for how to build the notebook using
-the provided data and template. Within the file, you can control details
+Within the configuration file, you can control details
 such as the cohorts to include and the outcomes relevant to the model.
 You can also provide supplemental model documentation to give data
 scientists and other report consumers working with the notebook
@@ -142,8 +141,7 @@ The following is an example of an events table.
 Provide Configuration Files
 ===========================
 
-The configuration file provides the instructions to the template for how
-to build the Notebook with the provided data. It allows you to define
+The configuration file allows you to define
 relevant cohorts including things like demographics, sensitive groups,
 and other criteria for evaluating model performance. You can define
 outcome and intervention events that relate to actions taken based on

docs/index.rst

@@ -11,7 +11,7 @@ Seismometer Documentation
         :class-card: intro-card
         :shadow: md
 
-        New to ``seismometer``? The Getting Started guide provides an introduction 
+        New to ``seismometer``? The Getting Started guide provides an introduction
         to ``seismometer``’s main concepts and details on gathering data for analysis.
 
         +++
@@ -28,7 +28,7 @@ Seismometer Documentation
         :class-card: intro-card
         :shadow: md
 
-        The User Guide provides details on the available templates 
+        The User Guide provides details on the available templates
         with explanations of the key concepts.
 
         +++
@@ -45,7 +45,7 @@ Seismometer Documentation
         :class-card: intro-card
         :shadow: md
 
-        The API Reference guide details the available ``seismometer`` APIs, 
+        The API Reference guide details the available ``seismometer`` APIs,
         including how the methods work and available parameters.
 
         +++
@@ -62,8 +62,8 @@ Seismometer Documentation
         :class-card: intro-card
         :shadow: md
 
-        Did you develop new guidelines or processes for AI model validation? 
-        Saw a typo in the documentation? Learn more about the process for 
+        Did you develop new guidelines or processes for AI model validation?
+        Saw a typo in the documentation? Learn more about the process for
         improving ``seismometer``.
 
         +++
@@ -85,10 +85,8 @@ Seismometer Documentation
    user_guide/index
    example_notebooks/index
    reference/index
-   cli/index
    development/index
    release_notes/index
    roadmap/index
    integration_guide/index
    faq/index
-

docs/reference/internals.rst

@@ -5,37 +5,6 @@
 Internals
 =========
 
-Command Line
-------------
-
-Extract
-~~~~~~~
-.. currentmodule:: seismometer.builder.extract
-.. autosummary::
-   :toctree: api/
-
-   extract_supplement
-   generate_data_dict_from_parquet
-
-Build
-~~~~~
-.. currentmodule:: seismometer.builder.compile
-.. autosummary::
-   :toctree: api/
-
-   compile_notebook
-
-Other
-~~~~~
-.. currentmodule:: seismometer.builder
-.. autosummary::
-   :toctree: api/
-
-   jupyter.contrib_cells
-   jupyter.get_id
-   jupyter.get_text
-
-
 .. currentmodule:: seismometer.plot.mpl
 
 Plotting

docs/user_guide/index.rst

@@ -38,48 +38,17 @@ you might not be familiar with:
 
 -  *Feature*. A column of data used as an input to the model.
 
-Generating a Notebook
+Creating a Notebook
 =====================
 
-Generating a Notebook requires three pieces of information:
+Creating a Seismogram (notebook) requires a couple distinct pieces of information:
 
-- Template Notebook: A template Notebook that is suitable for your model.
+- Example Notebook: Starting from example notebook, while not required, is expected to be the most straight-forward. Once serveral types of models are supported, it is expected that a CLI will further automate combining new content into the example structure.
 - Configuration files: A ``config.yml`` file to specify location of required data and/or other configuration files (refer to the :ref:`config-files`).
-- Supplemental info: Explanatory markdown files and model-specific supplements to guide the analysis (refer to the :ref:`config-files`).
+- Supplemental info: Explanatory model-specific supplements to guide the analysis.
 
-Each template Notebook is associated with a collection of markdown files. Your markdown files are used to fill the corresponding
-markdown file in the template Notebook to generate a Notebook. To extract the expected markdown files
-from the template Notebook, you can run the following:
+Update or replace the example notebook with content relevant to your model.
 
-.. code-block:: bash
-
-   seismometer extract --template binary
-
-If the command is not run from the same directory as your ``config.yml`` file, use
-
-.. code-block:: bash
-
-   seismometer extract --template binary --config_yaml {path_to_base_config_file}
-
-In the above example, we are using the ``binary`` template. Run
-
-.. code-block:: bash
-
-   seismometer extract --help
-
-for more details on available templates and arguments.
-
-Update the markdown files with content relevant to your model or replace them with model-specific markdown files
-provided by the model developer.
-
-After updating the markdown files with content for the model, generate a Notebook by running
-
-.. code-block:: bash
-
-   seismometer build [--config_yaml] {path_to_base_config_file}
-
-.. seealso::
-   :ref:`cli` for more details on the CLI and :ref:`api.internals` for more information on build and extract commands.
 
 Using the Binary Classifier Notebook
 ====================================
@@ -343,7 +312,7 @@ Notebook.
 Create Configuration Files
 --------------------------
 
-Configuration files provide the instructions and details needed to build
+Configuration files provide the instructions and details needed to create
 the Notebook for your dataset. It can be provided in one or several YAML
 files. The configuration includes several sections:
 
@@ -477,8 +446,7 @@ defined in a single YAML file.
       usage_config: "usage_config.yml"
       # Name of the template to use during generation
       template: "binary"
-      # Directory to the location of markdown
-      # Use seismometer extract to prepopulate these files
+      # Directory to write info during the notebook run
       info_dir: "outputs"
       # These two definitions define all the columns available
       event_definition: "dictionary.yml"

example-notebooks/binary-classifier/config.yml

@@ -3,8 +3,7 @@ other_info:
   usage_config: "usage_config.yml"
   # Name of the template to use during generation
   template: "binary"
-  # Directory to the location of markdown
-  # Use seismometer extract to prepopulate these files
+  # Directory to write info from and for the notebook run
   info_dir: "outputs"
   # These two definitions define all the columns available
   event_definition: "data_dictionary.yml"

setup.cfg

@@ -39,10 +39,6 @@ install_requires =
 [options.packages.find]
 where = src
 
-[options.entry_points]
-console_scripts =
-    seismometer = seismometer.builder:main_cli
-
 [options.extras_require]
 all =
     %(dev)s