Merge pull request #327 from ATOMScience-org/1.6.1

1.6.1

Author: mauvais2

atomsci/ddm/docs/source/get_started/install_with_docker.rst

@@ -2,7 +2,7 @@
 Install AMPL With Docker
 ########################
 
-This page provides an option to use Docker to install `AMPL <https://github.com/ATOMScience-org/AMPL>`_. For an alternate way, please see the "Getting Started" `Install <https://ampl.readthedocs.io/en/latest/getting_started/install.html>`_ page.
+This page provides an option to use Docker to install `AMPL <https://github.com/ATOMScience-org/AMPL>`_. For an alternate way, please see the "Getting Started" `Install <https://ampl.readthedocs.io/en/latest/get_started/install.html>`_ page.
 
 To install `AMPL <https://github.com/ATOMScience-org/AMPL>`_ software using Docker, the major steps are:
 

atomsci/ddm/docs/source/get_started/introduction.rst

@@ -7,6 +7,6 @@ The ATOM Modeling PipeLine `AMPL <https://github.com/ATOMScience-org/AMPL>`_ is
 
 There are two alternative paths for installing `AMPL <https://github.com/ATOMScience-org/AMPL>`_: 
 
-1. Cloning the git repo, setting up the pip environment and running the AMPL install command. Please refer to `Installation <https://ampl.readthedocs.io/en/latest/getting_started/install.html>`_.
+1. Cloning the git repo, setting up the pip environment and running the AMPL install command. Please refer to `Installation <https://ampl.readthedocs.io/en/latest/get_started/install.html>`_.
 
 2. `Install With Docker <https://ampl.readthedocs.io/en/latest/get_started/install_with_docker.html>`_. 

atomsci/ddm/docs/source/tutorials/03_train_regression_model.rst

@@ -32,8 +32,8 @@ using the following inputs:
 The tutorial will present the following functions and classes:
 
 -  `ModelPipeline <https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_pipeline>`_
--  `parameter_parser.wrapper <https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_pipeline>`_
--  `compare_models.get_filesystem_perf_results <https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_pipeline>`_
+-  `parameter_parser.wrapper <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.parameter_parser.wrapper>`_
+-  `compare_models.get_filesystem_perf_results <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.compare_models.get_filesystem_perf_results>`_
 
 We will explain the use of descriptors, how to evaluate model
 performance, and where the model is saved as a .tar.gz file.

atomsci/ddm/docs/source/tutorials/06_compare_models.rst

@@ -33,7 +33,7 @@ In this tutorial, we will focus on these functions:
 -  `plot_train_valid_test_scores <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.hyper_perf_plots.plot_train_valid_test_scores>`_
 -  `plot_split_perf <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.hyper_perf_plots.plot_split_perf>`_
 -  `plot_hyper_perf <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.hyper_perf_plots.plot_hyper_perf>`_
--  `get_score_types <https:.//ampl.readthedocs.io/en/latest/pipeline.html#pipeline.hyper_perf_plots.get_score_types>`_
+-  `get_score_types <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.hyper_perf_plots.get_score_types>`_
 -  `plot_xg_perf <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.hyper_perf_plots.plot_xg_perf>`_
 -  `plot_pred_vs_actual_from_file <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.perf_plots.plot_pred_vs_actual_from_file>`_
 

atomsci/ddm/docs/source/tutorials/08_visualizations_of_model_performance.rst

@@ -18,8 +18,8 @@ The tutorial will present the following functions, all from the
 ``perf_plots`` module: 
 
 -  `plot_perf_vs_epoch <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.perf_plots.plot_perf_vs_epoch>`_
--  `plot_pred_vs_actual <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.perf_plots.pred_vs_actual>`_
--  `plot_confusion_matrices <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.perf_plots.confusion_matrices>`_
+-  `plot_pred_vs_actual <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.perf_plots.plot_pred_vs_actual>`_
+-  `plot_confusion_matrices <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.perf_plots.plot_confusion_matrices>`_
 -  `plot_model_metrics <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.perf_plots.plot_model_metrics>`_
 -  `plot_ROC_curve <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.perf_plots.plot_ROC_curve>`_
 -  `plot_prec_recall_curve <https://ampl.readthedocs.io/en/latest/pipeline.html#pipeline.perf_plots.plot_prec_recall_curve>`_