Fix new plotting APIs with Triage's result schemas

.gitignore

@@ -6,6 +6,7 @@ dist/
 .cache/
 .coverage*
 .tox/
+docs/site/
 
 /.install.*.bash.inc
 /.python-version

.travis.yml

@@ -1,5 +1,6 @@
+dist: xenial
 language: python
-python: 3.6
+python: ["3.6", "3.7"]
 addons:
   postgresql: '9.5'
 services:
@@ -11,19 +12,29 @@ install:
 - pip install -r requirement/include/build.txt -r requirement/include/test-management.txt
 env:
   matrix:
-  - BOTO_CONFIG=/tmp/nowhere
+    - BOTO_CONFIG=/tmp/nowhere
   global:
     secure: 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
 script: tox
 notifications:
   email: false
 after_success: codecov
 deploy:
-  on:
+  -
     repo: dssg/triage
-    tags: true
-  distributions: sdist bdist_wheel
-  password:
-    secure: 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
-  provider: pypi
-  user: dssg
+    distributions: sdist bdist_wheel
+    password:
+      secure: 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
+    provider: pypi
+    user: dssg
+    on:
+       repo: dssg/triage
+       tags: true
+  -
+    provider: pages
+    skip_cleanup: true
+    keep_history: true
+    on:
+      tags: true
+    github_token:
+      secure: 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

CONTRIBUTING.md

@@ -34,8 +34,7 @@ pip install -r requirements/dev.txt
 
 Once this is done, you can modify any of the pages under the documentation root directory, and change general doc site configuration in [docs/mkdocs.yml](docs/mkdocs.yml). While modifying a documentation page, you can preview your changes by running the mkdocs dev server:
 ```
-cd docs
-mkdocs serve
+manage docs
 ```
 
 ### Submit Feedback

LICENSE

@@ -1,8 +1,8 @@
 BY DOWNLOADING triage PROGRAM YOU AGREE TO THE FOLLOWING TERMS OF USE:
 
-Copyright ©2017.  The University of Chicago (“Chicago”). All Rights Reserved.  
+Copyright (c)2017.  The University of Chicago ("Chicago"). All Rights Reserved.
 
-Permission to use, copy, modify, and distribute this software, including all object code and source code, and any accompanying documentation (together the “Program”) for educational and not-for-profit research purposes, without fee and without a signed licensing agreement, is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies, modifications, and distributions. For the avoidance of doubt, educational and not-for-profit research purposes excludes any service or part of selling a service that uses the Program. To obtain a commercial license for the Program, contact the Technology Commercialization and Licensing, Polsky Center for Entrepreneurship and Innovation, University of Chicago, 1452 East 53rd Street, 2nd floor, Chicago, IL 60615.
+Permission to use, copy, modify, and distribute this software, including all object code and source code, and any accompanying documentation (together the "Program") for educational and not-for-profit research purposes, without fee and without a signed licensing agreement, is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies, modifications, and distributions. For the avoidance of doubt, educational and not-for-profit research purposes excludes any service or part of selling a service that uses the Program. To obtain a commercial license for the Program, contact the Technology Commercialization and Licensing, Polsky Center for Entrepreneurship and Innovation, University of Chicago, 1452 East 53rd Street, 2nd floor, Chicago, IL 60615.
 
 Created by Data Science and Public Policy, University of Chicago
 

README.rst

@@ -13,9 +13,14 @@ Risk modeling and prediction
 .. image:: https://codeclimate.com/github/dssg/triage.png
    :target: https://codeclimate.com/github/dssg/triage
 
-Predictive analytics projects require the coordination of many different tasks, such as feature generation, classifier training, evaluation, and list generation. These tasks are complicated in their own right, but in addition have to be combined in different ways throughout the course of the project.
+Building systems that use predictive models require answering many design decisions, turning them into modeling choices, and technical tasks. Questions such as cohort selection, unit of analysis determination, outcome determination, feature (explanantory variables) generation, model/classifier training, evaluation, selection, and list generation are often complicated and hard to choose apriori. In addition, once these choices are made, they have to be combined in different ways throughout the course of a project.
+
+Triage aims to help solve these problems by:
+
+1. Guiding users (data scientists, analysts, researchers) through these design choices by highlighting operational use questions that are important.
+
+2. Providing interfaces to these different phases of a project, such as an ``Experiment``. Each phase is defined by a configuration (corresponding to a design choice) specific to the needs of the project, and an arrangement of core data science components that work together to produce the output of that phase. 
 
-Triage aims to provide interfaces to these different phases of a project, such as an ``Experiment``. Each phase is defined by configuration specific to the needs of the project, and an arrangement of core data science components that work together to produce the output of that phase.
 
 
 Installation

docs/mkdocs.yml

@@ -1,29 +1,92 @@
 site_name: Triage Documentation
-theme: readthedocs
+theme:
+  name: 'material'
+  palette:
+    primary: 'blue grey'
+    accent: 'deep orange'
+  font:
+    text: 'Ubuntu'
+    code: 'Ubuntu Mono'
+  logo:
+    icon: 'book'
+  favicon: 'assets/images/favicon.ico'
+
 docs_dir: sources
+repo_name: 'dssg/triage'
 repo_url: http://github.com/dssg/triage
-edit_uri: blob/master/docs/templates
+edit_uri: ''
 site_description: 'Documentation for Triage.'
 
+extra:
+  social:
+    - type: 'github'
+      link: 'https://github.com/dssg/hitchhikers-guide'
+    - type: 'twitter'
+      link: 'https://twitter.com/datascifellows'
+    - type: 'linkedin'
+      link: 'https://linkedin.com/company/center-for-data-science-and-public-policy-university-of-chicago'
+
+
 markdown_extensions:
-    - toc:
-        permalink: True
-        baselevel: 2
+  - toc:
+      permalink: True
+      baselevel: 2
+      toc_depth: 1
+  - admonition
+  - codehilite:
+      guess_lang: false
+  - def_list
+  - footnotes
+  - meta
+  - pymdownx.arithmatex
+  - pymdownx.b64
+  - pymdownx.caret
+  - pymdownx.critic
+  - pymdownx.details
+  - pymdownx.extrarawhtml
+  - pymdownx.keys
+  - pymdownx.highlight
+  - pymdownx.snippets
+  - pymdownx.superfences
+  - pymdownx.tasklist:
+      custom_checkbox: true
+  - pymdownx.tilde
+  - pymdownx.superfences
+
 extra_javascript:
     - "js/mermaid.min.js"
 
-pages:
+nav:
   - Home: index.md
-  - Dirty Duck Tutorial: https://dssg.github.io/dirtyduck
+  - Dirty Duck Tutorial:
+    - Welcome: dirtyduck/docs/index.md
+    - Choose your own adventure: dirtyduck/docs/choose_your_own_adventure.md
+    - Setup:
+      - For the impatient: dirtyduck/docs/for_the_impatient.md
+      - Infrastructure: dirtyduck/docs/infrastructure.md
+      - Data preparation: dirtyduck/docs/data_preparation.md
+    - Case studies:
+      - Problem description: dirtyduck/docs/intro.md
+      - Resource prioritization: dirtyduck/docs/inspections.md
+      - Early Warning System: dirtyduck/docs/eis.md
+    - Triage:
+      - A deeper look into triage: dirtyduck/docs/triage_intro.md
   - Experiment:
     - Defining an Experiment: experiments/defining.md
     - Testing Feature Configuration: experiments/feature-testing.md
+    - Experiment Configuration: https://github.com/dssg/triage/blob/master/example/config/README.md
     - Running an Experiment: experiments/running.md
-    - Upgrading an Experiment: experiments/upgrading.md
+    - Upgrading an Experiment:
+        - v6 -> v7: experiments/upgrade-to-v7.md
+        - v5 -> v6: experiments/upgrade-to-v6.md
+        - v3/v4 -> v5: experiments/upgrade-to-v5.md
     - Temporal Validation Deep Dive: experiments/temporal-validation.md
     - Cohort and Label Deep Dive: experiments/cohort-labels.md
+    - Prediction Ranking: experiments/prediction-ranking.md
     - Feature Generation Recipe Book: experiments/features.md
     - Experiment Algorithm: experiments/algorithm.md
     - Experiment Architecture: experiments/architecture.md
-  - Audition: https://github.com/dssg/triage/tree/master/src/triage/component/audition
+  - Model selection: dirtyduck/docs/audition.md
   - Postmodeling: postmodeling/index.md
+  - Model governance:  dirtyduck/docs/ml_governance.md
+  - Scaling up: dirtyduck/docs/aws_batch.md