Merge pull request #1 from yzhao062/dev

Add unit tests

Author: yzhao062

.circleci/config.yml

@@ -0,0 +1,55 @@
+# Python CircleCI 2.0 configuration file
+#
+# Check https://circleci.com/docs/2.0/language-python/ for more details
+# Adapted from https://github.com/NeuralEnsemble/python-neo
+version: 2
+workflows:
+  version: 2
+  test:
+    jobs:
+      - test-3.6
+jobs:
+  test-3.6:
+    docker:
+      - image: circleci/python:3.6-stretch
+
+    working_directory: ~/repo
+
+    steps:
+      - checkout
+      - run: sudo chown -R circleci:circleci /usr/local/bin
+
+      # Download and cache dependencies
+      - restore_cache:
+          keys:
+            - v1-py3-dependencies-{{ checksum "requirements_ci.txt" }}
+            # fallback to using the latest cache if no exact match is found
+            - v1-py3-dependencies-
+
+      - run:
+          name: install dependencies
+          command: |
+            python3 -m venv venv
+            . venv/bin/activate
+            pip install --upgrade pip
+            pip install -r requirements.txt
+            pip install pytest
+            pip install pytest-cov
+
+
+      - save_cache:
+          paths:
+            - ./venv
+          key: v1-py3-dependencies-{{ checksum "requirements.txt" }}
+
+
+      # run tests!
+      - run:
+          name: run tests
+          command: |
+            . venv/bin/activate
+            pytest
+
+      - store_artifacts:
+          path: test-reports
+          destination: test-reports

CHANGES.txt

@@ -1,2 +1,3 @@
 v<0.0.0>, <08/01/2020> -- Initial release.
 v<0.0.1>, <08/03/2020> -- Initial release & minor example fix.
+v<0.0.2>, <08/04/2020> -- Set up autotests.

README.rst

@@ -12,6 +12,15 @@ Python Library for Healthcare AI (PyHealth)
    :alt: Documentation status
 
 
+.. image:: https://travis-ci.org/yzhao062/pyhealth.svg?branch=master
+   :target: https://travis-ci.org/yzhao062/pyhealth
+   :alt: Build Status
+
+
+.. image:: https://circleci.com/gh/yzhao062/PyHealth.svg?style=svg
+   :target: https://circleci.com/gh/yzhao062/PyHealth
+   :alt: Circle CI
+
 
 .. image:: https://img.shields.io/github/stars/yzhao062/pyhealth.svg
    :target: https://github.com/yzhao062/pyhealth/stargazers
@@ -40,7 +49,7 @@ Python Library for Healthcare AI (PyHealth)
 
 -----
 
-**Development Status**: **As of 08/02/2020, PyHealth is under active development and in its alpha stage. Please follow, star, and fork to get the latest functions**!
+**Development Status**: **As of 08/04/2020, PyHealth is under active development and in its alpha stage. Please follow, star, and fork to get the latest functions**!
 
 
 **PyHealth** is a comprehensive and flexible **Python library** for **healthcare AI**, designed for both **ML researchers** and **medical practitioners**.
@@ -167,15 +176,18 @@ Alternatively, you could clone and run setup.py file:
 * joblib
 * numpy>=1.13
 * numba>=0.35
-* pandas>=0.24
-* scipy>=0.19.1
+* pandas>=0.25
+* scipy>=0.20
 * scikit_learn>=0.20
-* torch
+* tqdm
+* torch (this should be installed manually)
+* xgboost (this should be installed manually)
 * xlrd >= 1.0.0
 
 **Warning 1**\ :
 PyHealth has multiple neural network based models, e.g., LSTM, which are
-implemented in PyTorch. However, PyHealth does **NOT** install these DL libraries for you. This reduces the risk of interfering with your local copies.
+implemented in PyTorch. However, PyHealth does **NOT** install these DL libraries for you.
+This reduces the risk of interfering with your local copies.
 If you want to use neural-net based models, please make sure PyTorch is installed.
 Similarly, models depending on **xgboost**, would **NOT** enforce xgboost installation by default.