initial commit

.gitattributes

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+docs/* linguist-documentation
+notebooks/*.ipynb linguist-documentation
+examples/*.ipynb linguist-documentation=false

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.pytest_cache
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

.travis.yml

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+language: python
+dist: xenial
+
+env:
+  global:
+    PIP_PREFER_BINARY=true # https://github.com/numba/llvmlite/issues/471
+
+python:
+  - "3.5"  # disabled for now as warning messages crash travis ci. turn it back in 3.5.7
+  - "3.5-dev"  # 3.5 development branch
+  - "3.6"
+  - "3.6-dev"  # 3.6 development branch
+  - "3.7"  # 3.6 development branch
+
+install:
+  - pip install --upgrade pip
+  - pip install -r requirements.txt
+  - pip install pytest
+  - pip install pytest-cov
+  - pip install coveralls
+
+# command to run tests
+script:
+   pytest --cov=pyhealth/
+
+after_success:
+  - coveralls
+
+notifications:
+  email:
+    recipients:
+      - [email protected]
+  on_success: never # default: change
+  on_failure: always # default: always

CHANGES.txt

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+v<0.0.0>, <08/01/2020> -- Initial release.

LICENSE

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+BSD 2-Clause License
+
+Copyright (c) 2020, Yue Zhao, Zhi Qiao, Xiao Cao
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

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+prune examples
+prune notebooks
+prune pyhealth/test
+include README.rst
+include requirements.txt

README.rst

@@ -413,4 +413,4 @@ Reference
 
 .. [#Ma2017Dipole] Ma, F., Chitta, R., Zhou, J., You, Q., Sun, T. and Gao, J., 2017, August. Dipole: Diagnosis prediction in healthcare via attention-based bidirectional recurrent neural networks. In Proceedings of the 23rd ACM SIGKDD international conference on knowledge discovery and data mining (pp. 1903-1911).
 
-.. [#Xu2018RAIM] Xu, Y., Biswal, S., Deshpande, S.R., Maher, K.O. and Sun, J., 2018, July. Raim: Recurrent attentive and intensive model of multimodal patient monitoring data. In Proceedings of the 24th ACM SIGKDD international conference on Knowledge Discovery & Data Mining (pp. 2565-2573).
+.. [#Xu2018RAIM] Xu, Y., Biswal, S., Deshpande, S.R., Maher, K.O. and Sun, J., 2018, July. Raim: Recurrent attentive and intensive model of multimodal patient monitoring data. In Proceedings of the 24th ACM SIGKDD international conference on Knowledge Discovery & Data Mining (pp. 2565-2573).

appveyor.yml

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+build: off
+
+# branches to build
+branches:
+  # whitelist
+  only:
+    - master
+    - development
+environment:
+  matrix:
+    - PYTHON: "C:\\Python35-x64"
+    - PYTHON: "C:\\Python36-x64"
+
+skip_commits:
+  files:
+    - "*.yml"
+    - "*.rst"
+    - "*.md"
+    - "LICENSE"
+
+init:
+  - "ECHO %PYTHON% %PYTHON_VERSION% %PYTHON_ARCH%"
+
+install:
+  - "%PYTHON%\\python.exe -m pip install --upgrade pip setuptools"
+  - "%PYTHON%\\python.exe -m pip install wheel"
+  - "%PYTHON%\\python.exe -m pip install pytest"
+  - "%PYTHON%\\python.exe -m pip install -r requirements.txt"
+
+
+test_script:
+  - "%PYTHON%\\python.exe -m pytest"
+
+after_test:
+  - "%PYTHON%\\python.exe  setup.py bdist_wheel"
+
+artifacts:
+  - path: dist\*
+
+notifications:
+  - provider: Email
+    to:
+      - [email protected]
+    on_build_success: false
+    on_build_failure: true
+    on_build_status_changed: true