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How to set up your dev environment (Windows-specific)

Set up Git

Install healthcareai via these instuctions: https://github.com/HealthCatalystSLC/healthcareai-py/blob/master/README.rst

Install the IDE and clone the healthcareai-py repo

  1. Install PyCharm Community Edition
  2. Set path to git.exe via File -> settings -> Version Control -> Git
  3. Clone repo (if you haven't) via PyCharm -> VCS (at top) -> Checkout from version control -> Github
  • Grab .git url from HCRTools repo in Github
  • Set parent directory to C:/Source
  • Name directory healthcareai-py
  1. File -> Open and look for the healthcareai project (if it didn’t come up already)
  2. Create a destination table for the test predictions by executing this in SSMS:
CREATE TABLE [SAM].[dbo].[HCPyDeployClassificationBASE] (
[BindingID] [int] , [BindingNM] [varchar] (255), [LastLoadDTS] [datetime2] (7), [PatientEncounterID] [decimal] (38, 0), [PredictedProbNBR] [decimal] (38, 2), [Factor1TXT] [varchar] (255), [Factor2TXT] [varchar] (255), [Factor3TXT] [varchar] (255))
CREATE TABLE [SAM].[dbo].[HCPyDeployRegressionBASE] (
[BindingID] [int], [BindingNM] [varchar] (255), [LastLoadDTS] [datetime2] (7), [PatientEncounterID] [decimal] (38, 0), [PredictedValueNBR] [decimal] (38, 2), [Factor1TXT] [varchar] (255), [Factor2TXT] [varchar] (255), [Factor3TXT] [varchar] (255))
  1. Verify that unit tests pass
  • Right click on tests folder under healthcareai-py/healthcareai
  • Click on Run Nosetest in test
  1. Create test branch and push it to github
  • Note the text ‘Git: master’ in bottom-right of PyCharm
  • Create new test branch via VCS -> Git -> Branches -> New Branch
  • Push branch to github (ie, create origin) via VCS -> Git -> Push (CTRL-SHIFT-K)

Code Housekeeping

  1. Install the following packages via the command line: python -m pip install packagename
  • pylint
  • pyflakes
  1. Set these up via http://www.mantidproject.org/How_to_run_Pylint#PyCharm_-_JetBrains
  • If your python is installed in C:Pythonxx, then your parameters will be:
  • Program: C:Python34Scriptspylint.exe
  • Parameters: $FilePath$
  • Working dir: C:Python34Scripts
  • If you are using a different Python distribution, you may need to find where Pylint is installed. For example, the same three parameters from above might be:
  • C:Usersuser.name AppDataLocalContinuumAnaconda3Scriptspylint
  • Parameters: $FilePath$
  • C:Usersdavid.healeyAppDataLocalContinuumAnaconda3Scripts
  • Instead of using default parameter, use $FilePath$
  • For Anaconda, you may have to use C:Usersuser.name AppDataLocalContinuumAnaconda3Scriptspylint
  • Check all boxes
  1. Make sure pylint and pyflakes work
  • Right-click on relevant directory in PyCharm (this will be where you’ve done work)
  • Navigate to external tools
  • Run both pylint and pyflakes
  • Verify that there aren’t any issues with your code; please do this before sending pull requests
  1. Set maximum line width to 79 via Settings -> Editor -> Code Style -> Right margin
  2. Set tabs as spaces via Edit -> Convert Indents -> To Spaces
  3. Click Code -> Inspect code -> Whole project -> Look for section on Package requirements
  • Under the lines related to sklearn, click ‘Ignore Requirement’

Git config

Set up your email and username for git (otherwise no attribution in github)

  1. Set git user name and work email
  1. Configure line endings for windows: git config core.autocrlf true
  2. Make git case sensitive for file names: git config core.ignorecase false
  1. Set up SSH (if desired) so you can push to topic branch without password