idmtools-calibra 2.0.0.dev1

Calibration tool for IDM-Tools

![Staging: idmtools-calibra]

idmtools-calibra

Table of Contents

• User Installation
  • Pre-requisites
• Development Environment Setup
  • First Time Setup
  • Development Tips
  • Building docs
  • Resume Supports Parameters

User Installation

pip install idmtools-calibra

Pre-requisites

• Python 3.6/3.7 x64

Development Environment Setup

When setting up your environment for the first time, you can use the following instructions

First Time Setup

1. Clone the repository:

   > git clone https://github.com/InstituteforDiseaseModeling/idmtools_calibra.git
   

2. Create a virtualenv. On Windows, please use venv to create the environment python -m venv idmtools_calibra On Unix(Mac/Linux) you can use venv or virtualenv
3. Activate the virtualenv
4. Then run python ./.dev_scripts/bootstrap.py. This will install all the tools.

Development Tips

There is a Makefile file available for most common development tasks. Here is a list of commands

clean       -   Clean up temproary files
lint        -   Lint package and tests
test        -   Run All tests
coverage    -   Run tests and generate coverage report that is shown in browser

On Windows, you can use pymake instead of make

Building docs

From your virtualenv, install idmtools_calibra and all dependencies. Then from the docs folder, run pip install -r requirements.txt. You can build the docs from that folder using make html.

To pick up docstring changes, you must re-run the setup script to include those changes in the itertool installation. Then run make clean and re-run make html.

Documentation on Read the Docs is available at https://docs.idmod.org/projects/idmtools_calibra/en/latest/.

Resume Supports Parameters

CalibManager's run_calibration method supports the following parameters for resume action, for example:

run_calibration(resume=True, iteration=2, iter_step='analyze')

• resume: bool, default=False, required for resume Note: resume=True is required for resume, otherwise all the parameters will be ignored
• iteration: int, default=None, from which iteration to resume Note: in None case, calibra will detect and take the last iteration from last run
• iter_step: str, default=None, from which calibration step to resume Note: in None case, calibra will detect and take the valid step of the iteration
• loop: bool, default=True, if like to continue to next iteration Note: by default, resume will continue to run next iteration
• max_iterations, int, default=None, user can override the max_iterations defined in calib_manager Note: in None case, calibra will take max_iterations defined in calib_manager
• backup: bool, default=False, if like to backup Calibration.json Note: by default, resume will not make a backup of Calibration.json
• dry_run: bool, default=False, if like to really execute resume action Note: by default (dry_run= False), resume will go ahead to execute resume action

iter_step supports the following options:

• commission: will start to run a new iteration
• analyze: analyze the output data from given iteration
• plot: just plot for given iteration
• next_point: go directly to next iteration