A library to assist with running parameter sets across multiple systems. The goal of this library is to provide a tool set and pipeline that make organizing, running and analyzing a large amount of parameter easier. Some of the highlights include:
- Provide an easy way to run parameter sets.
- Protocol for allowing teams to run parameter sets concurrently.
- Use Google Sheets as a database to host and manage parameter sets.
- Access to the Box API which allows files to be uploaded to box.
When working on a project with or without access to high performance computing (HPC), there is often a need to perform large parameter sweeps. Before developing DAPT, there were several problems the ECM team in Dr. Paul Macklin's research lab identified. First, it was difficult to manage a large number of parameter sets with a large number of parameters. Second, it would be nice to use Google Sheets to run the parameters for easier collaboration and management. Third, only one person in the group would be running all the parameters, making their computer useless for the duration of the runs. Finally, we needed to upload the data to Box for permanent storage and to allow the rest of the team to view the data.
DAPT was written to solve these problems. A "database" (CSV or Google Sheet) is used to store a list of parameter sets. This database is managed by the Param class and provides methods to interact with and manage parameter sets. the Box class allows data to be uploaded to Box.com. Sensitive API credentials can be stored in a config file (via the Config class) which can also be accessed by users to get other variables.
Future versions of the project will work to improve documentation, add examples, cleanup current functionality and add more features. While most of the dapt module is documented, the intended way of using each method is not clearly explained. There are examples given for the main features, however, again there is not a satisfactory amount of documentation. Some of the exciting new features to come will be notification and logging integration. For example, we would like to add Slack notification so teams can be notified if there is an error with a test.
The easiest way to install DAPT is using pip. To do so type:
pip install dapt
Alternatively, you can dowload the project. It is recommended to download a release of the project from GitHub for improved stability. If you would like to download the most up to date version, then download the repo or clone it on your machine git clone https://github.com/BenSDuggan/DAPT. Once downloaded navigate to the root of the project (DAPT) and run pip install -r requirements.txt to install all of the dependences. If you use this method of installation, you will need to write all of your Python scripts using DAPT in the root directory of the project. For these reasons, it's recommended to only use this method if would like to contribute to the project.
You can then test to make sure everything installed by starting a python session and then running:
>>> import dapt
>>> dapt.__version__
0.9.3
Python: >=3.6
All dependence are located in requirements.txt.
You can view the most recent documentation on RTD here. Documentation is performed using Sphinx. The docs folder holds all of the resources to document the code.
To build docs on your local machine simply type make html inside the docs folder.
Examples of some basic uses of DAPT are located in the examples folder. Before running any of the tests, ensure that you have installed DAPT. If you just downloaded the repo and did not install using pip then move the tests into the root of the directory (i.e. DAPT/). This step is necessary to ensure that dapt can properly be imported.
If you would like to contribute please fork the repo and make a pull request explaining what you added/fixed and why you added it. If you are adding a new feature please write a unit test and example for it.
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├── dapt # The folder where the DAPT library is housed
├── docs # Documentation for project
├── examples # Python scripts showing examples of how to use the program
├── misc # Folder containing miscellaneous code
├── requirements.txt # List of Python requirements for DAPT
├── setup.py # Script to generate pyip package
└── tests # Unit tests for DAPT
Unit tests are ran using Pytest. You can install Pytest by running pip install pytest. The tests are located in the tests folder inside the root directory. The tests can be run pytest in the terminal. Travis CI is used for continuous integration. For more information on the tests go to the tests folder.