Welcome

Pepys-import is a Python library to be used in the parsing and collation of data to be used in platform based spatial analysis.

The library provides tools to help work through text data-files, and then push data measurements (and supporting metadata) to a databaes.

PostGres and SQLite databases are currently supported, with SQLite being the low-friction option favoured for getting started with Pepys-Import, or for project maintainers.

Here's a working demonstrator of datafile import: |binder|

.. |binder| image:: https://mybinder.org/badge_logo.svg :target: https://mybinder.org/v2/gh/debrief/pepys-import/develop?filepath=examples%2Fnotebooks%2Fdata_store_sqlite.ipynb

Online documentation

Learn more here: |docs|

.. |docs| image:: https://readthedocs.org/projects/pepys-import/badge/?version=latest :target: https://pepys-import.readthedocs.io/

Development

Code coverage

We're aiming for 100% code coverage on the project, track our progress here: |code_cov|

.. |code_cov| image:: https://codecov.io/gh/debrief/pepys-import/branch/develop/graph/badge.svg :target: https://codecov.io/gh/debrief/pepys-import/branch/develop

Upstream security

We have continuous vulnerability testing on the Open Source libraries we depend upon for development: |dev_req| and production: |plain_req|

.. |plain_req| image:: https://snyk.io/test/github/debrief/pepys-import/badge.svg?targetFile=requirements.txt :target: https://snyk.io/test/github/debrief/pepys-import?targetFile=requirements.txt

.. |dev_req| image:: https://snyk.io/test/github/debrief/pepys-import/badge.svg?targetFile=requirements_dev.txt :target: https://snyk.io/test/github/debrief/pepys-import?targetFile=requirements_dev.txt

Code Style

Black is used on the project: |black|

.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg :target: https://github.com/python/black

It is suggested to install a pre-commit hook in order to apply Black before pushing commits::

$ pip install pre-commit
$ pre-commit install

Project Progres

View the project Kanban board here <https://github.com/debrief/pepys-import/projects/3>_

Setup

To prepare for running ensure these tools and packages are installed:

• Python 3 - at least Python 3.6.4 or later
• SQL Alchemy 1.3

For Postgres support and unit tests these packages are also required:

• geoalchemy2
• psycopg2
• nose2 (0.9.1)

Dependencies

Install the python dependencies with: :code:pip install -r requirements.txt

Unit tests

• Run the unit test suite with: :code:coverage3 run -m unittest discover -v
• View the unit test coverage with: :code:coverage report

Command Line Instructions

To run from the command line go to the top level directory of the library in your bash shell or terminal program

Run by specifying the program as a module with :code:-m and leaving off the .py file extension

The exact executable name for invoking python will depend how you have it installed, but most commonly it's just :code:python

For example run the Sqlite example using: :code:python -m Experiments.DataStore_sqliteExperiment

IntelliJ Instructions

To run from inside IntelliJ open the project Mark the :code:Store package as source by right clicking on the directory and selecting :code:Mark Directory as -> Source Root

Open any python module you want to run in the main editor window, right click anywhere in the editor and choose the :code:Run or :code:Debug option