Transferred ownership to AguaClara Reach

• Transferred ownership to AguaClara Cornell to AguaClara Reach
• Created CITATION.cff for integration with Zenodo
  • Resolves #328
• Added automatic formatting and linting with black and flake8
  • Resolves #295
  • Resolves #308
• Removed deprecated functions from floc_model.py

Updated dependencies to fix import error

• Removing string from the beginning of unit_definitions.txt.
• Fixed the SyntaxWarning by changing is to == with string comparisons
• Updated dependencies so that package installation works correctly

Bumped Dependencies and Updates to pipes.py

Dependencies:

• Upgraded urllib3 to 1.26.4.
  Fixed: "Using default SSLContext for HTTPS requests in an HTTPS proxy doesn't verify certificate hostname for proxy connection [high severity]."
• Upgraded pillow to 8.1.2.
  Fixed: "Denial of Service by Uncontrolled Resource Consumption [high severity]."

Pipes module (PR #289)

• Addressed Issue #279
• module now includes schedules 80, 120, and 120
• methods that give the schedule and ND that fit requirements of a pipe

Documentation Site Upgrade

The aguaclara documentation has now been updated to consist of two main parts: an API reference (which was the bulk of the old documentation site) and a developer guide for helping new contributors. The README.md has also been updated to resemble the new documentation homepage, with installation instructions, basic code examples, and links to the API reference and developer guide.

Python >=3.8 Requirement and Migration to Github Actions

aguaclara now requires Python versions 3.8 and higher. Also, the package has migrated from Travis CI and Appveyor to Github Actions for continuous integration.

Documented CDC and deprecated estimated coagulant stock concentrations

This release:

• adds the cdc.py module to the Sphinx documentation
• deprecates estimated coagulant stock concentration and flow rate (coag_stock_conc_est and coag_q_max_est) in cdc.py and replaces them with exact concentration and flow rate (coag_stock_conc and coag_q_max)
• updates the utilities.ceil_nearest and utilities.floor_nearest functions to handle unsorted arrays and raise errors when values are out of range
• updates the environmental_processes_analysis.E_Advective_Dispersion function to return 0 instead of NaN when t=0
• updates the physchem viscosity functions to accept temperatures of 0ºC

Additional onshape_parser functionality

Added processes variable which is returned by get_parsed_measurements() in addition to measurements and templates.

Also fixes a bug which occurred when creating a folder in onshape_parser

Refactored onshape_parser

Extended test coverage and generalized the logic of onshape_parser.py so that it can work for both validation and documentation.

This is accomplished through the for_docs flag. By default this flag is true, so variables will be parsed into human readable strings.
When false, variables are returned as Pint quantities.

Introduction of onshape_parser

We are moving what was parse.py in aide_design_specs to the aguaclara package because it's being used by aide_validation as well, and Monroe would like to have it available for student use when he teaches at Ohio State this spring.

It's not fully tested, but that it is still experimental and will be refactored before being used publicly, at which point we'll ensure 100% test coverage.

Updates to procoda_parser

The following updates have been made to aguaclara.research.procoda_parser:

• addition of an intersect function for locating the intersections between two sets of data
• ability to read data from folder paths that are Github URLs
• addition of an elapsed time option to the get_data_by_time function