[WIP] Refactor software: step 1

[gmaze]

About Refactoring

Refactoring the software can be done in 2 steps:

1. Re-organise all functions into sub-modules, no changes in function name or content
2. Optimise sub-modules and functions to make them pythonic, and more efficient

This PR is a proposition for step 1: a new structure of the library where functions are now organized into sub-modules.

New positioning of functions

Note that functions name are not changed !

• pyowc/core

  • stats.py: brk_pt_fit, build_cov, covarxy_pv, covar_xyt_pv, noise_variance, signal_variance, fit_cond, nlbpfun
  • finders.py: find_10thetas, find_25boxes, find_besthit, find_ellipse, nearest_neighbour

• pyowc/data

  • fetchers.py: get_region_data, get_region_hist_locations, get_data, get_topo_grid
  • wrangling.py: interp_climatology, map_data_grid

• pyowc/plot

  • dashboard.py: plot_diagnostics
  • plots.py: cal_sal_curve_plot, sal_var_plot, t_s_profile_plot, theta_sal_plot, trajectory_plot
  • utils.py: create_dataframe

• pyowc/calibration.py: update_salinity_mapping, calc_piecewisefit

• pyowc/configuration.py: load_configuration, set_calseries, print_cfg

• pyowc/tests # Contain all the unit tests !

• pyowc/utilities.py: change_dates, cal2dec, potential_vorticity, wrap_longitudes, sorter, spatial_correlation

Usage

With this structure, we have a more elegant:

import pyowc as owc
FLOAT_NAME = "3901960"
USER_CONFIG = owc.configuration.load() # fetch the configuration and parameters set by the user
owc.calibration.update_salinity_mapping("/", FLOAT_NAME, USER_CONFIG)
owc.configuration.set_calseries("/", FLOAT_NAME, USER_CONFIG)
owc.calibration.calc_piecewisefit("/", FLOAT_NAME, USER_CONFIG)
owc.plot.dashboard("/", FLOAT_NAME, USER_CONFIG)

Remains to be done

• Settle on the sub-module names and content
• Consolidate unit testing

[codecov]

Codecov Report

Merging #26 into master will decrease coverage by 3.39%.
The diff coverage is 86.36%.

@@            Coverage Diff             @@
##           master      #26      +/-   ##
==========================================
- Coverage   91.38%   87.99%   -3.40%     
==========================================
  Files          65       12      -53     
  Lines        3145     1957    -1188     
==========================================
- Hits         2874     1722    -1152     
+ Misses        271      235      -36     

Flag	Coverage Δ
#unittests	87.99% <86.36%> (-3.40%)	⬇️

Impacted Files	Coverage Δ
setup.py	0.00% <0.00%> (ø)
start_with_pycharm.py	0.00% <0.00%> (ø)
pyowc/calibration.py	85.93% <76.38%> (ø)
pyowc/core/stats.py	80.77% <80.77%> (ø)
pyowc/configuration.py	84.72% <84.72%> (ø)
pyowc/data/fetchers.py	90.69% <90.69%> (ø)
pyowc/plot/plots.py	92.80% <92.80%> (ø)
pyowc/core/finders.py	93.84% <93.84%> (ø)
pyowc/data/wrangling.py	100.00% <100.00%> (ø)
pyowc/plot/dashboard.py	100.00% <100.00%> (ø)
... and 12 more

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[gmaze]

I think "calc_piecewisefit" should also go into the calibration.py module

[edsmall-bodc]

Apart from the above suggested changes, this looks good to me