fix(HeadUFile): repro & fix #1503, add tests

[wpbonelli]

This PR includes:

• add get_lni(ncpl, *nodes) function in flopy.utils.gridutil.py (convert node number to within-layer node index)
• use get_lni(ncpl, *nodes) in HeadUFile.get_ts(idx) (fix bug: error when call get_ts() function of class HeadUFile #1503)
• add get_lni(*nodes) method to Grid
• declare nlay property on Grid
• add addopts -ra to pytest.ini (show more info about skipped and xfailed tests)
• add pytest-cases to testing dependencies in setup.cfg and etc/environment.yml
• use pytest-cases to define grids in test_grid_cases.py and parametrize tests in test_grid.py
• run linter on example scripts, tutorials and tests
• mark EPSG-code related tests flaky

HeadUFile.get_ts() fix

As reported in #1503 HeadUFile.get_ts() was converting node number to within-layer node index incorrectly, causing an IndexError. This wasn't revealed before because it only happened for nodes in layers 2+ and tests only called get_ts() on nodes in layer 1. Now the index conversion is done in function get_lni(ncpl, *nodes) (for "layer-node-index") in new module flopy.utils.gridutil.py. The function's parameters are:

• ncpl: single int or collection of int if node count varies per layer
• *nodes zero or more node numbers

The return value is a tuple (layer, node index) if a single node number was provided, otherwise a list of tuples. If no node numbers are provided, the values for all nodes will be returned in ascending order by node number.

HeadUFile.get_ts(idx) is now tested for every node of a sample grid

Grid updates

Adds corresponding method get_lni(*nodes) to Grid, which uses the standalone function above internally.

Also adds unimplemented nlay property to Grid, following convention for other props shared by all grid types.

Test fixtures & parametrization

Per @Hofer-Julian's suggestion I tried out pytest-cases on some tests in test_grid.py. This plugin provides mechanisms to extend or work around limitations of pytest fixtures (e.g. the inability to use them to parametrize a test function).

A number of tests in test_grid.py previously built and tested their own custom grids. Some of these have been pulled into the GridCases class in test_grid_cases.py, which now holds a few examples of each grid type. Some tests in test_grid.py are now parametrized with some or all GridCases, depending whether properties under test are shared or specific to a grid type — pytest-cases lets you subset via prefix, e.g. naming structured grids structured_* and selecting with e.g. @parametrize_with_cases("grid", cases=GridCases, prefix="structured").

The grids are still defined by hand. A future option might be generating grids from a random seed and some size/complexity parameters. pytest-cases supports dynamically generating cases, if pytest_generate_tests is not sufficient. Maybe something like hypothesis could be useful, assuming it's compatible with pytest.

[codecov]

Codecov Report

Merging #1510 (c730428) into develop (58938b9) will decrease coverage by 0.0%.
The diff coverage is 85.7%.

❗ Current head c730428 differs from pull request most recent head 1d890bf. Consider uploading reports for the commit 1d890bf to get more accurate results

@@            Coverage Diff            @@
##           develop   #1510     +/-   ##
=========================================
- Coverage     72.4%   72.4%   -0.1%     
=========================================
  Files          250     251      +1     
  Lines        54039   54055     +16     
=========================================
+ Hits         39174   39183      +9     
- Misses       14865   14872      +7     

Impacted Files	Coverage Δ
flopy/discretization/unstructuredgrid.py	81.7% <60.0%> (-0.4%)	⬇️
flopy/discretization/grid.py	74.5% <66.6%> (-0.2%)	⬇️
flopy/utils/binaryfile.py	79.2% <91.6%> (+0.2%)	⬆️
flopy/utils/grid.py	100.0% <100.0%> (ø)
flopy/plot/crosssection.py	62.4% <0.0%> (-1.6%)	⬇️
flopy/utils/get_modflow.py	56.2% <0.0%> (+0.7%)	⬆️
flopy/utils/mfreadnam.py	78.7% <0.0%> (+1.5%)	⬆️

[Hofer-Julian]

Hypothesis is compatible with pytest. We use it successfully in multiple projects.

[langevin-usgs]

@w-bonelli go ahead and merge this in.