Test case for IWater and PWater subroutines

austinorr commented 2 months ago

Revisions include:

remove ACIDPH.py from importable modules -- this module looks like its under construction so it's been staged as a text file temporarily.
code coverage cannot be measured for jit-compiled functions or classes. This is ok though because numba code is also valid python code -- except for the special cases in the jitclass(spec) when we are spec'ing another jit class. To get past this barrier quickly I've just checked to see if we're running tests with the flag NUMBA_DISABLE_JIT=1. If set to one (jit disabled), we use the python class in the spec, if not we default to using the jitclass.
Added a test case and a helper function to eliminate the .h5 file intermediary (using version controllable json for now instead -- open to discussion on how to make this harder/better/faster/stronger)

no additional dependencies for now, but running the tests and measuring coverage is done with pytest and coverage like so:


(hsp2) aorr@POR-AORR:~/wsl-sources/HSPsquared$ NUMBA_DISABLE_JIT=1 coverage run --branch -m  pytest tests/ipwater  && coverage report
=========================================================== test session starts ============================================================
platform linux -- Python 3.11.5, pytest-7.4.3, pluggy-1.3.0
rootdir: /home/aorr/wsl-sources/HSPsquared
collected 2 items

tests/ipwater/test_ipwater.py .. [100%]

============================================================ 2 passed in 0.45s ============================================================= Name Stmts Miss Branch BrPart Cover

HSP2/ADCALC.py 155 141 76 0 10% HSP2/ATEMP.py 27 19 4 0 32% HSP2/CONS.py 154 143 54 0 6% HSP2/COPY.py 18 10 2 0 40% HSP2/GENER.py 104 70 20 0 27% HSP2/GQUAL.py 1136 1116 454 0 2% HSP2/HTRCH.py 309 296 102 0 4% HSP2/HYDR.py 477 455 196 0 4% HSP2/IQUAL.py 182 173 58 0 5% HSP2/IWATER.py 199 52 72 14 70% HSP2/IWTGAS.py 116 104 36 0 9% HSP2/NUTRX_Class.py 592 564 222 0 5% HSP2/OXRX_Class.py 141 127 32 0 9% HSP2/PHCARB_Class.py 130 117 32 0 9% HSP2/PLANK_Class.py 960 914 334 1 5% HSP2/PQUAL.py 264 252 74 0 4% HSP2/PSTEMP.py 145 136 58 0 5% HSP2/PWATER.py 534 154 168 34 68% HSP2/PWTGAS.py 269 256 92 0 4% HSP2/RQUAL.py 349 330 182 0 4% HSP2/RQUAL_Class.py 719 698 168 1 3% HSP2/RQUTIL.py 24 17 12 0 36% HSP2/SEDMNT.py 152 143 52 0 5% HSP2/SEDTRN.py 725 708 192 0 3% HSP2/SNOW.py 446 433 156 0 3% HSP2/SOLIDS.py 92 84 36 0 8% HSP2/SPECL.py 4 1 2 0 83% HSP2/init.py 4 0 0 0 100% HSP2/configuration.py 41 13 0 0 68% HSP2/main.py 291 277 144 0 3% HSP2/mainDoE.py 194 175 90 0 7% HSP2/state.py 117 90 26 0 20% HSP2/uci.py 14 10 0 0 29% HSP2/utilities.py 318 256 224 5 14% HSP2IO/io.py 48 34 10 0 24% HSP2IO/protocols.py 32 6 10 0 86% _version.py 1 0 0 0 100% tests/init.py 0 0 0 0 100% tests/ipwater/init.py 0 0 0 0 100% tests/ipwater/test_ipwater.py 46 0 16 0 100%

TOTAL 9529 8374 3406 55 11%


This shows the ~70% coverage for HSP2/IWater and HSP2/PWater modules.

We can also run the suite with the numba jit to ensure we didn't break anything.
```bash
(hsp2) aorr@POR-AORR:~/wsl-sources/HSPsquared$ coverage run --branch -m  pytest tests/ipwater  && coverage report
=========================================================== test session starts ============================================================
platform linux -- Python 3.11.5, pytest-7.4.3, pluggy-1.3.0
rootdir: /home/aorr/wsl-sources/HSPsquared
collected 2 items                                                                                                                          

tests/ipwater/test_ipwater.py ..                                                                                                     [100%]

============================================================ 2 passed in 4.52s =============================================================
Name                            Stmts   Miss Branch BrPart  Cover
-----------------------------------------------------------------
HSP2/ADCALC.py                    155    141     76      0    10%
HSP2/ATEMP.py                      27     19      4      0    32%
HSP2/CONS.py                      154    143     54      0     6%
HSP2/COPY.py                       18     10      2      0    40%
HSP2/GENER.py                     104     70     20      0    27%
HSP2/GQUAL.py                    1136   1116    454      0     2%
HSP2/HTRCH.py                     309    296    102      0     4%
HSP2/HYDR.py                      477    455    196      0     4%
HSP2/IQUAL.py                     182    173     58      0     5%
HSP2/IWATER.py                    199    166     72      3    17%
HSP2/IWTGAS.py                    116    104     36      0     9%
HSP2/NUTRX_Class.py               592    564    222      0     5%
HSP2/OXRX_Class.py                141    127     32      0     9%
HSP2/PHCARB_Class.py              130    117     32      0     9%
HSP2/PLANK_Class.py               960    914    334      1     5%
HSP2/PQUAL.py                     264    252     74      0     4%
HSP2/PSTEMP.py                    145    136     58      0     5%
HSP2/PWATER.py                    534    489    168      3     9%
HSP2/PWTGAS.py                    269    256     92      0     4%
HSP2/RQUAL.py                     349    330    182      0     4%
HSP2/RQUAL_Class.py               719    698    168      1     3%
HSP2/RQUTIL.py                     24     17     12      0    36%
HSP2/SEDMNT.py                    152    143     52      0     5%
HSP2/SEDTRN.py                    725    708    192      0     3%
HSP2/SNOW.py                      446    433    156      0     3%
HSP2/SOLIDS.py                     92     84     36      0     8%
HSP2/SPECL.py                       4      1      2      0    83%
HSP2/__init__.py                    4      0      0      0   100%
HSP2/configuration.py              41     13      0      0    68%
HSP2/main.py                      291    277    144      0     3%
HSP2/mainDoE.py                   194    175     90      0     7%
HSP2/state.py                     117     90     26      0    20%
HSP2/uci.py                        14     10      0      0    29%
HSP2/utilities.py                 318    256    224      5    14%
HSP2IO/io.py                       48     34     10      0    24%
HSP2IO/protocols.py                32      6     10      0    86%
_version.py                         1      0      0      0   100%
tests/__init__.py                   0      0      0      0   100%
tests/ipwater/__init__.py           0      0      0      0   100%
tests/ipwater/test_ipwater.py      46      0     16      0   100%
-----------------------------------------------------------------
TOTAL                            9529   8823   3406     13     7%

Here we see the tests pass, but line coverage can't be measured since it's all been compiled.

austinorr commented 2 months ago

Request review from @PaulDudaRESPEC and @rburghol

austinorr commented 2 months ago

@PaulDudaRESPEC yep, that sounds fine. Is that the long-term branch management pattern that this project intends to use, or is this just temporary while we manage the current push of changes?

austinorr commented 2 months ago

@PaulDudaRESPEC ok, rebased revisions on the develop branch.

respec / HSPsquared

Test case for IWater and PWater subroutines #151

============================================================ 2 passed in 0.45s ============================================================= Name Stmts Miss Branch BrPart Cover