Update to packaging push plus fixes #158

timcera · 2024-04-30T04:52:14Z

I was sitting on these changes because I couldn't find solutions to two problems. So thought to put this in a pull request for review and maybe someone will be able to figure them out.

Another reason to get this out there, is for the next two weeks or so I won't be able to work on this and I didn't want to slow progress down.

"pytest" works to test the new PWATER and IWATER tests. They both pass.

THE PROBLEMS:

Right now, using python 3.10 and a "pip install ." with the code in this pull request, the "readUCI" function in tests/test05/HSP2results/CompareHSP2.ipynb will only bring in the PERLND operation. IMPLND and RCHRES are ignored. No errors. I can't figure it out.
In tests/test10/HSP2results/TEST10_hsp2_compare.ipynb, when it is calculating RQUAL I get the error:

...
File [~/anaconda3/envs/hsp2_310/lib/python3.10/site-packages/HSP2/RQUAL.py:225](http://localhost:8888/home/tim/anaconda3/envs/hsp2_310/lib/python3.10/site-packages/HSP2/RQUAL.py#line=224), in rqual(io_manager, siminfo, uci, uci_oxrx, uci_nutrx, uci_plank, uci_phcarb, ts, monthdata)
    218 		ts['BINV'] = initm(siminfo, ui_plank, binvfg, 'MONTHLY[/BINV](http://localhost:8888/BINV)', binv_init)
    220 #---------------------------------------------------------------------
    221 # initialize & run integerated WQ simulation:
    222 #---------------------------------------------------------------------
    224 (err_oxrx, err_nutrx, err_plank, err_phcarb) \
--> 225 	= _rqual_run(siminfo_, ui, ui_oxrx, ui_nutrx, ui_plank, ui_phcarb, ts)
    227 #---------------------------------------------------------------------
    228 # compile errors & return:
    229 #---------------------------------------------------------------------
    231 (errors, ERRMSGS) = _compile_errors(NUTFG, PLKFG, PHFG, err_oxrx, err_nutrx, err_plank, err_phcarb)

SystemError: CPUDispatcher(<function _rqual_run at 0x7f67104b8ee0>) returned NULL without setting an exception

…ly, or annual

…g R scripts or even running R inside the dirs

Added a couple R files to ignore to keep the repo clean when includin…

recent small fixes into develop

First attempt to initiate automated testing

try to change to node20 from node16

2nd try node.js

use v4 instead of v3 - does this fix node js 20 issue?

simplified tests using newer info from https://docs.github.com/en/[email protected]/actions/automating-builds-and-tests/building-and-testing-python

try v5 since v4 still seems to be deprecated even though the docs "seem" to say going from 3 to 4 will fix.

try py 3.9

…uggests it should?)

ignore missing variables (since `_version` is loaded via an include). to fix CI script failure with code `F821` see respec#135 (comment)

ignore ACIDPH.py because it uses a weird sci notation format AC (i.e. I think `rkal1 = 1.03d-5` should be `rkal1 = 1.03e-5` etc)

merge recent minor changes to setup.py from tim cera into develop branch

Testing framework base deployment

Run tests on 3 branches

* Moved metadata from setup.py to pyproject.toml and removed setup.py * Moved README.md to README.rst and rewrote. * Made a VERSION file to contain version number. + Allows version number to be read by pyproject.toml. + Refactored _version.py to read version number from VERSION file. * Made a publish.py to ease and document publishing to pypi.

mando used old import locations for Collections.

Test case for IWater and PWater subroutines

(feat) change to a pyproject.toml to publish to pypi

…nflict

push contributing.md to develop

Fixes * Allow the HDF filename to be passed to main function instead of only io_manager instance. Having main only accept io_manager broke all ipython notebooks. * Removed "print(table)" from readUCI which I think was a debugging statement. * Removed what I hope are unnecessary "iter(llines)" statements from readUCI. IPython Notebook Fixes * Edited some of the ipython notebooks that tried to find an element time-series with an old name, for example tried to find "SURO" instead of the new name "SURO_sum". * Edited some of the ipython notebooks so that filenames were case sensitive. Deprecations * The append function is no longer available for DataFrames and changed to pd.concat form. * In pandas 3.0, to_hdf will require the "key" to be a keyword argument instead of a positional argument and made that change now to silence the deprecation message. Format * Removed trailing spaces from some files. * Fixed not a multiple of 4 spaces indentation in at least one file. * Renamed files with spaces in their names, replacing spaces with "_". Documentation * Additional edits to the README.rst. * Reshaped some docstrings into Numpy format.

timcera · 2024-04-30T04:53:49Z

I messed up the pull request so I am withdrawing and looks like I need to rebase.

PaulDudaRESPEC and others added 30 commits October 31, 2023 16:05

first cut at implementing other gener operations

e78f84c

first draft of enhancement to allow output aggregated to daily, month…

4431180

…ly, or annual

small clean-ups to fully implement GENER operations

9c435e3

Added a couple R files to ignore to keep the repo clean when includin…

9bb8109

…g R scripts or even running R inside the dirs

Merge pull request respec#124 from HARPgroup/devignore

e1140fc

Added a couple R files to ignore to keep the repo clean when includin…

Merge pull request respec#125 from respec/master

85ce951

recent small fixes into develop

clean up details of ParseTable.csv

fece38c

add hdf5 file name to output message

fc9846e

refinements to include multiple canopy layer enhancement

d2bc9cc

Create python-app.yml

274eaab

First attempt to initiate automated testing

Update python-app.yml

dfa9e75

try to change to node20 from node16

Update python-app.yml

34530b4

2nd try node.js

Update python-app.yml

26dd7aa

use v4 instead of v3 - does this fix node js 20 issue?

Update python-app.yml

4b938da

simplified tests using newer info from https://docs.github.com/en/[email protected]/actions/automating-builds-and-tests/building-and-testing-python

Update python-app.yml

aa625f3

try v5 since v4 still seems to be deprecated even though the docs "seem" to say going from 3 to 4 will fix.

Create python-app1.yml

32bf2a7

Update python-app.yml

23de13b

Update python-app.yml

b819471

Update python-app.yml

e15a76d

delete superfluous workflow

2a05f92

add actions folder to see if it fixes

3b718c0

Update python-app.yml

2f39354

try py 3.9

Update python-app.yml

419dc23

disable the custom action yml to see if it still works (as tutorial s…

20009c6

…uggests it should?)

Merge branch 'master' of github.com:HARPgroup/HSPsquared

92941eb

Update python-app.yml

40d52f5

ignore missing variables (since `_version` is loaded via an include). to fix CI script failure with code `F821` see respec#135 (comment)

Update python-app.yml

f996426

ignore ACIDPH.py because it uses a weird sci notation format AC (i.e. I think `rkal1 = 1.03d-5` should be `rkal1 = 1.03e-5` etc)

Update python-app.yml

c129dca

Update python-app.yml

2b5c89b

add ptest

238388e

Burgholzer and others added 28 commits February 29, 2024 10:18

adding new dev config from dependency_options branch

9e09e61

set py to 3.11 in dev

cfb12e5

info

98b3e21

rename scripts to show install env (i.e. pip / conda)

780c50f

attempt a conda install tester

45b48db

attempt a conda install tester

f79bc56

attempt a conda install tester

e3dfaf0

try looking for hsp2 in the CONDA path

4f31719

call hsp wihtout path

71f58d8

Merge pull request respec#144 from respec/master

5b6ca0a

merge recent minor changes to setup.py from tim cera into develop branch

merge in minor additions

ed3f2a5

merging in changes from HARPgroup

760b180

Merge branch 'develop' into testx

2df5a94

Merge pull request respec#142 from HARPgroup/testx

5e54508

Testing framework base deployment

only run tests on 3 branches

0bd5030

Merge pull request respec#148 from HARPgroup/testx

34a56c8

Run tests on 3 branches

ACIDPH.py is not yet valid python, preserving wip as text

e84924b

prepare for disabling the jit during tests to enable code coverage

07d1b78

tests passing for IWater and PWater under pytest with ~70% code coverage

1decc4f

(ci) update github workflows to work with pyproject.toml.

43af3bc

(fix) replaced mando with cltoolbox

1dca5ba

mando used old import locations for Collections.

Merge pull request respec#151 from Geosyntec/ipwater-tests

a6abcfb

Test case for IWater and PWater subroutines

Merge pull request respec#152 from timcera/pypi_package

3a40125

(feat) change to a pyproject.toml to publish to pypi

README.md -- restore this file temporarily while resolving a merge co…

681b842

…nflict

Merge pull request respec#153 from respec/master

d149b7d

push contributing.md to develop

Delete README.md after resolving merge conflict

fd31a26

timcera closed this Apr 30, 2024

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Update to packaging push plus fixes #158

Update to packaging push plus fixes #158

timcera commented Apr 30, 2024

timcera commented Apr 30, 2024

Update to packaging push plus fixes #158

Update to packaging push plus fixes #158

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timcera commented Apr 30, 2024

timcera commented Apr 30, 2024