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Update to version 0.7.0 #273

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Oct 24, 2023
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2c918b4
improve get_geotop
dbrakenhoff Jun 16, 2023
456b983
old get_geotop is renamed geotop_to_layermodel:
dbrakenhoff Jun 16, 2023
84593ce
clean up old code
dbrakenhoff Jun 16, 2023
62a9861
improve get_regis:
dbrakenhoff Jun 16, 2023
56a264e
add cache support for chunked datasets
dbrakenhoff Jun 16, 2023
68a4c1f
add log msg to split_layers
dbrakenhoff Jun 16, 2023
4ed3976
remove nan layer (value -127) from geo_eenheden
OnnoEbbens Jun 16, 2023
25f4f72
use values instead of data to deal with potential dask array
dbrakenhoff Jun 16, 2023
f9cc9d7
improve geotop:
dbrakenhoff Jun 20, 2023
34dfdcf
if caching with dask, close and reopen ds to ensure ds points to file
dbrakenhoff Jun 20, 2023
5376c19
Use dask delayed to read model output
dbrakenhoff Jun 21, 2023
2179557
add delayed, chunked kwargs to output methods
dbrakenhoff Jun 21, 2023
de54e3d
fix DeprecationWarning
dbrakenhoff Jun 21, 2023
5618671
improve log messages grid.py
dbrakenhoff Jun 21, 2023
758f87d
replace modflow with mf6 in logging
dbrakenhoff Jun 21, 2023
a70974a
replace modflow with mf6 in logging
dbrakenhoff Jun 21, 2023
5044c04
more info in log message
dbrakenhoff Jun 21, 2023
c6c1aa3
docstrings
dbrakenhoff Jun 21, 2023
87e7afe
fix tests
dbrakenhoff Jun 21, 2023
a6a26c5
fix geotop_lithok_in_cross_section
dbrakenhoff Jun 21, 2023
471e724
Rename geotop_to_layermodel to to_model_layers and remove convert_geo…
rubencalje Jun 23, 2023
26db2e8
Some minor changes
rubencalje Jun 23, 2023
a551f55
Fix combination of regis and geotop
rubencalje Jun 23, 2023
b4b5256
version bump
OnnoEbbens Jun 26, 2023
fd588c7
Improve `geotop.to_model_layers` and add method `insert_layer`
rubencalje Jul 3, 2023
776a654
Add extra legends for layer models
rubencalje Jul 3, 2023
ecbe766
Add Formatie van Nieuwkoop, Laagpakket van Nij Beets in geotop
rubencalje Jul 3, 2023
4fba381
shorten name model_dataset_created_on -> created_on
OnnoEbbens Jul 4, 2023
62eadc9
199 nlmodgwfic slow for uniform starting head (#200)
OnnoEbbens Jul 7, 2023
961f321
Update webservices.py
rubencalje Jul 10, 2023
e016683
Add test_insert_layer
rubencalje Jul 10, 2023
25ad000
Fix tests and codacy issues
rubencalje Jul 10, 2023
e9ab8c4
add contour-array flopy func
dbrakenhoff Jul 10, 2023
1011d6d
198 deal with outdated cache pickles (#201)
OnnoEbbens Jul 12, 2023
2813914
181 further improve caching by checking only relevant coordinates for…
OnnoEbbens Jul 12, 2023
fe016ec
Merge branch 'dev' into logging-and-docstrings
dbrakenhoff Jul 17, 2023
09cebd9
address @OnnoEbbens comments
dbrakenhoff Jul 17, 2023
c033401
Set the default of method_gullies to "add_to_layer_below"
rubencalje Jul 17, 2023
c45d9a0
Rename gullies to geulen and gully to geul
rubencalje Jul 17, 2023
ab47dfa
Make sure ss and sy are used from the dataset when they are present
rubencalje Jul 17, 2023
83bc51d
improve mfoutput
dbrakenhoff Jul 17, 2023
b4140db
resolve my own comments
dbrakenhoff Jul 17, 2023
345cbb7
Merge pull request #195 from ArtesiaWater/logging-and-docstrings
dbrakenhoff Jul 17, 2023
feec346
refactor mfoutput
dbrakenhoff Jul 19, 2023
f8d58e3
remove deprecation from docstring
dbrakenhoff Jul 19, 2023
17b121c
add test data and modify gitignore
dbrakenhoff Jul 19, 2023
09c5a7d
update PR
dbrakenhoff Jul 20, 2023
28ee878
please codacy
dbrakenhoff Jul 20, 2023
787e12c
Merge pull request #196 from ArtesiaWater/193-geotop
dbrakenhoff Jul 20, 2023
945e302
Merge pull request #194 from ArtesiaWater/mfoutput
dbrakenhoff Jul 20, 2023
a49d63c
improve log msg
dbrakenhoff Jul 20, 2023
827495c
208 gridrefine raises incomprehensible valueerror when there is a dat…
OnnoEbbens Jul 20, 2023
45a999a
small fixes
OnnoEbbens Jul 20, 2023
79e81fe
use get_extent for rotated grids in read.jarkus
dbrakenhoff Jul 27, 2023
19772a0
typo
dbrakenhoff Jul 27, 2023
be311e2
remove singleton dimensions in da_to_reclist for calculating mask
dbrakenhoff Jul 27, 2023
7f92794
deal with time dimension for steady state models for EVT pkg
dbrakenhoff Jul 27, 2023
2dfbdb7
add trap for adding SSM when no sinks/sources present
dbrakenhoff Jul 27, 2023
7904cac
add well logging
dbrakenhoff Jul 28, 2023
0ccc7ed
fix for extrapolate_ds
dbrakenhoff Jul 28, 2023
02fb015
add calculate resistance (C), #134
OnnoEbbens Jul 31, 2023
f47c2f3
improve docstring
OnnoEbbens Jul 31, 2023
865bcf5
add info about assigning resistance to a layer
OnnoEbbens Jul 31, 2023
10e9109
fix missing :
OnnoEbbens Jul 31, 2023
272f18d
fix new doc requirement
OnnoEbbens Aug 7, 2023
3ec05df
some extra checks to avoid errors
OnnoEbbens Aug 10, 2023
778dcd0
fix layer selection in animate_map
OnnoEbbens Aug 15, 2023
46de73e
Fix DatasetCrossSection for rotated grids
rubencalje Aug 16, 2023
50c31ce
Add layer argument to nlmod.gwf.chd and nlmod.gwf.ghb (just like nlmo…
rubencalje Aug 16, 2023
66d60b9
Improve docs of add_bathymetry_to_top_bot_kh_kv
rubencalje Aug 16, 2023
b8b5d75
Add downloads of boundaries of dutch municipalities and provinces
rubencalje Aug 16, 2023
06f0be4
fix #215 (#216)
OnnoEbbens Aug 22, 2023
e730a76
Make sure ssm_sources is a list (which is not the case when ds is loa…
rubencalje Aug 23, 2023
2757063
Rename pg to particlegroups, equal to flopy
rubencalje Aug 23, 2023
35c440d
Merge branch 'dev' into improve-plots
dbrakenhoff Aug 24, 2023
2e404d3
Merge pull request #230 from ArtesiaWater/improve-plots
dbrakenhoff Aug 24, 2023
056f209
Merge pull request #231 from ArtesiaWater/zeeland
dbrakenhoff Aug 24, 2023
d11b76d
Stop overwriting kh and gv of geotop in add_geotop_to_regis_layers
rubencalje Aug 24, 2023
41f8810
Update url for "level_areas" of "De Stichtse Rijnlanden"
rubencalje Aug 24, 2023
ca0c62a
save model dataset to model_ws instead of cachedir
OnnoEbbens Aug 24, 2023
e0a9aa7
rename _FillValue to nodata, see #218
OnnoEbbens Aug 24, 2023
fe3b788
Codacy
OnnoEbbens Aug 24, 2023
515afe3
Bumped dependency for netCDF4 to 1.6.3 (#232)
bdestombe Aug 24, 2023
14ef9a4
codacy fix
OnnoEbbens Aug 24, 2023
18af3e7
Merge branch 'dev' into 218-getting-an-extra-layer-when-reading-geoto…
OnnoEbbens Aug 24, 2023
8a12472
Merge branch 'dev' into 227-write-dataset-to-model-workspace-instead-…
OnnoEbbens Aug 24, 2023
0070aa6
Make recharge more uniform
OnnoEbbens Aug 24, 2023
6be2006
nb_path -> script_path
OnnoEbbens Aug 24, 2023
33d6478
fix Projection issue in backgroundmaps #240
dbrakenhoff Aug 24, 2023
93e5248
Add calculate_sea_coverage
rubencalje Aug 24, 2023
34e69f7
improve plotting in notebooks #224
dbrakenhoff Aug 24, 2023
9df355a
add calculate transmissivity #134
OnnoEbbens Aug 24, 2023
b4c3a96
Merge pull request #236 from ArtesiaWater/227-write-dataset-to-model-…
dbrakenhoff Aug 24, 2023
f21acbc
Add DatasetCrossSection.label_layers
rubencalje Aug 24, 2023
48ceacf
Merge pull request #239 from ArtesiaWater/210-nlmod-adding-rch-and-ev…
dbrakenhoff Aug 24, 2023
6afd58f
Merge branch 'dev' of github.com:ArtesiaWater/nlmod into dev
OnnoEbbens Aug 24, 2023
b391597
Merge branch 'dev' of github.com:ArtesiaWater/nlmod into dev
OnnoEbbens Aug 24, 2023
c066d31
nb_path -> script_path
OnnoEbbens Aug 24, 2023
918e35b
mostly typos and rename AHN -> DTM
dbrakenhoff Aug 24, 2023
d7b7e1e
Merge pull request #242 from ArtesiaWater/calculate_sea
dbrakenhoff Aug 24, 2023
7f3d31c
Add test
rubencalje Aug 24, 2023
3ce6ebd
Merge branch 'dev' into 218-getting-an-extra-layer-when-reading-geoto…
rubencalje Aug 25, 2023
2800853
Merge pull request #238 from ArtesiaWater/218-getting-an-extra-layer-…
dbrakenhoff Aug 25, 2023
021fc6a
Merge pull request #246 from ArtesiaWater/label_layers
dbrakenhoff Aug 25, 2023
0d9806e
fix typos
dbrakenhoff Aug 25, 2023
7469fd7
Merge remote-tracking branch 'origin/dev' into plotting-in-notebooks
dbrakenhoff Aug 25, 2023
1cf219a
update gwt nb
dbrakenhoff Aug 25, 2023
f4c40f7
Add caching for DataArrays as well
rubencalje Aug 25, 2023
8839d06
codacy, pass on fmt_base kwarg
dbrakenhoff Aug 25, 2023
959d436
Fix bug found by tests
rubencalje Aug 25, 2023
7ce393e
Update test_006_caching.py
rubencalje Aug 25, 2023
5d52ce2
Remove last empty cell again
rubencalje Aug 25, 2023
47d3de2
codacy suggestions
dbrakenhoff Aug 25, 2023
4fa08c8
rename backgroundmap to background everywhere
dbrakenhoff Aug 25, 2023
8ecca8a
Merge pull request #244 from ArtesiaWater/plotting-in-notebooks
dbrakenhoff Aug 25, 2023
c73f524
Merge pull request #241 from ArtesiaWater/epsg-28992-issue
dbrakenhoff Aug 25, 2023
3e61b49
Merge pull request #243 from ArtesiaWater/stop_overwriting_kh_and_kv_…
dbrakenhoff Aug 25, 2023
d5b8f70
Make write_and_run more consistent, #233
OnnoEbbens Aug 25, 2023
51f6853
remove all the unnecessary references on top of the modules
OnnoEbbens Aug 25, 2023
1961dfd
Merge branch 'dev' of github.com:ArtesiaWater/nlmod into dev
OnnoEbbens Aug 25, 2023
c9ad917
codacy fix
dbrakenhoff Aug 25, 2023
b25a209
codacy fix
dbrakenhoff Aug 25, 2023
46ccfbb
Add docstring to _check_for_data_array
rubencalje Aug 25, 2023
9161091
Merge pull request #248 from ArtesiaWater/codacy
dbrakenhoff Aug 25, 2023
f4ef09b
improve gwf bc pkgs
dbrakenhoff Aug 25, 2023
4ddd093
Remove idomain from Dataset
rubencalje Aug 25, 2023
cec77d4
Add docstring to get_idomain
rubencalje Aug 25, 2023
a9002da
Fix tests and rename "active" to "active_domain"
rubencalje Aug 25, 2023
94198fc
set idomain above/below the first/last active layer to 0
rubencalje Aug 25, 2023
f3fa3ee
Merge pull request #247 from ArtesiaWater/add_caching_data_array
rubencalje Aug 25, 2023
12175a3
Improve test for caching DataArrays
rubencalje Aug 25, 2023
5b8ccf0
Merge pull request #249 from ArtesiaWater/97-drn-riv-ghb-packages-in-…
dbrakenhoff Aug 25, 2023
a525f7d
Change typo
rubencalje Aug 25, 2023
2030fda
Merge pull request #250 from ArtesiaWater/calculate_idomain_on_the_fly
rubencalje Aug 25, 2023
dd9e478
Attributes encoding (#245)
bdestombe Aug 25, 2023
15d19e1
improve time discretization:
dbrakenhoff Aug 28, 2023
78b620c
update STO pkg
dbrakenhoff Aug 28, 2023
ec31953
update recharge pkg for new ds time discretization
dbrakenhoff Aug 28, 2023
f239cb2
update get_tdis_perioddata
dbrakenhoff Aug 28, 2023
36cebae
update tests for new time discretization
dbrakenhoff Aug 28, 2023
06c4e3c
black
dbrakenhoff Aug 28, 2023
c5ffc29
codacy
dbrakenhoff Aug 28, 2023
14bd019
Not all encodings were returned (#256)
bdestombe Aug 28, 2023
6082bd4
process @OnnoEbbens comments
dbrakenhoff Aug 30, 2023
21dd905
process @OnnoEbbens comments
dbrakenhoff Aug 30, 2023
505a985
remove commented code
dbrakenhoff Aug 31, 2023
361c509
pin pandas version < 2.1.0
dbrakenhoff Aug 31, 2023
9ff2a84
add pin to ci not RTD...
dbrakenhoff Aug 31, 2023
5bc7da3
process comments @rubencalje
dbrakenhoff Aug 31, 2023
54160a4
Add perlen and default value for start
rubencalje Aug 31, 2023
f5c5da2
minor docstring update
rubencalje Aug 31, 2023
3bfc28e
Allow time to be a single value as well
rubencalje Aug 31, 2023
d32c937
remove default value of start
rubencalje Aug 31, 2023
3322919
Fix tests
rubencalje Aug 31, 2023
d620084
Update notebooks
rubencalje Aug 31, 2023
fb17b73
Make sure time is converted to an iterable a bit earlier
rubencalje Aug 31, 2023
d796995
Add knmi bugfix
rubencalje Sep 1, 2023
f270efd
Fix new warning in pandas 2.1.0
rubencalje Sep 1, 2023
f7159c9
Fix other problems in notebooks
rubencalje Sep 1, 2023
cfa3d3a
Fix last notebook bugs
rubencalje Sep 1, 2023
e4d009f
Remove start_date_time check in modpath
rubencalje Sep 1, 2023
652196e
codacy + json error nb11
dbrakenhoff Sep 4, 2023
658b4ef
update log message
dbrakenhoff Sep 4, 2023
89fe3ea
Merge pull request #257 from ArtesiaWater/time_discretization_issues
dbrakenhoff Sep 4, 2023
d77a0da
Add dataframe_to_flopy_timeseries
rubencalje Sep 7, 2023
01be467
Many small fixes
rubencalje Sep 8, 2023
7906723
Allow stage to be a timeseries in build_spd
rubencalje Sep 11, 2023
db448d7
minor fix in DataSetCrossSection
rubencalje Sep 11, 2023
84ffcf9
Add get_layer_of_z
rubencalje Sep 12, 2023
15e3695
catch common error where user tries to plot a layered DataArray in nl…
rubencalje Sep 12, 2023
e3739ca
Add remove_thin_layers and minor changes
rubencalje Sep 20, 2023
22dfe25
update epsg code in plotutil
dbrakenhoff Sep 25, 2023
d4e7a03
Update download of provisional version of modpath
rubencalje Sep 27, 2023
66aa48a
UZF, RCH, EVT, WEL and MAW improvement (#263)
rubencalje Oct 6, 2023
386c916
Add function to compare model results with measurements (#258)
OnnoEbbens Oct 10, 2023
bfc1bc6
Add logos (#271)
rubencalje Oct 18, 2023
40989db
fix for #260 (#266)
OnnoEbbens Oct 18, 2023
7b72aec
Incomplete knmi ts breaks get_recharge function (#269)
bdestombe Oct 18, 2023
6ed4225
Time dimension attributes added to set_ds_time
bdestombe Oct 19, 2023
400b2e3
Update time.py
bdestombe Oct 19, 2023
c2d3efc
add more info on epsg 28892 definition, see comment Bas
OnnoEbbens Oct 20, 2023
b1775dc
typo in default ghb conductance var
dbrakenhoff Oct 20, 2023
933ce2e
black on kmi.py
dbrakenhoff Oct 20, 2023
0cdc603
deal with print_option kwarg
dbrakenhoff Oct 20, 2023
2c4c91c
remove one general exception for codacy
dbrakenhoff Oct 20, 2023
42c5fb1
update readme
dbrakenhoff Oct 20, 2023
5ec859f
update readme/docs
dbrakenhoff Oct 23, 2023
9aaa530
codacy fixes
OnnoEbbens Oct 23, 2023
1748780
fix typo
OnnoEbbens Oct 23, 2023
5129bb1
ignore new check
OnnoEbbens Oct 23, 2023
92e0cf5
remove pass
OnnoEbbens Oct 23, 2023
b3274b8
fix error
OnnoEbbens Oct 23, 2023
6da6e24
tuple comprehension
OnnoEbbens Oct 23, 2023
95be564
Update index.rst
rubencalje Oct 23, 2023
f84a399
Buisdrainage (#276)
rubencalje Oct 23, 2023
c777fa3
Fix codacy issue and improve documentation index
rubencalje Oct 24, 2023
46d7585
Fix remaining codacy issue
rubencalje Oct 24, 2023
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1 change: 0 additions & 1 deletion .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,6 @@ jobs:
run: |
py.test ./tests -m "not notebooks"


- name: Run codacy-coverage-reporter
uses: codacy/codacy-coverage-reporter-action@master
with:
Expand Down
8 changes: 7 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,13 @@ nlmod/bin/*
!nlmod/bin/
!nlmod/bin/mp7_2_002_provisional
flowchartnlmod.pptx
tests/data/

tests/data/*
!tests/data/**/
tests/data/mfoutput/*
!tests/data/mfoutput/vertex/*
!tests/data/mfoutput/structured/*

docs/examples/*/
!docs/examples/data/
!docs/examples/data/chloride_hbossche.nc
5 changes: 2 additions & 3 deletions .readthedocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@ version: 2

# Set the version of Python and other tools you might need
build:
os: ubuntu-20.04
os: ubuntu-22.04
tools:
python: "3.9"
python: "3.10"

# Build documentation in the docs/ directory with Sphinx
sphinx:
Expand All @@ -20,7 +20,6 @@ sphinx:

# Optionally declare the Python requirements required to build your docs
python:
system_packages: true
install:
- method: pip
path: .
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2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ Install the module with pip:

`pip install nlmod`

`nlmod` has many required dependencies: `flopy`, `xarray`, `netcdf4`, `rasterio`, `rioxarray`, `affine`, `geopandas`, `owslib`, `hydropandas`, `shapely`, `pyshp`, `rtree`, `matplotlib`, `dask` and `colorama`. On top of that there are some optional dependecies, only needed (and imported) in a single method. Examples of this are `bottleneck` (used in calculate_gxg), `geocube` (used in add_min_ahn_to_gdf), `h5netcdf` (used for hdf5 files backend in xarray). To install the nlmod with the optional dependencies use:
`nlmod` has many required dependencies: `flopy`, `xarray`, `netcdf4`, `rasterio`, `rioxarray`, `affine`, `geopandas`, `owslib`, `hydropandas`, `shapely`, `pyshp`, `rtree`, `matplotlib`, `dask` and `colorama`. On top of that there are some optional dependecies, only needed (and imported) in a single method. Examples of this are `bottleneck` (used in calculate_gxg), `geocube` (used in add_min_ahn_to_gdf), `h5netcdf` (used for hdf5 files backend in xarray), `scikit-image` (used in calculate_sea). To install the nlmod with the optional dependencies use:

`pip install nlmod[full]`

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1 change: 1 addition & 0 deletions docs/_static/logo_brabant_water.svg
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141 changes: 141 additions & 0 deletions docs/_static/logo_hhnk.svg
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