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Release v0.7.0: Adding cross-sections to TTim #86

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Dec 20, 2024
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f1bdd70
attempt notebook test change to improve performance
dbrakenhoff Sep 27, 2024
afde9bd
ruff
dbrakenhoff Sep 27, 2024
85ed067
add tests for numba bessel functions
dbrakenhoff Nov 7, 2024
7383401
use all close instead of exactly equal for besselk1cheb
dbrakenhoff Nov 7, 2024
ba53755
fix #78
dbrakenhoff Nov 7, 2024
6fe91fc
revert changes, lambda has to be a float and not an array, apparently
dbrakenhoff Nov 7, 2024
b3dcdca
convert lab to float for failing tests
dbrakenhoff Nov 7, 2024
8d1bc4c
minor improvements:
dbrakenhoff Nov 7, 2024
2de1e03
make elemenent AbstractBaseClass
dbrakenhoff Nov 7, 2024
f97363c
TTim plots (#76)
dbrakenhoff Nov 7, 2024
fa233cc
Merge branch 'dev' into elementABC
dbrakenhoff Nov 7, 2024
9061995
ruff
dbrakenhoff Nov 7, 2024
eed3372
Add LineSink1D:
dbrakenhoff Nov 7, 2024
ef083da
Merge pull request #79 from mbakker7/elementABC
dbrakenhoff Nov 7, 2024
96119ac
ruff
dbrakenhoff Nov 7, 2024
c2dcd7f
add timml for linesink1d notebook
dbrakenhoff Nov 8, 2024
1645f33
add linedoublet1d
dbrakenhoff Nov 8, 2024
7ba144d
add linedoublet1d
dbrakenhoff Nov 8, 2024
b0da425
Merge pull request #77 from mbakker7/numba_tests
dbrakenhoff Nov 8, 2024
9ff976e
renamed x coordinate
dbrakenhoff Nov 8, 2024
af372fa
Merge remote-tracking branch 'origin/dev' into linesink1d
dbrakenhoff Nov 8, 2024
f9283bd
example with variable entry resistance (#83)
mbakker7 Nov 8, 2024
d1fe487
add multi layer example for 1d linesinks and doublets
dbrakenhoff Nov 11, 2024
124b061
add HeadDiffLineSink1D and FluxDiffLineSink1D
dbrakenhoff Nov 11, 2024
99a63db
add HeadDiffEquation for continuity of head and FluxDiffEquation for …
dbrakenhoff Nov 11, 2024
0e73211
add tiny
dbrakenhoff Nov 11, 2024
6530419
add tiny
dbrakenhoff Nov 11, 2024
b23c252
remove parentheses for leaky layer parameter label on plot
dbrakenhoff Nov 11, 2024
c48f95f
use python conventions for function names
dbrakenhoff Nov 11, 2024
145ad51
add tiny
dbrakenhoff Nov 11, 2024
9517b7e
ruff
dbrakenhoff Nov 11, 2024
633bded
add inhom 1d element notebook
dbrakenhoff Nov 11, 2024
bf90ec1
Added boundary check on leaky wall example
mbakker7 Nov 12, 2024
5bf0c49
Add StripInhom elements
dbrakenhoff Dec 4, 2024
c6af896
add add_inhom to Aquifer class
dbrakenhoff Dec 4, 2024
5bd7ea9
force overloading of is_inside in AquiferData
dbrakenhoff Dec 4, 2024
ee58ac3
add is_inside to Aquifer class
dbrakenhoff Dec 4, 2024
d89c9b1
for RHS elements compute influence on xc (not xcin/xcout) and specify…
dbrakenhoff Dec 4, 2024
47f3831
add self.aq in LineSink1DBase
dbrakenhoff Dec 4, 2024
2dc2036
move initialize to ensure inhom elements are initialized prior to pop…
dbrakenhoff Dec 4, 2024
78a3073
add stripareasink element
dbrakenhoff Dec 4, 2024
c8756f8
reurn nb
dbrakenhoff Dec 4, 2024
74a7107
add examples
dbrakenhoff Dec 4, 2024
7d304bf
first attempt StripHstarInhom
dbrakenhoff Dec 5, 2024
a240601
first attempt StripHstarInhom
dbrakenhoff Dec 5, 2024
9ee8d5c
add plots for StripAreaSinkInhom and StripHstarInhom
dbrakenhoff Dec 5, 2024
b2b06c1
use super()
dbrakenhoff Dec 5, 2024
05cca3f
improve xsection plot for 1D elements
dbrakenhoff Dec 5, 2024
ab15a92
add StripHstarInhom example (not yet working)
dbrakenhoff Dec 5, 2024
73c4d76
Fix rhs in HeadDiffEquation
mbakker7 Dec 5, 2024
b6d6728
This notebook seems to run fine now
mbakker7 Dec 5, 2024
66ac4bf
Added check using numerical derivatives for stripinhom, 1 and 2 layers
mbakker7 Dec 6, 2024
bf6dbe0
Added strip river
mbakker7 Dec 8, 2024
483403d
Added comparison mf6 example river
mbakker7 Dec 9, 2024
bab8931
add optional name to AquiferData
dbrakenhoff Dec 10, 2024
2d4c284
make AquiferData repr more informative
dbrakenhoff Dec 10, 2024
8ccf9ff
make Aquifer repr more informative
dbrakenhoff Dec 10, 2024
e39f116
Add SimpleAquifer for cross-section models
dbrakenhoff Dec 10, 2024
daf39e5
convert inhom list to inhom dict
dbrakenhoff Dec 10, 2024
f591662
tag inhom elements in Element class
dbrakenhoff Dec 10, 2024
4d8de58
Add ModelXsection
dbrakenhoff Dec 10, 2024
ca0d20a
add disvecalongline
dbrakenhoff Dec 10, 2024
10b8572
avoid initializing aquifer in init?
dbrakenhoff Dec 10, 2024
49a2a48
remove unused addinhom method
dbrakenhoff Dec 10, 2024
9a0c690
improve model repr
dbrakenhoff Dec 10, 2024
f1f272d
remove inhomelements from element lists at start of intialize
dbrakenhoff Dec 10, 2024
2be2f31
add imports
dbrakenhoff Dec 10, 2024
87210d7
Improve 1D inhomogeneties
dbrakenhoff Dec 10, 2024
08cad59
improve inhom elements
dbrakenhoff Dec 10, 2024
f0b52b4
improve linesink1d
dbrakenhoff Dec 10, 2024
5926c32
improve Calibrate class
dbrakenhoff Dec 10, 2024
c45821f
leave out water level mark on plots
dbrakenhoff Dec 10, 2024
63e4683
update notebooks
dbrakenhoff Dec 10, 2024
2193c22
ruff
dbrakenhoff Dec 10, 2024
b697c6b
ruff
dbrakenhoff Dec 10, 2024
944e2f7
fix old calibrate notebooks with new layer specification method.
dbrakenhoff Dec 10, 2024
6280815
fix for pname in background aquifer
dbrakenhoff Dec 10, 2024
00bfa45
add inactive inhoms bounds check
dbrakenhoff Dec 11, 2024
3708554
add show_versions function
dbrakenhoff Dec 13, 2024
fcd788e
add show_versions function
dbrakenhoff Dec 13, 2024
a265ee1
allow passing kwargs to lmfit.minimize
dbrakenhoff Dec 13, 2024
0e6bde4
add aquifer parameter summary table
dbrakenhoff Dec 17, 2024
cc07811
allow old method of setting calibration parameters with deprecation w…
dbrakenhoff Dec 17, 2024
fa37d24
docstrings
dbrakenhoff Dec 17, 2024
b21c04f
docstrinsg
dbrakenhoff Dec 17, 2024
4f5fa60
add aquifer_summary method to Model classes
dbrakenhoff Dec 17, 2024
f7c680e
docs docs docs
dbrakenhoff Dec 17, 2024
aee20ec
added basic leastsq to fit
mbakker7 Dec 17, 2024
61097e6
first cut at howto xsection notebook
mbakker7 Dec 17, 2024
f79a934
Merge branch 'linesink1d' of https://github.com/mbakker7/ttim into li…
mbakker7 Dec 17, 2024
5730d58
fix xsection labels
dbrakenhoff Dec 18, 2024
cc55bb4
docstrings and add support for ml.plots.xsection() for cross-section …
dbrakenhoff Dec 18, 2024
06ba45c
minor style fixes
dbrakenhoff Dec 18, 2024
794826e
add howto tidal boundary notebook
dbrakenhoff Dec 18, 2024
29bf5ca
add a simpel watex example, calibrating aquifer parameters for a tida…
dbrakenhoff Dec 18, 2024
5b16771
add howtos to docs
dbrakenhoff Dec 18, 2024
2b3ad15
Update howto_xsection_model.ipynb
mbakker7 Dec 19, 2024
7e79c1a
Merge branch 'linesink1d' of https://github.com/mbakker7/ttim into li…
mbakker7 Dec 19, 2024
ce97262
fix from_lay to_lay
mbakker7 Dec 19, 2024
4b0127b
fix fit xsection multiple layers
mbakker7 Dec 19, 2024
27e7bae
fit by reference still needs a fix it seems
mbakker7 Dec 19, 2024
e2beb86
specify inhoms by tuple of names in calibrate
mbakker7 Dec 19, 2024
eec2a1a
added option x1=-np.inf, x2=+np.inf
mbakker7 Dec 19, 2024
91b1bc6
Rewrote howto tidal notebook
mbakker7 Dec 19, 2024
2955e39
removed leftover print statement
mbakker7 Dec 19, 2024
b7ef3ca
fixed sioux notebook
mbakker7 Dec 19, 2024
a47695b
ruff
mbakker7 Dec 19, 2024
457fcef
last ruff stuff
mbakker7 Dec 19, 2024
74d4ab3
Added explanations to the xsection howto
mbakker7 Dec 19, 2024
77bcb44
show warning when using old layer specification method
dbrakenhoff Dec 19, 2024
6eb0428
minor fixes to text in nb
dbrakenhoff Dec 19, 2024
c982386
minor fixes to text in nb
dbrakenhoff Dec 19, 2024
70c8f3a
final style/docs changes
dbrakenhoff Dec 19, 2024
7d5ca53
Merge pull request #81 from mbakker7/linesink1d
dbrakenhoff Dec 20, 2024
c86dbe3
up version for release
dbrakenhoff Dec 20, 2024
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7 changes: 6 additions & 1 deletion .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,12 @@ jobs:

- name: Run tests
run: |
py.test ./tests
pytest ./tests

- name: Numba coverage
run: |
NUMBA_DISABLE_JIT=1 pytest --cov-append ./tests/test_bessel.py


- name: Publish to coveralls.io
uses: coverallsapp/github-action@v2
Expand Down
302 changes: 302 additions & 0 deletions docs/01howto/howto_fluctuating_head_boundary.ipynb

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816 changes: 816 additions & 0 deletions docs/01howto/howto_xsection_model.ipynb

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6 changes: 4 additions & 2 deletions docs/01howto/index.rst
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@@ -1,10 +1,12 @@
How To Guides
=============

This section contains how to guides on building groundwater models with TTim.
This section contains how-to guides on building groundwater models with TTim.


.. toctree::
:maxdepth: 1

howto_pumpingtest
howto_pumpingtest
howto_xsection_model
howto_fluctuating_head_boundary
807 changes: 807 additions & 0 deletions docs/03examples/1d_elements.ipynb

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812 changes: 812 additions & 0 deletions docs/03examples/1d_inhom_elements.ipynb

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169 changes: 110 additions & 59 deletions docs/03examples/aem_ttim_sol.ipynb

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98 changes: 44 additions & 54 deletions docs/03examples/circareasink_example.ipynb

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89 changes: 58 additions & 31 deletions docs/03examples/compare_wells_linesink.ipynb

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2 changes: 2 additions & 0 deletions docs/03examples/data/mf6_ttim_xsec_riv1.txt
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1.000000000000000056e-01 2.000000000000000111e-01 3.000000000000000444e-01 4.000000000000000222e-01 5.000000000000000000e-01 5.999999999999999778e-01 6.999999999999999556e-01 7.999999999999999334e-01 8.999999999999999112e-01 9.999999999999998890e-01 1.099999999999999867e+00 1.199999999999999956e+00 1.300000000000000044e+00 1.400000000000000133e+00 1.500000000000000222e+00 1.600000000000000311e+00 1.700000000000000400e+00 1.800000000000000488e+00 1.900000000000000577e+00 2.000000000000000444e+00 2.100000000000000533e+00 2.200000000000000622e+00 2.300000000000000711e+00 2.400000000000000799e+00 2.500000000000000888e+00 2.600000000000000977e+00 2.700000000000001066e+00 2.800000000000001155e+00 2.900000000000001243e+00 3.000000000000001332e+00 3.100000000000001421e+00 3.200000000000001510e+00 3.300000000000001599e+00 3.400000000000001688e+00 3.500000000000001776e+00 3.600000000000001865e+00 3.700000000000001954e+00 3.800000000000002043e+00 3.900000000000002132e+00 4.000000000000001776e+00 4.100000000000001421e+00 4.200000000000001066e+00 4.300000000000000711e+00 4.400000000000000355e+00 4.500000000000000000e+00 4.599999999999999645e+00 4.699999999999999289e+00 4.799999999999998934e+00 4.899999999999998579e+00 5.000000000000000000e+00 5.099999999999999645e+00 5.199999999999999289e+00 5.299999999999998934e+00 5.399999999999998579e+00 5.499999999999998224e+00 5.599999999999997868e+00 5.699999999999997513e+00 5.799999999999997158e+00 5.899999999999996803e+00 5.999999999999996447e+00 6.099999999999996092e+00 6.199999999999995737e+00 6.299999999999995381e+00 6.399999999999995026e+00 6.499999999999994671e+00 6.599999999999994316e+00 6.699999999999993960e+00 6.799999999999993605e+00 6.899999999999993250e+00 6.999999999999992895e+00 7.099999999999992539e+00 7.199999999999992184e+00 7.299999999999991829e+00 7.399999999999991473e+00 7.499999999999991118e+00 7.599999999999990763e+00 7.699999999999990408e+00 7.799999999999990052e+00 7.899999999999989697e+00 7.999999999999989342e+00 8.099999999999988987e+00 8.199999999999988631e+00 8.299999999999988276e+00 8.399999999999987921e+00 8.499999999999987566e+00 8.599999999999987210e+00 8.699999999999986855e+00 8.799999999999986500e+00 8.899999999999986144e+00 8.999999999999985789e+00 9.099999999999985434e+00 9.199999999999985079e+00 9.299999999999984723e+00 9.399999999999984368e+00 9.499999999999984013e+00 9.599999999999983658e+00 9.699999999999983302e+00 9.799999999999982947e+00 9.899999999999982592e+00 1.000000000000000000e+01
1.159017167161723871e-01 1.951479064645816885e-01 2.544200683732626422e-01 3.010058575039881723e-01 3.387643380263183346e-01 3.700038247505645916e-01 3.962281425057884721e-01 4.184802117915192299e-01 4.375178703822047988e-01 4.539116951695496005e-01 4.681032487317482449e-01 4.804417418157326813e-01 4.912081921628182468e-01 5.006319634452204292e-01 5.089024569347744276e-01 5.161776045613933883e-01 5.225901836038792103e-01 5.282526066476443960e-01 5.332606184745887212e-01 5.376961926888864651e-01 5.416298314599240493e-01 5.451224126726975650e-01 5.482266888143778605e-01 5.509885143314257050e-01 5.534478587740685462e-01 5.556396491446045083e-01 5.575944747581775829e-01 5.593391804683748303e-01 5.608973685367534268e-01 5.622898252087923376e-01 5.635348848326486859e-01 5.646487418631130906e-01 5.656457191465746881e-01 5.665384993499099631e-01 5.673383251790988790e-01 5.680551730594405324e-01 5.686979041644691923e-01 5.692743960439513584e-01 5.697916575815853424e-01 5.702559295863320887e-01 5.706727729689822226e-01 5.710471461633391810e-01 5.713834732077194278e-01 5.716857036985120155e-01 5.719573656560053010e-01 5.722016121979379699e-01 5.724212627936292597e-01 5.726188397673240837e-01 5.727966006305248436e-01 5.729565667471094859e-01 6.890022654860391560e-01 7.683780756955553848e-01 8.277669509941412151e-01 8.744578507519991106e-01 9.123110091621650097e-01 9.436357909329928795e-01 9.699369632860055379e-01 9.922582928619395615e-01 1.011358377367433503e+00 1.027808476382900515e+00 1.042050765940109924e+00 1.054435008161286769e+00 1.065242716483590923e+00 1.074703700319298738e+00 1.083007761846358941e+00 1.090313193652035828e+00 1.096753097530023258e+00 1.102440178116962155e+00 1.107470443079265676e+00 1.111926102694645868e+00 1.115877872245733426e+00 1.119386821548318256e+00 1.122505875971647971e+00 1.125281045710751826e+00 1.127752440650453991e+00 1.129955114257956250e+00 1.131919769830818101e+00 1.133673354968975699e+00 1.135239564564473058e+00 1.136639268384368240e+00 1.137890876094886039e+00 1.139010650079591569e+00 1.140012974456728667e+00 1.140910587167013990e+00 1.141714780785140437e+00 1.142435576733606073e+00 1.143081876791956608e+00 1.143661595157213995e+00 1.144181773790982737e+00 1.144648683361460639e+00 1.145067911735885957e+00 1.145444441686290560e+00 1.145782719227390833e+00 1.146086713801202306e+00 1.146359971351087026e+00 1.146605661183011327e+00 1.146826617388872149e+00 1.147025375502409350e+00 1.147204204969099139e+00 1.147365137935320467e+00
3 changes: 3 additions & 0 deletions docs/03examples/data/mf6_ttim_xsec_riv2.txt
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