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Feature/introduce biota #83

Merged
merged 123 commits into from
Apr 13, 2022
Merged

Feature/introduce biota #83

merged 123 commits into from
Apr 13, 2022

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Carsopre
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DzimbaS and others added 30 commits March 16, 2022 09:31
@DzimbaS
new constants class
1d216af
@DzimbaS
new class colonization start
ef033b1
@DzimbaS
new class vegetation
93d37df
@DzimbaS
changes to veg_model
46039f5
@deboradta
created get_hydromorphodynamics and import vegetation model
99777ae
@deboradta
base_simulation.py - created initiate_hydromorphodynamics
3bd62d6 
delft3d.py - created update_hydromorphodynamics
@DzimbaS
Addition of vegetation characteristics method, growth and mortality c…
36f84b5 
…lasses. New veg_base_simulation.
@DzimbaS
Merge branch 'saltmarsh_debora' into SaltMarsh_Sarah
4238dd9 
# Conflicts:
#	src/core/bio_process/colonisation.py
@DzimbaS
Addition of vegetation characteristics method, growth and mortality c…
69e8e77 
…lasses. New veg_base_simulation.
@DzimbaS
add class Hydro_Morphodynamics, process in veg_base_simulation.py
fac4a49
@DzimbaS
changes to Hydro_Morphodynamics, process in veg_base_simulation.py
7a49900
@DzimbaS
changes to Hydro_Morphodynamics, process in veg_base_simulation.py, p…
df2a4d7 
…rogress in the veg bio-processes
@DzimbaS
changes to Hydro_Morphodynamics, process in veg_base_simulation.py, p…
d0ab434 
…rogress in the veg bio-processes
@DzimbaS
progress in mortality
5bbb8b4
@deboradta
output
66f7f72
@deboradta
updates to output
428c137
@DzimbaS
progress in mortality
fcbcfb9
@deboradta
Merge branch 'SaltMarsh_Sarah' into saltmarsh_debora
6aa5d37
@DzimbaS
Merge branch 'saltmarsh_debora' into SaltMarsh_Sarah
95d1c0f
@DzimbaS
account for maxAge vegetation in veg_growth
62727fa
@deboradta
Merge branch 'SaltMarsh_Sarah' into saltmarsh_debora
11b4004
@DzimbaS
account for maxAge vegetation in veg_growth
d5d4fc8
@deboradta
Merge branch 'SaltMarsh_Sarah' into saltmarsh_debora
a119170
@deboradta
updates to output
2d85f97
@DzimbaS
changes after debugging
c4e1589
@DzimbaS
simtest
eadb6ec
@DzimbaS
veg_delft3D_simulation file
861e7b8
@DzimbaS
changes to veg_model
967bd69
@deboradta
updates veg_model
15e4cd9
@DzimbaS
json file for constants and changes to constants class
5f67647
Carsopre and others added 26 commits April 12, 2022 21:06
@Carsopre
autoformat: isort & black
371ca4e
@DzimbaS
fix bugs in veg_mortality.py
b5e7467
@DzimbaS
autoformat: isort & black
04f1f38
@Carsopre
refactor(coral_simulation.py): Created intermediate coral simulation …
3625fdc 
…class
@Carsopre
refactor(src/coral): Extracted coral model and simulation from the co…
115e0fe 
…re module
@Carsopre
refactor(coral/model/coral_constants.py;coral/output/coral_output_wra…
8349d22 
…pper.py): Moved out coral constants and output_wrapper
@Carsopre
refactor(coral/output;core/output): Split coral from core output at p…
f6e1f6c 
…arameters and model levels
@Carsopre
Merge branch 'feature/introduce_biota' of https://github.com/Deltares…
bed10c3 
…/NBSDynamics into feature/introduce_biota
@Carsopre
chore(sm_plot.py): Moved custom script to tools
56c739b
@Carsopre
Merge branch 'feature/small-hackathon' into feature/introduce_biota
01413b8
@Carsopre
refactor(src/vegetation/model/veg_constants.py): Refactored the way w…
ac019ce 
…e are loading vegetation constants
@Carsopre
refactor(base_output): Renamed concrete output models to match their …
320e09a 
…biota type
@Carsopre
test(test/core/output/test_output_model.py): Adapted failing test to …
679a011 
…new structure
@Carsopre
autoformat: isort & black
b16a161
@Carsopre
Merge branch 'master' into feature/introduce_biota
da64d8e
@Carsopre
chore(master): Fixed some merge issues from master
c64839c
@Carsopre
chore(veg_mortality.py): Ensured fix was in the branch, added a few p…
8f81e15 
…ytypes
@Carsopre
Merge branch 'feature/introduce_biota' of https://github.com/Deltares…
e563107 
…/NBSDynamics into feature/introduce_biota
@Carsopre
autoformat: isort & black
cfab405
@Carsopre
refactor(coral/bio_process): Moved all from core all coral bioprocesses
8a07923
@Carsopre
Merge branch 'feature/introduce_biota' of https://github.com/Deltares…
57ced43 
…/NBSDynamics into feature/introduce_biota
@Carsopre
refactor(biota_models): Grouped vegetation and coral into biota_model…
e05d3b4 
…s parallel to core
@Carsopre
autoformat: isort & black
8d8ba44
@Carsopre
docs(../README.md;../docs/index.md): Updated main readme
c2214ad
@Carsopre
Merge branch 'feature/introduce_biota' of https://github.com/Deltares…
829bc60 
…/NBSDynamics into feature/introduce_biota
@Carsopre
docs(docs/reference): Updated code reference to mirror the src structure
709ba60
@sonarqubecloud
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SonarCloud Quality Gate failed.    Quality Gate failed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 97 Code Smells

64.8% 64.8% Coverage
2.8% 2.8% Duplication

@Carsopre Carsopre marked this pull request as ready for review April 13, 2022 11:31
@Carsopre Carsopre merged commit d160d8d into master Apr 13, 2022
@Carsopre Carsopre deleted the feature/introduce_biota branch April 13, 2022 11:32
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3 participants
@Carsopre @DzimbaS @deboradta