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Towards parcels v3.0 #1426

Merged
merged 227 commits into from
Oct 10, 2023
Merged

Towards parcels v3.0 #1426

merged 227 commits into from
Oct 10, 2023

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erikvansebille
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@erikvansebille erikvansebille commented Sep 8, 2023 •
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This PR collects all the changes that will be combined in Parcels v3.0. They include

And some general code cleanups (renaming of files, fixing Deprecation Warnings)

Still to add/fix/include

erikvansebille and others added 30 commits January 4, 2022 08:36
@erikvansebille
Fixing a bug in OperationCode.StopExecution
d1b6c7f
@erikvansebille
Adding unit test for sampling particle.xi
1403293 
This addresses #1145
@erikvansebille
Merge branch 'master' into xi_in_particlefile
747f889
@erikvansebille
Merge branch 'master' into xi_in_particlefile
52da1c0
@erikvansebille
Update test_kernel_execution.py
762c72e
@erikvansebille
Adding support for dcoord in JIT and Scipy mode
74d6c80
@erikvansebille
Renaming to particle_dlon, particle_dlat etc for easier use
294e787
@erikvansebille
Merge branch 'master' into bugfix_OperationCodeStopExecution
796c57f
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
e6e505b 
for more information, see https://pre-commit.ci
@erikvansebille
Merge branch 'master' into vectorial_summing_particle_moves_at_end_of…
57f4a4c 
…_kernel_list
@erikvansebille
Also using particle_dlon and particle_dlat in advectiondiffusion kernels
b826fef
@erikvansebille
Making sure extra kernels are only compiled once in scipy
ec9ead4
@erikvansebille
Making sure particle.dt can't get too small (zero) in RK45
830b3a9
@erikvansebille
Using explicit Euler Forward in Recovery Kernel
caf7418 
As calling functions is not possible anymore with new implementation
@erikvansebille
Merge branch 'master' into vectorial_summing_zarr_approach
a8b5745
@erikvansebille
Adding unit test for field sampling
eb9e54f
@erikvansebille
Removing Interpolation and sampling on time-varying Fields from tutor…
737d90d 
…ial_interpolation
@erikvansebille
Support for vectorial summing in Analytical Advection kernel
7ffb0d2
@erikvansebille
Removing write_ondelete option from particlefiel
c6669c0 
As it was not advertised/used, and with the new lazy loading schemes is not needed. It does complicate the code significantly
@erikvansebille
Adding extra variables lon_towrite, lat_towrite and depth_towrite
32ad39c
@erikvansebille
Minor fixes to code
84a9bf0
@erikvansebille
Fixing time-stepping for writing vectorial form
5c865fc
@erikvansebille
Fixing initialisation and printing of towrite variables
4d2f7f9
@erikvansebille
Changing AdvectionAnalytical to use particle.lon instead of dlon
2bff74c
@erikvansebille
Adding time_towrite to Particle
1ecf030
@erikvansebille
Updating timing of output in pset.execute
72a69e7
@erikvansebille
First attempt at rewrite of particle loop and Recovery-Kernels in scipy
3e1e6a3
@erikvansebille
Fixing particle.time updates in the JIT loop
84a8fa7
@erikvansebille
First update to codeconverter to remove RecoveryKernels
811c406
@erikvansebille
Fixing return error code in codeconverter
e4630ed
erikvansebille and others added 28 commits October 4, 2023 09:49
@erikvansebille
Fixing broken link in index.html
94158f4
@erikvansebille
Update tutorial_kernelloop.ipynb
3eb8957
@erikvansebille
Renumbering statuscodes so that they are increasing
b0fb29f
@erikvansebille
Merge pull request #1439 from OceanParcels/renumbering_statuscodes
bd9838b 
Renumbering statuscodes so that they are increasing
@erikvansebille
Merge branch 'v3.0' into xi_in_particlefile
71246ea
@erikvansebille
Simplifying ParticleNode in codegenerator
e7f8131
@erikvansebille
Fixing error message when particle Variable not known
4791b08
@erikvansebille
Repeat message that functions can be added to the list of kernels
014e14d
@erikvansebille
Removing stray debug message
d8eca54
@erikvansebille
Implement JIT version of sampling particle.xi on specific grid number
010b6c9
@erikvansebille
Fixing type-os in comments
99fe755
@erikvansebille
Changing neighbor and color to American English throughout
8e73e39
@erikvansebille
Cleaning up arguments of kernel.execute_python
f3c2231
@erikvansebille
Merge pull request #1147 from OceanParcels/xi_in_particlefile
ce3d8bd 
Storing particle.xi in output files
@erikvansebille
Fixing pydocstyle error
d5105a7
@erikvansebille
Using American English spelling in tutorials
ffa5a42
@erikvansebille
Changing to American spelling for analyze
6420c1a
@erikvansebille
Merge pull request #1438 from OceanParcels/codecleanups_v3
06709a0 
More small codecleanups in preparation for parcels v3
@erikvansebille
Simplifying binder environment file
ee65f68 
As typical binder user does not need full mpi and scikitlearn support
@erikvansebille
Merge pull request #1441 from OceanParcels/simplifying_binder_environ…
d9b7b44 
…ment

Simplifying binder environment file
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate
7e5b10e 
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0)
- [github.com/pycqa/flake8: 6.0.0 → 6.1.0](PyCQA/flake8@6.0.0...6.1.0)
@erikvansebille
Updating all tutorials with latest conda environment and parcels v3 code
f8cfabf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
b18b743 
for more information, see https://pre-commit.ci
@erikvansebille
Merge pull request #1442 from OceanParcels/pre-commit-ci-update-config
2f721d1 
[pre-commit.ci] pre-commit autoupdate
@erikvansebille
Updating stuck particles examples
d0cb411
@erikvansebille
Updating final few documentation tutorials that can be rerun
e4338aa
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
4d4b5eb 
for more information, see https://pre-commit.ci
@erikvansebille
Merge pull request #1443 from OceanParcels/rerunning_notebooks
8597833 
Updating all tutorials with latest conda environment and parcels v3 code
@erikvansebille erikvansebille merged commit 3662aa5 into master Oct 10, 2023
@erikvansebille erikvansebille deleted the v3.0 branch October 10, 2023 13:12
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2 participants
@erikvansebille @michaeldenes