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Fix compats #130

Merged
merged 193 commits into from
Apr 13, 2024
Merged

Fix compats #130

merged 193 commits into from
Apr 13, 2024

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richardreeve
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Compatibility updates to dev

claireh93 and others added 30 commits August 1, 2021 21:23
@claireh93
Add pluto notebook for introductory examples.
b9fcaba
@claireh93
Finish intro pluto notebook.
b811668
@claireh93
Add Pluto example to README.
db711c1
@claireh93
Move HPC code into own folder.
237a6fa
@claireh93
Put warning for Africa_run examples.
5f1ba76
@claireh93
Update README.
de40a1d
@claireh93
Start interactive example of Africa run.
99e82fb
@claireh93
Updates to pluto examples
c379fe2
@claireh93
Merge branch 'main' into claireh93/pluto
35ad9c7
@claireh93
Apply suggestions from code review
8e1b58d 
Co-authored-by: Richard Reeve <git@richardreeve.net>
(cherry picked from commit d2c6a93)
@claireh93
Update dicts.
d5bc644
@claireh93
Add relative paths for EcoSISTEM in Manifests.
6c81375
@richardreeve
Extra dependencies for examples.
3df9538
@richardreeve
More dependencies for Worldclim examples.
afc33fb
@claireh93
Add testing of a file in the examples folder.
a377a61
@github-actions
CompatHelper: bump compat for "SimpleSDMLayers" to "0.8"
40bff4f
@claireh93
Turn africa examples into abstract circles.
ebcbefe
@claireh93
Add some package compats.
bee8821
@claireh93
Update units.
2332cb0
@claireh93
Fix bug in units.
49f1045
@claireh93
Another unit bug.
3c4f554
@claireh93
A few small updates to Africa example for paper.
625f61f
@claireh93
Small change to retrigger workflow.
3de8e4d
@claireh93
Fix canonical biodiversity test.
875a97a
@claireh93
Fix test examples.
265ea0b
@github-actions
CompatHelper: bump compat for "ArchGDAL" to "0.8"
cc24087
@claireh93
Remove RCall - not used for anything anymore!
23d553a
@claireh93
Remove RCall from examples - not used.
d1714ad
@claireh93
Update examples.
6aef1c5
@claireh93 @richardreeve
Update test/canonical/test_biodiversity.jl
cd14aa0 
Co-authored-by: Richard Reeve <git@richardreeve.net>
@coveralls
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coveralls commented Dec 14, 2023 •
edited by github-actions bot
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Pull Request Test Coverage Report for Build 7242284207

  • 5 of 6 (83.33%) changed or added relevant lines in 1 file are covered.
  • 1 unchanged line in 1 file lost coverage.
  • Overall coverage decreased (-0.02%) to 72.574%
Changes Missing Coverage Covered Lines Changed/Added Lines %
src/Biodiversity/Dist.jl 5 6 83.33%
Files with Coverage Reduction New Missed Lines %
src/Biodiversity/Dist.jl 1 89.19%
Totals Coverage Status
Change from base Build 5748824405: -0.02%
Covered Lines: 2588
Relevant Lines: 3566
💛 - Coveralls

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codecov bot commented Dec 14, 2023 •
edited
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Codecov Report

Attention: Patch coverage is 78.93570% with 95 lines in your changes are missing coverage. Please review.

Project coverage is 81.78%. Comparing base (dab5f22) to head (3516c42).

Files Patch % Lines
src/Biodiversity/Generate.jl 77.27% 30 Missing ⚠️
src/Biodiversity/HabitatUpdate.jl 50.00% 23 Missing ⚠️
src/Biodiversity/AbioticEnv.jl 90.47% 14 Missing ⚠️
src/Biodiversity/Energy.jl 87.01% 10 Missing ⚠️
ext/EcoSISTEMDataPipelineExt.jl 0.00% 5 Missing ⚠️
src/Biodiversity/Cache.jl 0.00% 4 Missing ⚠️
ext/EcoSISTEMERAExt.jl 0.00% 3 Missing ⚠️
src/Biodiversity/Dist.jl 83.33% 3 Missing ⚠️
src/Biodiversity/DiversitySet.jl 0.00% 3 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##              dev     #130      +/-   ##
==========================================
+ Coverage   80.62%   81.78%   +1.16%     
==========================================
  Files          43       46       +3     
  Lines        2973     3064      +91     
==========================================
+ Hits         2397     2506     +109     
+ Misses        576      558      -18

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

richardreeve and others added 24 commits December 18, 2023 00:45
@richardreeve
Fix compats in Project.toml
363c870
@richardreeve
Updates to manifests
07e5c7c
@richardreeve
Fix docs
2eb0bd3
@richardreeve
Fix docs
ac32bb1
@richardreeve
Minor version updates
3b524a4
@richardreeve
Add modules to tests
2667b97
@richardreeve
Put tests into separate modules
6baa829
@richardreeve
Update workflows
1d95c68
@richardreeve
Update docs
887fdf2
@richardreeve
Doc cleaning and version bump
9047058
@richardreeve
Fix doc generation
b57172c
@richardreeve
Add in NEWS updates
c8f23c8
@richardreeve
Update workflows
a021f54
@richardreeve
Update codecov action and use token
404ad93
@richardreeve
Formatting cleanup
17b1a20
@richardreeve
Merge pull request #124 from EcoJulia/rr/testing
0ce4b7f
@richardreeve
Update Pluto notebooks
99ea0e2
@richardreeve
No point in caching for nightly runs
d4c8e18
@richardreeve
Remove Pluto dependency and better document use
820148d
@richardreeve
Merge pull request #134 from EcoJulia/rr/pluto
a746cf5 
Update Pluto notebooks
@richardreeve
Merge commit '404ad930898aede24d3aad9df59473fc39714c4c' into rr/compa…
dd4129a 
…t and update Julia and package versions

# Conflicts:
#	.github/workflows/testing.yaml
#	CONTRIBUTING.md
#	LICENSE.md
#	Project.toml
#	README.md
#	docs/Manifest.toml
#	docs/make.jl
#	docs/src/africa.md
#	docs/src/basics.md
#	docs/src/simulation-jl.md
#	examples/Biodiversity/Africa_run.jl
#	examples/Biodiversity/CirrusComp.jl
#	examples/Biodiversity/CirrusDiversity.jl
#	examples/Biodiversity/CirrusExample.jl
#	examples/Biodiversity/CirrusMPIRun.jl
#	examples/Biodiversity/CirrusRunUK.jl
#	examples/Biodiversity/CirrusSmallMPIRun.jl
#	examples/Biodiversity/CirrusSmallNonMPIRun.jl
#	examples/Biodiversity/CirrusSmallRun.jl
#	examples/Biodiversity/MPItest.jl
#	examples/Biodiversity/Project.toml
#	examples/Biodiversity/UK_mpi_cirrus1x1x36.bash
#	examples/Biodiversity/UK_mpi_cirrus20x2x34.bash
#	examples/Biodiversity/Worldclim_africa.jl
#	examples/Biodiversity/mpi_cirrus1x1x36.bash
#	examples/Biodiversity/mpi_cirrus1x2x18.bash
#	examples/Biodiversity/mpi_cirrus1x2x34.bash
#	examples/Biodiversity/mpi_cirrus1x2x36.bash
#	examples/Biodiversity/mpi_cirrus20x2x34.bash
#	examples/Biodiversity/mpi_cirrus4x1x36.bash
#	examples/Biodiversity/mpi_cirrus4x2x18.bash
#	examples/Biodiversity/mpi_cirrus4x2x34.bash
#	examples/CirrusComp.jl
#	examples/CirrusDiversity.jl
#	examples/CirrusExample.jl
#	examples/CirrusMPIRun.jl
#	examples/CirrusRunUK.jl
#	examples/CirrusSmallMPIRun.jl
#	examples/CirrusSmallNonMPIRun.jl
#	examples/CirrusSmallRun.jl
#	examples/HPC/CirrusComp.jl
#	examples/HPC/CirrusDiversity.jl
#	examples/HPC/CirrusExample.jl
#	examples/HPC/CirrusMPIRun.jl
#	examples/HPC/CirrusRunUK.jl
#	examples/HPC/CirrusSmallMPIRun.jl
#	examples/HPC/CirrusSmallNonMPIRun.jl
#	examples/HPC/CirrusSmallRun.jl
#	examples/HPC/MPItest.jl
#	examples/HPC/UK_mpi_cirrus1x1x36.bash
#	examples/HPC/UK_mpi_cirrus20x2x34.bash
#	examples/HPC/mpi_cirrus1x1x36.bash
#	examples/HPC/mpi_cirrus1x2x18.bash
#	examples/HPC/mpi_cirrus1x2x34.bash
#	examples/HPC/mpi_cirrus1x2x36.bash
#	examples/HPC/mpi_cirrus20x2x34.bash
#	examples/HPC/mpi_cirrus4x1x36.bash
#	examples/HPC/mpi_cirrus4x2x18.bash
#	examples/HPC/mpi_cirrus4x2x34.bash
#	examples/MPItest.jl
#	examples/Manifest.toml
#	examples/UK_mpi_cirrus1x1x36.bash
#	examples/UK_mpi_cirrus20x2x34.bash
#	examples/mpi_cirrus1x1x36.bash
#	examples/mpi_cirrus1x2x18.bash
#	examples/mpi_cirrus1x2x34.bash
#	examples/mpi_cirrus1x2x36.bash
#	examples/mpi_cirrus20x2x34.bash
#	examples/mpi_cirrus4x1x36.bash
#	examples/mpi_cirrus4x2x18.bash
#	examples/mpi_cirrus4x2x34.bash
#	src/Biodiversity/Dist.jl
#	src/Biodiversity/Generate.jl
#	src/Biodiversity/Habitats.jl
#	src/Biodiversity/MPIEcosystem.jl
#	src/Biodiversity/MPIGenerate.jl
#	src/Biodiversity/MPILandscape.jl
#	src/Biodiversity/SpeciesList.jl
#	src/ClimatePref/ClimatePref.jl
#	src/ClimatePref/ERA5_tools.jl
#	src/ClimatePref/Plotting.jl
#	src/ClimatePref/ReadData.jl
#	src/EcoSISTEM.jl
#	src/Ecosystem.jl
#	src/Helper.jl
#	src/plotting.jl
#	test/canonical/test_biodiversity.jl
#	test/examples/RunSim.jl
#	test/test_AbioticEnv.jl
#	test/test_Ecosystem.jl
#	test/test_Generate.jl
#	test/test_Helper.jl
#	test/test_ReadData.jl
@richardreeve
Merge commit '0ce4b7fc889d8ecdf8c4990d493a00cb23a78abd' into rr/compa…
8db5f0b 
…t and reformat code.

# Conflicts:
#	CONTRIBUTING.md
#	Project.toml
#	docs/Manifest.toml
#	docs/make.jl
#	docs/src/simulation-jl.md
#	examples/Biodiversity/Africa_run.jl
#	examples/Biodiversity/CirrusComp.jl
#	examples/Biodiversity/CirrusDiversity.jl
#	examples/Biodiversity/CirrusExample.jl
#	examples/Biodiversity/CirrusMPIRun.jl
#	examples/Biodiversity/CirrusRunUK.jl
#	examples/Biodiversity/CirrusSmallMPIRun.jl
#	examples/Biodiversity/CirrusSmallNonMPIRun.jl
#	examples/Biodiversity/CirrusSmallRun.jl
#	examples/Biodiversity/MPItest.jl
#	examples/Biodiversity/UK_mpi_cirrus1x1x36.bash
#	examples/Biodiversity/UK_mpi_cirrus20x2x34.bash
#	examples/Biodiversity/Worldclim_africa.jl
#	examples/Biodiversity/exampleModels.jl
#	examples/Biodiversity/mpi_cirrus1x1x36.bash
#	examples/Biodiversity/mpi_cirrus1x2x18.bash
#	examples/Biodiversity/mpi_cirrus1x2x34.bash
#	examples/Biodiversity/mpi_cirrus1x2x36.bash
#	examples/Biodiversity/mpi_cirrus20x2x34.bash
#	examples/Biodiversity/mpi_cirrus4x1x36.bash
#	examples/Biodiversity/mpi_cirrus4x2x18.bash
#	examples/Biodiversity/mpi_cirrus4x2x34.bash
#	examples/CirrusComp.jl
#	examples/CirrusDiversity.jl
#	examples/CirrusExample.jl
#	examples/CirrusMPIRun.jl
#	examples/CirrusRunUK.jl
#	examples/CirrusSmallMPIRun.jl
#	examples/CirrusSmallNonMPIRun.jl
#	examples/CirrusSmallRun.jl
#	examples/HPC/CirrusComp.jl
#	examples/HPC/CirrusDiversity.jl
#	examples/HPC/CirrusExample.jl
#	examples/HPC/CirrusMPIRun.jl
#	examples/HPC/CirrusRunUK.jl
#	examples/HPC/CirrusSmallMPIRun.jl
#	examples/HPC/CirrusSmallNonMPIRun.jl
#	examples/HPC/CirrusSmallRun.jl
#	examples/HPC/MPItest.jl
#	examples/HPC/UK_mpi_cirrus1x1x36.bash
#	examples/HPC/UK_mpi_cirrus20x2x34.bash
#	examples/HPC/mpi_cirrus1x1x36.bash
#	examples/HPC/mpi_cirrus1x2x18.bash
#	examples/HPC/mpi_cirrus1x2x34.bash
#	examples/HPC/mpi_cirrus1x2x36.bash
#	examples/HPC/mpi_cirrus20x2x34.bash
#	examples/HPC/mpi_cirrus4x1x36.bash
#	examples/HPC/mpi_cirrus4x2x18.bash
#	examples/HPC/mpi_cirrus4x2x34.bash
#	examples/MPItest.jl
#	examples/Manifest.toml
#	examples/Project.toml
#	examples/UK_mpi_cirrus1x1x36.bash
#	examples/UK_mpi_cirrus20x2x34.bash
#	examples/mpi_cirrus1x1x36.bash
#	examples/mpi_cirrus1x2x18.bash
#	examples/mpi_cirrus1x2x34.bash
#	examples/mpi_cirrus1x2x36.bash
#	examples/mpi_cirrus20x2x34.bash
#	examples/mpi_cirrus4x1x36.bash
#	examples/mpi_cirrus4x2x18.bash
#	examples/mpi_cirrus4x2x34.bash
#	ext/EcoSISTEMDataPipelineExt.jl
#	ext/EcoSISTEMERAExt.jl
#	ext/EcoSISTEMMPIExt.jl
#	notebooks/InteractiveAfrica.jl
#	notebooks/Introduction.jl
#	src/Biodiversity/AbioticEnv.jl
#	src/Biodiversity/AdditionalDiversity.jl
#	src/Biodiversity/Cache.jl
#	src/Biodiversity/Dist.jl
#	src/Biodiversity/Energy.jl
#	src/Biodiversity/Generate.jl
#	src/Biodiversity/HabitatUpdate.jl
#	src/Biodiversity/Habitats.jl
#	src/Biodiversity/Landscape.jl
#	src/Biodiversity/MPIEcosystem.jl
#	src/Biodiversity/MPIGenerate.jl
#	src/Biodiversity/MPILandscape.jl
#	src/Biodiversity/Phylo.jl
#	src/Biodiversity/Scenarios.jl
#	src/Biodiversity/SpeciesList.jl
#	src/Biodiversity/Traitfuns.jl
#	src/Biodiversity/Traits.jl
#	src/ClimatePref/ClimatePref.jl
#	src/ClimatePref/ClimateTypes.jl
#	src/ClimatePref/DataCleaning.jl
#	src/ClimatePref/ERA5_tools.jl
#	src/ClimatePref/ExtractClimate.jl
#	src/ClimatePref/Plotting.jl
#	src/ClimatePref/ReadData.jl
#	src/EcoSISTEM.jl
#	src/Ecosystem.jl
#	src/Helper.jl
#	src/plotting.jl
#	src/units.jl
#	test/SmallMPItest.jl
#	test/canonical/test_biodiversity.jl
#	test/examples/CreateEco.jl
#	test/examples/RunSim.jl
#	test/examples/Scenarios.jl
#	test/runtests.jl
#	test/test_AbioticEnv.jl
#	test/test_AdditionalDiversity.jl
#	test/test_Ecosystem.jl
#	test/test_Energy.jl
#	test/test_Generate.jl
#	test/test_HabitatUpdate.jl
#	test/test_Helper.jl
#	test/test_MPI.jl
#	test/test_Movement.jl
#	test/test_ReadData.jl
#	test/test_Scenario.jl
#	test/test_SpeciesList.jl
#	test/test_Traitfuns.jl
@richardreeve
Merge branch 'main' into rr/compat.
bc857f4 
# Conflicts:
#	docs/Manifest.toml
#	examples/Biodiversity/Manifest.toml
#	notebooks/InteractiveAfrica.jl
#	notebooks/Introduction.jl
@richardreeve
Test fixes.
3516c42
@richardreeve richardreeve merged commit 11c2baa into dev Apr 13, 2024
8 of 9 checks passed
@richardreeve richardreeve deleted the rr/compat branch April 13, 2024 05:04
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4 participants
@richardreeve @coveralls @claireh93 @JuliaRegistrator