Fix compats #130

richardreeve · 2023-12-14T04:09:10Z

Compatibility updates to dev

Co-authored-by: Richard Reeve <[email protected]> (cherry picked from commit d2c6a93)

Co-authored-by: Richard Reeve <[email protected]>

coveralls · 2023-12-14T04:31:06Z

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
Change from base Build 5748824405:	-0.02%
Covered Lines:	2588
Relevant Lines:	3566

💛 - Coveralls

codecov · 2023-12-14T04:32:35Z

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.
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Update Pluto notebooks

…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

…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

# Conflicts: # docs/Manifest.toml # examples/Biodiversity/Manifest.toml # notebooks/InteractiveAfrica.jl # notebooks/Introduction.jl

claireh93 and others added 30 commits August 1, 2021 21:23

Add pluto notebook for introductory examples.

b9fcaba

Finish intro pluto notebook.

b811668

Add Pluto example to README.

db711c1

Move HPC code into own folder.

237a6fa

Put warning for Africa_run examples.

5f1ba76

Update README.

de40a1d

Start interactive example of Africa run.

99e82fb

Updates to pluto examples

c379fe2

Merge branch 'main' into claireh93/pluto

35ad9c7

Apply suggestions from code review

8e1b58d

Co-authored-by: Richard Reeve <[email protected]> (cherry picked from commit d2c6a93)

Update dicts.

d5bc644

Add relative paths for EcoSISTEM in Manifests.

6c81375

Extra dependencies for examples.

3df9538

More dependencies for Worldclim examples.

afc33fb

Add testing of a file in the examples folder.

a377a61

CompatHelper: bump compat for "SimpleSDMLayers" to "0.8"

40bff4f

Turn africa examples into abstract circles.

ebcbefe

Add some package compats.

bee8821

Update units.

2332cb0

Fix bug in units.

49f1045

Another unit bug.

3c4f554

A few small updates to Africa example for paper.

625f61f

Small change to retrigger workflow.

3de8e4d

Fix canonical biodiversity test.

875a97a

Fix test examples.

265ea0b

CompatHelper: bump compat for "ArchGDAL" to "0.8"

cc24087

Remove RCall - not used for anything anymore!

23d553a

Remove RCall from examples - not used.

d1714ad

Update examples.

6aef1c5

Update test/canonical/test_biodiversity.jl

cd14aa0

Co-authored-by: Richard Reeve <[email protected]>

richardreeve added 2 commits December 14, 2023 00:45

Merge branch 'main' into rr/testing

8d54853

Fix compats

261cb13

richardreeve and others added 24 commits December 18, 2023 00:45

Fix compats in Project.toml

363c870

Updates to manifests

07e5c7c

Fix docs

2eb0bd3

Fix docs

ac32bb1

Minor version updates

3b524a4

Add modules to tests

2667b97

Put tests into separate modules

6baa829

Update workflows

1d95c68

Update docs

887fdf2

Doc cleaning and version bump

9047058

Fix doc generation

b57172c

Add in NEWS updates

c8f23c8

Update workflows

a021f54

Update codecov action and use token

404ad93

Formatting cleanup

17b1a20

Merge pull request #124 from EcoJulia/rr/testing

0ce4b7f

Update Pluto notebooks

99ea0e2

No point in caching for nightly runs

d4c8e18

Remove Pluto dependency and better document use

820148d

Merge pull request #134 from EcoJulia/rr/pluto

a746cf5

Update Pluto notebooks

Merge branch 'main' into rr/compat.

bc857f4

# Conflicts: # docs/Manifest.toml # examples/Biodiversity/Manifest.toml # notebooks/InteractiveAfrica.jl # notebooks/Introduction.jl

Test fixes.

3516c42

richardreeve merged commit 11c2baa into dev Apr 13, 2024
8 of 9 checks passed

richardreeve deleted the rr/compat branch April 13, 2024 05:04

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Fix compats #130

Fix compats #130

richardreeve commented Dec 14, 2023

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Fix compats #130

Fix compats #130

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Pull Request Test Coverage Report for Build 7242284207

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