PlantSimEngine v0.13.2

Merged pull requests: - Fix printing of ModelList (#150) (@VEZY)

Closed issues: - Don't print the graph if too many models (#109) - Information display, printing (#133) - Regression in benchmark for ModelList (#145)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] 11 months ago

PlantSimEngine v0.13.1

Diff since v0.13.0

Patch

Fixing performance regressions:

Add dependency graph into model list by @VEZY in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/149
Fixing #146: performance regression by @VEZY in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/147

Full Changelog: https://github.com/VirtualPlantLab/PlantSimEngine.jl/compare/v0.13.0...v0.14.0

Merged pull requests: - Fixing #146: performance regression (#147) (@VEZY) - Add dependency graph into model list (#149) (@VEZY)

Closed issues: - Add dependency tree in the ModelList (#29) - Change default output structure (#123) - Improve performance of inputs pre-allocation step in run! (#146) - Improve performance of dependency graph creation (#148)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] 11 months ago

PlantSimEngine - v0.13.0

PlantSimEngine v0.13.0

Diff since v0.12.0

Breaking changes

PRs: * Multiscale outputs struct rework by @Samuel-amap in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/134 * Dev by @Samuel-amap in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/137

Summary: The outputs are now stored differently during the simulation for better performance. You now need to call convert_outputs on the outputs of the simulation, e.g. if the simulation outputs are stored outputs_sim:

julia df_dict = convert_outputs(outputs_sim, DataFrame)

df_dict will be a dictionary of dataframes, with the scale as the key and the results for this scale as the value.

Full Changelog: https://github.com/VirtualPlantLab/PlantSimEngine.jl/compare/v0.12.0...v0.13.0

Merged pull requests: - Multiscale outputs struct rework (#134) (@Samuel-amap) - Dev (#137) (@Samuel-amap)

Closed issues: - ModelList -> better manage models that takes values from the previous time-step (#85) - BoundsError with a single model and several Weather timesteps (#86) - XPalm Github action for testing (#90) - Non-obvious Julia errors (#92) - Documentation improvements (#93) - Collapse similar codepaths, and create a mapping for single-scale simulations (#101) - No outputs when simulating a mapping with one meteo timestep (#105) - Multiscale : outputs not saved when dependency graph only has one depth level (#111)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] about 1 year ago

PlantSimEngine - PlantSimEngine v0.12.0

Release notes:

Breaking changes

Most of the main features are breaking changes. You can update by simply updating function names and kwargs as mentioned in these release notes, or read the new documentation.

Expect an upcoming release of downstream packages PlantBiophysics and XPalm to update to the API changes.

Main features

Added a means of filtering outputs in ModelList mode, to align with multi-scale simulations, via a tracked_outputs keyword argument, changing the simulation output structure
Major documentation overhaul, with several more pages, extended examples/tutorials, a multi-scale toy plant example with PlantGeom 3D visualization, additional explanations on subtler aspects of simulations, specific pages explaining how to work with data or troubleshoot issues...

API changes

Removed Multi-object parallelisation, to be potentially reintroduced later
Renamed the outputs kwarg to tracked_outputs in multi-scale mode
Handle corner cases where user-requested outputs were empty in multi-scale mode, or missing weather data
Renamed some of the outputs functions to convert_outputs, for clarity
Changed mapping kwarg to mapped_variables for MultiScaleModel objects
The run! function returns the output data instead of the whole GraphSimulation in multi-scale mode
Some run! function default behaviours are changed to be made consistent between single- and multi-scale.
A couple of warnings may have changed.

CI-related changes

Added benchmarks and performance-related tests, as well as a Github Action tracking changes over time. More work needed.
Added a test to validate output filtering changes, that combines a meteo, a modellist and a list of outputs and runs it in ModelList mode, then converts to multiscale and compares results
Added a naive test that tries different meteo/modellist-mapping/outputs combos and expects either a successful run! or a dimensional mismatch

Fixed issues

86, #105, #111

Generated release notes:

What's Changed

Adding benchmarks and extra sanity checks (memory allocations, type stability, ...) by @Samuel-amap in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/115
Remove multi-object parallelisation by @Samuel-amap in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/127
Benchmark tracking via Github action by @Samuel-amap in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/129
Outputs filtering by @Samuel-amap in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/128

Full Changelog: https://github.com/VirtualPlantLab/PlantSimEngine.jl/compare/v0.11.3...v0.12.0

Scientific Software - Peer-reviewed - Julia
Published by Samuel-amap about 1 year ago

PlantSimEngine - v0.11.3

PlantSimEngine v0.11.3

Diff since v0.11.2

Merged pull requests: - Incomplete working version of a modellist to mapping conversion function (#122) (@Samuel-amap)

Closed issues: - API : enable passing in a vector providing values per timestep in multi-scale modelling (#117)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 1 year ago

PlantSimEngine - v0.11.2

PlantSimEngine v0.11.2

Diff since v0.11.1

Merged pull requests: - Add corner case tests (#110) (@Samuel-amap) - Update save_results.jl (#112) (@VEZY) - Bump codecov/codecov-action from 4 to 5 (#113) (@dependabot[bot])

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 1 year ago

PlantSimEngine - v0.11.1

PlantSimEngine v0.11.1

Diff since v0.11.0

Merged pull requests: - Fix issue of overspecialisation of outputs Dict of variables requested by the user (#104) (@Samuel-amap)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 1 year ago

PlantSimEngine - v0.11.0

PlantSimEngine v0.11.0

Diff since v0.10.3

Bug fixes

Fixes many bugs in the computation of the dependency graph. See #83 for more details.

Merged pull requests: - Multiscale hard dependencies (#83) (@VEZY)

Closed issues: - Check on model dependency not working (#77) - Incorrect state on nested HardDependencyNode if the child is created before the parent (#99)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 1 year ago

PlantSimEngine - v0.10.3

PlantSimEngine v0.10.3

Diff since v0.10.2

Bug fixes

Allow requiring outputs for organs that do not exist in the MTG yet. This is because some organs may only appear after the beginning of the simulation. In this case we now create a fake node for this organ, and use the initialisation function on that node to get its status, and hence get the right type for the vector on which the outputs will be listed. See afeeba0 and 33cc0af for more details.

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 2 years ago

PlantSimEngine - v0.10.2

PlantSimEngine v0.10.2

Diff since v0.10.1

What's Changed

Add status to the nodes so we get a circular reference by @VEZY in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/75
Fix #78 by @VEZY in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/79

Full Changelog: https://github.com/VirtualPlantLab/PlantSimEngine.jl/compare/v0.10.1...v0.11.0

Merged pull requests: - Add status to the nodes so we get a circular reference (#75) (@VEZY) - Fix #78 (#79) (@VEZY)

Closed issues: - Multiple variables with shared name (#78)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 2 years ago

PlantSimEngine - v0.10.1

PlantSimEngine v0.10.1

Diff since v0.10.0

Merged pull requests: - Bump julia-actions/cache from 1 to 2 (#71) (@dependabot[bot]) - CompatHelper: bump compat for MultiScaleTreeGraph to 0.14, (keep existing compat) (#72) (@github-actions[bot])

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] about 2 years ago

PlantSimEngine - v0.10.0

PlantSimEngine v0.10.0

Diff since v0.9.0

Breaking changes

Rewrite of the code for multiscale simulations: change how we build the dependency graph, how we compute the mapping, and how we compute basically everything for that.
Detect if the graph is cyclic, and return an helpful message with the cycle
Add PreviousTimeStep for multiscale mapping: 61 add a way to not use an input variable to build the dependency graph by @VEZY in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/66
Add a mapping format to rename a variable at the same scale (useful when models don't share the same variable name)
Fix a lot of issues related to the dependency graph

Changes:

Update TagBot.yml by @VEZY in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/52
CompatHelper: bump compat for MultiScaleTreeGraph to 0.13, (keep existing compat) by @github-actions in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/55
Bump julia-actions/setup-julia from 1 to 2 by @dependabot in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/59
61 add a way to not use an input variable to build the dependency graph by @VEZY in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/66

New Contributors

@dependabot made their first contribution in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/59

Full Changelog: https://github.com/VirtualPlantLab/PlantSimEngine.jl/compare/v0.9.0...v0.10.0

Merged pull requests: - CompatHelper: bump compat for MultiScaleTreeGraph to 0.13, (keep existing compat) (#55) (@github-actions[bot]) - Bump julia-actions/setup-julia from 1 to 2 (#59) (@dependabot[bot]) - 61 add a way to not use an input variable to build the dependency graph (#66) (@VEZY)

Closed issues: - inputs and outpus: always return the default values (#41) - Improve to_initialize(mapping, graph) (#56) - Multiscale mapping to other variable name (#57) - Add a way to not use an input variable to build the dependency graph. (#61) - Allow variable renaming (#62) - Use the outputs from other scales (used as input for this scale) as a dependency for the node (#63) - Remove the notion of PlantMeteo.prev_value (#64)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] about 2 years ago

PlantSimEngine - v0.9.0

What's Changed

Improve how computations are made over MTGs by @VEZY in https://github.com/VirtualPlantLab/PlantSimEngine.jl/pull/51

Full Changelog: https://github.com/VirtualPlantLab/PlantSimEngine.jl/compare/v0.8.2...v0.9.0

Scientific Software - Peer-reviewed - Julia
Published by VEZY over 2 years ago

PlantSimEngine - v0.8.2

Uses MultiScaleTreeGraph v0.12, which is a breaking release due to the removal of the node type.

Full Changelog: https://github.com/VirtualPlantLab/PlantSimEngine.jl/compare/v0.8.1...v0.8.2

Scientific Software - Peer-reviewed - Julia
Published by VEZY almost 3 years ago

PlantSimEngine - v0.8.1: release for JOSS

Full Changelog: https://github.com/VirtualPlantLab/PlantSimEngine.jl/compare/v0.8.0...v0.8.1

This is the release of the package for the publication in JOSS.

Scientific Software - Peer-reviewed - Julia
Published by VEZY about 3 years ago

PlantSimEngine - v0.8.0

PlantSimEngine v0.8.0

Diff since v0.7.0

Closed issues: - Add a nsteps argument to the ModelList (#43) - Corrections in PlantSImEngine tutorial (#45) - Fix Aqua ambiguities problem (#47)

Merged pull requests: - CompatHelper: bump compat for MultiScaleTreeGraph to 0.11, (keep existing compat) (#46) (@github-actions[bot])

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] about 3 years ago

PlantSimEngine - v0.7.0

PlantSimEngine v0.7.0

Diff since v0.6.1

Closed issues: - [REVIEW] Add complete (if basic) usage example to docs homepage and README (#32) - [REVIEW] Add "real" multi-component leaf/plant model example (#33) - [REVIEW] Justify (or tone-down) performance claims in paper and docs (#34) - [REVIEW] Add CONTRIBUTING.md file (#35) - Clarify how we make simulations over tables or singleton-alike input types (#36) - Issue when simulating several time-steps in parallel (#39)

Merged pull requests: - CompatHelper: bump compat for PlantMeteo to 0.4, (keep existing compat) (#37) (@github-actions[bot])

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] about 3 years ago

PlantSimEngine - v0.6.1

PlantSimEngine v0.6.1

Diff since v0.6.0

Merged pull requests: - CompatHelper: bump compat for MultiScaleTreeGraph to 0.10, (keep existing compat) (#31) (@github-actions[bot])

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.6.0

PlantSimEngine v0.6.0

Diff since v0.5.1

Closed issues: - Define the workflow for simulation of MTGs (#28)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.5.1

PlantSimEngine v0.5.1

Diff since v0.5.0

Merged pull requests: - CompatHelper: bump compat for Term to 2, (keep existing compat) (#26) (@github-actions[bot]) - CompatHelper: bump compat for PlantMeteo to 0.3, (keep existing compat) (#27) (@github-actions[bot])

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.5.0

PlantSimEngine v0.5.0

Diff since v0.4.0

Closed issues: - Add macro to generate model templates (#17) - Move the fit function from plantbiophysics to here (#24)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.4.0

PlantSimEngine v0.4.0

Diff since v0.3.2

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.3.2

PlantSimEngine v0.3.2

Diff since v0.3.1

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.3.1

PlantSimEngine v0.3.1

Diff since v0.3.0

Closed issues: - Update doc following run method implementation (#20)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.3.0

PlantSimEngine v0.3.0

Diff since v0.2.1

Closed issues: - Detect automatically which process is simulated in the ModelList for each model (#10) - Model simulation order (#18) - [dummy examples] process4 should have process1 listed as a soft dependency (#19)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.2.1

What's Changed

CompatHelper: bump compat for MultiScaleTreeGraph to 0.9, (keep existing compat) by @github-actions in https://github.com/VEZY/PlantSimEngine.jl/pull/15
CompatHelper: bump compat for PlantMeteo to 0.2, (keep existing compat) by @github-actions in https://github.com/VEZY/PlantSimEngine.jl/pull/16

Full Changelog: https://github.com/VEZY/PlantSimEngine.jl/compare/v0.1.9...v0.2.1

Scientific Software - Peer-reviewed - Julia
Published by VEZY over 3 years ago

PlantSimEngine - v0.1.9

PlantSimEngine v0.1.9

Diff since v0.1.8

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.1.8

PlantSimEngine v0.1.8

Diff since v0.1.7

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.1.7

PlantSimEngine v0.1.7

Diff since v0.1.6

Closed issues: - Add tests on simulations (with one ts or several, one meteo or several) (#11) - Add simulation tests on MTG (#12)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.1.6

PlantSimEngine v0.1.6

Diff since v0.1.5

Merged pull requests: - CompatHelper: add new compat entry for CSV at version 0.10, (keep existing compat) (#9) (@github-actions[bot])

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.1.5

PlantSimEngine v0.1.5

Diff since v0.1.4

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.1.4

PlantSimEngine v0.1.4

Diff since v0.1.3

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.1.3

PlantSimEngine v0.1.3

Diff since v0.1.2

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.1.2

PlantSimEngine v0.1.2

Diff since v0.1.1

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.1.1

PlantSimEngine v0.1.1

Diff since v0.1.0

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

PlantSimEngine - v0.1.0

PlantSimEngine v0.1.0

Merged pull requests: - CompatHelper: add new compat entry for AbstractTrees at version 0.4, (keep existing compat) (#1) (@github-actions[bot]) - CompatHelper: add new compat entry for DataFrames at version 1, (keep existing compat) (#2) (@github-actions[bot]) - CompatHelper: add new compat entry for Tables at version 1, (keep existing compat) (#3) (@github-actions[bot]) - CompatHelper: add new compat entry for Term at version 1, (keep existing compat) (#4) (@github-actions[bot]) - CompatHelper: add new compat entry for MultiScaleTreeGraph at version 0.8, (keep existing compat) (#5) (@github-actions[bot]) - CompatHelper: add new compat entry for PlantMeteo at version 0.1, (keep existing compat) (#7) (@github-actions[bot])

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 3 years ago

Recent Releases of PlantSimEngine

PlantSimEngine - v0.13.2

PlantSimEngine v0.13.2

PlantSimEngine - v0.13.1

PlantSimEngine v0.13.1

Patch

PlantSimEngine - v0.13.0

PlantSimEngine v0.13.0

Breaking changes

PlantSimEngine - PlantSimEngine v0.12.0

Release notes:

Breaking changes

Main features

API changes

CI-related changes

Fixed issues

86, #105, #111

Generated release notes:

What's Changed

PlantSimEngine - v0.11.3

PlantSimEngine v0.11.3

PlantSimEngine - v0.11.2

PlantSimEngine v0.11.2

PlantSimEngine - v0.11.1

PlantSimEngine v0.11.1

PlantSimEngine - v0.11.0

PlantSimEngine v0.11.0

Bug fixes

PlantSimEngine - v0.10.3

PlantSimEngine v0.10.3

Bug fixes

PlantSimEngine - v0.10.2

PlantSimEngine v0.10.2

What's Changed

PlantSimEngine - v0.10.1

PlantSimEngine v0.10.1

PlantSimEngine - v0.10.0

PlantSimEngine v0.10.0

Breaking changes

Changes:

New Contributors

PlantSimEngine - v0.9.0

What's Changed

PlantSimEngine - v0.8.2

PlantSimEngine - v0.8.1: release for JOSS

PlantSimEngine - v0.8.0

PlantSimEngine v0.8.0

PlantSimEngine - v0.7.0

PlantSimEngine v0.7.0

PlantSimEngine - v0.6.1

PlantSimEngine v0.6.1

PlantSimEngine - v0.6.0

PlantSimEngine v0.6.0

PlantSimEngine - v0.5.1

PlantSimEngine v0.5.1

PlantSimEngine - v0.5.0

PlantSimEngine v0.5.0

PlantSimEngine - v0.4.0

PlantSimEngine v0.4.0

PlantSimEngine - v0.3.2

PlantSimEngine v0.3.2

PlantSimEngine - v0.3.1

PlantSimEngine v0.3.1

PlantSimEngine - v0.3.0

PlantSimEngine v0.3.0

PlantSimEngine - v0.2.1

What's Changed

PlantSimEngine - v0.1.9

PlantSimEngine v0.1.9

PlantSimEngine - v0.1.8

PlantSimEngine v0.1.8

PlantSimEngine - v0.1.7

PlantSimEngine v0.1.7

PlantSimEngine - v0.1.6

PlantSimEngine v0.1.6

PlantSimEngine - v0.1.5

PlantSimEngine v0.1.5

PlantSimEngine - v0.1.4

PlantSimEngine v0.1.4

PlantSimEngine - v0.1.3