Lumen refactoring #49

Perro2110 · 2025-03-28T08:58:40Z

For possible registration of SolePostHoc.

…odels.jl into gio/refractoring

alberto-paparella · 2025-03-28T13:53:58Z

Dear @Perro2110, can you update the cirrus.yaml file updating the freebsd version to 14.2, so that we can make sure that all tests are successfull?

Perro2110 · 2025-04-01T16:24:47Z

Good evening everyone!
Even after updating the image family, I'm still getting errors but I noticed that these errors were already present before this pull request. Is there anything else I can do? Once this branch is moved from dev to main, SolePostHoc will have one less dependency on packages not in main, leaving only one more package to fix and then we're done! After that, PostHoc will be ready !

SoleBase = "0.11 - 0.13"

giopaglia · 2025-04-01T20:46:09Z

I cant see the error as the log is too long and I'm on my mobile. Can you link to the specific log line?

giopaglia · 2025-04-01T20:46:53Z

On another note could the log be made shorter? I think it's full of debug info that can be hidden for clarity

Perro2110 · 2025-04-02T06:40:30Z

On another note could the log be made shorter? I think it's full of debug info that can be hidden for clarity

I'm not sure if you want this but in case I'll forward it to you:
in one of the FreeBSD JULIA_VERSION 1:

TEST: base.jl
TEST: test_tree.jl
Models: Error During Test at /tmp/cirrus-ci-build/test/runtests.jl:33
  Got exception outside of a @test
  LoadError: UndefVarError: `parsebaseformula` not defined in `SoleLogics`
  Stacktrace:
    [1] getproperty(x::Module, f::Symbol)
      @ Base ./Base.jl:42
    [2] top-level scope
      @ ~/tmp/cirrus-ci-build/test/test_tree.jl:16
    [3] include
      @ ./sysimg.jl:38 [inlined]
    [4] run_tests(list::Vector{String})
      @ Main ~/tmp/cirrus-ci-build/test/runtests.jl:11
    [5] macro expansion
      @ ~/tmp/cirrus-ci-build/test/runtests.jl:34 [inlined]
    [6] macro expansion
      @ ~/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
    [7] macro expansion
      @ ~/tmp/cirrus-ci-build/test/runtests.jl:34 [inlined]
    [8] macro expansion
      @ ~/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
    [9] top-level scope
      @ ~/tmp/cirrus-ci-build/test/runtests.jl:29
   [10] include(fname::String)
      @ Main ./sysimg.jl:38
   [11] top-level scope
      @ none:6
   [12] eval
      @ ./boot.jl:430 [inlined]
   [13] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:296
   [14] _start()
      @ Base ./client.jl:531
  in expression starting at /tmp/cirrus-ci-build/test/test_tree.jl:16

and:

##################################################
TEST: /tmp/cirrus-ci-build/pluto-demo.jl

##################################################
[.....]

1.0, lift = 3.75, natoms = 16)
▣ ((sepal_length < 5.55)) ∧ ((petal_width ≥ 1.0)) ∧ ((petal_width < 0.75)) ∧ ((petal_length < 2.7)) ∧ ((petal_width < 1.7000000000000002)) ∧ ((petal_length < 2.5)) ∧ ((petal_width < 0.8)) ∧ ((petal_width ≥ 0.7)) ∧ ((sepal_length ≥ 6.15)) ∧ ((petal_width < 1.7000000000000002)) ∧ ((petal_width ≥ 0.7)) ∧ ((petal_width ≥ 1.65)) ∧ ((sepal_length < 5.45)) ∧ ((sepal_width ≥ 2.65)) ∧ ((petal_length < 2.5)) ∧ ((petal_length < 2.5999999999999996))  ↣  setosa : (ninstances = 30, ncovered = 8, coverage = 0.27, confidence = 1.0, lift = 3.75, natoms = 16)ERROR: Package SoleModels errored during testing (received signal: KILL)
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types ~/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68
 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
   @ Pkg.Operations ~/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2118
 [3] test
   @ ~/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2003 [inlined]
 [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}})
   @ Pkg.API ~/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:481
 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{coverage::Bool})
   @ Pkg.API ~/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159
 [6] test(; name::Nothing, uuid::Nothing, version::Nothing, url::Nothing, rev::Nothing, path::Nothing, mode::Pkg.Types.PackageMode, subdir::Nothing, kwargs::@Kwargs{coverage::Bool})
   @ Pkg.API ~/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:174
 [7] top-level scope
   @ none:3
�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������
[....]

in FreeBsd JULIA_VERSION:1.9

[...]
  ✓ MLJTuning
  ✓ SoleModels
  ✓ MLJ
  ✓ SoleModels → DecisionTreeExt
  ✓ SoleModels → XGBoostExt
  244 dependencies successfully precompiled in 230 seconds. 4 already precompiled.
  11 dependencies had output during precompilation:
┌ InverseFunctionsDatesExt [33677a4c-2dac-51eb-93f3-7ff1c38acef2]
│  ┌ Warning: Module InverseFunctionsDatesExt with build ID ffffffff-ffff-ffff-0000-004713b98708 is missing from the cache.
│  │ This may mean InverseFunctionsDatesExt [33677a4c-2dac-51eb-93f3-7ff1c38acef2] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1793
│  ┌ Error: Error during loading of extension InverseFunctionsDatesExt of InverseFunctions, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │    @ Base ./loading.jl:1797
│  │      [2] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │    @ Base ./loading.jl:1660
│  │      [3] _require_prelocked(uuidkey::Base.PkgId)
│  │    @ Base ./loading.jl:1658
│  │      [4] run_extension_callbacks(extid::Base.ExtensionId)
│  │    @ Base ./loading.jl:1255
│  │      [5] run_extension_callbacks(pkgid::Base.PkgId)
│  │    @ Base ./loading.jl:1290
│  │      [6] run_package_callbacks(modkey::Base.PkgId)
│  │    @ Base ./loading.jl:1124
│  │      [7] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │    @ Base ./loading.jl:1667
│  │      [8] macro expansion
[...]

various dependencies like:

└  
┌ TimeseriesFeatures [f3112013-b923-4dfa-b867-8806c885f823]
│  WARNING: Wrapping `Vararg` directly in UnionAll is deprecated (wrap the tuple instead).
└  
┌ FilePathsBaseMmapExt [968c5e7e-8fc3-5f0f-93d2-8a5e0e125e4f]
│  ┌ Warning: Module FilePathsBaseMmapExt with build ID ffffffff-ffff-ffff-0000-004bf37d83dc is missing from the cache.
│  │ This may mean FilePathsBaseMmapExt [968c5e7e-8fc3-5f0f-93d2-8a5e0e125e4f] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1793
│  ┌ Error: Error during loading of extension FilePathsBaseMmapExt of FilePathsBase, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │    @ Base ./loading.jl:1797
│  │      [2] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │    @ Base ./loading.jl:1660
│  │      [3] _require_prelocked(2

and then:

##################################################
TEST: base.jl
TEST: test_tree.jl
Models: Error During Test at /tmp/cirrus-ci-build/test/runtests.jl:33
  Got exception outside of a @test
  LoadError: UndefVarError: `parsebaseformula` not defined
  Stacktrace:
    [1] getproperty(x::Module, f::Symbol)
      @ Base ./Base.jl:31
    [2] top-level scope
      @ ~/tmp/cirrus-ci-build/test/test_tree.jl:16
    [3] include
      @ ./client.jl:478 [inlined]
    [4] run_tests(list::Vector{String})
      @ Main ~/tmp/cirrus-ci-build/test/runtests.jl:11
    [5] macro expansion
      @ ~/tmp/cirrus-ci-build/test/runtests.jl:34 [inlined]
    [6] macro expansion
      @ ~/julia/share/julia/stdlib/v1.9/Test/src/Test.jl:1498 [inlined]
    [7] macro expansion
      @ ~/tmp/cirrus-ci-build/test/

…Models.jl into lumen-refactoring

giopaglia · 2025-04-02T16:02:50Z

parsebaseformula is an obsolete function. Pushed a fix for this error.

giopaglia · 2025-04-02T16:05:17Z

src/SoleModels.jl

@@ -93,7 +93,7 @@ export subtreeheight
 include("symbolic-utils.jl")

 export PlainRuleExtractor
-export extractrules, listrules, joinrules
+export modalextractrules, listrules, joinrules


I want to stress the fact that I'm not bothered by the function being called "modalextractrules". But we need to be able to call it "extractrules". So again my suggestion is on of the following:

rename the function into "extractrules", and then put a "const modalextractrules = extractrules; export modalextractrules" in a deprecate.jl file

keep the name "modalextractrules", but also put a "const extractrules = modalextractrules; export xtractrules" in a deprecate.jl file

Ok, I fully agree, I chose the first option: rename the function into "extractrules", and then put a "const modalextractrules = extractrules; export modalextractrules" in a deprecate.jl file

giopaglia · 2025-04-27T12:26:05Z

I accidentally closed the pr, as I have deleted the dev branch (this was in the plans). Let's see if we can make this merge into main.

giopaglia · 2025-04-27T12:26:37Z

Okay should be good to remove dev now

codecov · 2025-06-07T14:41:50Z

Codecov Report

Attention: Patch coverage is 74.13793% with 30 lines in your changes missing coverage. Please review.

Project coverage is 56.03%. Comparing base (6668e77) to head (d3f8dfe).
Report is 109 commits behind head on main.

Files with missing lines	Patch %	Lines
src/utils/models/ensembles.jl	58.33%	15 Missing ⚠️
src/utils/models/leaf.jl	20.00%	8 Missing ⚠️
src/evaluate.jl	0.00%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #49      +/-   ##
==========================================
+ Coverage   50.91%   56.03%   +5.11%     
==========================================
  Files          16       21       +5     
  Lines         927     1260     +333     
==========================================
+ Hits          472      706     +234     
- Misses        455      554      +99

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

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

PasoStudio73 · 2025-06-07T15:04:12Z

Now everything is working, test passed both local than on codecov.
This is a summary list of what's changed:

porting from Cirrus to GitHub CI workflow
Lumen implementation
clean unused packages and deps
external packages "DecisiontreeExt" and "XgboostExt" implemented and working
minor

PasoStudio73 · 2025-06-07T16:03:17Z

Ready to merge on branch Main and register a new version.

Perro2110 and others added 5 commits January 13, 2025 14:41

fix if 1 lmf [TodoReview this]

e4d257d

Add test, add iscomplete

67af772

Merge branch 'gio/refractoring' of https://github.com/aclai-lab/SoleM…

ebe5d9d

…odels.jl into gio/refractoring

refactoring name

a287352

minor fix

b2312c1

Perro2110 requested review from ferdiu, giopaglia, mauro-milella and alberto-paparella March 28, 2025 08:58

Perro2110 self-assigned this Mar 28, 2025

Perro2110 and others added 2 commits March 29, 2025 10:21

update image_family

4bc2854

decisiontree and xgboost ext working

afd1161

minor fix in Project.toml for compatibility

183de68

SoleBase = "0.11 - 0.13"

giopaglia added 2 commits April 2, 2025 18:02

Fix

8ee5cf3

Merge branch 'lumen-refactoring' of https://github.com/aclai-lab/Sole…

8ef0051

…Models.jl into lumen-refactoring

giopaglia reviewed Apr 2, 2025

View reviewed changes

PasoStudio73 added 8 commits April 2, 2025 21:35

debug xgboost, not yet ready

d870851

Refining XGBoost

5de4302

xgboost float predict issue

2ad6442

xgboost predict found areas requireing fixes

dd23501

XGBoost test passed

93fba4d

working on tests

ae4e5a1

codecov working

52deed0

removed MLJXGBoostInterface in tests

7c4f025

Perro2110 and others added 4 commits April 18, 2025 18:26

minor add in TODO

d26e198

fix tests & deps

9638489

posthoc

b2a4869

Merge branch 'devTest' into lumen-refactoring

16476a9

Perro2110 requested a review from PasoStudio73 April 26, 2025 21:56

test fixed

1b5a6c6

giopaglia deleted the branch main April 27, 2025 11:55

giopaglia closed this Apr 27, 2025

giopaglia reopened this Apr 27, 2025

giopaglia changed the base branch from dev to main April 27, 2025 12:26

PasoStudio73 added 12 commits April 27, 2025 17:59

fix extras deps

dbe8e83

cleaned unused packages, tests still working

6c34e4d

updated SoleData dep

bcefa20

updated solelogics dep

ba4d143

added a @show for checking

72efb54

removed guard

bd889ac

test working

83ffb33

updated github ci

54ae95f

added distributed package

4275b3d

added MLJXGBoostInterface package

42c052e

fix XGB

1218cb1

added MMI

37daad6

Merge branch 'main' into lumen-refactoring

d3f8dfe

PasoStudio73 merged commit eafd7a9 into main Jun 7, 2025
9 checks passed

PasoStudio73 deleted the lumen-refactoring branch June 7, 2025 16:04

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Lumen refactoring #49

Lumen refactoring #49

Uh oh!

Perro2110 commented Mar 28, 2025

Uh oh!

alberto-paparella commented Mar 28, 2025 •

edited

Loading

Uh oh!

Perro2110 commented Apr 1, 2025

Uh oh!

giopaglia commented Apr 1, 2025

Uh oh!

giopaglia commented Apr 1, 2025

Uh oh!

Perro2110 commented Apr 2, 2025

Uh oh!

giopaglia commented Apr 2, 2025

Uh oh!

giopaglia Apr 2, 2025

Uh oh!

Perro2110 Apr 18, 2025

Uh oh!

giopaglia commented Apr 27, 2025

Uh oh!

giopaglia commented Apr 27, 2025

Uh oh!

codecov bot commented Jun 7, 2025 •

edited

Loading

Uh oh!

PasoStudio73 commented Jun 7, 2025

Uh oh!

PasoStudio73 commented Jun 7, 2025

Uh oh!

Uh oh!

Uh oh!

Lumen refactoring #49

Lumen refactoring #49

Uh oh!

Conversation

Perro2110 commented Mar 28, 2025

Uh oh!

alberto-paparella commented Mar 28, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Perro2110 commented Apr 1, 2025

Uh oh!

giopaglia commented Apr 1, 2025

Uh oh!

giopaglia commented Apr 1, 2025

Uh oh!

Perro2110 commented Apr 2, 2025

Uh oh!

giopaglia commented Apr 2, 2025

Uh oh!

giopaglia Apr 2, 2025

Choose a reason for hiding this comment

Uh oh!

Perro2110 Apr 18, 2025

Choose a reason for hiding this comment

Uh oh!

giopaglia commented Apr 27, 2025

Uh oh!

giopaglia commented Apr 27, 2025

Uh oh!

codecov bot commented Jun 7, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

PasoStudio73 commented Jun 7, 2025

Uh oh!

PasoStudio73 commented Jun 7, 2025

Uh oh!

Uh oh!

Uh oh!

alberto-paparella commented Mar 28, 2025 •

edited

Loading

codecov bot commented Jun 7, 2025 •

edited

Loading