Upgrade to Legolas 0.5 (#97)

* Project file

* update lighthouse eval

* update lightouse observation

* update lightouse class

* update lightouse labeled metrics

* update lightouse hardened metrics

* update lightouse tradeoff metrics

* formatting

* comment for evaluation

* comment for observation

* upgrade comments

* small changes based on huddle

* export and legolas

* Starting updating tests

* Use Legolas v0.5 records

* Prefer using term record to row

* Fix `_values_or_missing`

* Address MakieLayout deprecation

* Fix mistake where rho was replace with p

* Fix `test_evaluation_metrics_roundtrip`

* Use `IOBuffer` for `roundtrip_row`

* Documentation update

* Documentation changes

* Use modern Makie which deprecates MakieLayout

* updates documentation failures updating Row to V1

* format

* workflow

* run format

* un-mangle

* Update docs/Project.toml

* docstring format

* deprecation (with error)

* yasg demands return

Co-authored-by: Curtis Vogt <curtis.vogt@gmail.com>
Co-authored-by: Nader Bagherzadeh <nader.b@beacon.bio>
Co-authored-by: Dave Kleinschmidt <dave.f.kleinschmidt@gmail.com>

Author: 4 people

.github/workflows/format.yml

@@ -0,0 +1,37 @@
+name: YASG-enforcer
+on:
+  push:
+    branches:
+      - 'main'
+    tags: '*'
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    # note: keep in sync with `format/run.jl`
+    paths:
+      - 'src/**'
+      - 'test/**'
+      - '.github/workflows/format.yml'
+      - 'format/**'
+jobs:
+  format-check:
+    name: YASG Enforcement (Julia ${{ matrix.julia-version }} - ${{ github.event_name }})
+    # Run on push's or non-draft PRs
+    if: (github.event_name == 'push') || (github.event.pull_request.draft == false)
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        julia-version: [1.8]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+      - uses: actions/checkout@v1
+      - name: Instantiate `format` environment and format
+        run: |
+          julia --project=format -e 'using Pkg; Pkg.instantiate()'
+          julia --project=format 'format/run.jl'
+      - uses: reviewdog/action-suggester@v1
+        if: github.event_name == 'pull_request'
+        with:
+          tool_name: JuliaFormatter
+          fail_on_error: true

Project.toml

@@ -1,7 +1,7 @@
 name = "Lighthouse"
 uuid = "ac2c24cd-07f0-4848-96b2-1b82c3ea0e59"
 authors = ["Beacon Biosignals, Inc."]
-version = "0.14.16"
+version = "0.15.0"
 
 [deps]
 ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd"
@@ -23,8 +23,8 @@ Arrow = "2.3"
 ArrowTypes = "1, 2"
 CairoMakie = "0.7, 0.8"
 DataFrames = "1.3"
-Legolas = "0.3"
-Makie = "0.16.5, 0.17, 0.18"
+Legolas = "0.5"
+Makie = "0.17.4, 0.18"
 StatsBase = "0.33"
 Tables = "1.7"
 TensorBoardLogger = "0.1"

docs/Project.toml

@@ -4,5 +4,4 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 
 [compat]
-CairoMakie = "0.7.4"
 Documenter = "0.25"

docs/make.jl

@@ -7,7 +7,7 @@ makedocs(; modules=[Lighthouse], sitename="Lighthouse",
                 "Plotting" => "plotting.md"],
          # makes docs fail hard if there is any error building the examples,
          # so we don't just miss a build failure!
-         strict = true)
+         strict=true)
 
-deploydocs(repo="github.com/beacon-biosignals/Lighthouse.jl.git",
+deploydocs(; repo="github.com/beacon-biosignals/Lighthouse.jl.git",
            devbranch="main", push_preview=true)

docs/src/index.md

@@ -66,23 +66,23 @@ accuracy
 binary_statistics
 cohens_kappa
 calibration_curve
-EvaluationRow
-ObservationRow
+EvaluationV1
+ObservationV1
 Lighthouse.evaluation_metrics
-Lighthouse._evaluation_row_dict
-Lighthouse.evaluation_metrics_row
-Lighthouse.ClassRow
-TradeoffMetricsRow
+Lighthouse._evaluation_dict
+Lighthouse.evaluation_metrics_record
+Lighthouse.ClassV1
+TradeoffMetricsV1
 get_tradeoff_metrics
 get_tradeoff_metrics_binary_multirater
-HardenedMetricsRow
+HardenedMetricsV1
 get_hardened_metrics
 get_hardened_metrics_multirater
 get_hardened_metrics_multiclass
-LabelMetricsRow
+LabelMetricsV1
 get_label_metrics_multirater
 get_label_metrics_multirater_multiclass
-Lighthouse._evaluation_row
+Lighthouse._evaluation_record
 Lighthouse._calculate_ea_kappas
 Lighthouse._calculate_ira_kappas
 Lighthouse._calculate_spearman_correlation

docs/src/plotting.md

@@ -274,8 +274,8 @@ data["optimal_threshold"] = missing
 evaluation_metrics_plot(data)
 ```
 
-Plots can also be generated directly from an `EvaluationRow`:
+Plots can also be generated directly from an `EvaluationV1`:
 ```@example 1
-data_row = EvaluationRow(data)
+data_row = EvaluationV1(data)
 evaluation_metrics_plot(data_row)
 ```

format/Manifest.toml

@@ -0,0 +1,226 @@
+# This file is machine-generated - editing it directly is not advised
+
+julia_version = "1.8.3"
+manifest_format = "2.0"
+project_hash = "30b405be1c677184b7703a9bfb3d2100029ccad0"
+
+[[deps.ArgTools]]
+uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
+version = "1.1.1"
+
+[[deps.Artifacts]]
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+
+[[deps.Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[deps.CSTParser]]
+deps = ["Tokenize"]
+git-tree-sha1 = "3ddd48d200eb8ddf9cb3e0189fc059fd49b97c1f"
+uuid = "00ebfdb7-1f24-5e51-bd34-a7502290713f"
+version = "3.3.6"
+
+[[deps.CommonMark]]
+deps = ["Crayons", "JSON", "URIs"]
+git-tree-sha1 = "86cce6fd164c26bad346cc51ca736e692c9f553c"
+uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6"
+version = "0.8.7"
+
+[[deps.Compat]]
+deps = ["Dates", "LinearAlgebra", "UUIDs"]
+git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a"
+uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
+version = "4.5.0"
+
+[[deps.CompilerSupportLibraries_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
+version = "0.5.2+0"
+
+[[deps.Crayons]]
+git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
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+version = "4.1.1"
+
+[[deps.DataStructures]]
+deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
+git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0"
+uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+version = "0.18.13"
+
+[[deps.Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[deps.Downloads]]
+deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
+uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+version = "1.6.0"
+
+[[deps.FileWatching]]
+uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
+
+[[deps.Glob]]
+git-tree-sha1 = "4df9f7e06108728ebf00a0a11edee4b29a482bb2"
+uuid = "c27321d9-0574-5035-807b-f59d2c89b15c"
+version = "1.3.0"
+
+[[deps.InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[deps.JSON]]
+deps = ["Dates", "Mmap", "Parsers", "Unicode"]
+git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e"
+uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+version = "0.21.3"
+
+[[deps.JuliaFormatter]]
+deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "Tokenize"]
+git-tree-sha1 = "76ee67858b65133b2460b0eebf52e49950bb90a3"
+uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+version = "1.0.16"
+
+[[deps.LibCURL]]
+deps = ["LibCURL_jll", "MozillaCACerts_jll"]
+uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
+version = "0.6.3"
+
+[[deps.LibCURL_jll]]
+deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
+uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
+version = "7.84.0+0"
+
+[[deps.LibGit2]]
+deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[deps.LibSSH2_jll]]
+deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
+uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
+version = "1.10.2+0"
+
+[[deps.Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[deps.LinearAlgebra]]
+deps = ["Libdl", "libblastrampoline_jll"]
+uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[deps.Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[deps.Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[deps.MbedTLS_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+version = "2.28.0+0"
+
+[[deps.Mmap]]
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+
+[[deps.MozillaCACerts_jll]]
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+
+[[deps.NetworkOptions]]
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+[[deps.OpenBLAS_jll]]
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+[[deps.OrderedCollections]]
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+[[deps.Pkg]]
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+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
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+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[deps.Random]]
+deps = ["SHA", "Serialization"]
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+[[deps.Sockets]]
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+[[deps.UUIDs]]
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+[[deps.Unicode]]
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+
+[[deps.Zlib_jll]]
+deps = ["Libdl"]
+uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+version = "1.2.12+3"
+
+[[deps.libblastrampoline_jll]]
+deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
+uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
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+
+[[deps.nghttp2_jll]]
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format/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+
+[compat]
+JuliaFormatter = "1"

format/run.jl

@@ -0,0 +1,14 @@
+using JuliaFormatter
+
+function main()
+    perfect = format(joinpath(@__DIR__, ".."); style=YASStyle())
+    if perfect
+        @info "Linting complete - no files altered"
+    else
+        @info "Linting complete - files altered"
+        run(`git status`)
+    end
+    return nothing
+end
+
+main()

src/LearnLogger.jl

@@ -45,8 +45,9 @@ function log_plot!(logger::LearnLogger, field::AbstractString, plot, plot_data)
     return plot
 end
 
-function log_line_series!(logger::LearnLogger, field::AbstractString, curves, labels=1:length(curves))
-    @warn "`log_line_series!` not implemented for `LearnLogger`" maxlog=1
+function log_line_series!(logger::LearnLogger, field::AbstractString, curves,
+                          labels=1:length(curves))
+    @warn "`log_line_series!` not implemented for `LearnLogger`" maxlog = 1
     return nothing
 end