Fix CI (#612)

Author: DilumAluthge

.github/workflows/ci.yml

@@ -15,16 +15,23 @@ jobs:
   CI:
     runs-on: ${{ matrix.os }}
     strategy:
-      matrix:
-        julia-version: ["1", "nightly"]
-        julia-arch: [x64]
-        os: [macos-latest, ubuntu-latest]
       fail-fast: false
+      matrix:
+        julia-version:
+          - "1.5"
+          - "1"
+          - "nightly"
+        arch:
+          - x64
+        os:
+          - macos-latest
+          - ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia-version }}
+          arch: ${{ matrix.arch }}
       - if: startsWith(matrix.os, 'ubuntu')
         run: |
           sudo apt-get update
@@ -33,8 +40,8 @@ jobs:
         run: |
           brew update
           brew install pdf2svg tree
-          brew cask install basictex
-          echo "::add-path::/Library/TeX/texbin"
+          brew install --cask basictex
+          echo "/Library/TeX/texbin" >> $GITHUB_PATH
       - if: startsWith(matrix.os, 'macOS')
         run: |
           sudo tlmgr update --self || sudo tlmgr update --self || sudo tlmgr update --self
@@ -44,7 +51,7 @@ jobs:
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
         env:
-          JULIA_DEBUG: "all"
+          # JULIA_DEBUG: "all"
           PREDICTMD_OPEN_PLOTS_DURING_TESTS: "true"
           PREDICTMD_TEST_GROUP: "all"
           PREDICTMD_TEST_PLOTS: "true"

Project.toml

@@ -2,13 +2,11 @@ name = "PredictMD"
 uuid = "3e7d7328-36f8-4388-bd01-4613c92c7370"
 authors = ["Dilum Aluthge <[email protected]>", "Ishan Sinha <[email protected]>", "Paul Stey <[email protected]>", "Isabel Restrepo <[email protected]>", "Elizabeth Chen <[email protected]>", "Neil Sarkar <[email protected]>", "Brown Center for Biomedical Informatics <[email protected]>"]
 doi = "10.5281/zenodo.1291209"
-version = "0.34.19"
+version = "0.34.20"
 
 [deps]
-Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
 CSVFiles = "5d742f6a-9f54-50ce-8119-2520741973ca"
-CUDAapi = "3895d2a7-ec45-59b8-82bb-cfc6a382f9b3"
 Cassette = "7057c7e9-c182-5462-911a-8362d720325c"
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 ClassImbalance = "04a18a73-7590-580c-b363-eeca0919eb2a"
@@ -56,10 +54,8 @@ UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
 ValueHistories = "98cad3c8-aec3-5f06-8e41-884608649ab7"
 
 [compat]
-Adapt = "1"
 BSON = "0.2"
 CSVFiles = "0.16, 1.0"
-CUDAapi = "2, 3, 4"
 Cassette = "0.2, 0.3"
 CategoricalArrays = "0.7, 0.8"
 ClassImbalance = "0.8"
@@ -100,7 +96,7 @@ StatsModels = "0.6"
 TikzPictures = "3"
 UnicodePlots = "1"
 ValueHistories = "0.5"
-julia = "1.1"
+julia = "1.5"
 
 [extras]
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"

src/toplevel/always-loaded/neuralnetwork/flux.jl

@@ -1,5 +1,3 @@
-import Adapt
-import CUDAapi
 # import Flux
 # import GPUArrays
 # import NNlib

src/toplevel/always-loaded/neuralnetwork/knet.jl

@@ -1,4 +1,3 @@
-import CUDAapi
 # import GPUArrays
 import Knet
 import ProgressMeter

src/toplevel/always-loaded/utils/constant_columns.jl

@@ -1,24 +1,4 @@
 import DataFrames
-import StatsBase
-
-function get_countmap(itr; skip_missings::Bool = true)
-    if skip_missings
-        result = get_countmap_skip_missings(itr)
-    else
-        result = get_countmap_include_missings(itr)
-    end
-    return result
-end
-
-function get_countmap_skip_missings(itr)
-    result = StatsBase.countmap(collect(skipmissing(itr)))
-    return result
-end
-
-function get_countmap_include_missings(itr)
-    result = StatsBase.countmap(collect(itr))
-    return result
-end
 
 function get_unique_values(itr; skip_missings::Bool = true)
     if skip_missings
@@ -30,13 +10,11 @@ function get_unique_values(itr; skip_missings::Bool = true)
 end
 
 function get_unique_values_skip_missings(itr)
-    result = keys(get_countmap_skip_missings(itr))
-    return result
+    return unique(skipmissing(collect(itr)))
 end
 
-function get_unique_values_include_missings(itr)
-    result = keys(get_countmap_include_missings(itr))
-    return result
+function get_unique_values_include_missings(itr) 
+    return unique(collect(itr))
 end
 
 function get_number_of_unique_values(itr; skip_missings::Bool = true)::Int

test/Project.toml

@@ -1,8 +1,6 @@
 [deps]
-Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
 CSVFiles = "5d742f6a-9f54-50ce-8119-2520741973ca"
-CUDAapi = "3895d2a7-ec45-59b8-82bb-cfc6a382f9b3"
 Cassette = "7057c7e9-c182-5462-911a-8362d720325c"
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 ClassImbalance = "04a18a73-7590-580c-b363-eeca0919eb2a"

test/unit/toplevel/utils/constant_columns.jl

@@ -4,19 +4,6 @@ import Test
 
 x = Union{Missing, String}["foo", "bar", "foo", missing, "bar"]
 
-Test.@test(
-    length(keys(PredictMD.get_countmap(x; skip_missings = true))) == 2
-    )
-Test.@test(
-    length(keys(PredictMD.get_countmap(x; skip_missings = false))) == 3
-    )
-Test.@test(
-    length(keys(PredictMD.get_countmap_skip_missings(x))) == 2
-    )
-Test.@test(
-    length(keys(PredictMD.get_countmap_include_missings(x))) == 3
-    )
-
 Test.@test(
     length(PredictMD.get_unique_values(x; skip_missings = true)) == 2
     )