Merge branch 'master' of github.com:MillironX/docker-JuliaPro

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>

.github/workflows/build_docker.yml

@@ -14,9 +14,6 @@ jobs:
       - name: Extract Tag Name 🕵️
         id: tag-name
         uses: olegtarasov/get-tag@v2.1
-      - name: Extract Short Hash 🕵️
-        id: hash
-        uses: pr-mpt/actions-commit-hash@v1
       - name: Install QEMU 🖥️
         uses: docker/setup-qemu-action@v1
       - name: Install Docker 🐋
@@ -43,9 +40,9 @@ jobs:
         with:
           push: true
           tags: |
-            millironx/biojulia:latest
+            millironx/juliapro:latest
-            millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}
+            millironx/juliapro:${{ steps.tag-name.outputs.tag }}
-            quay.io/millironx/biojulia:latest
+            quay.io/millironx/juliapro:latest
-            quay.io/millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}
+            quay.io/millironx/juliapro:${{ steps.tag-name.outputs.tag }}
-            ghcr.io/millironx/biojulia:latest
+            ghcr.io/millironx/juliapro:latest
-            ghcr.io/millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}
+            ghcr.io/millironx/juliapro:${{ steps.tag-name.outputs.tag }}

.github/workflows/update.yml

@@ -0,0 +1,40 @@
+name: Update Packages
+on:
+  schedule:
+    - cron: "0 0 1,15 * *"
+  workflow_dispatch:
+
+jobs:
+  pkg_up:
+    name: Update Packages
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: "1.6"
+      - id: julia_ver
+        run: |
+          echo "::set-output name=version::$(julia -v | awk '{print $3}')"
+      - run: |
+          julia --project=${GITHUB_WORKSPACE} -e '
+            using Pkg
+            Pkg.instantiate()
+            Pkg.update()'
+      - id: time
+        uses: nanzm/get-time-action@v1.1
+        with:
+          format: "YYYY-MM-DD"
+      - uses: devops-infra/action-commit-push@v0.9.0
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          commit_message: "[⚡ AUTOMATED]: Pkg upgrade for ${{ steps.time.outputs.time }}"
+      - id: hash
+        run: |
+          echo "::set-output name=short_hash::$(git rev-parse --short HEAD)"
+          echo "::set-output name=long_hash::$(git rev-parse HEAD)"
+      - uses: mathieudutour/github-tag-action@v6.0
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          commit_sha: ${{ steps.hash.outputs.long_hash }}
+          custom_tag: ${{ steps.julia_ver.outputs.version }}-${{ steps.hash.outputs.short_hash }}

Dockerfile

@@ -1,4 +1,4 @@
-FROM julia:1.6.5-bullseye
+FROM julia:1.6-bullseye
 
 ENV JULIA_DEPOT_PATH="/usr/local/share/julia"
 
@@ -12,7 +12,7 @@ COPY Project.toml /
 COPY Manifest.toml /
 
 RUN julia -e 'using Pkg; Pkg.instantiate()'
-RUN julia --project=/ -e 'using Pkg; Pkg.instantiate()'
+RUN julia --project=/ -e 'using Pkg; Pkg.instantiate(); Pkg.update()'
 RUN \
   mv /Project.toml ${JULIA_DEPOT_PATH}/environments/v1.6/ && \
   mv /Manifest.toml ${JULIA_DEPOT_PATH}/environments/v1.6/

Manifest.toml

@@ -17,6 +17,12 @@ git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 version = "3.3.3"
 
+[[ArgParse]]
+deps = ["Logging", "TextWrap"]
+git-tree-sha1 = "3102bce13da501c9104df33549f511cd25264d7d"
+uuid = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
+version = "1.1.4"
+
 [[ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
 
@@ -78,9 +84,9 @@ version = "1.0.1"
 
 [[AxisArrays]]
 deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"]
-git-tree-sha1 = "d127d5e4d86c7680b20c35d40b503c74b9a39b5e"
+git-tree-sha1 = "cf6875678085aed97f52bfc493baaebeb6d40bcb"
 uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
-version = "0.4.4"
+version = "0.4.5"
 
 [[BBI]]
 deps = ["BioCore", "Libz"]
@@ -617,9 +623,9 @@ version = "3.3.10+0"
 
 [[FastBroadcast]]
 deps = ["LinearAlgebra", "Polyester", "Static"]
-git-tree-sha1 = "f39bcc05eb0dcbd2c0195762df7a5737041289b9"
+git-tree-sha1 = "b6bf57ec7a3f294c97ae46124705a9e6b906a209"
 uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
-version = "0.1.14"
+version = "0.1.15"
 
 [[FastClosures]]
 git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef"
@@ -695,10 +701,10 @@ uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7"
 version = "2.10.4+0"
 
 [[FreeTypeAbstraction]]
-deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics", "StaticArrays"]
+deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"]
-git-tree-sha1 = "8e76bcd47f98ee25c8f8be4b9a1c60f48efa4f9e"
+git-tree-sha1 = "b5c7fe9cea653443736d264b85466bad8c574f4a"
 uuid = "663a7486-cb36-511b-a19d-713bb74d65c9"
-version = "0.9.7"
+version = "0.9.9"
 
 [[FriBidi_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -729,9 +735,9 @@ version = "3.3.6+0"
 
 [[GLM]]
 deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "StatsModels"]
-git-tree-sha1 = "fb764dacfa30f948d52a6a4269ae293a479bbc62"
+git-tree-sha1 = "609115155b0dc532fa5130de65ed086efd27bfbd"
 uuid = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
-version = "1.6.1"
+version = "1.6.2"
 
 [[GMP_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -1153,9 +1159,9 @@ version = "2.1.2+0"
 
 [[JuliaInterpreter]]
 deps = ["CodeTracking", "InteractiveUtils", "Random", "UUIDs"]
-git-tree-sha1 = "9c43a2eb47147a8776ca2ba489f15a9f6f2906f8"
+git-tree-sha1 = "cd6ce9cee498f6b044357cb439f2a3fea3d450df"
 uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a"
-version = "0.9.11"
+version = "0.9.12"
 
 [[JuliaWebAPI]]
 deps = ["Base64", "HTTP", "JSON", "Serialization", "Sockets", "ZMQ"]
@@ -1189,9 +1195,9 @@ version = "0.2.5"
 
 [[Krylov]]
 deps = ["LinearAlgebra", "Printf", "SparseArrays"]
-git-tree-sha1 = "a024280a69c49f51ba29d2deb66f07508f0b9b49"
+git-tree-sha1 = "82f5afb342a5624dc4651981584a841f6088166b"
 uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
-version = "0.7.13"
+version = "0.8.0"
 
 [[KrylovKit]]
 deps = ["LinearAlgebra", "Printf"]
@@ -1347,9 +1353,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[LinearSolve]]
 deps = ["ArrayInterface", "DocStringExtensions", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "SuiteSparse", "UnPack"]
-git-tree-sha1 = "a25bc80647e44d0e1e1694b47000603497700b18"
+git-tree-sha1 = "6eb8e10ed29b85673495c29bd77ee0dfa8929977"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "1.13.0"
+version = "1.15.0"
 
 [[LittleCMS_jll]]
 deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pkg"]
@@ -1368,9 +1374,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[LoopVectorization]]
 deps = ["ArrayInterface", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDDualNumbers", "SLEEFPirates", "SpecialFunctions", "Static", "ThreadingUtilities", "UnPack", "VectorizationBase"]
-git-tree-sha1 = "077c7c9d746cbe30ac5f001ea4c1277f64cc5dad"
+git-tree-sha1 = "aa73a4f9379db5b4d573bce890289fb34239403d"
 uuid = "bdcacae8-1622-11e9-2a5c-532679323890"
-version = "0.12.103"
+version = "0.12.105"
 
 [[Lz4_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -1650,9 +1656,9 @@ version = "1.4.1"
 
 [[OrdinaryDiffEq]]
 deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
-git-tree-sha1 = "509aa6d3b2773e5109d4a4dd9a300259ac727961"
+git-tree-sha1 = "adb3b4eec5bd0234dc55b7459d61276a870436c2"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.7.1"
+version = "6.8.0"
 
 [[PCRE_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -1725,10 +1731,10 @@ uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688"
 version = "0.1.1"
 
 [[PlotThemes]]
-deps = ["PlotUtils", "Requires", "Statistics"]
+deps = ["PlotUtils", "Statistics"]
-git-tree-sha1 = "a3a964ce9dc7898193536002a6dd892b1b5a6f1d"
+git-tree-sha1 = "8162b2f8547bc23876edd0c5181b27702ae58dce"
 uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a"
-version = "2.0.1"
+version = "3.0.0"
 
 [[PlotUtils]]
 deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"]
@@ -1738,9 +1744,9 @@ version = "1.2.0"
 
 [[Plots]]
 deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"]
-git-tree-sha1 = "edec0846433f1c1941032385588fd57380b62b59"
+git-tree-sha1 = "88ee01b02fba3c771ac4dce0dfc4ecf0cb6fb772"
 uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "1.27.4"
+version = "1.27.5"
 
 [[PoissonRandom]]
 deps = ["Random", "Statistics", "Test"]
@@ -1866,9 +1872,9 @@ version = "0.16.3"
 
 [[Quaternions]]
 deps = ["DualNumbers", "LinearAlgebra", "Random"]
-git-tree-sha1 = "522770af103809e8346aefa4b25c31fbec377ccf"
+git-tree-sha1 = "3754f35199da1bb4a55211ddbfd64cb1efee2272"
 uuid = "94ee1d12-ae83-5a48-8b1c-48b8ff168ae0"
-version = "0.5.3"
+version = "0.5.4"
 
 [[REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
@@ -1979,9 +1985,9 @@ version = "0.3.0+0"
 
 [[Roots]]
 deps = ["CommonSolve", "Printf", "Setfield"]
-git-tree-sha1 = "6085b8ac184add45b586ed8d74468310948dcfe8"
+git-tree-sha1 = "838b60ee62bebc794864c880a47e331e00c47505"
 uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
-version = "1.4.0"
+version = "1.4.1"
 
 [[Rotations]]
 deps = ["LinearAlgebra", "Quaternions", "Random", "StaticArrays", "Statistics"]
@@ -2153,9 +2159,9 @@ version = "0.33.16"
 
 [[StatsFuns]]
 deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
-git-tree-sha1 = "25405d7016a47cf2bd6cd91e66f4de437fd54a07"
+git-tree-sha1 = "72e6abd6fc9ef0fa62a159713c83b7637a14b2b8"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "0.9.16"
+version = "0.9.17"
 
 [[StatsModels]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsBase", "StatsFuns", "Tables"]
@@ -2183,9 +2189,9 @@ version = "6.46.0"
 
 [[StrideArraysCore]]
 deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "Requires", "SIMDTypes", "Static", "ThreadingUtilities"]
-git-tree-sha1 = "28debdcb4371020f89ffce06af4f7f68905a5fec"
+git-tree-sha1 = "c7e0392560f15771003cce388fe8471d17941374"
 uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da"
-version = "0.2.15"
+version = "0.2.19"
 
 [[StringEncodings]]
 deps = ["Libiconv_jll"]
@@ -2273,6 +2279,11 @@ version = "0.1.1"
 deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
+[[TextWrap]]
+git-tree-sha1 = "9250ef9b01b66667380cf3275b3f7488d0e25faf"
+uuid = "b718987f-49a8-5099-9789-dcd902bef87d"
+version = "1.0.1"
+
 [[ThreadingUtilities]]
 deps = ["ManualMemory"]
 git-tree-sha1 = "f8629df51cab659d70d2e5618a430b4d3f37f2c3"
@@ -2346,9 +2357,9 @@ version = "0.4.1"
 
 [[UnicodePlots]]
 deps = ["ColorTypes", "Contour", "Crayons", "Dates", "FileIO", "FreeTypeAbstraction", "LinearAlgebra", "MarchingCubes", "NaNMath", "SparseArrays", "StaticArrays", "StatsBase", "Unitful"]
-git-tree-sha1 = "e7b68f6d25a79dff79acbd3bcf324db4385c2c6f"
+git-tree-sha1 = "c3bab41f0910b8e3e70d88ee24a68ab952ec0a76"
 uuid = "b8865327-cd53-5732-bb35-84acbb429228"
-version = "2.10.1"
+version = "2.10.3"
 
 [[Unitful]]
 deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"]
@@ -2369,9 +2380,9 @@ version = "0.5.3"
 
 [[VectorizationBase]]
 deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "Hwloc", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"]
-git-tree-sha1 = "a48484def839a98571683a8b5b942fc910329480"
+git-tree-sha1 = "460aacceb20a12ec187eb8ca183c5944dc6c99c4"
 uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"
-version = "0.21.26"
+version = "0.21.28"
 
 [[VertexSafeGraphs]]
 deps = ["Graphs"]

Project.toml

@@ -2,6 +2,7 @@
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
 BED = "8e4a8c10-cb6b-11e8-08d2-83478d609d67"
 BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 BigWig = "9d649c22-cb6b-11e8-1fa9-f3896fced444"
 BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"