diff --git a/.github/workflows/build.yml b/.github/workflows/build_docker.yml similarity index 69% rename from .github/workflows/build.yml rename to .github/workflows/build_docker.yml index 1c66726..cdf416c 100644 --- a/.github/workflows/build.yml +++ b/.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/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} - quay.io/millironx/biojulia:latest - quay.io/millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} - ghcr.io/millironx/biojulia:latest - ghcr.io/millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} + millironx/juliapro:latest + millironx/juliapro:${{ steps.tag-name.outputs.tag }} + quay.io/millironx/juliapro:latest + quay.io/millironx/juliapro:${{ steps.tag-name.outputs.tag }} + ghcr.io/millironx/juliapro:latest + ghcr.io/millironx/juliapro:${{ steps.tag-name.outputs.tag }} diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml new file mode 100644 index 0000000..da12f18 --- /dev/null +++ b/.github/workflows/update.yml @@ -0,0 +1,40 @@ +name: Update Packages +on: + schedule: + - cron: "0 0 1,15 * *" + workflow_dispatch: + +jobs: + pkg_up: + name: Update Packages + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - uses: julia-actions/setup-julia@v1 + with: + version: "1.6" + - id: julia_ver + run: | + echo "::set-output name=version::$(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 }} diff --git a/Dockerfile b/Dockerfile index 65876ca..e279405 100644 --- a/Dockerfile +++ b/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/ diff --git a/Manifest.toml b/Manifest.toml index 815d9a3..8c51f0e 100644 --- a/Manifest.toml +++ b/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"] -git-tree-sha1 = "8e76bcd47f98ee25c8f8be4b9a1c60f48efa4f9e" +deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] +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"] -git-tree-sha1 = "a3a964ce9dc7898193536002a6dd892b1b5a6f1d" +deps = ["PlotUtils", "Statistics"] +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"] diff --git a/Project.toml b/Project.toml index c72beaa..7719911 100644 --- a/Project.toml +++ b/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"