diff --git a/.github/actions/install-julia/action.yaml b/.github/actions/install-julia/action.yaml index b28c75f78..5456288f2 100644 --- a/.github/actions/install-julia/action.yaml +++ b/.github/actions/install-julia/action.yaml @@ -16,6 +16,7 @@ runs: key: julia-binary-${{ inputs.version }} restore-keys: | julia-binary-${{ inputs.version }} + - name: Install Julia if: steps.cache-julia.outputs.cache-hit != 'true' run: | @@ -23,10 +24,14 @@ runs: version=$(echo ${{ inputs.version }} | cut -d. -f1,2) wget https://julialang-s3.julialang.org/bin/linux/x64/$version/julia-${{ inputs.version }}-linux-x86_64.tar.gz -O ~/julia/julia.tar.gz shell: bash - - run: tar -xzf ~/julia/julia.tar.gz -C ~/julia --strip-components=1 + + - name: Unzip Julia + run: tar -xzf ~/julia/julia.tar.gz -C ~/julia --strip-components=1 shell: bash + - run: echo "$HOME/julia/bin" >> $GITHUB_PATH shell: bash + - uses: actions/cache@v3 with: path: | diff --git a/.github/workflows/test-EpiAware.yaml b/.github/workflows/test-EpiAware.yaml new file mode 100644 index 000000000..b5450c972 --- /dev/null +++ b/.github/workflows/test-EpiAware.yaml @@ -0,0 +1,17 @@ +name: Test EpiAware + +on: + pull_request: + push: + branches: [main] + +jobs: + test-EpiAware: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - uses: ./.github/actions/install-julia + with: + version: '1.10.0' + - name: Run unit tests for EpiAware + run: julia --project=EpiAware -e 'using Pkg; Pkg.test()' diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9a211540b..1d393e5a9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -25,4 +25,4 @@ repos: hooks: - id: detect-secrets args: ['--baseline', '.secrets.baseline'] - exclude: EpiAware/Manifest.toml + exclude: '.*/Manifest\.toml$' diff --git a/EpiAware/Manifest.toml b/EpiAware/Manifest.toml index db059e653..468231f77 100644 --- a/EpiAware/Manifest.toml +++ b/EpiAware/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.0" manifest_format = "2.0" -project_hash = "994dd97f3407acb923def45029b96a36ab4b1ffe" +project_hash = "b4d488971893c2da3a7e5ee0a7a6da358a2c3ba6" [[deps.ADTypes]] git-tree-sha1 = "41c37aa88889c171f1300ceac1313c06e891d245" diff --git a/EpiAware/Project.toml b/EpiAware/Project.toml index a40dab87f..af39a406e 100644 --- a/EpiAware/Project.toml +++ b/EpiAware/Project.toml @@ -5,7 +5,6 @@ version = "0.1.0-DEV" [deps] Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" -DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" Optim = "429524aa-4258-5aef-a3af-852621145aeb" @@ -19,9 +18,3 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] julia = "1.9,1.10" - -[extras] -Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" - -[targets] -test = ["Test"] diff --git a/EpiAware/test/Manifest.toml b/EpiAware/test/Manifest.toml new file mode 100644 index 000000000..e763aaa09 --- /dev/null +++ b/EpiAware/test/Manifest.toml @@ -0,0 +1,1369 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.10.0" +manifest_format = "2.0" +project_hash = "4e801d137527f7d9f5c027430e922fb6b4f9c643" + +[[deps.ADTypes]] +git-tree-sha1 = "41c37aa88889c171f1300ceac1313c06e891d245" +uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" +version = "0.2.6" + +[[deps.AbstractFFTs]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.5.0" +weakdeps = ["ChainRulesCore", "Test"] + + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" + AbstractFFTsTestExt = "Test" + +[[deps.AbstractMCMC]] +deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] +git-tree-sha1 = "63ae0647e8db221d63256820d1e346216c65ac66" +uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" +version = "5.0.0" + +[[deps.AbstractPPL]] +deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] +git-tree-sha1 = "917ad8da4becae82028aba80b7e25197f0c76dd1" +uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" +version = "0.7.0" + +[[deps.AbstractTrees]] +git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" +uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" +version = "0.4.4" + +[[deps.Accessors]] +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Test"] +git-tree-sha1 = "cb96992f1bec110ad211b7e410e57ddf7944c16f" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.35" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + Requires = "ae029012-a4dd-5104-9daa-d747884805df" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + +[[deps.Adapt]] +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608" +uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" +version = "3.7.2" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" + +[[deps.AdvancedHMC]] +deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] +git-tree-sha1 = "dfa0e3508fc3df81d28624b328f3b937c1df8bc2" +uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" +version = "0.6.1" + + [deps.AdvancedHMC.extensions] + AdvancedHMCCUDAExt = "CUDA" + AdvancedHMCMCMCChainsExt = "MCMCChains" + AdvancedHMCOrdinaryDiffEqExt = "OrdinaryDiffEq" + + [deps.AdvancedHMC.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" + OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" + +[[deps.AdvancedMH]] +deps = ["AbstractMCMC", "Distributions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "Random", "Requires"] +git-tree-sha1 = "1cc336be36fef7df68473a7d0d60ebba25958b9e" +uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" +version = "0.8.0" +weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"] + + [deps.AdvancedMH.extensions] + AdvancedMHForwardDiffExt = ["DiffResults", "ForwardDiff"] + AdvancedMHMCMCChainsExt = "MCMCChains" + AdvancedMHStructArraysExt = "StructArrays" + +[[deps.AdvancedPS]] +deps = ["AbstractMCMC", "Distributions", "Random", "Random123", "Requires", "StatsFuns"] +git-tree-sha1 = "672f7ce648e06f93fceefde463c5855d77b6915a" +uuid = "576499cb-2369-40b2-a588-c64705576edc" +version = "0.5.4" +weakdeps = ["Libtask"] + + [deps.AdvancedPS.extensions] + AdvancedPSLibtaskExt = "Libtask" + +[[deps.AdvancedVI]] +deps = ["Bijectors", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] +git-tree-sha1 = "1f919a9c59cf3dfc68b64c22c453a2e356fca473" +uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" +version = "0.2.4" + +[[deps.ArgCheck]] +git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" +uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" +version = "2.3.0" + +[[deps.ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" + +[[deps.ArrayInterface]] +deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "bbec08a37f8722786d87bedf84eae19c020c4efa" +uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" +version = "7.7.0" + + [deps.ArrayInterface.extensions] + ArrayInterfaceBandedMatricesExt = "BandedMatrices" + ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" + ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" + ArrayInterfaceTrackerExt = "Tracker" + + [deps.ArrayInterface.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + +[[deps.Artifacts]] +uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" + +[[deps.Atomix]] +deps = ["UnsafeAtomics"] +git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" +uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" +version = "0.1.0" + +[[deps.AxisAlgorithms]] +deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] +git-tree-sha1 = 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BijectorsTrackerExt = "Tracker" + BijectorsZygoteExt = "Zygote" + + [deps.Bijectors.weakdeps] + DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.CEnum]] +git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" +uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" +version = "0.5.0" + +[[deps.Calculus]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" +uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" +version = "0.5.1" + +[[deps.ChainRules]] +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = 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