From 1c35b63793005ddf7b0a0a834c7c96a631526162 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 10 Jun 2020 00:23:05 +0000 Subject: [PATCH 1/2] CompatHelper: bump compat for "BlochSim" to "0.4" --- Project.toml | 2 +- test/Manifest.toml | 100 ++++++++++++++++++++------------------------- 2 files changed, 45 insertions(+), 57 deletions(-) diff --git a/Project.toml b/Project.toml index 9914c98..cda24d6 100644 --- a/Project.toml +++ b/Project.toml @@ -8,5 +8,5 @@ BlochSim = "5c0f8cbe-99a4-11e9-108b-216da9629524" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [compat] -BlochSim = "0.2, 0.3" +BlochSim = "0.2, 0.3, 0.4" julia = "1.2" diff --git a/test/Manifest.toml b/test/Manifest.toml index 14ce776..004e7ad 100644 --- a/test/Manifest.toml +++ b/test/Manifest.toml @@ -3,23 +3,17 @@ [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -[[BinDeps]] -deps = ["Libdl", "Pkg", "SHA", "URIParser", "Unicode"] -git-tree-sha1 = "66158ad56b4bf6cc8413b37d0b7bc52402682764" -uuid = "9e28174c-4ba2-5203-b857-d8d62c4213ee" -version = "1.0.0" - -[[BinaryProvider]] -deps = ["Libdl", "SHA"] -git-tree-sha1 = "5b08ed6036d9d3f0ee6369410b830f8873d4024c" -uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232" -version = "0.5.8" - [[Blosc]] -deps = ["BinaryProvider", "CMakeWrapper", "Compat", "Libdl"] -git-tree-sha1 = "71fb23581e1f0b0ae7be8ccf0ebfb3600e23ca41" +deps = ["Blosc_jll"] +git-tree-sha1 = "84cf7d0f8fd46ca6f1b3e0305b4b4a37afe50fd6" uuid = "a74b3585-a348-5f62-a45c-50e91977d574" -version = "0.5.1" +version = "0.7.0" + +[[Blosc_jll]] +deps = ["Libdl", "Lz4_jll", "Pkg", "Zlib_jll", "Zstd_jll"] +git-tree-sha1 = "aa9ef39b54a168c3df1b2911e7797e4feee50fbe" +uuid = "0b7ba130-8d10-5ba8-a3d6-c5182647fed9" +version = "1.14.3+1" [[BufferedStreams]] deps = ["Compat", "Test"] @@ -27,29 +21,17 @@ git-tree-sha1 = "5d55b9486590fdda5905c275bb21ce1f0754020f" uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d" version = "1.0.0" -[[CMake]] -deps = ["BinDeps"] -git-tree-sha1 = "50a8b41d2c562fccd9ab841085fc7d1e2706da82" -uuid = "631607c0-34d2-5d66-819e-eb0f9aa2061a" -version = "1.2.0" - -[[CMakeWrapper]] -deps = ["BinDeps", "CMake", "Libdl", "Parameters", "Test"] -git-tree-sha1 = "16d4acb3d37dc05b714977ffefa8890843dc8985" -uuid = "d5fb7624-851a-54ee-a528-d3f3bac0b4a0" -version = "0.2.3" - [[CodecZlib]] -deps = ["BinaryProvider", "Libdl", "TranscodingStreams"] -git-tree-sha1 = "05916673a2627dd91b4969ff8ba6941bc85a960e" +deps = ["TranscodingStreams", "Zlib_jll"] +git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.6.0" +version = "0.7.0" [[Compat]] -deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "ed2c4abadf84c53d9e58510b5fc48912c2336fbb" +deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] +git-tree-sha1 = "37964a28fa8231d769faa10eec8c4436253c48ba" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "2.2.0" +version = "3.11.0" [[Dates]] deps = ["Printf"] @@ -64,10 +46,16 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[HDF5]] -deps = ["BinaryProvider", "Blosc", "CMakeWrapper", "Libdl", "Mmap"] -git-tree-sha1 = "d3ea5532668bf9bdd5e8d5f16571e0b520cbbb9f" +deps = ["Blosc", "HDF5_jll", "Libdl", "Mmap", "Random"] +git-tree-sha1 = "7048678fa1970aaf867f3e99b90f3e85a9847124" uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" -version = "0.12.5" +version = "0.13.2" + +[[HDF5_jll]] +deps = ["Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "85bd2e586a10ae0eab856125bf5245e0d36384a7" +uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" +version = "1.10.5+5" [[InteractiveUtils]] deps = ["Markdown"] @@ -86,11 +74,17 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" +[[Lz4_jll]] +deps = ["Libdl", "Pkg"] +git-tree-sha1 = "e1a93171a400d4578193eaa39edd2d3f5db08fb6" +uuid = "5ced341a-0733-55b8-9ab6-a4889d929147" +version = "1.9.2+0" + [[MAT]] deps = ["BufferedStreams", "CodecZlib", "HDF5", "SparseArrays"] -git-tree-sha1 = "33db0ab3000dabd036867b3dd09b41c29a31ed9a" +git-tree-sha1 = "6a48d291b26d295c62670d956e083926332befb3" uuid = "23992714-dd62-5051-b70f-ba57cb901cac" -version = "0.7.0" +version = "0.8.0" [[Markdown]] deps = ["Base64"] @@ -99,18 +93,6 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" -[[OrderedCollections]] -deps = ["Random", "Serialization", "Test"] -git-tree-sha1 = "c4c13474d23c60d20a67b217f1d7f22a40edf8f1" -uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.1.0" - -[[Parameters]] -deps = ["OrderedCollections"] -git-tree-sha1 = "b62b2558efb1eef1fa44e4be5ff58a515c287e38" -uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" -version = "0.12.0" - [[Pkg]] deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Test", "UUIDs"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" @@ -158,15 +140,21 @@ git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.9.5" -[[URIParser]] -deps = ["Test", "Unicode"] -git-tree-sha1 = "6ddf8244220dfda2f17539fa8c9de20d6c575b69" -uuid = "30578b45-9adc-5946-b283-645ec420af67" -version = "0.4.0" - [[UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" [[Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" + +[[Zlib_jll]] +deps = ["Libdl", "Pkg"] +git-tree-sha1 = "a2e0d558f6031002e380a90613b199e37a8565bf" +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.11+10" + +[[Zstd_jll]] +deps = ["Libdl", "Pkg"] +git-tree-sha1 = "b25b0fb10176c42e9a5a20e1f40d570ac0288d4e" +uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" +version = "1.4.5+0" From edfdc3b0eb1b20062ffe540a7825b6fb49a130ba Mon Sep 17 00:00:00 2001 From: StevenWhitaker Date: Tue, 9 Jun 2020 21:16:20 -0400 Subject: [PATCH 2/2] Use `BlochSim.combine` (`combine` no longer exported). --- src/blochsim.jl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/blochsim.jl b/src/blochsim.jl index cac8d46..c5cb5a9 100644 --- a/src/blochsim.jl +++ b/src/blochsim.jl @@ -266,7 +266,7 @@ function stfrblochsim( Dtg = freeprecess(spin, Tg, grad) # Calculate steady-state magnetization immediately following excitation - (A, B) = combine(Dte, Dtr, Dtu, Dtg, Dtd) + (A, B) = BlochSim.combine(Dte, Dtr, Dtu, Dtg, Dtd) M = (Diagonal(ones(Bool, size(A, 1))) - A) \ B # Calculate steady-state signal at echo time @@ -304,7 +304,7 @@ function stfrblochsim( Dtg = freeprecess(spin, Tg - rfduration, grad) # Calculate steady-state magnetization immediately following excitation - (A, B) = combine(Dte, Dtr, Dtu, Dtg, Dtd) + (A, B) = BlochSim.combine(Dte, Dtr, Dtu, Dtg, Dtd) M = (Diagonal(ones(Bool, size(A, 1))) - A) \ B # Calculate steady-state signal at echo time @@ -330,7 +330,7 @@ function stfrblochsim( # Precompute spin dynamics Dte = freeprecess(spin, TE) Dtr = freeprecess(spin, Tfree - TE) - Dtetr = combine(Dte, Dtr) + Dtetr = BlochSim.combine(Dte, Dtr) Dtg = freeprecess(spin, Tg, grad) # Initialize RF spoiling parameters @@ -386,7 +386,7 @@ function stfrblochsim( # Precompute spin dynamics Dte = freeprecess(spin, TE - rfduration) Dtr = freeprecess(spin, Tfree - TE) - Dtetr = combine(Dte, Dtr) + Dtetr = BlochSim.combine(Dte, Dtr) Dtg = freeprecess(spin, Tg - rfduration, grad) # Initialize RF spoiling parameters