Merge branch 'master' of https://github.com/FluxML/Flux.jl

Author: Dhairya Gandhi

.fluxbot/Manifest.toml

@@ -0,0 +1,152 @@
+# This file is machine-generated - editing it directly is not advised
+
+[[Artifacts]]
+deps = ["Pkg"]
+git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744"
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+version = "1.3.0"
+
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[Distributed]]
+deps = ["Random", "Serialization", "Sockets"]
+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[FluxBot]]
+deps = ["GitHub", "Glob", "Pkg", "Sockets"]
+git-tree-sha1 = "b9e6fca2afde87f29efa248edba9699e4ce746be"
+repo-rev = "master"
+repo-url = "https://github.com/dhairyagandhi96/FluxBot.jl"
+uuid = "352bd040-0f98-11ea-1faf-6f930ca83554"
+version = "0.1.0"
+
+[[GitHub]]
+deps = ["Base64", "Dates", "HTTP", "JSON", "MbedTLS", "Sockets", "SodiumSeal"]
+git-tree-sha1 = "a4f61fc1b1724e6eec1d9333eac2d4b01d8fcc8f"
+uuid = "bc5e4493-9b4d-5f90-b8aa-2b2bcaad7a26"
+version = "5.4.0"
+
+[[Glob]]
+git-tree-sha1 = "4df9f7e06108728ebf00a0a11edee4b29a482bb2"
+uuid = "c27321d9-0574-5035-807b-f59d2c89b15c"
+version = "1.3.0"
+
+[[HTTP]]
+deps = ["Base64", "Dates", "IniFile", "MbedTLS", "Sockets", "URIs"]
+git-tree-sha1 = "63055ee44b5c2b95ec1921edcf856c60124ff0c3"
+uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
+version = "0.9.2"
+
+[[IniFile]]
+deps = ["Test"]
+git-tree-sha1 = "098e4d2c533924c921f9f9847274f2ad89e018b8"
+uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f"
+version = "0.5.0"
+
+[[InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[JLLWrappers]]
+git-tree-sha1 = "a431f5f2ca3f4feef3bd7a5e94b8b8d4f2f647a0"
+uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
+version = "1.2.0"
+
+[[JSON]]
+deps = ["Dates", "Mmap", "Parsers", "Unicode"]
+git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4"
+uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+version = "0.21.1"
+
+[[LibGit2]]
+deps = ["Printf"]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[MbedTLS]]
+deps = ["Dates", "MbedTLS_jll", "Random", "Sockets"]
+git-tree-sha1 = "1c38e51c3d08ef2278062ebceade0e46cefc96fe"
+uuid = "739be429-bea8-5141-9913-cc70e7f3736d"
+version = "1.0.3"
+
+[[MbedTLS_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "0eef589dd1c26a3ac9d753fe1a8bcad63f956fa6"
+uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+version = "2.16.8+1"
+
+[[Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[Parsers]]
+deps = ["Dates"]
+git-tree-sha1 = "50c9a9ed8c714945e01cd53a21007ed3865ed714"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "1.0.15"
+
+[[Pkg]]
+deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[SodiumSeal]]
+deps = ["Base64", "Libdl", "libsodium_jll"]
+git-tree-sha1 = "80cef67d2953e33935b41c6ab0a178b9987b1c99"
+uuid = "2133526b-2bfb-4018-ac12-889fb3908a75"
+version = "0.1.1"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[URIs]]
+git-tree-sha1 = "7855809b88d7b16e9b029afd17880930626f54a2"
+uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
+version = "1.2.0"
+
+[[UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[libsodium_jll]]
+deps = ["Libdl", "Pkg"]
+git-tree-sha1 = "7127f5f40332ccfa43ee07dcd0c4d81a27d9bb23"
+uuid = "a9144af2-ca23-56d9-984f-0d03f7b5ccf8"
+version = "1.0.18+1"

.fluxbot/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+FluxBot = "352bd040-0f98-11ea-1faf-6f930ca83554"

.github/workflows/fluxbot.yml

@@ -0,0 +1,28 @@
+name: FluxBot
+
+on:
+  issue_comment:
+    types: [created, edited]
+
+jobs:
+  build:
+    if: contains(github.event.comment.body, '@ModelZookeeper')
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1.5.0]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: actions/checkout@af513c7a016048ae468971c52ed77d9562c7c819 # v1.0.0
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+      - name: Install dependencies
+        run: julia --project=.fluxbot/ -e 'using Pkg; Pkg.instantiate()'
+      - name: FluxBot.respond
+        env:
+          FLUXBOT_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BOT_SECRET: ${{ secrets.BOT_SECRET }}
+          MODELZOO_TRIGGER_TOKEN: ${{ secrets.MODELZOO_TRIGGER_TOKEN }}
+        run: julia --project=.fluxbot -e 'using FluxBot; FluxBot.trial()'

Manifest.toml

@@ -14,9 +14,9 @@ version = "0.3.3"
 
 [[Adapt]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "27edd95a09fd428113ca019c092e8aeca2eb1f2d"
+git-tree-sha1 = "87491f7d03ae1b423a353aff99cf61a45e3c993a"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "3.0.0"
+version = "3.1.0"
 
 [[Artifacts]]
 deps = ["Pkg"]
@@ -40,21 +40,21 @@ version = "0.4.1"
 
 [[CUDA]]
 deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CompilerSupportLibraries_jll", "DataStructures", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "Logging", "MacroTools", "NNlib", "Pkg", "Printf", "Random", "Reexport", "Requires", "SparseArrays", "Statistics", "TimerOutputs"]
-git-tree-sha1 = "39f6f584bec264ace76f924d1c8637c85617697e"
+git-tree-sha1 = "6ccc73b2d8b671f7a65c92b5f08f81422ebb7547"
 uuid = "052768ef-5323-5732-b1bb-66c8b64840ba"
-version = "2.4.0"
+version = "2.4.1"
 
 [[ChainRules]]
 deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "Reexport", "Requires", "Statistics"]
-git-tree-sha1 = "31b28f5123afa5e5ca0c885e4051896032754578"
+git-tree-sha1 = "6ba8100fa9356807f1d0df6468ae463c67627c30"
 uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2"
-version = "0.7.45"
+version = "0.7.49"
 
 [[ChainRulesCore]]
-deps = ["LinearAlgebra", "MuladdMacro", "SparseArrays"]
-git-tree-sha1 = "15081c431bb25848ad9b0d172a65794f3a3e197a"
+deps = ["Compat", "LinearAlgebra", "SparseArrays"]
+git-tree-sha1 = "53fed426c9af1eb68e63b3999e96454c2db79757"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "0.9.24"
+version = "0.9.27"
 
 [[CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
@@ -99,9 +99,9 @@ version = "1.4.0"
 
 [[DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "fb0aa371da91c1ff9dc7fbed6122d3e411420b9c"
+git-tree-sha1 = "4437b64df1e0adccc3e5d1adbc3ac741095e4677"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.18.8"
+version = "0.18.9"
 
 [[Dates]]
 deps = ["Printf"]
@@ -134,9 +134,9 @@ version = "0.1.3"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "ff537e5a3cba92fb48f30fec46723510450f2c0e"
+git-tree-sha1 = "8bd8e47ff5d34b20f0aa9641988eb660590008bc"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.10.2"
+version = "0.11.0"
 
 [[FixedPointNumbers]]
 deps = ["Statistics"]
@@ -146,15 +146,15 @@ version = "0.8.4"
 
 [[ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"]
-git-tree-sha1 = "8de2519a83c6c1c2442c2f481dd9a8364855daf4"
+git-tree-sha1 = "c26b56e9b9f0687f7ca887f6b6ded03d269e0e35"
 uuid = "f6369f11-7733-5829-9624-2563aa707210"
-version = "0.10.14"
+version = "0.10.15"
 
 [[Functors]]
 deps = ["MacroTools"]
-git-tree-sha1 = "f40adc6422f548176bb4351ebd29e4abf773040a"
+git-tree-sha1 = "cd79039c468eac0a15256c55f260eec7ce551d07"
 uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
-version = "0.1.0"
+version = "0.2.0"
 
 [[GPUArrays]]
 deps = ["AbstractFFTs", "Adapt", "LinearAlgebra", "Printf", "Random", "Serialization"]
@@ -191,9 +191,9 @@ version = "0.8.4"
 
 [[LLVM]]
 deps = ["CEnum", "Libdl", "Printf", "Unicode"]
-git-tree-sha1 = "d0d99629d6ae4a3e211ae83d8870907bd842c811"
+git-tree-sha1 = "b616937c31337576360cb9fb872ec7633af7b194"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "3.5.2"
+version = "3.6.0"
 
 [[LibGit2]]
 deps = ["Printf"]
@@ -234,16 +234,11 @@ version = "0.4.4"
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
-[[MuladdMacro]]
-git-tree-sha1 = "c6190f9a7fc5d9d5915ab29f2134421b12d24a68"
-uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
-version = "0.2.2"
-
 [[NNlib]]
-deps = ["ChainRulesCore", "LinearAlgebra", "Pkg", "Requires", "Statistics"]
-git-tree-sha1 = "13fd29731c7f609cb82a3a544c5538584d22c153"
+deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Pkg", "Requires", "Statistics"]
+git-tree-sha1 = "573cc0d31f9697b9d2b060130a7a3c05a4f36b78"
 uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
-version = "0.7.11"
+version = "0.7.12"
 
 [[NaNMath]]
 git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb"
@@ -282,10 +277,9 @@ deps = ["Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[Reexport]]
-deps = ["Pkg"]
-git-tree-sha1 = "7b1d07f411bc8ddb7977ec7f377b97b158514fe0"
+git-tree-sha1 = "57d8440b0c7d98fc4f889e478e80f268d534c9d5"
 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
-version = "0.2.0"
+version = "1.0.0"
 
 [[Requires]]
 deps = ["UUIDs"]
@@ -381,9 +375,9 @@ version = "1.2.11+18"
 
 [[Zygote]]
 deps = ["AbstractFFTs", "ChainRules", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"]
-git-tree-sha1 = "d88a7e71fc2eef9510187b1c7d4af7a5177633d0"
+git-tree-sha1 = "746c9de7fb87a341c809437007cbd172c4d494b4"
 uuid = "e88e6eb3-aa80-5325-afca-941959d7151f"
-version = "0.6.0"
+version = "0.6.2"
 
 [[ZygoteRules]]
 deps = ["MacroTools"]

NEWS.md

@@ -6,11 +6,12 @@
 * Dense and Conv layers no longer perform  [implicit type conversion](https://github.com/FluxML/Flux.jl/pull/1394).
 * Excise datasets in favour of other providers in the julia ecosystem.
 * Added option to set `bias` to [false](https://github.com/FluxML/Flux.jl/pull/1379) to eliminating `bias` from being trained.
+* Add [CTC loss function](https://github.com/FluxML/Flux.jl/pull/1287) to Losses module
 * Removed kwarg only constructors for [`convolutional layers`](https://github.com/FluxML/Flux.jl/pull/1379).
 * Add [sparse initialization](https://github.com/FluxML/Flux.jl/pull/1454) as described in [Deep learning via Hessian-free optimization](https://dl.acm.org/doi/abs/10.5555/3104322.3104416).
 * Moved GPU CI to use buildkite instead of GitLab
 * New [`Parallel` layer](https://github.com/FluxML/Flux.jl/pull/1462) adds inception module-like building blocks.
-* Other new features and bug fixes (see GitHub releases page)
+
 
 ## v0.11.2
 

Project.toml

@@ -31,7 +31,7 @@ Adapt = "2.0, 3.0"
 CUDA = "2.1"
 CodecZlib = "0.7"
 Colors = "0.12"
-Functors = "0.1"
+Functors = "0.1, 0.2"
 Juno = "0.8"
 MacroTools = "0.5"
 NNlib = "0.7.10"

docs/src/ecosystem.md

@@ -17,4 +17,4 @@ machine learning and deep learning workflows:
 - [ProgressMeters.jl](https://github.com/timholy/ProgressMeter.jl): progress meters for long-running computations
 - [TensorBoardLogger.jl](https://github.com/PhilipVinc/TensorBoardLogger.jl): easy peasy logging to [tensorboard](https://www.tensorflow.org/tensorboard) in Julia
 
-This tight integration among Julia pakages is shown in some of the examples in the [model-zoo](https://github.com/FluxML/model-zoo) repository.
+This tight integration among Julia packages is shown in some of the examples in the [model-zoo](https://github.com/FluxML/model-zoo) repository.

docs/src/training/training.md

@@ -7,13 +7,36 @@ To actually train a model we need four things:
 * A collection of data points that will be provided to the objective function.
 * An [optimiser](optimisers.md) that will update the model parameters appropriately.
 
-With these we can call `train!`:
+Training a model is typically an iterative process, where we go over the data set,
+calculate the objective function over the datapoints, and optimise that.
+This can be visualised in the form of a simple loop.
+
+```julia
+for d in datapoints
+
+  # `d` should produce a collection of arguments
+  # to the loss function
+
+  # Calculate the gradients of the parameters
+  # with respect to the loss function
+  grads = Flux.gradient(parameters) do
+    loss(d...)
+  end
+
+  # Update the parameters based on the chosen
+  # optimiser (opt)
+  Flux.Optimise.update!(opt, parameters, grads)
+end
+```
+
+To make it easy, Flux defines `train!`:
 
 ```@docs
 Flux.Optimise.train!
 ```
 
-There are plenty of examples in the [model zoo](https://github.com/FluxML/model-zoo).
+There are plenty of examples in the [model zoo](https://github.com/FluxML/model-zoo), and
+more information can be found on [Custom Training Loops](../models/advanced.md).
 
 ## Loss Functions