Merge branch 'main' into compathelper/new_version/2024-07-30-00-57-20…

…-657-04239093220

.JuliaFormatter.toml

@@ -5,5 +5,5 @@ indent = 4
 format_docstrings = true
 separate_kwargs_with_semicolon = true
 always_for_in = true
-join_lines_based_on_source = false
+join_lines_based_on_source = true
 annotate_untyped_fields_with_any = false

.buildkite/testing.yml

@@ -54,5 +54,4 @@ steps:
               - "1"
 
 env:
-  JULIA_NUM_THREADS: 4
-  SECRET_CODECOV_TOKEN: "PxSr3Y7vdbiwaoX51uGykPsogxmP1IOBt5Z8TwP9GqDxIrvFocEVV2DR4Bebee12G/HYvXtQTyYXH49DpzlsfJ7ri1GQZxd9WRr+aM1DDYmzfDCfpadp4hMoJ5NQvmc/PzeGrNWOOaewaLTUP1eEaG4suygZN0lc5q9BCchIJeqoklGms5DVt/HtfTmwoD/s4wGoIJINi4RoFgnCAkzSh11hTAkyjVerfBGWEi/8E6+WBq3UKwaW4HnT02wG9qFnD4XkHpIpjMxJTpdBn5ufKI+QoJ7qJHlwqgDCtsOCblApccLTjH/BnTahNoSb/b0wdS/cblOTrtdPGzZ5UvmQ4Q==;U2FsdGVkX1/Ji2Nqeq3tqTYCBik6iXILP+rriPRqj/qxhFu4vBWWT3UnlfqDzj6oVdXyuKt0+5e+x33x2S0mBw=="
+  SECRET_CODECOV_TOKEN: "gZlC/IAmeUJehhP5mP2QuUV5a1qV61cvo4PUCLkA9vVkt3x6wgD6fTZmCm+f+gHkmkssFxX+q2h1Ud00XXc75H2LrjyR/cDTIthcO46BBOidYocv/U0gfhp6uT2IZ9fi+ryFfTVVpZ0RIUGmDTj0O/b5qt4oaTriAArLAq6mMipbIR9YCz7ZD/hWQXx8oDeAbnDpwQaddwPyhJhz95nayknOpuJj+ClaVOxgsLGZc3ZWiTj1QxkXBNwxLD2ALeG16Qxs9h7eK87sdcbWeTihvJ6OooARgpoVJAa2pJCFYOGy4Bh07c0VTZmicN2M3GIi74Y5T1PWNaz7nGeANO5Pow==;U2FsdGVkX1843DHkbGWCV9PArLBw0rNqmdy56VOTRNTifBSpkC796Oez1lMFU+yDtkElbcrRSIlS5hRFqpsaFA=="

.github/workflows/CI.yml

@@ -77,9 +77,6 @@ jobs:
       - uses: julia-actions/julia-downgrade-compat@v1
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
-        env:
-          RETESTITEMS_NWORKERS: 4
-          RETESTITEMS_NWORKER_THREADS: 2
       - uses: julia-actions/julia-processcoverage@v1
         with:
           directories: src,ext
@@ -121,5 +118,3 @@ jobs:
 
 env:
   BACKEND_GROUP: "CPU"
-  RETESTITEMS_NWORKERS: 4
-  RETESTITEMS_NWORKER_THREADS: 2

.github/workflows/CompatHelper.yml

@@ -37,8 +37,10 @@ jobs:
       - name: "Run CompatHelper"
         run: |
           import CompatHelper
-          CompatHelper.main()
+          subdirs = ["", "docs", "test"]
+          append!(subdirs, joinpath.(("examples",), filter(p -> isdir(joinpath("examples", p)), readdir("examples"))))
+          CompatHelper.main(; subdirs)
         shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/DocCleanUp.yml

@@ -0,0 +1,26 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "avik-pal"
+              git config user.email "[email protected]"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

.github/workflows/Documentation.yml

@@ -0,0 +1,53 @@
+# Sample workflow for building and deploying a VitePress site to GitHub Pages
+#
+name: Documenter
+
+on:
+  # Runs on pushes targeting the `master` branch. Change this to `main` if you're
+  # using the `main` branch as the default branch.
+  push:
+    branches:
+      - main
+    tags: ["*"]
+  pull_request:
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  actions: write
+  contents: write
+  pages: write
+  id-token: write
+  statuses: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v2
+      - name: Pull Julia cache
+        uses: julia-actions/cache@v2
+      - name: Install documentation dependencies
+        run: julia --project=docs -e 'using Pkg; Pkg.develop(Pkg.PackageSpec(path=".")); Pkg.instantiate(); Pkg.precompile(); Pkg.status()'
+      - name: Build the tutorials
+        run: julia --project=docs docs/tutorials.jl
+      - name: Build and deploy docs
+        uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+          GKSwstype: "100" # for Plots.jl plots (if you have them)
+          JULIA_DEBUG: "Documenter"
+          DATADEPS_ALWAYS_ACCEPT: true

.github/workflows/FormatPR.yml

@@ -15,7 +15,7 @@ jobs:
       # https://github.com/peter-evans/create-pull-request#reference-example
       - name: Create Pull Request
         id: cpr
-        uses: peter-evans/create-pull-request@v6
+        uses: peter-evans/create-pull-request@v7
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           commit-message: Format .jl files

.github/workflows/QualityCheck.yml

@@ -16,4 +16,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.23.5
+        uses: crate-ci/typos@v1.24.6

.gitignore

@@ -10,3 +10,9 @@ docs/site
 
 scripts
 test_ext
+
+package-lock.json
+node_modules
+
+*.cov
+tutorial_deps/

Artifacts.toml

@@ -1,111 +1,71 @@
 [alexnet]
-git-tree-sha1 = "8904a6756649aa4cd264328430b829dafde95645"
+git-tree-sha1 = "f1739363d54a358cae904133699a93eca7b7a028"
 lazy = true
 
     [[alexnet.download]]
-    sha256 = "e20107404aba1c2c0ed3fad4314033a2fa600cdc0c55d03bc1bfe4f8e5031105"
-    url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/alexnet.tar.gz"
-
-# [resnet101]
-# git-tree-sha1 = "6c9143d40950726405b88db0cc021fa1dcbc0896"
-# lazy = true
-
-#     [[resnet101.download]]
-#     sha256 = "3840f05b3d996b2b3ea1e8fb6617775fd60ad6b8769402200fdc9c8b8dca246f"
-#     url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/resnet101.tar.gz"
-
-# [resnet152]
-# git-tree-sha1 = "892915c44de37537aad97da3de8a4458dfa36297"
-# lazy = true
-
-#     [[resnet152.download]]
-#     sha256 = "6033a1ecc46d7f4ed1139067c5f9f5ea0d247656e9abbbe755c4702ec5a636d6"
-#     url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/resnet152.tar.gz"
-
-# [resnet18]
-# git-tree-sha1 = "1d4a46fee1bb87eeef0ce2c85f63cfe0ff47d4de"
-# lazy = true
-
-#     [[resnet18.download]]
-#     sha256 = "f4041ea1d1ec9bba86c7a5a519daaa49bb096a55fcd4ebf74f0743c8bdcb1c35"
-#     url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/resnet18.tar.gz"
-
-# [resnet34]
-# git-tree-sha1 = "306a8055ae9207ae2a316e31b376254557e481c9"
-# lazy = true
-
-#     [[resnet34.download]]
-#     sha256 = "d62e40ee9213ea9611e3fcedc958df4011da1fa108fb1537bac91e6b7778a3c8"
-#     url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/resnet34.tar.gz"
-
-# [resnet50]
-# git-tree-sha1 = "8c5866edb29b53f581a9ed7148efa1dbccde6133"
-# lazy = true
-
-#     [[resnet50.download]]
-#     sha256 = "275365d76e592c6ea35574853a75ee068767641664e7817aedf394fcd7fea25a"
-#     url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/resnet50.tar.gz"
+    sha256 = "feb3e1600179ba00b72a68759c7f3b12f400f6d59b28ac72b48614cbafa187d8"
+    url = "https://huggingface.co/LuxDL/alexnet/resolve/2c48051ecb131d38f2209470cdda70a343289db1/alexnet.tar.gz"
 
 [vgg11]
-git-tree-sha1 = "ea7e8ef9399a0fe0aad2331781af5d6435950d36"
+git-tree-sha1 = "2468801ab9bc7343c02a141e145e95209236b218"
 lazy = true
 
     [[vgg11.download]]
-    sha256 = "a88b78c4e939138270068933f6278fa6392ce699991385000b1b9bb0ff53fa3e"
-    url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/vgg11.tar.gz"
+    sha256 = "509567b428c02f7e9fa69ad7b6e0f62a1347ce6ec7fbad4e4cb4fddbf4f66b60"
+    url = "https://huggingface.co/LuxDL/vgg/resolve/ac7292d920627cdb66caee17420bfee5dbfe0f61/vgg11.tar.gz"
 
 [vgg11_bn]
-git-tree-sha1 = "6bb8128b150ac7ca30c32e34295d8d7403471942"
+git-tree-sha1 = "e444f279f7b6641da80f4910362d0ccb37a5fe96"
 lazy = true
 
     [[vgg11_bn.download]]
-    sha256 = "159392d11cb5ced5bfe66dc9da7bd12fbbf92687bbea9e9bb96bf0c6b58c9ef2"
-    url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/vgg11_bn.tar.gz"
+    sha256 = "8ed6002ccad7e204276d638e8bc288cce85f6b26f0a6d7cb5a85d714750a0cc7"
+    url = "https://huggingface.co/LuxDL/vgg/resolve/0ecfa4aea43abc4bbf27fd7f185ffda3fdc5d31a/vgg11_bn.tar.gz"
 
 [vgg13]
-git-tree-sha1 = "260246834e15048ec128fadc6d1a5dd050dd0928"
+git-tree-sha1 = "d9b0cc88a71a8eabe3375e9bb92b601cb0c984a5"
 lazy = true
 
     [[vgg13.download]]
-    sha256 = "757c555f47e2dd4898e89fcb6fb94f1a7a9977e4cdbdba5502eacd1d3496cf3b"
-    url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/vgg13.tar.gz"
+    sha256 = "4c554fb0d7ed976019c0d03ffe9ec6ed0cc88d8fa94a3405c65b55e138c5a7b7"
+    url = "https://huggingface.co/LuxDL/vgg/resolve/f4a690e83af5a8f9e907e33de0b2d53b8a6ad1cc/vgg13.tar.gz"
 
 [vgg13_bn]
-git-tree-sha1 = "623d2ae96cbf935ae09067fb7e85ca6894b79447"
+git-tree-sha1 = "12ac8f1c9fadfcd4fb80db270ffa17ec96375fb7"
 lazy = true
 
     [[vgg13_bn.download]]
-    sha256 = "3ccfb481b79bf56e6b70fefbc727127f5eb6de6478b1c57be669e5e5bb007377"
-    url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/vgg13_bn.tar.gz"
+    sha256 = "e6f69a7580a9af6eedbbb11c1c590ad6da4e57872dfdb2ac38f2e085d50b429b"
+    url = "https://huggingface.co/LuxDL/vgg/resolve/5f6acdbc972e0455428c4618c41ebedcd7d5b14b/vgg13_bn.tar.gz"
 
 [vgg16]
-git-tree-sha1 = "0e4d8a869e2688c765a3126c8a8c59e4a58fe97d"
+git-tree-sha1 = "8b85924419036f584e32aac9500b1d198a3b748a"
 lazy = true
 
     [[vgg16.download]]
-    sha256 = "79463750e1fd2424928b21a8d5d0cb2328c46e5cf39252600e0d132570bfd931"
-    url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/vgg16.tar.gz"
+    sha256 = "9e2905a02c4f2425e199b5d7b47aad9c6d2029850d2f2fd4d9c1a9d26dafb163"
+    url = "https://huggingface.co/LuxDL/vgg/resolve/d05baefb64db70c66ccfe6daa6e2a3b7ce8b3021/vgg16.tar.gz"
 
 [vgg16_bn]
-git-tree-sha1 = "b93f35dddcaec69444e0cfb709a19be4fb6be53f"
+git-tree-sha1 = "46d8299cc071102ceaf9e7d84699a7029dc0293a"
 lazy = true
 
     [[vgg16_bn.download]]
-    sha256 = "98f3e88c12fd07faa20505c864bfe2afc17e714ac5ddb4b05018fab25d9b3373"
-    url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/vgg16_bn.tar.gz"
+    sha256 = "b0fb3382434fd4f025f2e5517fc29b787aca093300d1a683d4dc10d380d102ed"
+    url = "https://huggingface.co/LuxDL/vgg/resolve/79b657b252c9b9a2f0fecb67c10ba4ec6c4fed0b/vgg16_bn.tar.gz"
 
 [vgg19]
-git-tree-sha1 = "8c0f1bdb7e540f1529a4038a0c73971debb1634b"
+git-tree-sha1 = "4dfc386f5da165daf80429b15a9a6bf7c2bf1b3b"
 lazy = true
 
     [[vgg19.download]]
-    sha256 = "2cedf1574207abe1989619aab292c51964dc27226b8852f0ce8a5acbc66ded31"
-    url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/vgg19.tar.gz"
+    sha256 = "662c7a63b07fdf52bb548a2019c31dd19d43e8675beb8fecf9ff3901ba36ef6e"
+    url = "https://huggingface.co/LuxDL/vgg/resolve/0268c4327e5ab4ae7172755bb767bf80dd792b0c/vgg19.tar.gz"
 
 [vgg19_bn]
-git-tree-sha1 = "fb3ec225e8a0b2eb838be682c6facceaa5b8aad3"
+git-tree-sha1 = "c0db4c840ae575da62ed28b3fcb29e3ca4da570a"
 lazy = true
 
     [[vgg19_bn.download]]
-    sha256 = "7a8d3d43ea092db4f53e721015078fcba4980dd5534a743f2b388165f8af185d"
-    url = "https://github.com/LuxDL/Lux.jl/releases/download/weights/vgg19_bn.tar.gz"
+    sha256 = "43a0005b4f4ad261773e5a9dd2241165c211be476d6bce8493fd470bfe16ef5f"
+    url = "https://huggingface.co/LuxDL/vgg/resolve/9b3f3be58a84e52b40f5489c481d954d0cf4f2b4/vgg19_bn.tar.gz"

Project.toml

@@ -1,82 +1,74 @@
 name = "Boltz"
 uuid = "4544d5e4-abc5-4dea-817f-29e4c205d9c8"
 authors = ["Avik Pal <[email protected]> and contributors"]
-version = "0.3.10"
+version = "1.0.0"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 ArgCheck = "dce04be8-c92d-5529-be00-80e4d2c0e197"
 Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 ConcreteStructs = "2569d6c7-a4a2-43d3-a901-331e8e4be471"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
 GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
-JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 Lux = "b2108857-7c20-44ae-9111-449ecde12c47"
 LuxCore = "bb33d45b-7691-41d6-9220-0943567d0623"
-LuxDeviceUtils = "34f89e08-e1d5-43b4-8944-0b49ac560553"
+MLDataDevices = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
 NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 WeightInitializers = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d"
 
 [weakdeps]
 DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
+DynamicExpressions = "a40a106e-89c9-4ca8-8020-a735e8728b6b"
+JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 Metalhead = "dbeba491-748d-5e0e-a39e-b530a07fa0cc"
+ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
+Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [extensions]
 BoltzDataInterpolationsExt = "DataInterpolations"
+BoltzDynamicExpressionsExt = "DynamicExpressions"
+BoltzJLD2Ext = "JLD2"
 BoltzMetalheadExt = "Metalhead"
+BoltzReverseDiffExt = "ReverseDiff"
+BoltzTrackerExt = "Tracker"
 BoltzZygoteExt = "Zygote"
 
 [compat]
-ADTypes = "1.3"
-Aqua = "0.8.7"
+ADTypes = "1.5"
 ArgCheck = "2.3"
 Artifacts = "1.10"
 ChainRulesCore = "1.24"
-ComponentArrays = "0.15.13"
+Compat = "4.15"
 ConcreteStructs = "0.2.3"
 DataInterpolations = "< 5.3, 6"
-ExplicitImports = "1.9"
+DynamicExpressions = "0.16, 0.17, 0.18, 0.19"
 ForwardDiff = "0.10.36"
+Functors = "0.4.12"
 GPUArraysCore = "0.1.6"
-JLD2 = "0.4.48"
+JLD2 = "0.5"
 LazyArtifacts = "1.10"
-Lux = "0.5.60"
-LuxCore = "0.1.16"
-LuxDeviceUtils = "0.1.26"
-LuxLib = "0.3.26"
-LuxTestUtils = "0.1.18"
+Lux = "1"
+LuxCore = "1"
+MLDataDevices = "1.1"
 Markdown = "1.10"
-Metalhead = "0.9"
-NNlib = "0.9.17"
-Pkg = "1.10"
+Metalhead = "0.9.4"
+NNlib = "0.9.21"
 Random = "1.10"
-ReTestItems = "1.24.0"
 Reexport = "1.2.2"
+ReverseDiff = "1.15"
+Static = "1.1.1"
 Statistics = "1.10"
-Test = "1.10"
-WeightInitializers = "0.1.7, 1"
+Tracker = "0.2.34"
+WeightInitializers = "1"
 Zygote = "0.6.70"
 julia = "1.10"
-
-[extras]
-Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
-ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
-DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
-ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
-LuxLib = "82251201-b29d-42c6-8e01-566dec8acb11"
-LuxTestUtils = "ac9de150-d08f-4546-94fb-7472b5760531"
-Metalhead = "dbeba491-748d-5e0e-a39e-b530a07fa0cc"
-Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-ReTestItems = "817f1d60-ba6b-4fd5-9520-3cf149f6a823"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
-
-[targets]
-test = ["Aqua", "ComponentArrays", "DataInterpolations", "ExplicitImports", "LuxLib", "LuxTestUtils", "Metalhead", "Pkg", "ReTestItems", "Test", "Zygote"]