refactor: general cleanup of internals and documentation

.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

.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 +1,51 @@
+# 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@v1
+      - name: Pull Julia cache
+        uses: julia-actions/cache@v1
+      - name: Install documentation dependencies
+        run: julia --project=docs -e 'using Pkg; pkg"dev ."; Pkg.instantiate(); Pkg.precompile(); Pkg.status()'
+      - 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

.gitignore

@@ -10,3 +10,6 @@ docs/site
 
 scripts
 test_ext
+
+package-lock.json
+node_modules

Project.toml

@@ -1,13 +1,14 @@
 name = "Boltz"
 uuid = "4544d5e4-abc5-4dea-817f-29e4c205d9c8"
 authors = ["Avik Pal <[email protected]> and contributors"]
-version = "0.3.11"
+version = "0.3.12"
 
 [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"
 GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
@@ -36,23 +37,24 @@ BoltzZygoteExt = "Zygote"
 [compat]
 ADTypes = "1.5"
 ArgCheck = "2.3"
-Artifacts = "1.10, 1"
+Artifacts = "1.10"
 ChainRulesCore = "1.24"
+Compat = "4.15"
 ConcreteStructs = "0.2.3"
 DataInterpolations = "< 5.3"
 ForwardDiff = "0.10.36"
 GPUArraysCore = "0.1.6"
 JLD2 = "0.4.48"
 LazyArtifacts = "1.10"
-Lux = "0.5.62"
-LuxCore = "0.1.21"
-MLDataDevices = "1.0.0"
+Lux = "0.5.65"
+LuxCore = "0.1.24"
+MLDataDevices = "1.0.1"
 Markdown = "1.10"
 Metalhead = "0.9"
 NNlib = "0.9.21"
 Random = "1.10"
 Reexport = "1.2.2"
 Statistics = "1.10"
-WeightInitializers = "0.1.7, 1"
+WeightInitializers = "1"
 Zygote = "0.6.70"
 julia = "1.10"

README.md

@@ -1,13 +1,18 @@
 # Boltz ⚡
 
-[![Join the chat at https://julialang.zulipchat.com #machine-learning](https://img.shields.io/static/v1?label=Zulip&message=chat&color=9558b2&labelColor=389826)](https://julialang.zulipchat.com/#narrow/stream/machine-learning)
-[![Latest Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://lux.csail.mit.edu/dev/api/Domain_Specific_Modeling/Boltz)
-[![Stable Docs](https://img.shields.io/badge/docs-stable-blue.svg)](https://lux.csail.mit.edu/stable/api/Domain_Specific_Modeling/Boltz)
+[![GitHub Discussions](https://img.shields.io/github/discussions/LuxDL/Lux.jl?color=white&logo=github&label=Discussions)](https://github.com/LuxDL/Lux.jl/discussions)
+[![Latest Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://luxdl.github.io/Boltz.jl/stable/)
+[![Stable Docs](https://img.shields.io/badge/docs-stable-blue.svg)](https://luxdl.github.io/Boltz.jl/dev/)
 
 [![CI](https://github.com/LuxDL/Boltz.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/LuxDL/Boltz.jl/actions/workflows/CI.yml)
+[![Build status](https://badge.buildkite.com/33d66eb556ba88f60e733e97ff65c133fdb5f0ac683e823cfb.svg?branch=main)](https://buildkite.com/julialang/boltz-dot-jl)
 [![codecov](https://codecov.io/gh/LuxDL/Boltz.jl/branch/main/graph/badge.svg?token=YBImUxz5qO)](https://codecov.io/gh/LuxDL/Boltz.jl)
-[![Package Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/Boltz)](https://pkgs.genieframework.com?packages=Boltz)
 
+[![Downloads](https://img.shields.io/badge/dynamic/json?url=http%3A%2F%2Fjuliapkgstats.com%2Fapi%2Fv1%2Fmonthly_downloads%2FBoltz&query=total_requests&suffix=%2Fmonth&label=Downloads)](https://juliapkgstats.com/pkg/Boltz)
+[![Downloads](https://img.shields.io/badge/dynamic/json?url=http%3A%2F%2Fjuliapkgstats.com%2Fapi%2Fv1%2Ftotal_downloads%2FBoltz&query=total_requests&&label=Total%20Downloads)](https://juliapkgstats.com/pkg/Boltz)
+
+[![JET Testing](https://img.shields.io/badge/%F0%9F%9B%A9%EF%B8%8F_tested_with-JET.jl-233f9a)](https://github.com/aviatesk/JET.jl)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
 [![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)
 
@@ -25,20 +30,5 @@ Pkg.add("Boltz")
 ```julia
 using Boltz, Lux, Metalhead
 
-model, ps, st = resnet(:alexnet; pretrained=true)
+model, ps, st = Vision.AlexNet(; pretrained=true)
 ```
-
-## Changelog
-
-
-### Updating from v0.2 to v0.3
-
-CUDA is not loaded by default. To use GPUs follow
-[Lux.jl documentation](https://lux.csail.mit.edu/stable/manual/gpu_management/).
-
-### Updating from v0.1 to v0.2
-
-We have moved some dependencies into weak dependencies. This means that you will have to
-manually load them for certain features to be available.
-
-* To load Flux & Metalhead models, do `using Metalhead`.

docs/Project.toml

@@ -0,0 +1,7 @@
+[deps]
+Boltz = "4544d5e4-abc5-4dea-817f-29e4c205d9c8"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+DocumenterVitepress = "4710194d-e776-4893-9690-8d956a29c365"
+Lux = "b2108857-7c20-44ae-9111-449ecde12c47"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

docs/make.jl

@@ -0,0 +1,42 @@
+using Documenter, DocumenterVitepress, DocumenterCitations, Boltz
+
+#! format: off
+pages = [
+    "Boltz.jl" => "index.md",
+    "Tutorials" => [
+        "Getting Started" => "tutorials/getting_started.md",
+    ],
+    "API Reference" => [
+        "Index" => "api/index.md",
+        "Basis Functions" => "api/basis.md",
+        "Layers API" => "api/layers.md",
+        "Vision Models" => "api/vision.md",
+        "Private API" => "api/private.md",
+    ]
+]
+#! format: on
+
+bib = CitationBibliography(
+    joinpath(@__DIR__, "ref.bib");
+    style=:authoryear
+)
+
+deploy_config = Documenter.auto_detect_deploy_system()
+deploy_decision = Documenter.deploy_folder(deploy_config; repo="github.com/LuxDL/Boltz.jl",
+    devbranch="main", devurl="dev", push_preview=true)
+
+makedocs(; sitename="Boltz.jl Docs",
+    authors="Avik Pal et al.",
+    clean=true,
+    doctest=false,  # We test it in the CI, no need to run it here
+    modules=[Boltz],
+    linkcheck=true,
+    repo="https://github.com/LuxDL/Boltz.jl/blob/{commit}{path}#{line}",
+    format=DocumenterVitepress.MarkdownVitepress(;
+        repo="github.com/LuxDL/Boltz.jl", devbranch="main", devurl="dev", deploy_decision),
+    draft=false,
+    plugins=[bib],
+    pages)
+
+deploydocs(; repo="github.com/LuxDL/Boltz.jl.git",
+    push_preview=true, target="build", devbranch="main")

docs/package.json

@@ -0,0 +1,18 @@
+{
+    "devDependencies": {
+        "markdown-it": "^14.1.0",
+        "markdown-it-mathjax3": "^4.3.2",
+        "vitepress": "^1.0.2",
+        "vitepress-plugin-tabs": "^0.5.0",
+        "vitest": "^1.3.0"
+    },
+    "scripts": {
+        "docs:dev": "vitepress dev build/.documenter",
+        "docs:build": "vitepress build build/.documenter",
+        "docs:preview": "vitepress preview build/.documenter"
+    },
+    "dependencies": {
+        "@shikijs/transformers": "^1.1.7",
+        "markdown-it-footnote": "^4.0.0"
+    }
+}

docs/ref.bib

@@ -0,0 +1,91 @@
+@article{dosovitskiy2020image,
+  title   = {An image is worth 16x16 words: Transformers for image recognition at scale},
+  author  = {Dosovitskiy, Alexey and Beyer, Lucas and Kolesnikov, Alexander and Weissenborn, Dirk and Zhai, Xiaohua and Unterthiner, Thomas and Dehghani, Mostafa and Minderer, Matthias and Heigold, Georg and Gelly, Sylvain and others},
+  journal = {arXiv preprint arXiv:2010.11929},
+  year    = {2020}
+}
+
+@article{simonyan2014very,
+  title   = {Very deep convolutional networks for large-scale image recognition},
+  author  = {Simonyan, Karen},
+  journal = {arXiv preprint arXiv:1409.1556},
+  year    = {2014}
+}
+
+@article{greydanus2019hamiltonian,
+  title   = {Hamiltonian neural networks},
+  author  = {Greydanus, Samuel and Dzamba, Misko and Yosinski, Jason},
+  journal = {Advances in neural information processing systems},
+  volume  = {32},
+  year    = {2019}
+}
+
+@article{krizhevsky2012imagenet,
+  title   = {Imagenet classification with deep convolutional neural networks},
+  author  = {Krizhevsky, Alex and Sutskever, Ilya and Hinton, Geoffrey E},
+  journal = {Advances in neural information processing systems},
+  volume  = {25},
+  year    = {2012}
+}
+
+@inproceedings{he2016deep,
+  title     = {Deep residual learning for image recognition},
+  author    = {He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian},
+  booktitle = {Proceedings of the IEEE conference on computer vision and pattern recognition},
+  pages     = {770--778},
+  year      = {2016}
+}
+
+@inproceedings{xie2017aggregated,
+  title     = {Aggregated residual transformations for deep neural networks},
+  author    = {Xie, Saining and Girshick, Ross and Doll{\'a}r, Piotr and Tu, Zhuowen and He, Kaiming},
+  booktitle = {Proceedings of the IEEE conference on computer vision and pattern recognition},
+  pages     = {1492--1500},
+  year      = {2017}
+}
+
+@inproceedings{szegedy2015going,
+  title     = {Going deeper with convolutions},
+  author    = {Szegedy, Christian and Liu, Wei and Jia, Yangqing and Sermanet, Pierre and Reed, Scott and Anguelov, Dragomir and Erhan, Dumitru and Vanhoucke, Vincent and Rabinovich, Andrew},
+  booktitle = {Proceedings of the IEEE conference on computer vision and pattern recognition},
+  pages     = {1--9},
+  year      = {2015}
+}
+
+@inproceedings{huang2017densely,
+  title     = {Densely connected convolutional networks},
+  author    = {Huang, Gao and Liu, Zhuang and Van Der Maaten, Laurens and Weinberger, Kilian Q},
+  booktitle = {Proceedings of the IEEE conference on computer vision and pattern recognition},
+  pages     = {4700--4708},
+  year      = {2017}
+}
+
+@article{trockman2022patches,
+  title   = {Patches are all you need?},
+  author  = {Trockman, Asher and Kolter, J Zico},
+  journal = {arXiv preprint arXiv:2201.09792},
+  year    = {2022}
+}
+
+@article{howard2017mobilenets,
+  title   = {MobileNets: Efficient Convolutional Neural Networks for Mobile Vision Applications},
+  author  = {Howard, Andrew G},
+  journal = {arXiv preprint arXiv:1704.04861},
+  year    = {2017}
+}
+
+@inproceedings{sandler2018mobilenetv2,
+  title     = {Mobilenetv2: Inverted residuals and linear bottlenecks},
+  author    = {Sandler, Mark and Howard, Andrew and Zhu, Menglong and Zhmoginov, Andrey and Chen, Liang-Chieh},
+  booktitle = {Proceedings of the IEEE conference on computer vision and pattern recognition},
+  pages     = {4510--4520},
+  year      = {2018}
+}
+
+@inproceedings{howard2019searching,
+  title     = {Searching for mobilenetv3},
+  author    = {Howard, Andrew and Sandler, Mark and Chu, Grace and Chen, Liang-Chieh and Chen, Bo and Tan, Mingxing and Wang, Weijun and Zhu, Yukun and Pang, Ruoming and Vasudevan, Vijay and others},
+  booktitle = {Proceedings of the IEEE/CVF international conference on computer vision},
+  pages     = {1314--1324},
+  year      = {2019}
+}