Move domain-specific functionality to subpackages (#240)

* Move domain-specific functionality to subpackages * Add FastMakie.jl * Update tests * Add subpackage CI * run SciMLStyle * Add sysimage example * Update documentation * Rerun notebooks
FluxML · Jul 3, 2022 · c0cbc53 · c0cbc53
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diff --git a/.github/workflows/ci-fastmakie.yml b/.github/workflows/ci-fastmakie.yml
@@ -0,0 +1,57 @@
+name: CI - FastMakie
+on:
+  push:
+    paths-ignore:
+      - 'docs/**'
+      - 'FastTabular/**'
+      - 'FastText/**'
+      - 'FastVision/**'
+      - '*.md'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - name: Dev FastAI
+        run: |
+          julia --color=yes --project=./FastMakie -e 'using Pkg; pkg"dev ."'
+        shell: bash
+      - name: Dev test dependencies
+        run: |
+          julia --color=yes --project=./FastMakie/test -e 'using Pkg; pkg"dev . ./FastMakie "'
+        shell: bash
+      - uses: julia-actions/julia-buildpkg@latest
+        with:
+          project: './FastMakie/'
+      - name: Run tests
+        run: |
+          julia --color=yes --depwarn=yes --project=./FastMakie/test -e 'include("FastMakie/test/runtests.jl")'
+        continue-on-error: ${{ matrix.version == 'nightly' }}
+        shell: bash
diff --git a/.github/workflows/ci-fasttabular.yml b/.github/workflows/ci-fasttabular.yml
@@ -0,0 +1,56 @@
+name: CI - FastTabular
+on:
+  push:
+    paths-ignore:
+      - 'docs/**'
+      - 'FastMakie/**'
+      - 'FastText/**'
+      - 'FastVision/**'
+      - '*.md'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+        arch:
+          - x64
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - name: Dev FastAI
+        run: |
+          julia --color=yes --project=./FastTabular -e 'using Pkg; pkg"dev ."'
+        shell: bash
+      - name: Dev test dependencies
+        run: |
+          julia --color=yes --project=./FastTabular/test -e 'using Pkg; pkg"dev . ./FastTabular "'
+        shell: bash
+      - uses: julia-actions/julia-buildpkg@latest
+        with:
+          project: './FastTabular/'
+      - name: Run tests
+        run: |
+          julia --color=yes --depwarn=yes --project=./FastTabular/test -e 'include("FastTabular/test/runtests.jl")'
+        continue-on-error: ${{ matrix.version == 'nightly' }}
+        shell: bash
diff --git a/.github/workflows/ci-fasttext.yml b/.github/workflows/ci-fasttext.yml
@@ -0,0 +1,57 @@
+name: CI - FastText
+on:
+  push:
+    paths-ignore:
+      - 'docs/**'
+      - 'FastMakie/**'
+      - 'FastTabular/**'
+      - 'FastVision/**'
+      - '*.md'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - name: Dev FastAI
+        run: |
+          julia --color=yes --project=./FastText -e 'using Pkg; pkg"dev ."'
+        shell: bash
+      - name: Dev test dependencies
+        run: |
+          julia --color=yes --project=./FastText/test -e 'using Pkg; pkg"dev . ./FastText "'
+        shell: bash
+      - uses: julia-actions/julia-buildpkg@latest
+        with:
+          project: './FastText/'
+      - name: Run tests
+        run: |
+          julia --color=yes --depwarn=yes --project=./FastText/test -e 'include("FastText/test/runtests.jl")'
+        continue-on-error: ${{ matrix.version == 'nightly' }}
+        shell: bash
diff --git a/.github/workflows/ci-fastvision.yml b/.github/workflows/ci-fastvision.yml
@@ -0,0 +1,61 @@
+name: CI - FastVision
+on:
+  push:
+    paths-ignore:
+      - 'docs/**'
+      - 'FastTabular/**'
+      - 'FastText/**'
+      - '*.md'
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - 'FastTabular/**'
+      - 'FastText/**'
+      - '*.md'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+        arch:
+          - x64
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - name: Dev FastAI
+        run: |
+          julia --color=yes --project=./FastVision -e 'using Pkg; pkg"dev ."'
+        shell: bash
+      - name: Dev test dependencies
+        run: |
+          julia --color=yes --project=./FastVision/test -e 'using Pkg; pkg"dev . ./FastVision ./FastMakie"'
+        shell: bash
+      - uses: julia-actions/julia-buildpkg@latest
+        with:
+          project: './FastVision/'
+      - name: Run tests
+        run: |
+          julia --color=yes --depwarn=yes --project=./FastVision/test -e 'include("FastVision/test/runtests.jl")'
+        continue-on-error: ${{ matrix.version == 'nightly' }}
+        shell: bash
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,7 +1,21 @@
 name: CI
 on:
-  - push
-  - pull_request
+  push:
+    paths-ignore:
+      - 'docs/**'
+      - 'FastMakie/**'
+      - 'FastVision/**'
+      - 'FastTabular/**'
+      - 'FastText/**'
+      - '*.md'
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - 'FastMakie/**'
+      - 'FastVision/**'
+      - 'FastTabular/**'
+      - 'FastText/**'
+      - '*.md'
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}

diff --git a/.github/workflows/pollenbuild.yml b/.github/workflows/pollenbuild.yml
@@ -1,4 +1,4 @@
-name: pollenbuild
+name: Documentation - Build
 
 on:
   push:
@@ -19,7 +19,7 @@ jobs:
           version: '1.7'
       - name: "Install package and docs dependencies"
         run: |
-          julia --color=yes --project=./docs -e 'using Pkg; Pkg.add([Pkg.PackageSpec(path="."), Pkg.PackageSpec(url="https://github.com/c42f/JuliaSyntax.jl"), Pkg.PackageSpec(url="https://github.com/lorenzoh/ModuleInfo.jl"), Pkg.PackageSpec(url="https://github.com/lorenzoh/Pollen.jl", rev="main")]); Pkg.instantiate();'
+          julia --color=yes --project=./docs -e 'using Pkg; pkg"dev . ./FastVision ./FastMakie ./FastTabular https://github.com/c42f/JuliaSyntax.jl https://github.com/lorenzoh/ModuleInfo.jl https://github.com/lorenzoh/Pollen.jl"; Pkg.instantiate();'
       - name: Build
         run: |
           julia --color=yes --project=./docs ./docs/make.jl ./pollen/dev/

diff --git a/.github/workflows/pollenpr.yml b/.github/workflows/pollenpr.yml
@@ -0,0 +1,33 @@
+name: Documentation - PR
+
+on:
+  - pr
+
+jobs:
+  pollen:
+    name: "Pollen - test documentation build"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/checkout@v2
+        with:
+          ref: pollen
+          path: pollen
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.7'
+      - name: "Install package and docs dependencies"
+        run: |
+          julia --color=yes --project=./docs -e 'using Pkg; pkg"dev . ./FastVision ./FastMakie ./FastTabular https://github.com/c42f/JuliaSyntax.jl https://github.com/lorenzoh/ModuleInfo.jl https://github.com/lorenzoh/Pollen.jl"; Pkg.instantiate();'
+      - name: Build
+        run: |
+          julia --color=yes --project=./docs ./docs/make.jl ./pollen/dev/
+      - name: Deploy
+        run: |
+          cd pollen
+          git config user.name github-actions
+          git config user.email [email protected]
+          git add .
+          git commit -m "Build documentation data (Pollen.jl)"
+          git push
+
diff --git a/.github/workflows/pollenstatic.yml b/.github/workflows/pollenstatic.yml
@@ -1,4 +1,4 @@
-name: pollenstatic
+name: Documentation - Deploy
 
 on:
   push:

diff --git a/.gitignore b/.gitignore
@@ -3,4 +3,5 @@ test/Manifest.toml
 docs/Manifest.toml
 development/**
 Manifest.toml
-**/*.jld2
+**/*.jld2
+*.so
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,12 +9,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
-- (BREAKING) Now uses [MLUtils.jl](https://github.com/JuliaML/MLUtils.jl) to create and load datasets and data containers
+- (BREAKING): Now uses [MLUtils.jl](https://github.com/JuliaML/MLUtils.jl) to create and load datasets and data containers
     - Replaces dependencies MLDataPattern.jl, LearnBase.jl, and DataLoaders.jl
     - Data containers must now implement the `Base.getindex`/`MLUtils.getobs` and `Base.length`/`MLUtils.numobs` interfaces.
     - Previously exported `MLDataPattern.datasubset` has been replaced by `MLUtils.ObsView`
     - Documentation has been updated appropriately
-
+- (BREAKING): `FastAI.Vision` now lives in a separate package `FastVision` that holds all computer vision-related functionality. 
+- (BREAKING): `FastAI.Tabular` now lives in a separate package `FastTabular` that holds all tabular data-related functionality. 
+
+### Removed
+
+- (BREAKING): `FastAI.Models` submodule. `Models` submodule of domain libraries, e.g. `FastVision.Models` should now be used.
 
 ## v0.4.3 (2022/05/14)
 
@@ -105,7 +110,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - New interfaces
     - `blockbackbone` creates a default backbone for an input block
 - Support for tabular data along with recipes and learning methods:
-    - [Tabular classification tutorial](https://fluxml.ai/FastAI.jl/dev/notebooks/tabularclassification.ipynb.html)
+    - [Tabular classification tutorial](https://fluxml.ai/FastAI.jl/dev/docs/notebooks/tabularclassification.ipynb.html)
     - [`TabularPreprocessing`](https://fluxml.ai/FastAI.jl/dev/REFERENCE/FastAI.TabularPreprocessing.html), [`TableRow`](https://fluxml.ai/FastAI.jl/dev/REFERENCE/FastAI.TableRow.html), [`TableDataset`](https://fluxml.ai/FastAI.jl/dev/REFERENCE/FastAI.Datasets.TableDataset.html), [`TabularClassificiationSingle`](https://fluxml.ai/FastAI.jl/dev/REFERENCE/FastAI.TabularClassificationSingle.html), [`TabularRegression`](https://fluxml.ai/FastAI.jl/dev/REFERENCE/FastAI.TabularRegression.html)
 
 
@@ -115,7 +120,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
     - [README](https://fluxml.ai/FastAI.jl/dev/README.md.html)
     - [Introduction](https://fluxml.ai/FastAI.jl/dev/docs/introduction.md.html)
     - [Data containers](https://fluxml.ai/FastAI.jl/dev/docs/data_containers.md.html)
-    - Combined how-tos on training [into a single page](https://fluxml.ai/FastAI.jl/dev/notebooks/training.ipynb.html)
+    - Combined how-tos on training [into a single page](https://fluxml.ai/FastAI.jl/dev/docs/notebooks/training.ipynb.html)
 - Breaking changes to [`methodlearner`](https://fluxml.ai/FastAI.jl/dev/REFERENCE/FastAI.methodlearner.html):
     - now accepts `callbacks` as kwarg
     - `validdata` no longer keyword

diff --git a/FastMakie/Project.toml b/FastMakie/Project.toml
@@ -0,0 +1,14 @@
+name = "FastMakie"
+uuid = "ca994201-3d74-4fad-8816-f8bc5449c7c3"
+authors = ["Lorenz Ohly", "Julia Community"]
+version = "0.1.0"
+
+[deps]
+FastAI = "5d0beca9-ade8-49ae-ad0b-a3cf890e669f"
+InlineTest = "bd334432-b1e7-49c7-a2dc-dd9149e4ebd6"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
+
+[compat]
+FastAI = "0.5"
+Makie = "0.17"
diff --git a/FastMakie/src/FastMakie.jl b/FastMakie/src/FastMakie.jl
@@ -0,0 +1,21 @@
+module FastMakie
+
+import FastAI: FastAI, createhandle, showblock!, AbstractBlock, OneHotTensor,
+               OneHotTensorMulti,
+               Label, LabelMulti, ShowBackend, ShowMakie, axiskwargs, showblock,
+               showblocks!, showblocks
+using InlineTest
+import Makie
+import NNlib: softmax, sigmoid
+
+include("axis.jl")
+include("showmakie.jl")
+include("blocks.jl")
+include("lrfind.jl")
+
+function __init__()
+    # When loaded, set default show backend
+    FastAI.SHOW_BACKEND[] = ShowMakie()
+end
+
+end