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Merge pull request #211 from JuliaAI/dev
For a 3.2.0 release
2 parents 990cb81 + 76f9c30 commit 2ff6a83

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‎.github/codecov.yml‎

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coverage:
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status:
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project:
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default:
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threshold: 0.5%
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removed_code_behavior: fully_covered_patch
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patch:
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default:
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target: 80

‎.github/workflows/ci.yml‎

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name: CI
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on:
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pull_request:
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branches:
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- master
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- dev
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push:
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branches:
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- master
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- dev
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tags: '*'
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branches: [master, dev]
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tags: ["*"]
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pull_request:
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jobs:
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test:
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name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
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fail-fast: false
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matrix:
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version:
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- '1' # automatically expands to the latest stable 1.x release of Julia
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- '1.10'
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- '1' # automatically expands to the latest stable 1.x release of Julia.
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os:
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- ubuntu-latest
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- windows-latest
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arch:
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- x64
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include:
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- os: macOS-latest
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arch: aarch64
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version: 1
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v4
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- uses: julia-actions/setup-julia@v2
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with:
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version: ${{ matrix.version }}
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arch: ${{ matrix.arch }}
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- uses: julia-actions/cache@v2
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env:
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cache-name: cache-artifacts
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with:
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path: ~/.julia/artifacts
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key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
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restore-keys: |
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${{ runner.os }}-test-${{ env.cache-name }}-
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${{ runner.os }}-test-
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${{ runner.os }}-
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- uses: julia-actions/julia-buildpkg@v1
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- uses: julia-actions/julia-runtest@v1
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- uses: julia-actions/julia-processcoverage@v1
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- uses: codecov/codecov-action@v5
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with:
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files: lcov.info
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token: ${{ secrets.CODECOV_TOKEN }}
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fail_ci_if_error: false
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verbose: true
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docs:
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name: Documentation
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: julia-actions/setup-julia@v2
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with:
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version: '1'
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- shell: julia --color=yes {0}
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run: |
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function set_environment_variable(name::AbstractString, value::AbstractString)
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github_env = ENV["GITHUB_ENV"]
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touch(github_env)
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open(github_env, "a") do io
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println(io, "$(name)=$(value)")
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end
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end
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event_name = "${{ github.event_name }}"
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if event_name == "pull_request"
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base_ref = "${{ github.base_ref }}"
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head_ref = "${{ github.head_ref }}"
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base_repository = "${{ github.repository }}"
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head_repository = "${{ github.event.pull_request.head.repo.full_name }}"
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build_docs = (base_ref == "master") && (head_ref == "dev") && (base_repository == head_repository)
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elseif event_name == "push"
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ref = "${{ github.ref }}"
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build_docs = (ref == "refs/heads/master") || (startswith(ref, "refs/tags/"))
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elseif event_name == "schedule"
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build_docs = ref == "refs/heads/master"
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elseif event_name == "workflow_dispatch"
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build_docs = ref == "refs/heads/master"
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else
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build_docs = false
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end
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if build_docs
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@info("We will build the docs")
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set_environment_variable("BUILD_DOCS", "true")
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else
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@info("We will NOT build the docs")
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set_environment_variable("BUILD_DOCS", "false")
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end
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- name: Instantiate docs environment
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shell: julia --color=yes --project=docs {0}
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run: |
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if ENV["BUILD_DOCS"] == "true"
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using Pkg
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Pkg.develop(PackageSpec(path=pwd()))
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Pkg.instantiate()
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end
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- name: Run doctests
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shell: julia --color=yes --project=docs {0}
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run: |
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if ENV["BUILD_DOCS"] == "true"
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using Documenter: doctest
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using ScientificTypes
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@info "attempting to run the doctests"
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doctest(ScientificTypes)
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else
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@info "skipping the doctests"
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end
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- name: Build documentation
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shell: julia --color=yes --project=docs {0}
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run: |
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if ENV["BUILD_DOCS"] == "true"
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@info "attempting to build the docs"
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run(`julia --project=docs docs/make.jl`)
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@info "successfully built the docs"
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else
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@info "skipping the docs build"
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end
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- uses: actions/checkout@v4
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- uses: julia-actions/julia-buildpkg@latest
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- uses: julia-actions/julia-docdeploy@latest
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

‎Project.toml‎

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name = "ScientificTypes"
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uuid = "321657f4-b219-11e9-178b-2701a2544e81"
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authors = ["Anthony D. Blaom <anthony.blaom@gmail.com>"]
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version = "3.1.2"
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version = "3.2.0"
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[deps]
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CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
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Distributions = "0.25.1"
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PrettyTables = "3"
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Reexport = "1.2"
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ScientificTypesBase = "3.0"
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ScientificTypesBase = "3.1"
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StatisticalTraits = "3.0"
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Tables = "1.6.1"
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julia = "1.10"

‎docs/Project.toml‎

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CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
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DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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ScientificTypes = "321657f4-b219-11e9-178b-2701a2544e81"
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ScientificTypesBase = "30f210dd-8aff-4c5f-94ba-8e64358c1161"
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Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
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[compat]
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Documenter = "0.25"
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ScientificTypesBase = "3"
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Documenter = "1"

‎docs/make.jl‎

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using Documenter, ScientificTypes, ScientificTypesBase
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using Documenter, ScientificTypes
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import ScientificTypesBase
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const REPO = Remotes.GitHub("JuliaAI", "ScientificTypes.jl")
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makedocs(
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modules = [ScientificTypes, ScientificTypesBase],
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format = Documenter.HTML(
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prettyurls = !("local" in ARGS),
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),
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sitename = "ScientificTypes.jl",
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authors = "Anthony Blaom, Thibaut Lienart, and contributors.",
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format=Documenter.HTML(
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prettyurls = true,
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collapselevel = 1,
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),
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pages = [
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"Home" => "index.md",
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]
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"Reference" => "reference.md",
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],
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sitename = "ScientificTypes.jl",
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authors = "Anthony Blaom, Thibaut Lienart, and contributors.",
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warnonly = [:cross_references, :missing_docs],
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repo = REPO
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)
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deploydocs(
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repo = "github.com/JuliaAI/ScientificTypes.jl",
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push_preview = true
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devbranch="dev",
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push_preview=false,
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repo="github.com/JuliaAI/ScientificTypes.jl.git",
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)

‎docs/src/index.md‎

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Unknown
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```
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For more on specific types, see the [Reference](@ref) section.
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Additionally, we regard the Julia native types `Missing` and `Nothing`
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as scientific types as well.
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One should check and possibly modify the returned dictionary
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before passing to `coerce`.
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## API reference
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```@docs
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ScientificTypes.scitype
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coerce
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autotype
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```

‎docs/src/reference.md‎

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# Reference
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- [Types](@ref)
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- [Methods](@ref)
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## Types
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- [Finite](@ref)
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- [Multiclass](@ref)
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- [OrderedFactor](@ref)
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- [Infinite](@ref)
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- [Continuous](@ref)
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- [Count](@ref)
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- [Image](@ref)
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- [ColorImage](@ref)
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- [GrayImage](@ref)
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- [Sampleable](@ref)
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- [Density](@ref)
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- [Table](@ref)
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- [Textual](@ref)
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```@docs
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Finite
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Multiclass
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OrderedFactor
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Infinite
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Continuous
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Count
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Image
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ColorImage
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GrayImage
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Sampleable
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Density
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Table
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Textual
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```
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## Methods
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- [scitype](@ref)
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- [schema](@ref)
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- [coerce](@ref)
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- [autotype](@ref)
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```@docs
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scitype
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schema
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coerce
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autotype
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```

‎src/convention/scitype.jl‎

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"""
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scitype(X)
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The scientific type (interpretation) of `X`, as distinct from its machine type. Atomic
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scientific types (`Continuous`, `Multiclass`, etc) are mostly abstract types defined in
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the package ScientificTypesBase.jl. Scientific types do not ordinarily have instances.
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Return the scientific type (interpretation) of `X`, as distinct from its machine
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type. Atomic scientific types (`Continuous`, `Multiclass`, etc) are mostly abstract types
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defined in the package ScientificTypesBase.jl. Scientific types do not ordinarily have
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instances.
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!!! note
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Third party packages may extend the behavior of `scitype`: Objects previously having
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`Unknown` scitype may no longer do so.
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To display the active scientific type hierarchy (excluding `Missing` and `Nothing`) do
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`scitype()`.
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### Examples
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```
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```
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Column scitpes of a table can also be inspected with [`schema`](@ref).
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Column scitypes of a table can also be inspected with [`schema`](@ref).
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The behavior of `scitype` is detailed in the [ScientificTypes
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documentation](https://juliaai.github.io/ScientificTypes.jl/dev/#Summary-of-the-default-convention).
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`Missing`, Julia types that are also regarded as scientific.
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See also [`coerce`](@ref), [`autotype`](@ref), [`schema`](@ref).
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!!! note
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"""
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scitype(X) = ST.scitype(X, CONV)
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"""
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scitype(; io=stdout)
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Third party packages may extend the behavior of `scitype`: Objects
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previously having `Unknown` scitype may no longer do so.
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Print to `io` the scitype hierarchy, beginning at `Found` (and so excluding `Missing` and
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`Nothing`).
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See also [`coerce`](@ref), [`autotype`](@ref), [`schema`](@ref).
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Note that third party packages can extend the hierarchy, so output is not static.
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"""
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scitype(X) = ST.scitype(X, CONV)
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scitype(; kwargs...) = ST.scitype(; kwargs...)
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function ST.scitype(@nospecialize(X), C::DefaultConvention)
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return _scitype(X, C, vtrait(X))

‎test/convention/scitype.jl‎

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@testset "type hierarch display" begin
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str = sprint(io -> scitype(;io))
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# only smoke tests, to save maintenance:
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@test contains(str, "Found\n Known\n")
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@test contains(str, "Multiclass")
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@test contains(str, "Textual")
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end
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@testset "Explicit Scitype tests" begin
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STB = ScientificTypesBase
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ST = ScientificTypes

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