Sync changes, add workflows

.github/workflows/CompatHelper.yml

@@ -0,0 +1,45 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1.9'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/Documenter.yml

@@ -0,0 +1,40 @@
+name: Documentation
+on:
+  push:
+    branches:
+      - main # update to match your development branch (master, main, dev, trunk, ...)
+    tags: '*'
+  pull_request:
+jobs:
+  build:
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.9'
+      - uses: actions/cache@v3
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-docs-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-docs-${{ env.cache-name }}-
+            ${{ runner.os }}-docs-
+            ${{ runner.os }}-
+      - name: Install binary dependencies
+        run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev
+      - name: Install Julia dependencies
+        run: >
+          DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24'
+          julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+        run: >
+          DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24'
+          julia --project=docs --color=yes docs/make.jl

.github/workflows/Formatter.yml

@@ -0,0 +1,36 @@
+name: FormatCheck
+on:
+  push:
+    branches:
+      - 'main'
+    tags: '*'
+  pull_request:
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v3
+      - name: Install JuliaFormatter and format
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

.github/workflows/TagBot.yml

@@ -0,0 +1,33 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          # Edit the following line to reflect the actual name of the GitHub Secret containing your private key
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          # ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}

.github/workflows/Tests.yml

@@ -0,0 +1,35 @@
+name: Tests
+on:
+  push:
+    branches:
+      - main # update to match your development branch (master, main, dev, trunk, ...)
+    tags: '*'
+  pull_request:
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        julia_version: ['1.9']
+        os: [ubuntu-latest]
+    steps:
+      - uses: actions/checkout@v3
+      - name: "Set up Julia"
+        uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia_version }}
+      - uses: actions/cache@v3
+        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: "Build package"
+        uses: julia-actions/julia-buildpkg@latest
+      - name: "Run tests"
+        uses: julia-actions/julia-runtest@latest

Project.toml

@@ -1,6 +1,6 @@
 name = "CEED"
 uuid = "e939450b-799e-4198-a5f5-3f2f7fb1c671"
-version = "0.3.0"
+version = "0.3.4"
 
 [deps]
 Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
@@ -38,7 +38,7 @@ Distances = "0.10"
 POMDPs = "0.9"
 JSON = "0.21"
 Clustering = "0.15"
-MCTS = "0.5"
+MCTS = "0.5.5"
 MLJ = "0.19"
 Requires = "1.3"
 POMDPSimulators = "0.3"

docs/make.jl

@@ -4,7 +4,7 @@ using CEED
 # Literate for tutorials
 const literate_dir = joinpath(@__DIR__, "..", "tutorials")
 const tutorials_src =
-    ["StaticDesigns.jl", "StaticDesignsFiltration.jl", "GenerativeDesigns.jl", "paper.jl"]
+    ["StaticDesigns.jl", "StaticDesignsFiltration.jl", "GenerativeDesigns.jl"]
 const generated_dir = joinpath(@__DIR__, "src", "tutorials/")
 
 # copy tutorials src

docs/src/api.md

@@ -14,13 +14,19 @@ CEED.StaticDesigns.evaluate_experiments
 ## `GenerativeDesigns`
 
 ```@docs
-CEED.GenerativeDesigns.ResearchMDP
+CEED.GenerativeDesigns.UncertaintyReductionMDP
+CEED.GenerativeDesigns.EfficientValueMDP
 CEED.GenerativeDesigns.State
-CEED.GenerativeDesigns.efficient_designs
 CEED.GenerativeDesigns.Variance
 CEED.GenerativeDesigns.Entropy
 ```
 
+```@docs
+CEED.GenerativeDesigns.efficient_design
+CEED.GenerativeDesigns.efficient_designs
+CEED.GenerativeDesigns.efficient_value
+```
+
 ### Distance-Based Sampling
 
 ```@docs

docs/src/index.md

@@ -29,4 +29,6 @@ At the beginning of the triage process, an entity's prior data is used to projec
 <a><img src="assets/search_tree.png" align="left" alt="code" width="400"></a>
 ```
 
-We conceptualized the triage as a Markov decision process, in which we iteratively choose to conduct a subset of experiments and then, based on the experimental evidence, update our belief about the distribution of outcomes for the experiments that have not yet been conducted. The information value associated with the state, derived from experimental evidence, can be modeled through any statistical or information-theoretic measure such as the variance or uncertainty associated with the target variable posterior.
+We conceptualized the triage as a Markov decision process, in which we iteratively choose to conduct a subset of experiments and then, based on the experimental evidence, update our belief about the distribution of outcomes for the experiments that have not yet been conducted. The information value associated with the state, derived from experimental evidence, can be modeled through any statistical or information-theoretic measure such as the variance or uncertainty associated with the target variable posterior.
+
+We implemented the following two variants of the decision-making process: Firstly, assuming that the decision-making process only terminates when the uncertainty drops below a given threshold, we minimize the expected resource spend. Secondly, we can optimize the value of experimental evidence, adjusted for the incurred experimental costs.