feature: hBayesDM version 2.0

.github/workflows/Python.yaml

@@ -0,0 +1,62 @@
+name: Python
+
+on:
+  push:
+    branches: [master, develop]
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest:
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.os }} (Python ${{ matrix.python-version }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.13"]
+
+    env:
+      CMDSTAN_VERSION: "2.36.0"
+
+    defaults:
+      run:
+        working-directory: ./Python
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --all-groups
+
+      - name: Cache CmdStan
+        id: cmdstan-cache
+        uses: actions/cache@v4
+        with:
+          path: ~/.cmdstan
+          key: cmdstan-${{ runner.os }}-${{ env.CMDSTAN_VERSION }}
+
+      - name: Install CmdStan
+        if: steps.cmdstan-cache.outputs.cache-hit != 'true'
+        shell: bash
+        run: |
+          uv run python -c "import cmdstanpy; cmdstanpy.install_cmdstan(version='${CMDSTAN_VERSION}', cores=2)"
+
+      - name: Lint
+        run: uv run ruff check hbayesdm
+        continue-on-error: true
+
+      - name: Run user-facing tests
+        run: uv run pytest tests/test_user_facing.py -v --reruns 2

.github/workflows/R.yaml

@@ -0,0 +1,88 @@
+name: R
+
+on:
+  push:
+    branches: [master, develop]
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (R ${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,  r: '4.4'}
+          - {os: windows-latest, r: '4.4'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      CMDSTAN_VERSION: "2.36.0"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          working-directory: ./R
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::covr
+            stan-dev/cmdstanr
+          needs: check
+
+      - name: Cache CmdStan
+        id: cmdstan-cache
+        uses: actions/cache@v4
+        with:
+          path: ~/.cmdstan
+          key: cmdstan-${{ runner.os }}-${{ env.CMDSTAN_VERSION }}
+
+      - name: Install CmdStan
+        if: steps.cmdstan-cache.outputs.cache-hit != 'true'
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE, quiet = FALSE)
+          cmdstanr::install_cmdstan(version = Sys.getenv("CMDSTAN_VERSION"), cores = 2)
+        shell: Rscript {0}
+
+      - name: R CMD check
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          working-directory: ./R
+          args: 'c("--no-manual", "--as-cran", "--no-build-vignettes", "--no-tests", "--no-examples")'
+          error-on: '"warning"'
+
+      - name: Install hBayesDM
+        shell: bash
+        run: R CMD INSTALL R
+
+      - name: Run user-facing tests
+        env:
+          NOT_CRAN: "true"
+          TEST_FILE: ${{ github.workspace }}/R/tests/testthat/test_user_facing.R
+        run: |
+          Rscript -e "testthat::test_file(Sys.getenv('TEST_FILE'), reporter = 'progress')"
+
+      - name: Upload coverage to codecov
+        if: matrix.config.os == 'ubuntu-latest'
+        env:
+          NOT_CRAN: "true"
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          TEST_FILE: ${{ github.workspace }}/R/tests/testthat/test_user_facing.R
+        run: |
+          Rscript -e "covr::codecov(path = 'R', quiet = FALSE, type = 'none', code = sprintf('testthat::test_file(\"%s\", reporter = \"progress\")', Sys.getenv('TEST_FILE')))"

.github/workflows/pkgdown.yaml

@@ -16,38 +16,38 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CMDSTAN_VERSION: "2.36.0"
 
     steps:
       - uses: actions/checkout@v4
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
+          r-version: '4.4'
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "../.github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), "../.github/R-version")
-        shell: Rscript {0}
-        working-directory: ./R
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          working-directory: ./R
+          extra-packages: |
+            any::pkgdown
+            stan-dev/cmdstanr
+          needs: website
+
+      - name: Cache CmdStan
+        id: cmdstan-cache
         uses: actions/cache@v4
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('**/.github/R-version') }}-1-${{ hashFiles('**/.github/depends.Rds') }}
+          path: ~/.cmdstan
+          key: cmdstan-${{ runner.os }}-${{ env.CMDSTAN_VERSION }}
 
-      - name: Install dependencies
+      - name: Install CmdStan
+        if: steps.cmdstan-cache.outputs.cache-hit != 'true'
         run: |
-          install.packages("remotes")
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary", quiet = TRUE)
+          cmdstanr::install_cmdstan(version = Sys.getenv("CMDSTAN_VERSION"), cores = 2)
         shell: Rscript {0}
-        working-directory: ./R
 
       - name: Install package
         run: R CMD INSTALL .

.gitignore

@@ -356,3 +356,6 @@ CRAN-RELEASE
 Python/.idea
 Python/hbayesdm/version.py
 
+# compiled stan objects
+commons/stan_files/*
+!commons/stan_files/*.stan

.readthedocs.yml

@@ -2,17 +2,18 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-# Required
 version: 2
 
-# Build documentation in the docs/ directory with Sphinx
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.13"
+
 sphinx:
   configuration: Python/docs/conf.py
 
-# Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
   install:
-    - requirements: Python/requirements.txt
+    - requirements: Python/docs/requirements.txt
     - method: pip
       path: ./Python