Amended all ymls files

.github/workflows/R-CMD-check.yml

@@ -33,11 +33,8 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install matplotlib numpy>=1.8 packaging parameterized pandas>=1.4 tqdm
-          # Install pyEpiabm in development mode to ensure it's in PYTHONPATH
-          git clone https://github.com/SABS-R3-Epidemiology/epiabm.git
-          cd epiabm
-          pip install -e .
-          cd ..
+          python -m pip install git+https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm\&subdirectory=pyEpiabm
+
 
       - name: Set up R ${{ matrix.config.r }}
         uses: r-lib/actions/setup-r@v2

.github/workflows/lint.yaml

@@ -1,10 +1,11 @@
-name: R Package Check
+name: Lint
 
 on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
+    branches:
+      - '**'
 
 jobs:
   check:

.github/workflows/pkgdown.yaml

@@ -1,41 +1,105 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+# Workflow for building and deploying package documentation
+name: pkgdown
+
 on:
   push:
     branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
-
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_LIBS_USER: ${{ github.workspace }}/R/library
+      RETICULATE_PYTHON: ${{ github.workspace }}/.venv/bin/python
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.8'
+          cache: 'pip'
+
+      - name: Create Python virtual environment
+        run: |
+          python -m venv .venv
+          source .venv/bin/activate
+          python -m pip install --upgrade pip
+          pip install numpy>=1.8 pandas>=1.4 matplotlib packaging parameterized tqdm
+          pip install git+https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm\&subdirectory=pyEpiabm
+
+      - name: Set up reticulate configuration
+        run: |
+          mkdir -p ~/.R
+          echo "RETICULATE_PYTHON='${{ github.workspace }}/.venv/bin/python'" >> ~/.R/Makevars
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: https://inla.r-inla-download.org/R/stable
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libharfbuzz-dev libfribidi-dev
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::., any::XML
+          extra-packages: |
+            any::pkgdown
+            any::XML
+            any::devtools
+            any::reticulate
+            local::.
           needs: website
 
+      - name: Check DESCRIPTION file format
+        run: |
+          echo "" >> DESCRIPTION  # Ensure there's a newline at the end
+          Rscript -e 'if(length(readLines("DESCRIPTION")) == 0) stop("Empty DESCRIPTION file")'
+
+      - name: Configure reticulate
+        run: |
+          Rscript -e 'Sys.setenv(RETICULATE_PYTHON = "${{ github.workspace }}/.venv/bin/python")'
+          Rscript -e 'reticulate::use_virtualenv("${{ github.workspace }}/.venv")'
+
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
-        shell: Rscript {0}
-
+        run: |
+          Rscript -e '
+          options(pkgdown.internet = FALSE)
+          pkgdown::build_site_github_pages(
+            new_process = FALSE,
+            install = FALSE,
+            examples = TRUE,
+            run_dont_run = FALSE
+          )'
+
       - name: Deploy to GitHub pages
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@4.1.4
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           clean: false
           branch: gh-pages
           folder: docs
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Upload documentation artifacts
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: pkgdown-artifacts
+          path: |
+            docs/
+            pkgdown/
+            .venv/
+            *.Rcheck/
+            *.log

.github/workflows/test_macos.yml

@@ -9,57 +9,95 @@ on:
       - '**'
 
 jobs:
-
   test:
     name: tests on macOS with R ${{ matrix.R }}
     runs-on: macos-latest
+    env:
+      R_LIBS_USER: ${{ github.workspace }}/R/library
+      RETICULATE_PYTHON: ${{ github.workspace }}/.venv/bin/python
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     strategy:
       fail-fast: false
       matrix:
         R: [ '4.1.0' ]
 
     steps:
-
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.R }}
           Ncpus: 2
-
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.8'
+          cache: 'pip'
+
+      - name: Create Python virtual environment
+        run: |
+          python -m venv .venv
+          source .venv/bin/activate
+          python -m pip install --upgrade pip
+          pip install numpy>=1.8 pandas>=1.4 matplotlib packaging parameterized tqdm
+          pip install git+https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm\&subdirectory=pyEpiabm
+
       - name: Query dependencies
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
-        
-      - name: cache R installed packages
-        uses: actions/cache@v2
+
+      - name: Restore R package cache
+        uses: actions/cache@v3
         id: cache
         with:
-          path: |
-            ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-R${{ matrix.R }}-2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-R${{ matrix.R }}-2-
-
-      - name: Install packages
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.R }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.R }}-
+
+      - name: Install system dependencies
+        run: |
+          brew install curl openssl libxml2
+          
+      - name: Install R dependencies
+        if: steps.cache.outputs.cache-hit != 'true'
         run: |
-          install.packages(c("devtools"))
+          install.packages(c("devtools", "reticulate", "withr", "rappdirs"))
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
+      - name: Check DESCRIPTION file format
+        run: |
+          echo "" >> DESCRIPTION  # Ensure there's a newline at the end
+          Rscript -e 'if(length(readLines("DESCRIPTION")) == 0) stop("Empty DESCRIPTION file")'
+
+      - name: Set up reticulate configuration
+        run: |
+          mkdir -p ~/.R
+          echo "RETICULATE_PYTHON='${{ github.workspace }}/.venv/bin/python'" >> ~/.R/Makevars
+
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: |
           options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
+          Sys.setenv(RETICULATE_PYTHON = '${{ github.workspace }}/.venv/bin/python')
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ runner.os }}-r${{ matrix.R }}-results
+          path: check

.github/workflows/test_ubuntu.yml

@@ -9,62 +9,101 @@ on:
       - '**'
 
 jobs:
-
   test:
     name: tests on Ubuntu with R ${{ matrix.R }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
+    env:
+      R_LIBS_USER: ${{ github.workspace }}/R/library
+      RETICULATE_PYTHON: ${{ github.workspace }}/.venv/bin/python
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     strategy:
       fail-fast: false
       matrix:
         R: [ '4.1.0' ]
 
     steps:
-
       - name: Checkout repository
-        uses: actions/checkout@v2
-
-      - name: Install build dependencies
-        run: |
-          sudo apt update
-          sudo apt install libcurl4-openssl-dev
+        uses: actions/checkout@v3
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.R }}
           Ncpus: 2
-
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.8'
+          cache: 'pip'
+
+      - name: Create Python virtual environment
+        run: |
+          python -m venv .venv
+          source .venv/bin/activate
+          python -m pip install --upgrade pip
+          pip install numpy>=1.8 pandas>=1.4 matplotlib packaging parameterized tqdm
+          pip install git+https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm\&subdirectory=pyEpiabm
+
       - name: Query dependencies
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
-        
-      - name: cache R installed packages
-        uses: actions/cache@v2
+
+      - name: Restore R package cache
+        uses: actions/cache@v3
         id: cache
         with:
-          path: |
-            ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-R${{ matrix.R }}-2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-R${{ matrix.R }}-2-
-
-      - name: Install packages
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.R }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.R }}-
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y --no-install-recommends \
+            libcurl4-openssl-dev \
+            libssl-dev \
+            libxml2-dev \
+            libharfbuzz-dev \
+            libfribidi-dev
+
+      - name: Install R dependencies
+        if: steps.cache.outputs.cache-hit != 'true'
         run: |
-          install.packages(c("devtools"))
+          install.packages(c("devtools", "reticulate", "withr", "rappdirs"))
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
+      - name: Check DESCRIPTION file format
+        run: |
+          echo "" >> DESCRIPTION  # Ensure there's a newline at the end
+          Rscript -e 'if(length(readLines("DESCRIPTION")) == 0) stop("Empty DESCRIPTION file")'
+
+      - name: Set up reticulate configuration
+        run: |
+          mkdir -p ~/.R
+          echo "RETICULATE_PYTHON='${{ github.workspace }}/.venv/bin/python'" >> ~/.R/Makevars
+
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: |
           options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
+          Sys.setenv(RETICULATE_PYTHON = '${{ github.workspace }}/.venv/bin/python')
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ runner.os }}-r${{ matrix.R }}-results
+          path: check