Merge branch 'r_replication_k' into r_replication

.Rbuildignore

@@ -0,0 +1,12 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$
+^codecov\.yml$
+^CRAN-RELEASE$
+^cran-comments\.md$
+^\.github$
+^doc$
+^Meta$
+^windows\\i386\*
+^i386\.*$
+.lintr

.github/workflows/pkgdown.yaml

@@ -2,7 +2,11 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: 
+      - '**'
+  pull_request:
+    branches:
+      - '**'
   release:
     types: [published]
   workflow_dispatch:
@@ -28,9 +32,16 @@ jobs:
           extra-packages: any::pkgdown, local::., any::XML
           needs: website
 
-      - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
+
+      - name: Setup r-reticulate env
+        run: reticulate::virtualenv_create("r-reticulate", Sys.which("python"))
         shell: Rscript {0}
+
+      - name: Build site
+        run: Rscript -e "pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
 
       - name: Deploy to GitHub pages
         if: github.event_name != 'pull_request'

.github/workflows/test_macos.yml

@@ -3,7 +3,7 @@ name: "Unit tests: macOS"
 on:
   push:
     branches:
-      - main
+      - '**'
   pull_request:
     branches:
       - '**'
@@ -22,6 +22,10 @@ jobs:
 
       - name: Checkout repository
         uses: actions/checkout@v2
+
+      - name: Install build dependencies
+        run: |
+          brew install curl
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
@@ -49,6 +53,7 @@ jobs:
           install.packages(c("devtools"))
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
+          reticulate::install_python(version = "3.9:latest")
         shell: Rscript {0}
 
       - name: Check
@@ -62,4 +67,4 @@ jobs:
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+        shell: bash

.github/workflows/test_ubuntu.yml

@@ -3,7 +3,7 @@ name: "Unit tests: Ubuntu"
 on:
   push:
     branches:
-      - main
+      - '**'
   pull_request:
     branches:
       - '**'

.github/workflows/test_windows.yml

@@ -3,13 +3,12 @@ name: "Unit tests: Windows"
 on:
   push:
     branches:
-      - main
+      - '**'
   pull_request:
     branches:
       - '**'
 
 jobs:
-
   test:
     name: tests on Windows with R ${{ matrix.R }}
     runs-on: windows-latest
@@ -19,6 +18,13 @@ jobs:
         R: [ '4.1.0' ]
 
     steps:
+      - name: Check Windows architecture
+        run: |
+          if (-not [Environment]::Is64BitOperatingSystem) { throw "Not 64-bit Windows" }
+          Write-Host "OS Architecture: $([Environment]::Is64BitOperatingSystem)"
+          Write-Host "Process Architecture: $([Environment]::Is64BitProcess)"
+          systeminfo | findstr /B /C:"OS Name" /C:"OS Version" /C:"System Type"
+        shell: pwsh
 
       - name: Checkout repository
         uses: actions/checkout@v2
@@ -28,22 +34,31 @@ jobs:
         with:
           r-version: ${{ matrix.R }}
           Ncpus: 2
-
+          r-arch: 'x64'
+
+      - name: Verify R architecture
+        run: |
+          Rscript -e "if(R.version$arch != 'x64') stop('R architecture is not 64-bit!')"
+          Rscript -e "cat('R Architecture:', R.version$arch, '\n')"
+          Rscript -e "cat('.Machine$sizeof.pointer:', .Machine$sizeof.pointer, '\n')"
+          Rscript -e "cat('Using R at:', R.home(), '\n')"
+        shell: cmd
+
       - 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
+      - name: Cache R packages
         uses: actions/[email protected]
         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
         run: |
           install.packages(c("devtools"))
@@ -56,10 +71,10 @@ jobs:
           _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")
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran" ,'--no-multiarch'), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+        shell: bash

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: R-Wrapper of Epiabm
 Version: 0.0.2
 Authors@R: c(
-    person('Anita', 'Applegarth', role = c('aut', 'cre', 'cph'), email = 'anita.applegarth@reub.ox.ac.uk'),
+    person('Anita', 'Applegarth', role = c('aut', 'cre', 'cph'), email = 'anita.applegarth@reuben.ox.ac.uk'),
     person('Kingsley', 'Oguma', role = 'aut', email = "[email protected]")
     )
 Description: Wraps the epiabm Python module in R.
@@ -12,20 +12,23 @@ Encoding: UTF-8
 Archs: x64
 SystemRequirements: Python (>= 2.7.0)
 Suggests: tinytest
-Imports: ggplot2, here
-Depends: 
-    reticulate (>= 1.14),
-    R (>= 3.3.0)
+Imports: 
+    ggplot2,
+    here,
+    tidyr,
+    reticulate (>= 1.14)
+Depends: R (>= 3.3.0)
 Config/reticulate:
     list(
         packages = list(
             list(package = "numpy", pip = TRUE),
-	    list(package = "pandas", pip = TRUE),
+            list(package = "pandas", pip = TRUE),
             list(package = "matplotlib", pip = TRUE),
             list(
                 package = "pyEpiabm",
                 pip = TRUE,
-                pip_options = "--index-url git+https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm&subdirectory=pyEpiabm"
+                pip_options = "--extra-index-url https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm&subdirectory=pyEpiabm"
             )
         )
     )
+RoxygenNote: 7.3.2

NAMESPACE

@@ -1 +1,4 @@
-import(reticulate)
+# Generated by roxygen2: do not edit by hand
+
+export(check_python_env)
+export(initialize_python_env)

R/simulation_flow_check.R

@@ -2,15 +2,20 @@
 # Example simulation script with data output
 #
 # Import dependencies
+source("R/zzz.R")
+initialize_python_env()
+check_python_env()
 
 library(reticulate)
+#library(rEpiabm)
 library(here)
+library(tidyr)
 
-os <- import("os")
-logging <- import("logging")
-pd <- import("pandas")
-plt <- import("matplotlib.pyplot")
-pe <- import("pyEpiabm")
+os <- import("os", delay_load = TRUE)
+logging <- import("logging", delay_load = TRUE)
+pd <- import("pandas", delay_load = TRUE)
+plt <- import("matplotlib.pyplot", delay_load = TRUE)
+pe <- import("pyEpiabm", delay_load = TRUE)
 
 # Set working directory for relative directory references
 base_dir <- here()
@@ -91,12 +96,8 @@ sim$compress_csv()
 
 # Create dataframe for plots
 filename <- here("simulation_outputs", "output.csv")
-df <- pd$read_csv(filename)
+df <- read.csv(filename)
 
-# Convert pandas dataframe to R dataframe
-df_r <- as.data.frame(df)
-
-# Load library for plotting
 library(ggplot2)
 
 # Reshape the data from wide to long format using base R
@@ -105,13 +106,15 @@ status_columns <- c("InfectionStatus.Susceptible",
                     "InfectionStatus.Recovered",
                     "InfectionStatus.Dead")
 
-df_long <- data.frame(
-  time = rep(df_r$time, length(status_columns)),
-  Status = factor(rep(status_columns, each = nrow(df_r)),
-                  levels = status_columns,
-                  labels = c("Susceptible", "Infected", "Recovered", "Dead")),
-  Count = unlist(df_r[status_columns])
+df_long <- pivot_longer(
+  df,
+  cols = all_of(status_columns),
+  names_to = "Status",
+  values_to = "Count"
 )
+df_long$Status <- factor(df_long$Status,
+                        levels = status_columns,
+                        labels = c("Susceptible", "Infected", "Recovered", "Dead"))
 
 # Create the plot
 p <- ggplot(df_long, aes(x = time, y = Count, color = Status)) +