Release/v0.4.1

.Rbuildignore

@@ -20,3 +20,8 @@
 ^SLiM$
 ^SLiM_build$
 ^cran-comments\.md$
+^\.claude$
+^FORK_AND_PR_INSTRUCTIONS\.md$
+^IMPROVEMENTS_SUMMARY\.md$
+^PR_DESCRIPTION\.md$
+^\.\.Rcheck$

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

@@ -22,11 +22,11 @@ jobs:
         config:
           - {os: windows-latest, r: 'release', slim: 'yes', conda: 'no'}
           - {os: windows-latest, r: 'release', slim: 'no', conda: 'no'}
-          - {os: macOS-latest, r: 'release', slim: 'yes', conda: 'no'}
-          - {os: macOS-latest, r: 'devel', slim: 'yes', conda: 'no'}
+          - {os: macos-14, r: 'release', slim: 'yes', conda: 'no'}
+          - {os: macos-14, r: 'devel', slim: 'yes', conda: 'no'}
           - {os: macOS-latest, r: 'release', slim: 'no', conda: 'yes'}
-          - {os: ubuntu-20.04, r: 'release', slim: 'yes', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", conda: 'no'}
-          - {os: ubuntu-20.04, r: 'release', slim: 'no', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", conda: 'yes'}
+          - {os: ubuntu-latest, r: 'release', slim: 'yes', conda: 'no'}
+          - {os: ubuntu-latest, r: 'release', slim: 'no', conda: 'yes'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -51,18 +51,19 @@ jobs:
            mingw-w64-x86_64-toolchain
            mingw-w64-x86_64-cmake
 
+      # Download SLiM 4.2.2 (last version compatible with current slimr)
       - name: Download SLiM on Windows
         if: runner.os == 'Windows' && matrix.config.slim == 'yes'
         shell: msys2 {0}
         run: |
           cd /d/a
-          wget http://benhaller.com/slim/SLiM.zip
+          wget https://github.com/MesserLab/SLiM/releases/download/v4.2.2/SLiM.zip
 
       - name: Download SLiM on non-Windows
         if: runner.os != 'Windows' && matrix.config.slim == 'yes'
         run: |
           cd ${{ github.workspace }}
-          wget http://benhaller.com/slim/SLiM.zip
+          wget https://github.com/MesserLab/SLiM/releases/download/v4.2.2/SLiM.zip
 
       # - name: Cache SLiM on Windows
       #   id: cache-slim-win
@@ -98,7 +99,7 @@ jobs:
           cd ../../..
           mkdir SLiM_build
           cd SLiM_build
-          cmake -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release ../SLiM
+          cmake -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ../SLiM
           make -j 2
 
       - name: Install SLiM on Windows Part 2
@@ -119,7 +120,7 @@ jobs:
           unzip -o SLiM.zip
           mkdir SLiM_build
           cd SLiM_build
-          cmake -DCMAKE_BUILD_TYPE=Release ../SLiM
+          cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ../SLiM
           make
 
       - name: Install SLiM on non-Windows Part 2
@@ -141,6 +142,13 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - name: Setup Miniconda for conda-based tests
+        if: matrix.config.conda == 'yes'
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: "3.10"
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: slimr
 Title: Create, Run and Post-Process 'SLiM' Population Genetics Forward Simulations
-Version: 0.4.0.9000
+Version: 0.4.1
 Authors@R: 
     c(person(given = "Russell",
              family = "Dinnage",
@@ -32,11 +32,11 @@ Encoding: UTF-8
 LazyData: true
 URL: https://rdinnager.github.io/slimr, https://rdinnager.github.io/slimr/index.html, https://github.com/rdinnager/slimr
 BugReports: https://github.com/rdinnager/slimr/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.3
 Language: en-GB
 Depends: 
     R (>= 2.10)
-Imports: 
+Imports:
     stringr,
     processx,
     readr,
@@ -51,8 +51,7 @@ Imports:
     tidyr,
     zeallot,
     utils,
-    stats,
-    codetools
+    stats
 Suggests: 
     ape,
     covr,

NEWS.md

@@ -1,5 +1,16 @@
 # slimr (development version)
 
+# slimr 0.4.1
+
+* Enhanced `slim_setup()` function with improved reliability and user experience:
+  - Added automatic conda Terms of Service acceptance to prevent installation failures
+  - Implemented download retry logic with exponential backoff for more reliable binary downloads
+  - Added structured error messages with platform-specific guidance and troubleshooting steps
+  - Added post-installation verification that automatically tests the SLiM installation
+  - Added informative progress messages throughout the installation process
+  - `slim_version` parameter now accepts specific version numbers (e.g., "4.2.2", "5.1") in addition to "stable" (default: SLiM 4.2.2)
+  - Warns users about potential compatibility issues when installing SLiM 5.x
+
 # slimr 0.4.0
 
 * Updated `slimr` to be fully compatible with SLiM v4.1 updates