add renv lock file to reproduce env

Author: lpantano

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/run_visium_qc.yaml

@@ -0,0 +1,41 @@
+name: R Restore and Run
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  r-restore:
+    runs-on: ubuntu-latest
+
+    env:
+      RENV_PATHS_ROOT: ~/.local/share/renv  # persistent cache location
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Cache R packages (renv)
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.RENV_PATHS_ROOT }}
+          key: ${{ runner.os }}-renv-${{ hashFiles('renv.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-renv-
+
+      - name: Restore environment from renv.lock
+        run: |
+          install.packages("renv", repos = "https://cloud.r-project.org")
+          renv::restore(prompt = FALSE)
+        shell: Rscript {0}
+
+      - name: Get data
+        run: Rscript visium/download-test-data.R
+
+      - name: Run visium quality assessment
+        run: Rscript visium/01_quality_assessment/quality_assessment.qmd

.gitignore

@@ -4,4 +4,7 @@
 **qs
 **rds
 **html
-*results*
+*results*
+# pixi environments
+.pixi
+*.egg-info

install_dependencies.R

@@ -1,6 +1,15 @@
+options(repos = c(CRAN = "https://cloud.r-project.org"))
+options(BioC_mirror = "https://bioconductor.org")
+
 install.packages("BiocManager")
 BiocManager::install("renv")
 BiocManager::install(renv::dependencies(path = ".")[["Package"]])
 BiocManager::install("dmcable/spacexr")
 BiocManager::install("prabhakarlab/Banksy")
 BiocManager::install("satijalab/seurat-wrappers")
+
+# Only scan "scripts/" and "analysis.R"
+renv::snapshot(
+  prompt = FALSE,
+  packages = renv::dependencies(path = ".")[["Package"]]
+)