Update RStudio server (& python venv)

.dockerignore

@@ -20,6 +20,7 @@
 !/RNA-seq
 !/scRNA-seq
 !/scRNA-seq-advanced
+!/spatial
 
 # still ignore data directories
 **/data/*

.github/workflows/build-docker.yml

@@ -90,7 +90,7 @@ jobs:
         with:
           push: ${{ github.event_name == 'push' }}
           secrets: |
-            GITHUB_TOKEN=${{ secrets.GITHUB_TOKEN }}
+            GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}
           platforms: ${{ matrix.platform }}
           outputs: type=image,push-by-digest=true,name-canonical=true
           labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -67,6 +67,22 @@ RUN apt-get update -qq \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
+# Update RStudio if needed
+ARG RSTUDIO_MIN=2026.09.0+174
+
+RUN set -eux; \
+    ARCH=$(dpkg --print-architecture); \
+    CUR_VER=$(dpkg-query -W -f='${Version}' rstudio-server 2>/dev/null || echo 0); \
+    if dpkg --compare-versions "$CUR_VER" lt "$RSTUDIO_MIN"; then \
+      curl -fsSL "https://dl.dailies.rstudio.com/server/jammy/${ARCH}/rstudio-server-$(echo "$RSTUDIO_MIN" | tr + -)-${ARCH}.deb" \
+        -o /tmp/rstudio-server.deb; \
+      gdebi --non-interactive /tmp/rstudio-server.deb; \
+      rm /tmp/rstudio-server.deb; \
+      ln -fs /usr/lib/rstudio-server/bin/rstudio-server /usr/local/bin; \
+      ln -fs /usr/lib/rstudio-server/bin/rserver /usr/local/bin; \
+    fi; \
+    rm -rf /var/lib/apt/lists/*
+
 # FastQC
 RUN apt-get update -qq \
     && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
@@ -77,16 +93,26 @@ RUN apt-get update -qq \
 # Get rclone
 RUN curl -L https://rclone.org/install.sh | bash
 
-# Python packages
-COPY requirements.txt requirements.txt
-RUN pip install -r requirements.txt --break-system-packages
+# Python packages in a venv that is set as default for users
+COPY requirements.txt /tmp/requirements.txt
+RUN python3 -m venv /opt/venv \
+    && /opt/venv/bin/pip install --no-cache-dir -r /tmp/requirements.txt \
+    && rm /tmp/requirements.txt \
+    && chgrp -R staff /opt/venv && chmod -R g+ws /opt/venv \
+    && echo '[ "$(id -u)" -ne 0 ] && export PATH=/opt/venv/bin:$PATH' > /etc/profile.d/venv.sh \
+    && cat >> "$(R RHOME)/etc/Rprofile.site" <<'EOF'
+Sys.setenv(
+    RETICULATE_PYTHON = "/opt/venv/bin/python",
+    VIRTUAL_ENV_DISABLE_PROMPT = "1"
+  )
+EOF
 
 # Use renv for R packages
 WORKDIR /usr/local/renv
 COPY renv.lock renv.lock
 ENV RENV_CONFIG_CACHE_ENABLED=FALSE
 ENV RENV_CONFIG_INSTALL_STAGED=FALSE
-RUN --mount=type=secret,id=GITHUB_TOKEN,env=GITHUB_PAT,required=false \
+RUN --mount=type=secret,id=GITHUB_PAT,env=GITHUB_PAT,required=false \
     Rscript - <<'RSCRIPT_EOF'
 # Some challenges with multi-arch builds and Bioconductor binaries mean we
 # want to be sure to set up repos manually here, lest the ones recorded in the
@@ -128,5 +154,8 @@ RUN python3 ${template_dir}/scripts/setup-skel.py \
     --skel-dir /etc/skel \
     --module-file ${template_dir}/current-modules.json
 
+# Disable Posit Assistant
+RUN echo "posit-assistant-enabled=0" >> /etc/rstudio/rsession.conf
+
 WORKDIR /home/rstudio
 

renv.lock

@@ -3218,7 +3218,7 @@
     },
     "RcppParallel": {
       "Package": "RcppParallel",
-      "Version": "6.1.1",
+      "Version": "6.2.1",
       "Source": "Repository",
       "Type": "Package",
       "Title": "Parallel Programming Tools for 'Rcpp'",
@@ -5640,8 +5640,7 @@
       "URL": "https://www.rforge.net/base64enc",
       "BugReports": "https://github.com/s-u/base64enc/issues",
       "NeedsCompilation": "yes",
-      "Repository": "CRAN",
-      "Encoding": "UTF-8"
+      "Repository": "CRAN"
     },
     "batchelor": {
       "Package": "batchelor",
@@ -14139,28 +14138,28 @@
     },
     "qs2": {
       "Package": "qs2",
-      "Version": "0.2.2",
+      "Version": "0.3.1",
       "Source": "Repository",
       "Type": "Package",
       "Title": "Efficient Serialization of R Objects",
-      "Date": "2026-06-02",
+      "Date": "2026-08-19",
       "Authors@R": "c( person(\"Travers\", \"Ching\", email = \"traversc@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Yann\", \"Collet\", role = c(\"ctb\", \"cph\"), comment = \"Yann Collet is the author of the bundled zstd\"), person(\"Facebook, Inc.\", role = \"cph\", comment = \"Facebook is the copyright holder of the bundled zstd code\"), person(\"Reichardt\", \"Tino\", role = c(\"ctb\", \"cph\"), comment = \"Contributor/copyright holder of zstd bundled code\"), person(\"Skibinski\", \"Przemyslaw\", role = c(\"ctb\", \"cph\"), comment = \"Contributor/copyright holder of zstd bundled code\"), person(\"Mori\", \"Yuta\", role = c(\"ctb\", \"cph\"), comment = \"Contributor/copyright holder of zstd bundled code\"), person(\"Francesc\", \"Alted\", role = c(\"ctb\", \"cph\"), comment = \"Shuffling routines derived from Blosc library\"))",
       "Maintainer": "Travers Ching <traversc@gmail.com>",
       "Description": "Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.",
       "License": "GPL-3",
       "LazyData": "true",
       "Biarch": "true",
       "Depends": [
-        "R (>= 3.5.0)"
+        "R (>= 3.6.0)"
       ],
       "Imports": [
         "Rcpp",
-        "RcppParallel",
+        "RcppParallel (>= 6.1.1)",
         "stringfish (>= 0.18.0)"
       ],
       "LinkingTo": [
         "Rcpp",
-        "RcppParallel"
+        "RcppParallel (>= 6.1.1)"
       ],
       "Suggests": [
         "knitr",
@@ -14171,11 +14170,11 @@
       ],
       "SystemRequirements": "GNU make, C++17",
       "Encoding": "UTF-8",
-      "RoxygenNote": "7.3.3",
       "VignetteBuilder": "knitr",
       "Copyright": "This package includes code from the 'zstd' library owned by Facebook, Inc. and created by Yann Collet; and code derived from the 'Blosc' library created and owned by Francesc Alted.",
       "URL": "https://github.com/qsbase/qs2",
       "BugReports": "https://github.com/qsbase/qs2/issues",
+      "Config/roxygen2/version": "8.0.0",
       "NeedsCompilation": "yes",
       "Author": "Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd), Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled zstd code), Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled code), Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd bundled code), Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled code), Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc library)",
       "Repository": "CRAN"
@@ -17011,11 +17010,11 @@
     },
     "stringfish": {
       "Package": "stringfish",
-      "Version": "0.19.0",
+      "Version": "0.19.2",
       "Source": "Repository",
       "Title": "Alt String Implementation",
-      "Date": "2026-04-18",
-      "Authors@R": "c( person(\"Travers\", \"Ching\", email = \"traversc@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Phillip\", \"Hazel\", role = c(\"ctb\"), comment = \"Bundled PCRE2 code\"), person(\"Zoltan\", \"Herczeg\", role = c(\"ctb\", \"cph\"), comment = \"Bundled PCRE2 code\"), person(\"University of Cambridge\", role = c(\"cph\"), comment = \"Bundled PCRE2 code\"), person(\"Tilera Corporation\", role = c(\"cph\"), comment = \"Stack-less Just-In-Time compiler bundled with PCRE2\"), person(\"Yann\", \"Collet\", role = c(\"ctb\", \"cph\"), comment = \"Yann Collet is the author of the bundled xxHash code\"))",
+      "Date": "2026-08-04",
+      "Authors@R": "c( person(\"Travers\", \"Ching\", email = \"traversc@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Phillip\", \"Hazel\", role = c(\"ctb\"), comment = \"Bundled PCRE2 code\"), person(\"Zoltan\", \"Herczeg\", role = c(\"ctb\", \"cph\"), comment = \"Bundled PCRE2 code\"), person(\"University of Cambridge\", role = c(\"cph\"), comment = \"Bundled PCRE2 code\"), person(\"Tilera Corporation\", role = c(\"cph\"), comment = \"Stack-less Just-In-Time compiler bundled with PCRE2\"), person(\"Yann\", \"Collet\", role = c(\"ctb\", \"cph\"), comment = \"Yann Collet is the author of the bundled xxHash code\"), person(\"Martin\", \"Leitner-Ankerl\", role = c(\"ctb\", \"cph\"), comment = \"Bundled ankerl::unordered_dense code\"))",
       "Maintainer": "Travers Ching <traversc@gmail.com>",
       "Description": "Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.",
       "License": "GPL-3",
@@ -17027,7 +17026,7 @@
       "SystemRequirements": "GNU make, C++17",
       "LinkingTo": [
         "Rcpp (>= 0.12.18.3)",
-        "RcppParallel (>= 5.1.4)"
+        "RcppParallel (>= 6.1.1)"
       ],
       "Imports": [
         "Rcpp",
@@ -17038,12 +17037,12 @@
         "rmarkdown"
       ],
       "VignetteBuilder": "knitr",
-      "RoxygenNote": "7.3.3",
-      "Copyright": "Copyright for the bundled 'PCRE2' library is held by University of Cambridge, Zoltan Herczeg and Tilera Corporation (Stack-less Just-In-Time compiler); Copyright for the bundled 'xxHash' code is held by Yann Collet.",
+      "Copyright": "Copyright for the bundled 'PCRE2' library is held by University of Cambridge, Zoltan Herczeg and Tilera Corporation (Stack-less Just-In-Time compiler); Copyright for the bundled 'xxHash' code is held by Yann Collet; Copyright for the bundled 'ankerl::unordered_dense' code is held by Martin Leitner-Ankerl.",
       "URL": "https://github.com/traversc/stringfish",
       "BugReports": "https://github.com/traversc/stringfish/issues",
+      "Config/roxygen2/version": "8.0.0",
       "NeedsCompilation": "yes",
-      "Author": "Travers Ching [aut, cre, cph], Phillip Hazel [ctb] (Bundled PCRE2 code), Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code), University of Cambridge [cph] (Bundled PCRE2 code), Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with PCRE2), Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash code)",
+      "Author": "Travers Ching [aut, cre, cph], Phillip Hazel [ctb] (Bundled PCRE2 code), Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code), University of Cambridge [cph] (Bundled PCRE2 code), Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with PCRE2), Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash code), Martin Leitner-Ankerl [ctb, cph] (Bundled ankerl::unordered_dense code)",
       "Repository": "CRAN"
     },
     "stringi": {
@@ -18124,8 +18123,7 @@
       "URL": "https://www.rforge.net/uuid",
       "BugReports": "https://github.com/s-u/uuid/issues",
       "NeedsCompilation": "yes",
-      "Repository": "CRAN",
-      "Encoding": "UTF-8"
+      "Repository": "CRAN"
     },
     "uwot": {
       "Package": "uwot",