pull changes from main

.Rbuildignore

@@ -14,3 +14,5 @@ src/Makevars$
 autobrew
 configure.log
 ^[.]?air[.]toml$
+^\.positai$
+^\.claude$

.github/workflows/check.yml → .github/legacy/check.yml

@@ -181,6 +181,7 @@ jobs:
           BiocManager::install('SpatialExperiment')
           install.packages('dplyr')
           BiocManager::install('DESeq2')
+          install.packages('harmony')
           install.packages('ggnewscale')
           install.packages('patchwork')
           devtools::install_github('vitessce/vitessceR')

.github/workflows/claude-code-review.yml

@@ -0,0 +1,46 @@
+name: Claude Code Review
+
+on:
+  pull_request:
+    types: [opened, synchronize, ready_for_review, reopened]
+    # Optional: Only run on specific file changes
+    # paths:
+    #   - "src/**/*.ts"
+    #   - "src/**/*.tsx"
+    #   - "src/**/*.js"
+    #   - "src/**/*.jsx"
+
+jobs:
+  claude-review:
+    # Optional: Filter by PR author
+    # if: |
+    #   github.event.pull_request.user.login == 'external-contributor' ||
+    #   github.event.pull_request.user.login == 'new-developer' ||
+    #   github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR'
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code Review
+        id: claude-review
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          plugin_marketplaces: 'https://github.com/anthropics/claude-code.git'
+          plugins: 'code-review@claude-code-plugins'
+          prompt: '/code-review:code-review ${{ github.repository }}/pull/${{ github.event.pull_request.number }}'
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://code.claude.com/docs/en/cli-reference for available options
+          claude_args: |
+            --model claude-opus-4-8
+

.github/workflows/claude.yml

@@ -0,0 +1,51 @@
+name: Claude Code
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  claude:
+    if: |
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
+      (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+      actions: read # Required for Claude to read CI results on PRs
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code
+        id: claude
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+
+          # This is an optional setting that allows Claude to read CI results on PRs
+          additional_permissions: |
+            actions: read
+
+          # Optional: Give a custom prompt to Claude. If this is not specified, Claude will perform the instructions specified in the comment that tagged it.
+          # prompt: 'Update the pull request description to include a summary of changes.'
+
+          # Optional: Add claude_args to customize behavior and configuration
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://code.claude.com/docs/en/cli-reference for available options
+          claude_args: |
+            --model claude-opus-5
+

.github/workflows/r-universe.yml

@@ -0,0 +1,11 @@
+name: R-universe test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  build:
+    name: R-universe testing
+    uses: r-universe-org/workflows/.github/workflows/build.yml@v3

.gitignore

@@ -16,4 +16,5 @@ Makevars
 dev
 *.tar.xz
 cleanup
-inst/share
+inst/share
+.positai

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: VoltRon
 Type: Package
 Title: VoltRon for Spatial Omics Data Integration and Analysis
-Version: 0.2.6
+Version: 0.3.0
 Depends: R (>= 4.6.0)
 Author@R: 
 	person("Artür", "Manukyan", 
@@ -30,7 +30,6 @@ License: MIT + file LICENSE
 SystemRequirements: OpenCV 4.8 (or higher): libopencv-dev (Debian, Ubuntu) or 
                     opencv-devel (Fedora)
 Encoding: UTF-8
-RoxygenNote: 7.3.3
 biocViews:
 Imports: utils, methods, grDevices, data.table, Matrix, S4Arrays, S4Vectors, 
          ids, RcppAnnoy, RANN, igraph, dplyr, ggplot2, ggrepel, ggpubr, 
@@ -64,22 +63,22 @@ Collate:
     'visualization.R'
 Suggests:
     testthat (>= 3.0.0),
+    arrow,
+    RBioFormats,
+    basilisk,
+    reticulate,
     DelayedArray,
     DelayedMatrixStats,
     BiocParallel,
     rhdf5,
     Rarr,
     ZarrArray,
-    basilisk,
-    reticulate,
-    RBioFormats,
-    VoltRonStore,
+    VoltRonStore (>= 0.1.2),
     BPCells,
     HDF5Array,
     HDF5DataFrame,
     ZarrDataFrame,
     ImageArray,
-    viridisLite,
     SpatialExperiment,
     SingleCellExperiment,
     SummarizedExperiment,
@@ -93,19 +92,17 @@ Suggests:
     sf,
     ComplexHeatmap,
     xlsx,
-    reshape2,
-    arrow,
     vitessceR,
-    geojsonR,
     circlize,
     rstudioapi,
     ggforce,
     ggnewscale,
     anndataR,
     anndata,
-    SimpleITK
+    SimpleITK,
+    harmony
 Remotes:
-	  stla/RCDT,
+    stla/RCDT,
     BIMSBbioinfo/VoltRonStore,
     bnprks/BPCells/r@v0.3.0,
     BIMSBbioinfo/VoltRon,
@@ -114,3 +111,4 @@ Remotes:
 Config/testthat/edition: 3
 LazyData: true
 LazyDataCompression: gzip
+Config/roxygen2/version: 8.1.0

Dockerfile

@@ -9,6 +9,9 @@ RUN apt-get install -y libssl-dev libcurl4-openssl-dev libgit2-dev libxml2-dev l
 # RCDT/rgl dependencies
 RUN apt-get install -y libglu1-mesa libglu1-mesa-dev libxext6 libsm6 libxrender1
 
+# sf dependencies
+RUN apt-get install -y libuv1-dev
+
 # Install required R packages
 RUN R -e "install.packages(c('shiny', 'devtools', 'BiocManager'), repos='http://cran.rstudio.com/')"
 
@@ -37,6 +40,7 @@ RUN R -e "BiocManager::install('SingleCellExperiment')"
 RUN R -e "BiocManager::install('SpatialExperiment')"
 RUN R -e "install.packages('dplyr')"
 RUN R -e "BiocManager::install('DESeq2')"
+RUN R -e "install.packages('harmony')"
 RUN R -e "install.packages('ggnewscale')"
 RUN R -e "install.packages('patchwork')"
 RUN R -e "install.packages('anndata')"