From aabaf6ecbb0449ba7761a3afd80f0015c940c2a1 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Mon, 22 Jan 2024 11:57:37 -0600
Subject: [PATCH] Prepare for seurat 5 compatibility (#40)

* Prepare for seurat 5 compatibility
* Remove unnecessary fixed versions
---
 .github/workflows/R-CMD-check.yaml | 16 +++-------------
 DESCRIPTION                        |  2 +-
 Dockerfile                         |  9 ++-------
 3 files changed, 6 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index f2be0b2..8e45034 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -50,8 +50,7 @@ jobs:
 
       - name: Setup CoNGA
         run: |
-          # NOTE: seaborn added for: https://github.com/scverse/scanpy/issues/2680
-          python3 -m pip install --user scanpy fastcluster seaborn==0.12.2
+          python3 -m pip install --user scanpy
           cd ../
           git clone -b rhesus https://github.com/phbradley/conga.git conga
           cd conga/tcrdist_cpp
@@ -105,17 +104,8 @@ jobs:
         run: |
           getOption('repos');
           print(paste0("R_BIOC_VERSION: ", Sys.getenv("R_BIOC_VERSION")));
-          # TODO: remove this once Seurat 5 is supported. Install RIRA and CellMembrane first, since it depends on seurat 4.4 and the upgrade would otherwise force-update it: 
-          devtools::install_version('Seurat', version = '4.4.0', ask = FALSE, upgrade = 'never', type = 'source', repos = 'https://cloud.r-project.org')
-          devtools::install_github(repo = 'bimberlabinternal/RIRA', ref = 'master', dependencies = TRUE, upgrade = 'never')
-          devtools::install_github(repo = 'bimberlabinternal/CellMembrane', ref = 'master', dependencies = TRUE, upgrade = 'never')
-          devtools::install_github(repo = 'bimberlab/cellhashR', ref = 'master', dependencies = TRUE, upgrade = 'never')
-          remotes::install_deps(dependencies = TRUE, upgrade = "never")
-          # Force 4.x for Seurat 
-          devtools::install_version('Seurat', version = '4.4.0', ask = FALSE, upgrade = 'never')
+          remotes::install_deps(dependencies = TRUE, upgrade = "always")
           remotes::install_cran("rcmdcheck")
-          # Due to Matrix/SeuratObject: https://github.com/mojaveazure/seurat-object/issues/166
-          install.packages('SeuratObject', ask = FALSE, force = TRUE, type = 'source', repos = 'https://cloud.r-project.org')
         shell: Rscript {0}
 
       - name: Session info
@@ -140,5 +130,5 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@main
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc${{ matrix.config.bioc }}-results
           path: check
diff --git a/DESCRIPTION b/DESCRIPTION
index e3ac4ba..2940ba4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -10,7 +10,7 @@ Encoding: UTF-8
 Depends:
     R (>= 4.3.0)
 Imports:
-    Seurat (<= 4.4.0),
+    Seurat,
     dplyr,
     naturalsort,
     Rlabkey,
diff --git a/Dockerfile b/Dockerfile
index 1b4d02c..cd147a4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -15,8 +15,7 @@ RUN echo "local({r <- getOption('repos') ;r['CRAN'] = 'https://packagemanager.rs
         wget \
         git \
     && python3 -m pip install --upgrade pip \
-    #  NOTE: seaborn added for: https://github.com/scverse/scanpy/issues/2680
-    && pip3 install umap-learn phate scanpy fastcluster seaborn==0.12.2 \
+    && pip3 install umap-learn phate scanpy \
     && mkdir /conga \
     && cd /conga \
     && git clone https://github.com/phbradley/conga.git \
@@ -46,11 +45,7 @@ RUN --mount=type=secret,id=GITHUB_PAT \
     && export GITHUB_PAT="$(cat /run/secrets/GITHUB_PAT)" \
     && echo "GH: $GITHUB_PAT" \
     && Rscript -e "BiocManager::install(ask = F, upgrade = 'always');" \
-    # Force 4.x for Seurat
-    && Rscript -e "devtools::install_version('Seurat', version = '4.4.0', upgrade = 'never')" \
-    && Rscript -e "devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade = 'never');" \
-    # Due to Matrix/SeuratObject: https://github.com/mojaveazure/seurat-object/issues/166
-    && Rscript -e "install.packages('SeuratObject', ask = FALSE, force = TRUE, type = 'source', repos = 'https://cloud.r-project.org')" \
+    && Rscript -e "devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade = 'always');" \
     && R CMD build . \
     && R CMD INSTALL --build *.tar.gz \
     && rm -Rf /tmp/downloaded_packages/ /tmp/*.rds