Switch to {rhdf5} for HDF5 reading/writing (#283)

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Co-authored-by: LouiseDck <louise.deconinck@gmail.com>

Author: 3 people

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

@@ -25,7 +25,8 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest, r: 'release'}
-          - {os: ubuntu-latest, r: 'oldrel-1'}
+          # Fails due to #248, resolved with Bioconductor 3.22 release (October 2025)
+          # - {os: ubuntu-latest, r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -34,6 +35,12 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get -y install libsz2 libaec-dev
+
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
@@ -47,6 +54,22 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
+      # Avoid a caching issue where {rhdf5} was not restored properly
+      - name: Reinstall {rhdf5} on Linux
+        if: runner.os == 'Linux'
+        run: |
+          BiocManager::install(c("rhdf5", "Rhdf5lib"), force = TRUE)
+        shell: Rscript {0}
+
+      - name: Check {rhdf5} availability
+        run: |
+          if (requireNamespace("rhdf5")) {
+            cat(as.character(packageVersion("rhdf5")))
+          } else {
+            stop("rhdf5 not found")
+          }
+        shell: Rscript {0}
+
       - name: Install h5diff
         run: |
           if [ "$RUNNER_OS" == "Linux" ]; then

.github/workflows/pkgdown.yaml

@@ -23,6 +23,12 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get -y install libsz2
+
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
@@ -34,6 +40,18 @@ jobs:
           extra-packages: local::.
           needs: website
 
+      # Avoid a caching issue where {rhdf5} was not restored properly
+      - name: Reinstall {rhdf5} and check availability
+        run: |
+          BiocManager::install(c("rhdf5", "Rhdf5lib"), force = TRUE)
+
+          if (requireNamespace("rhdf5")) {
+            cat(as.character(packageVersion("rhdf5")))
+          } else {
+            stop("rhdf5 not found")
+          }
+        shell: Rscript {0}
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: anndataR
 Title: AnnData interoperability in R
-Version: 0.1.0.9009
+Version: 0.1.0.9010
 Authors@R: c(
     person("Robrecht", "Cannoodt", , "robrecht@data-intuitive.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")),
@@ -45,10 +45,10 @@ Imports:
 Suggests:
     anndata,
     BiocStyle,
-    hdf5r (>= 1.3.11),
     knitr,
     processx,
     reticulate (>= 1.41.1),
+    rhdf5,
     rmarkdown,
     S4Vectors,
     Seurat,

NEWS.md

@@ -1,38 +1,46 @@
-# anndataR 0.1.0.9009
+# anndataR devel
 
-- Fix execution of roundtrip tests
-- 
-# anndataR 0.1.0.9008
+## anndataR 0.1.0.9010
+
+- Switch HDF5 back end from **{hdf5r}** to **{rhdf5}** (PR #283, Fixes #272, #175, #299)
+  - Includes improved compatibility with H5AD files written by Python **anndata**
+- Improvements to rountrip testing (PR #283)
+
+## anndataR 0.1.0.9009
+
+- Fix execution of roundtrip tests (PR #293)
+
+## anndataR 0.1.0.9008
 
-- Add Bioconductor installation instructions in preparation of submission
+- Add Bioconductor installation instructions in preparation of submission (PR #297)
 
-# anndataR 0.1.0.9007
+## anndataR 0.1.0.9007
 
-- Refactor superfluous for loops
+- Refactor superfluous for loops (PR #298)
 - 
-# anndataR 0.1.0.9006
+## anndataR 0.1.0.9006
 
-- ignore `development_status.Rmd` vignette when building package
+- Ignore `development_status.Rmd` vignette when building package (PR #296)
 
-# anndataR 0.1.0.9005
+## anndataR 0.1.0.9005
 
-- Bypass requiring a `counts` or `data` layer during `Seurat` conversion
+- Bypass requiring a `counts` or `data` layer during `Seurat` conversion (PR #284)
 
-# anndataR 0.1.0.9004
+## anndataR 0.1.0.9004
 
-- Use accessors instead of direct slot access where possible
+- Use accessors instead of direct slot access where possible (PR #291)
 
-# anndataR 0.1.0.9003
+## anndataR 0.1.0.9003
 
-- Simplify & update vignetttes
+- Simplify and update vignettes (PR #282)
 
-# anndataR 0.1.0.9002
+## anndataR 0.1.0.9002
 
-- remove `anndataR.Rproj` file from repository
+- Remove `anndataR.Rproj` file from repository (PR #292)
 
-# anndataR 0.1.0.9001
+## anndataR 0.1.0.9001
 
-- change uses of `sapply` to `vapply`
+- Change uses of `sapply()` to `vapply()` (PR #294)
 
 # anndataR 0.1.0 (inital release candidate)