Update classes to match the new tatami interface, improve caching. (#10)

The Extractor interface updates allow users to directly pass an oracle during
construction, which eliminates the messy work required to choose between the
with- and without-oracle behavior after construction. We also use the new
SparsifiedWrapper classes for efficiently dense output from a sparse matrix.

We improve chunk caching by accepting arbitrary chunkGrids rather than being
limited to regular chunk intervals. We simplify cache management by not
considering R-allocated memory in the cache size limit, which allows us to copy
over the data into our own slab cache managers from tatami_chunked. This
allows us to actually use the LRU and oracular caches to their full extent.

We also remove the COO matrix parser, on the understanding that this is superceded
by the SVT matrices in the latest versions of DelayedArray. (Nonetheless, we add
an R-side fallback to convert COO to SVT just in case.)

Finally, we greatly enhanced the scale of the tests to cover the new code.

.github/workflows/check-install.yaml

@@ -23,6 +23,13 @@ jobs:
         cmake -S . -B build -DTATAMI_TESTS=OFF
         sudo cmake --install build
 
+    - name: Install tatami-chunked
+      run: |
+        git clone https://github.com/tatami-inc/tatami_chunked dep-tatami_chunked --depth=1
+        cd dep-tatami_chunked
+        cmake -S . -B build -DTATAMI_CHUNKED_TESTS=OFF
+        sudo cmake --install build
+
     - name: Install manticore
       run: |
         git clone https://github.com/tatami-inc/manticore dep-manticore --depth=1

.github/workflows/run-tests.yaml

@@ -10,7 +10,7 @@ jobs:
   build:
     name: Run tests
     runs-on: ubuntu-latest
-    container: bioconductor/bioconductor_docker:devel
+    container: bioconductor/bioconductor_docker:RELEASE_3_19
     strategy:
       fail-fast: false
       matrix:

CMakeLists.txt

@@ -18,7 +18,7 @@ else()
     find_package(tatami_manticore CONFIG REQUIRED)
 endif()
 
-target_link_libraries(tatami_r INTERFACE tatami::tatami tatami::manticore)
+target_link_libraries(tatami_r INTERFACE tatami::tatami tatami::tatami_chunked tatami::manticore)
 
 # Switch between include directories depending on whether the downstream is
 # using the build directly or is using the installed package.

cmake/Config.cmake.in

@@ -2,6 +2,7 @@
 
 include(CMakeFindDependencyMacro)
 find_dependency(tatami_tatami CONFIG REQUIRED)
+find_dependency(tatami_tatami_chunked CONFIG REQUIRED)
 find_dependency(tatami_manticore CONFIG REQUIRED)
 
 include("${CMAKE_CURRENT_LIST_DIR}/tatami_tatami_rTargets.cmake")

extern/CMakeLists.txt

@@ -6,7 +6,11 @@ FetchContent_Declare(
   GIT_TAG master
 )
 
-FetchContent_MakeAvailable(tatami)
+FetchContent_Declare(
+  tatami_chunked
+  GIT_REPOSITORY https://github.com/tatami-inc/tatami_chunked
+  GIT_TAG master
+)
 
 FetchContent_Declare(
   manticore
@@ -15,3 +19,5 @@ FetchContent_Declare(
 )
 
 FetchContent_MakeAvailable(manticore)
+FetchContent_MakeAvailable(tatami)
+FetchContent_MakeAvailable(tatami_chunked)