Update to the latest tatami interface.

.github/workflows/run-tests.yaml

@@ -21,12 +21,12 @@ jobs:
           }
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Get latest CMake
       uses: lukka/get-cmake@latest
 
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       id: cache
       with:
         path: libtiledb
@@ -51,7 +51,15 @@ jobs:
     - name: Run the tests
       run: |
         cd build
-        ctest
+        # Avoid using ctest because it's so slow; it starts a
+        # new process for each individual test, which is crazy.
+        for exe in $(ctest --show-only=json-v1 | jq -r ".tests[] | .command | .[0]"  | sort | uniq)
+        do
+            echo "#### RUNNING ${exe} ####"
+            echo 
+            ${exe} --gtest_brief=1
+            echo
+        done 
 
     - name: Generate code coverage
       if: ${{ matrix.config.cov }}
@@ -61,6 +69,8 @@ jobs:
 
     - name: Upload to Codecov
       if: ${{ matrix.config.cov }}
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         directory: build/tests/CMakeFiles/
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

README.md

@@ -17,25 +17,18 @@ Any matrix stored as a 2-dimensional TileDB array (dense or sparse) can be repre
 ```cpp
 #include "tatami_tiledb/tatami_tiledb.hpp"
 
-tatami_tiledb::TileDbDenseMatrix<double, int> dense_mat("some_dir", "attr_name");
-tatami_tiledb::TileDbSparseMatrix<double, int> sparse_mat("some_dir", "attr_name");
-```
-
-If the dense/sparse nature is not known beforehand, we can use the `make_TileDbMatrix()` function to decide for us instead:
-
-```cpp
-auto some_mat = tatami_tiledb::make_TileDbMatrix("some_dir", "attr_name");
+tatami_tiledb::DenseMatrix<double, int> dense_mat("some_dir", "attr_name");
+tatami_tiledb::SparseMatrix<double, int> sparse_mat("some_dir", "attr_name");
 ```
 
 Advanced users can fiddle with the options, in particular the size of the tile cache.
 For example, we could force the matrix to use no more than 200 MB of memory in the cache:
 
 ```cpp
-tatami_tiledb::TileDbOptions opt;
+tatami_tiledb::DenseMatrixOptions opt;
 opt.maximum_cache_size = 200000000;
 opt.require_minimum_cache = false; // don't allow the cache to automatically expand.
-
-auto some_mat2 = tatami_tiledb::make_TileDbMatrix("some_dir", "attr_name", opt);
+tatami_tiledb::DenseMatrix<double, int> some_mat2("some_dir", "attr_name", opt);
 ```
 
 Check out the [reference documentation](https://tatami-inc.github.io/tatami_tiledb) for more details.
@@ -50,7 +43,7 @@ If you're using CMake, you just need to add something like this to your `CMakeLi
 include(FetchContent)
 
 FetchContent_Declare(
-  tatami
+  tatami_tiledb
   GIT_REPOSITORY https://github.com/tatami-inc/tatami_tiledb
   GIT_TAG master # or any version of interest
 )