Miscellaneous clean-ups for the docs, CI checks.

libscran · Jul 15, 2024 · bcb6dbc · bcb6dbc
1 parent 4be2deb
commit bcb6dbc
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Showing 5 changed files with 10 additions and 10 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -23,8 +23,8 @@ if(SCRAN_MARKERS_FETCH_EXTERN)
     add_subdirectory(extern)
 else()
     find_package(tatami_tatami 3.0.0 CONFIG REQUIRED)
-    find_package(tatami_tatami_stats 1.1.0 CONFIG REQUIRED)
-    find_package(scran_blocks 1.0.0 CONFIG REQUIRED)
+    find_package(tatami_tatami_stats 1.0.0 CONFIG REQUIRED)
+    find_package(libscran_scran_blocks 1.0.0 CONFIG REQUIRED)
 endif()
 
 target_link_libraries(scran_markers INTERFACE tatami::tatami tatami::tatami_stats libscran::scran_blocks)

diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@ const tatami::Matrix<double, int>& matrix = some_data_source();
 std::vector<int> groupings = some_groupings();
 
 scran_markers::ScoreMarkersSummaryOptions opt;
-auto res = scran::score_markers_summary(matrix, groupings.data(), opt);
+auto res = scran_markers::score_markers_summary(matrix, groupings.data(), opt);
 
 res.mean[0]; // mean of each gene in the first group.
 res.detected[0]; // detected proportion of each gene in the first group.
@@ -52,7 +52,7 @@ This performs the comparisons within each level of the blocking factor so as to
 // Array containing integer assignments to blocks 0, 1, 2, etc.
 std::vector<int> blocks = some_blocks();
 
-auto block_res = scran::score_markers_summary_blocked(
+auto block_res = scran_markers::score_markers_summary_blocked(
     matrix,
     groupings.data(), 
     blocks.data(),
@@ -65,7 +65,7 @@ If more detail is necessary, we can obtain effect sizes from all pairwise compar
 ```cpp
 scran_markers::ScoreMarkersPairwiseOptions popt;
 
-auto pair_res = scran::score_markers_pairwise(
+auto pair_res = scran_markers::score_markers_pairwise(
     matrix,
     groupings.data(),
     popt
@@ -134,7 +134,7 @@ cmake --build . --target install
 
 By default, this will use `FetchContent` to fetch all external dependencies.
 If you want to install them manually, use `-DSCRAN_MARKERS_FETCH_EXTERN=OFF`.
-See the commit hashes in [`extern/CMakeLists.txt`](extern/CMakeLists.txt) to find compatible versions of each dependency.
+See the tags in [`extern/CMakeLists.txt`](extern/CMakeLists.txt) to find compatible versions of each dependency.
 
 ### Manual
 

diff --git a/cmake/Config.cmake.in b/cmake/Config.cmake.in
@@ -2,7 +2,7 @@
 
 include(CMakeFindDependencyMacro)
 find_dependency(tatami_tatami 3.0.0 CONFIG REQUIRED)
-find_dependency(tatami_tatami_stats 1.1.0 CONFIG REQUIRED)
-find_dependency(scran_blocks 1.0.0 CONFIG REQUIRED)
+find_dependency(tatami_tatami_stats 1.0.0 CONFIG REQUIRED)
+find_dependency(libscran_scran_blocks 1.0.0 CONFIG REQUIRED)
 
 include("${CMAKE_CURRENT_LIST_DIR}/libscran_scran_markersTargets.cmake")
diff --git a/docs/Doxyfile b/docs/Doxyfile
@@ -1293,7 +1293,7 @@ HTML_STYLESHEET        =
 # list). For an example see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  =
+HTML_EXTRA_STYLESHEET  = doxygen-awesome.css
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note

diff --git a/extern/CMakeLists.txt b/extern/CMakeLists.txt
@@ -9,7 +9,7 @@ FetchContent_Declare(
 FetchContent_Declare(
   tatami_stats
   GIT_REPOSITORY https://github.com/tatami-inc/tatami_stats
-  GIT_TAG master # ^1.1.0
+  GIT_TAG master # ^1.0.0
 )
 
 FetchContent_Declare(