Merge pull request #37 from VeryAmazed/docs

Docs

.github/workflows/clang-format.yml

@@ -8,3 +8,5 @@ jobs:
     - uses: actions/checkout@v4
     - name: Run clang-format style check for C/C++/Protobuf programs.
       uses: jidicula/[email protected]
+      with:
+        clang-format-version: '17'

README.md

@@ -1,7 +1,7 @@
 # Digest
 C++ library which supports various minimizer schemes for digestion of DNA sequences  
 
-# Implementation (Most of the documentation is in the code)
+# Implementation
 Supports Mod Minimizers, Window Minimizers, and Syncmers  
 
 Uses the cyclic or hash provided by [ntHash](https://github.com/bcgsc/ntHash). For now I just downloaded the essential files off their github and compiled it myself but I may change how I link in ntHash in the future.  
@@ -28,11 +28,8 @@ This will generate `include` and `lib` folders.
 
 # Usage
 [Documentation](https://veryamazed.github.io/digest/)
-* Headers at `#include <digest/___.hpp>`
-* Classes are in `digest` namespace
-* example compile: `g++ file.cpp -IPREFIX/include -LPREFIX/lib -ldigest`
-* may need `std=c++17`
-* ntHash does not support `large_window < 4`
+* Digest objects require that the input string is kept in memory, unmodified.
+* requires `c++17`
 
 # Example
 ```cpp
@@ -44,28 +41,15 @@ Example snippet to collect up to 100000 indices of minimizers.
 A vector must be passed in, which will be appended to.
 Each WindowMin / Syncmer object is templated by the algorithm / data structure to find minimizers.
 
-# Selecting the correct `data_structure`
-our general guidelines:
-* for `large_window` < 12, use Naive
-* for 12 <= `large_window` <= 16 use SegmentTree
-* for `large_window` > 16 use Naive2
-
-adaptive performs at worst about 10% slower than best  
-adaptive64 performs at worst about 100% slower than best
+A complete example and cli can be found [here](https://github.com/BenLangmead/gester/tree/main)
 
 # Contributing
-run
-```bash
-ninja clang-format
-ninja clang-tidy
-ninja docs
-```
+Use clang format version 17.  
+run `ninja clang-format` before submitting a PR.
 
 # Benchmark / Tests
 ```bash
 meson setup build
 cd build && meson compile
 ```
 this will generate proper executables for benchmark/testing
-
-add to forked repo

docs/Doxyfile

@@ -588,7 +588,7 @@ RESOLVE_UNNAMED_PARAMS = YES
 # section is generated. This option has no effect if EXTRACT_ALL is enabled.
 # The default value is: NO.
 
-HIDE_UNDOC_MEMBERS     = NO
+HIDE_UNDOC_MEMBERS     = YES
 
 # If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
 # undocumented classes that are normally visible in the class hierarchy. If set
@@ -949,7 +949,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = include/digest
+INPUT                  = README.md include/digest
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1054,7 +1054,7 @@ RECURSIVE              = NO
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                =
+EXCLUDE                = # ./include/digest/data_structure.hpp
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -1165,7 +1165,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = README.md
 
 # The Fortran standard specifies that for fixed formatted Fortran code all
 # characters from position 72 are to be considered as comment. A common