Adding clang-format and formatting sources

.clang-format

@@ -0,0 +1,34 @@
+# MIT License
+#
+# Copyright (c) 2024 Andrew Smith
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+BasedOnStyle: LLVM
+ColumnLimit: 80
+IndentWidth: 2
+AlwaysBreakAfterReturnType: All
+ContinuationIndentWidth: 2
+ConstructorInitializerIndentWidth: 2
+BraceWrapping:
+  BeforeElse: true
+  BeforeCatch: true
+BreakBeforeBraces: Custom
+BreakConstructorInitializers: AfterColon
+SpacesBeforeTrailingComments: 2

.gitignore

@@ -1,13 +1,32 @@
-*
-!.gitignore
-!docs/*
-!src
-!src/*pp
-!m4
-!src/smithlab_cpp/*pp
-!Makefile
-!Makefile.am
-!configure.ac
-!README.md
-!LICENSE
-!autogen.sh
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app

src/AbismalAlign.hpp

@@ -1,4 +1,4 @@
-/* Copyright (C) 2019-2023 Andrew D. Smith and Guilherme Sena
+/* Copyright (C) 2019-2025 Andrew D. Smith and Guilherme Sena
  *
  * Authors: Andrew D. Smith and Guilherme Sena
  *