Merge pull request #75 from smithlabcode/linting

Linting and formatting code

.clang-format

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+# This file is part of preseq
+#
+# Copyright (C) 2024: Andrew D. Smith
+#
+# Authors: Andrew D. Smith
+#
+# This is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This software is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+
+BasedOnStyle: LLVM
+ColumnLimit: 80
+IndentWidth: 2
+AlwaysBreakAfterReturnType: TopLevel
+ContinuationIndentWidth: 2
+ConstructorInitializerIndentWidth: 2
+BraceWrapping:
+  BeforeElse: true
+  BeforeCatch: true
+BreakBeforeBraces: Custom
+BreakConstructorInitializers: AfterColon
+SpacesBeforeTrailingComments: 2

.github/workflows/clang-format.yml

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+# This file is part of preseq
+#
+# Copyright (C) 2024: Andrew D. Smith
+#
+# Authors: Andrew D. Smith
+#
+# This is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This software is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+
+name: Source formatting with clang-format
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  workflow_dispatch:
+
+jobs:
+  clang-format:
+    runs-on: ubuntu-24.04
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Install dependencies
+      run: sudo apt-get install -y clang-format
+
+    - name: Run clang-format
+      run: |
+        clang-format --dry-run -Werror $(git ls-files '*.*pp')

.github/workflows/cpplint.yml

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+# This file is part of preseq
+#
+# Copyright (C) 2024: Andrew D. Smith
+#
+# Authors: Andrew D. Smith
+#
+# This is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This software is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+
+name: Linting with cpplint
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+  workflow_dispatch:
+
+jobs:
+  cpplint:
+    runs-on: ubuntu-24.04
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Python setup ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install cpplint
+      run: |
+        python -m pip install --upgrade pip
+        pip install cpplint
+
+    - name: Check cpplint version
+      run: cpplint --version
+
+    - name: Run cpplint
+      run: |
+        cpplint --quiet --repository=. $(git ls-files '*.*pp')

CPPLINT.cfg

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+# This file is part of preseq
+#
+# Copyright (C) 2024: Andrew D. Smith
+#
+# Authors: Andrew D. Smith
+#
+# This is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This software is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+
+set noparent
+filter=-runtime/references
+filter=-build/include_subdir
+filter=-build/include_order
+filter=-build/c++11
+filter=-build/c++17
+# Formatting below handled by clang-format
+filter=-whitespace/line_length
+filter=-whitespace/newline
+filter=-readability/braces
+filter=-whitespace/semicolon
+filter=-whitespace/indent

autogen.sh

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+#!/bin/sh
+#
+# Run 'autoreconf -i' to generate 'configure', 'Makefile.in', etc.
+#
+# The first time this is run on a new cloned git repo the configure
+# script will not be present, only the configure.ac and
+# Makefile.am. The rest must be generated by `autoreconf -i`.
+#
+# If you are working with a distribution (file ending with ".tar.gz"
+# or similar) then this script should not be needed, and should not be
+# present, as all the files should already exist. You should only run
+# this script if you know what you are doing with autoreconf.
+#
+# This script will only work with an argument to confirm the help
+# message has been read.
+
+runautoreconf() {
+    autoreconf -i;
+}
+
+if test -d .git && test "$(basename "${PWD}")" = "preseq"
+then
+    runautoreconf
+    exit 0
+else
+    echo "  It seems you are either attempting to run this script       "
+    echo "  from the wrong directory, or in a source tree that was      "
+    echo "  not obtained by cloning the preseq git repo.                "
+    echo "                                                              "
+    echo "  ./autogen.sh generates the configure script. Only run       "
+    echo "                                                              "
+    echo "  Only run this if you know what you are doing with           "
+    echo "  autoreconf and are simply avoiding doing that. If you       "
+    echo "  just want to use the software, download a release and       "
+    echo "  this script will not be needed.                             "
+    exit 1
+fi