Improve Testing, Documentation, and CI/CD for GLIMPSE2 DevelopmentSome

.devcontainer/.bashrc

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+# ~/.bashrc: executed by bash(1) for non-login shells.
+# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
+# for examples
+
+# If not running interactively, don't do anything
+case $- in
+    *i*) ;;
+      *) return;;
+esac
+
+# don't put duplicate lines or lines starting with space in the history.
+# See bash(1) for more options
+HISTCONTROL=ignoreboth
+
+# append to the history file, don't overwrite it
+shopt -s histappend
+
+# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
+HISTSIZE=1000
+HISTFILESIZE=2000
+
+# check the window size after each command and, if necessary,
+# update the values of LINES and COLUMNS.
+shopt -s checkwinsize
+
+# If set, the pattern "**" used in a pathname expansion context will
+# match all files and zero or more directories and subdirectories.
+#shopt -s globstar
+
+# make less more friendly for non-text input files, see lesspipe(1)
+#[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"
+
+# set variable identifying the chroot you work in (used in the prompt below)
+if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
+    debian_chroot=$(cat /etc/debian_chroot)
+fi
+
+# set a fancy prompt (non-color, unless we know we "want" color)
+case "$TERM" in
+    xterm-color|*-256color) color_prompt=yes;;
+esac
+
+# uncomment for a colored prompt, if the terminal has the capability; turned
+# off by default to not distract the user: the focus in a terminal window
+# should be on the output of commands, not on the prompt
+#force_color_prompt=yes
+
+if [ -n "$force_color_prompt" ]; then
+    if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
+	# We have color support; assume it's compliant with Ecma-48
+	# (ISO/IEC-6429). (Lack of such support is extremely rare, and such
+	# a case would tend to support setf rather than setaf.)
+	color_prompt=yes
+    else
+	color_prompt=
+    fi
+fi
+
+if [ "$color_prompt" = yes ]; then
+    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
+else
+    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
+fi
+unset color_prompt force_color_prompt
+
+# If this is an xterm set the title to user@host:dir
+case "$TERM" in
+xterm*|rxvt*)
+    PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
+    ;;
+*)
+    ;;
+esac
+
+# enable color support of ls and also add handy aliases
+if [ -x /usr/bin/dircolors ]; then
+    test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
+    alias ls='ls --color=auto'
+    #alias dir='dir --color=auto'
+    #alias vdir='vdir --color=auto'
+
+    #alias grep='grep --color=auto'
+    #alias fgrep='fgrep --color=auto'
+    #alias egrep='egrep --color=auto'
+fi
+
+# colored GCC warnings and errors
+#export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'
+
+# some more ls aliases
+#alias ll='ls -l'
+#alias la='ls -A'
+#alias l='ls -CF'
+
+# Alias definitions.
+# You may want to put all your additions into a separate file like
+# ~/.bash_aliases, instead of adding them here directly.
+# See /usr/share/doc/bash-doc/examples in the bash-doc package.
+
+if [ -f ~/.bash_aliases ]; then
+    . ~/.bash_aliases
+fi
+
+# enable programmable completion features (you don't need to enable
+# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
+# sources /etc/bash.bashrc).
+if ! shopt -oq posix; then
+  if [ -f /usr/share/bash-completion/bash_completion ]; then
+    . /usr/share/bash-completion/bash_completion
+  elif [ -f /etc/bash_completion ]; then
+    . /etc/bash_completion
+  fi
+fi
+# bash theme - partly inspired by https://github.com/ohmyzsh/ohmyzsh/blob/master/themes/robbyrussell.zsh-theme
+__bash_prompt() {
+    local userpart='`export XIT=$? \
+        && [ ! -z "${GITHUB_USER:-}" ] && echo -n "\[\033[0;32m\]@${GITHUB_USER:-} " || echo -n "\[\033[0;32m\]\u " \
+        && [ "$XIT" -ne "0" ] && echo -n "\[\033[1;31m\]➜" || echo -n "\[\033[0m\]➜"`'
+    local gitbranch='`\
+        if [ "$(git config --get devcontainers-theme.hide-status 2>/dev/null)" != 1 ] && [ "$(git config --get codespaces-theme.hide-status 2>/dev/null)" != 1 ]; then \
+            export BRANCH="$(git --no-optional-locks symbolic-ref --short HEAD 2>/dev/null || git --no-optional-locks rev-parse --short HEAD 2>/dev/null)"; \
+            if [ "${BRANCH:-}" != "" ]; then \
+                echo -n "\[\033[0;36m\](\[\033[1;31m\]${BRANCH:-}" \
+                && if [ "$(git config --get devcontainers-theme.show-dirty 2>/dev/null)" = 1 ] && \
+                    git --no-optional-locks ls-files --error-unmatch -m --directory --no-empty-directory -o --exclude-standard ":/*" > /dev/null 2>&1; then \
+                        echo -n " \[\033[1;33m\]✗"; \
+                fi \
+                && echo -n "\[\033[0;36m\]) "; \
+            fi; \
+        fi`'
+    local lightblue='\[\033[1;34m\]'
+    local removecolor='\[\033[0m\]'
+    PS1="${userpart} ${lightblue}\w ${gitbranch}${removecolor}\$ "
+    unset -f __bash_prompt
+}
+__bash_prompt
+export PROMPT_DIRTRIM=4
+
+# Check if the terminal is xterm
+if [[ "$TERM" == "xterm" ]]; then
+    # Function to set the terminal title to the current command
+    preexec() {
+        local cmd="${BASH_COMMAND}"
+        echo -ne "\033]0;${USER}@${HOSTNAME}: ${cmd}\007"
+    }
+
+    # Function to reset the terminal title to the shell type after the command is executed
+    precmd() {
+        echo -ne "\033]0;${USER}@${HOSTNAME}: ${SHELL}\007"
+    }
+
+    # Trap DEBUG signal to call preexec before each command
+    trap 'preexec' DEBUG
+
+    # Append to PROMPT_COMMAND to call precmd before displaying the prompt
+    PROMPT_COMMAND="${PROMPT_COMMAND:+$PROMPT_COMMAND; }precmd"
+fi

.devcontainer/Dockerfile

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+FROM ubuntu:20.04
+
+LABEL org.opencontainers.image.created="2022-11-30"
+LABEL org.opencontainers.image.url="https://github.com/odelaneau/GLIMPSE"
+LABEL org.opencontainers.image.version="2.0.0"
+LABEL org.opencontainers.image.licences="MIT"
+LABEL org.opencontainers.image.title="glimpse"
+LABEL org.opencontainers.image.authors="simone.rubinacci@unil.ch"
+
+WORKDIR /docker_build/
+# Set non-interactive mode for apt-get
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=America/New_York
+
+# Install required packages for build
+RUN apt-get update && apt-get install -y build-essential=12.8ubuntu1.1 \
+                                         libbz2-dev=1.0.8-2 \
+                                         libcurl4-openssl-dev=7.68.0-1ubuntu2.25 \
+                                         autoconf=2.69-11.1 \
+                                         libssl-dev=1.1.1f-1ubuntu2.24 \
+                                         wget=1.20.3-1ubuntu2.1 \
+                                         zlib1g-dev=1:1.2.11.dfsg-2ubuntu1.5 \
+                                         liblzma-dev=5.2.4-1ubuntu1.1 \
+                                         libdeflate-dev=1.5-3 \
+                                         python3=3.8.2-0ubuntu2 \
+                                         libboost-regex-dev=1.71.0.0ubuntu2\
+                                         libboost-iostreams-dev=1.71.0.0ubuntu2\
+                                         libboost-program-options-dev=1.71.0.0ubuntu2\
+                                         libhts-dev=1.10.2-3ubuntu0.1\
+                                         libboost-serialization-dev=1.71.0.0ubuntu2\
+                                         graphviz=2.42.2-3build2
+# Install Doxygen 1.9.5
+RUN wget https://www.doxygen.nl/files/doxygen-1.9.5.linux.bin.tar.gz && \
+    tar -xzf doxygen-1.9.5.linux.bin.tar.gz && \
+    mv doxygen-1.9.5 /opt/ && \
+    ln -sf /opt/doxygen-1.9.5/bin/doxygen /usr/local/bin/doxygen && \
+    rm doxygen-1.9.5.linux.bin.tar.gz
+
+# Install required packages for docs 
+RUN apt-get update && apt-get install -y ruby-full=1:2.7+1
+RUN gem install bundler -v 2.3.27
+
+# Download and build boost program_options and iostreams
+RUN wget https://archives.boost.io/release/1.78.0/source/boost_1_78_0.tar.gz && \
+tar -xf boost_1_78_0.tar.gz && \
+rm boost_1_78_0.tar.gz && \
+cd boost_1_78_0/ && \
+./bootstrap.sh --with-libraries=iostreams,program_options,serialization --prefix=../boost && \
+./b2 install && \
+cd .. && \
+cp boost/lib/libboost_iostreams.a boost/lib/libboost_program_options.a boost/lib/libboost_serialization.a /usr/local/lib/ && \
+cp -r boost/include/boost/ /usr/include/ && \
+rm -r boost_1_78_0 boost
+
+# Download and build htslib
+RUN wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 && \
+tar -xf htslib-1.16.tar.bz2 && \
+rm htslib-1.16.tar.bz2 && \
+cd htslib-1.16 && \
+autoheader && \
+autoconf && \
+./configure --enable-libcurl && \
+make install && \
+cd .. && \
+rm -r htslib-1.16
+
+# Install github
+RUN apt-get install -y --no-install-recommends git=1:2.25.1-1ubuntu3.14
+
+# Install cmake
+RUN mkdir -p /usr/local
+RUN cd /usr/local &&\
+    wget https://github.com/Kitware/CMake/releases/download/v4.0.2/cmake-4.0.2-linux-x86_64.sh &&\
+    chmod +x cmake-4.0.2-linux-x86_64.sh &&\
+    ./cmake-4.0.2-linux-x86_64.sh --skip-license
+
+# Install required packages to debug
+ARG INSTALL_DEBUG_TOOLS=true
+RUN if [ "$INSTALL_DEBUG_TOOLS" = "true" ]; then \
+    apt-get install -y --no-install-recommends openssh-client=1:8.2p1-4ubuntu0.13 &&\
+    apt-get install -y --no-install-recommends gdb=9.2-0ubuntu1~20.04.2 &&\
+    apt-get install -y --no-install-recommends bcftools=1.10.2-2 &&\
+    apt-get install -y --no-install-recommends less=551-1ubuntu0.3 &&\
+    apt-get install -y --no-install-recommends samtools=1.10-3 &&\
+    apt-get install -y --no-install-recommends bash-completion=1:2.10-1ubuntu1 ;\
+    fi
+
+# Set up terminal 
+COPY .devcontainer/.bashrc /root/.bashrc
+
+
+# Set workspace
+RUN mkdir -p /workspace
+WORKDIR /workspace

.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile
+{
+	"name": "Dev Container",
+	"build": {
+		// Sets the run context to one level up instead of the .devcontainer folder.
+		"context": "..",
+		// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+		"dockerfile": "Dockerfile"
+	},
+	"postCreateCommand": "git config --global core.editor 'code --wait' && git remote add odelaneau git@github.com:odelaneau/GLIMPSE.git",
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"github.vscode-pull-request-github",
+				"ms-azuretools.vscode-docker",
+				"ms-vscode.cmake-tools",
+				"ms-vscode.cpptools",
+				"ms-vscode.cpptools-extension-pack",
+				"ms-vscode.cpptools-themes"
+			]
+		}
+	},
+	"remoteUser": "root",  
+	"mounts": [
+		"source=${localEnv:HOME}/.ssh,target=/root/.ssh,type=bind,consistency=cached"
+	]
+}

.github/workflows/docker-build.yml

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+name: Build & Push Devcontainer Image
+
+on:
+  workflow_dispatch:
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to GHCR
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and Push Docker image
+        run: |
+          # Convert GitHub username to lowercase
+          USERNAME=$(echo "${GITHUB_REPOSITORY_OWNER}" | tr '[:upper:]' '[:lower:]')
+          IMAGE_NAME=ghcr.io/$USERNAME/glimpse2-dev:latest
+          echo "Building Docker image $IMAGE_NAME"
+          docker build -t $IMAGE_NAME -f .devcontainer/Dockerfile .
+          echo "Pushing Docker image $IMAGE_NAME"
+          docker push $IMAGE_NAME

.github/workflows/doxygen.yml

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+name: Build & Deploy Docs
+
+on:
+  workflow_dispatch:
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build and run container dynamically (lowercase)
+        run: |
+          # Lowercase the GitHub repository owner
+          USERNAME=$(echo "$GITHUB_REPOSITORY_OWNER" | tr '[:upper:]' '[:lower:]')
+
+          # Build full image name
+          IMAGE="ghcr.io/$USERNAME/glimpse2-dev:latest"
+          echo "Using image $IMAGE"
+
+          # Run container and build docs
+          docker run --rm -v "$PWD":/workspace -w /workspace $IMAGE \
+            /bin/bash -c "cmake -S . -B build -DTEST=OFF -DDOXY=ON && cmake --build build && touch docs/html/.nojekyll"
+
+      - name: Deploy to GitHub Pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages
+          folder: docs/html

.gitignore

@@ -45,6 +45,7 @@
 
 # CMake
 cmake-build-*/
+build
 
 
 ##### Eclipse
@@ -105,3 +106,12 @@ tutorial/GLIMPSE_concordance/
 tutorial/bin/
 
 3rd_party/
+
+
+# Testing files
+*.txt.gz
+*chr*.txt
+
+# Ignore docs
+docs/html
+docs/latex

.vscode/c_cpp_properties.json

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+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "${workspaceFolder}/concordance/src/containers",
+                "${workspaceFolder}/build"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "c17",
+            "cppStandard": "gnu++17",
+            "intelliSenseMode": "linux-gcc-x64",
+            "configurationProvider": "ms-vscode.makefile-tools"
+        }
+    ],
+    "version": 4
+}