Merge branch 'development' into chore-docs-update

.dockerignore

@@ -0,0 +1,36 @@
+/.phpunit.cache
+/node_modules
+/public/build
+/public/hot
+/public/storage
+/storage/*.key
+/storage/app/public
+/storage/debugbar
+/storage/ssr
+/storage/clockwork
+/storage/logs
+/storage/pail
+.phpunit.result.cache
+Homestead.json
+Homestead.yaml
+npm-debug.log
+yarn-error.log
+/vendor
+.env.backup
+/.idea/sonarlint
+.phpstorm.meta.php
+_ide_helper_models.php
+_ide_helper.php
+.php-cs-fixer.cache
+.husky
+/.vscode
+**/.DS_Store
+/public/page-cache
+.phpunit.database.checksum
+.phpunit.cache
+rr
+.rr.yaml
+frankenphp
+.config
+.data
+.git

.github/workflows/build.yml

@@ -0,0 +1,53 @@
+
+# This worklflow will perform following actions when the code is pushed to development branch:
+# - Build the latest docker image in development.
+# - Push the latest docker image to Google Artifact Registry-Dev.
+# - Rollout the latest image in GKE.
+# 
+# Maintainers:
+#   - name: Chandu Nainala
+#   - email: [email protected]
+
+name : Build COCONUT image
+
+on:
+  push:
+    branches: [development]
+
+env:
+  PROJECT_ID: ${{ secrets.GKE_PROJECT }}
+  REPOSITORY_NAME: coconut
+  DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }}
+  DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
+  APP_IMAGE: coconut-app
+  REPOSITORY_NAMESPACE: nfdi4chem
+
+jobs:
+  setup-build-publish-deploy-dev:
+    name: Build & deploy to development
+    runs-on: ubuntu-latest
+    environment:
+      name: Dev
+    steps:
+    # Checkout code
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    # Login to Docker
+    - name: Log in to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ env.DOCKER_HUB_USERNAME  }}
+        password: ${{ env.DOCKER_HUB_PASSWORD  }}
+
+    # Build and push the app Docker image
+    - name: Build and push App Docker image
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        file: ./FrankenPHP.Dockerfile
+        push: true
+        build-args: |
+          RELEASE_VERSION=latest
+          COMPOSER_AUTH=${{ secrets.COMPOSER_AUTH }}
+        tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:latest

.gitignore

@@ -3,7 +3,10 @@
 /public/build
 /public/hot
 /public/storage
+/resources/scripts/python/20*
 /storage/*.key
+/storage/molecules_2d*
+/storage/molecules_3d*
 /vendor
 .env
 .env.backup
@@ -20,5 +23,8 @@ yarn-error.log
 storage/*.tsv
 storage/*.csv
 .DS_store
+**/caddy
+frankenphp
+frankenphp-worker.php
 /docs/.vitepress/cache
 /docs/.vitepress/dist

FrankenPHP.Alpine.Dockerfile

@@ -0,0 +1,174 @@
+# Accepted values: 8.3 - 8.2
+ARG PHP_VERSION=8.3
+
+ARG FRANKENPHP_VERSION=latest
+
+ARG COMPOSER_VERSION=latest
+
+###########################################
+# Build frontend assets with Bun
+###########################################
+
+ARG BUN_VERSION="latest"
+
+FROM oven/bun:${BUN_VERSION} AS build
+
+ENV ROOT=/var/www/html
+
+WORKDIR ${ROOT}
+
+COPY --link package.json bun.lockb* ./
+
+RUN bun install --frozen-lockfile
+
+COPY --link . .
+
+RUN bun run build
+
+###########################################
+
+FROM composer:${COMPOSER_VERSION} AS vendor
+
+FROM dunglas/frankenphp:${FRANKENPHP_VERSION}-php${PHP_VERSION}-alpine
+
+LABEL maintainer="SMortexa <[email protected]>"
+LABEL org.opencontainers.image.title="Laravel Octane Dockerfile"
+LABEL org.opencontainers.image.description="Production-ready Dockerfile for Laravel Octane"
+LABEL org.opencontainers.image.source=https://github.com/exaco/laravel-octane-dockerfile
+LABEL org.opencontainers.image.licenses=MIT
+
+ARG WWWUSER=1000
+ARG WWWGROUP=1000
+ARG TZ=UTC
+ARG APP_DIR=/var/www/html
+
+ENV TERM=xterm-color \
+    WITH_HORIZON=false \
+    WITH_SCHEDULER=false \
+    OCTANE_SERVER=frankenphp \
+    USER=octane \
+    ROOT=${APP_DIR} \
+    COMPOSER_FUND=0 \
+    COMPOSER_MAX_PARALLEL_HTTP=24 \
+    XDG_CONFIG_HOME=${APP_DIR}/.config \
+    XDG_DATA_HOME=${APP_DIR}/.data
+
+WORKDIR ${ROOT}
+
+SHELL ["/bin/sh", "-eou", "pipefail", "-c"]
+
+RUN ln -snf /usr/share/zoneinfo/${TZ} /etc/localtime \
+    && echo ${TZ} > /etc/timezone
+
+RUN apk update; \
+    apk upgrade; \
+    apk add --no-cache \
+    curl \
+    wget \
+    vim \
+    git \
+    ncdu \
+    procps \
+    ca-certificates \
+    supervisor \
+    libsodium-dev \
+    # Install PHP extensions (included with dunglas/frankenphp)
+    && install-php-extensions \
+    bz2 \
+    pcntl \
+    mbstring \
+    bcmath \
+    sockets \
+    pgsql \
+    pdo_pgsql \
+    opcache \
+    exif \
+    pdo_mysql \
+    zip \
+    intl \
+    gd \
+    redis \
+    rdkafka \
+    memcached \
+    igbinary \
+    ldap \
+    swoole \
+    && docker-php-source delete \
+    && rm -rf /var/cache/apk/* /tmp/* /var/tmp/*
+
+RUN arch="$(apk --print-arch)" \
+    && case "$arch" in \
+    armhf) _cronic_fname='supercronic-linux-arm' ;; \
+    aarch64) _cronic_fname='supercronic-linux-arm64' ;; \
+    x86_64) _cronic_fname='supercronic-linux-amd64' ;; \
+    x86) _cronic_fname='supercronic-linux-386' ;; \
+    *) echo >&2 "error: unsupported architecture: $arch"; exit 1 ;; \
+    esac \
+    && wget -q "https://github.com/aptible/supercronic/releases/download/v0.2.29/${_cronic_fname}" \
+    -O /usr/bin/supercronic \
+    && chmod +x /usr/bin/supercronic \
+    && mkdir -p /etc/supercronic \
+    && echo "*/1 * * * * php ${ROOT}/artisan schedule:run --no-interaction" > /etc/supercronic/laravel
+
+RUN addgroup -g ${WWWGROUP} ${USER} \
+    && adduser -D -h ${ROOT} -G ${USER} -u ${WWWUSER} -s /bin/sh ${USER}
+
+RUN mkdir -p /var/log/supervisor /var/run/supervisor \
+    && chown -R ${USER}:${USER} ${ROOT} /var/log /var/run \
+    && chmod -R a+rw ${ROOT} /var/log /var/run
+
+RUN cp ${PHP_INI_DIR}/php.ini-production ${PHP_INI_DIR}/php.ini
+
+USER ${USER}
+
+COPY --link --chown=${WWWUSER}:${WWWUSER} --from=vendor /usr/bin/composer /usr/bin/composer
+COPY --link --chown=${WWWUSER}:${WWWUSER} composer.json composer.lock ./
+
+RUN composer install \
+    --no-dev \
+    --no-interaction \
+    --no-autoloader \
+    --no-ansi \
+    --no-scripts \
+    --audit
+
+COPY --link --chown=${WWWUSER}:${WWWUSER} . .
+COPY --link --chown=${WWWUSER}:${WWWUSER} --from=build ${ROOT}/public public
+
+RUN mkdir -p \
+    storage/framework/sessions \
+    storage/framework/views \
+    storage/framework/cache \
+    storage/framework/testing \
+    storage/logs \
+    bootstrap/cache && chmod -R a+rw storage
+
+COPY --link --chown=${WWWUSER}:${WWWUSER} deployment/supervisord.conf /etc/supervisor/
+COPY --link --chown=${WWWUSER}:${WWWUSER} deployment/octane/FrankenPHP/supervisord.frankenphp.conf /etc/supervisor/conf.d/
+COPY --link --chown=${WWWUSER}:${WWWUSER} deployment/supervisord.*.conf /etc/supervisor/conf.d/
+COPY --link --chown=${WWWUSER}:${WWWUSER} deployment/start-container /usr/local/bin/start-container
+COPY --link --chown=${WWWUSER}:${WWWUSER} deployment/healthcheck /usr/local/bin/healthcheck
+COPY --link --chown=${WWWUSER}:${WWWUSER} deployment/php.ini ${PHP_INI_DIR}/conf.d/99-octane.ini
+
+# FrankenPHP embedded PHP configuration
+COPY --link --chown=${WWWUSER}:${WWWUSER} deployment/php.ini /lib/php.ini
+
+RUN composer install \
+    --classmap-authoritative \
+    --no-interaction \
+    --no-ansi \
+    --no-dev \
+    && composer clear-cache
+
+RUN chmod +x /usr/local/bin/start-container /usr/local/bin/healthcheck
+
+RUN cat deployment/utilities.sh >> ~/.bashrc
+
+EXPOSE 8000
+EXPOSE 443
+EXPOSE 443/udp
+EXPOSE 2019
+
+ENTRYPOINT ["start-container"]
+
+HEALTHCHECK --start-period=5s --interval=2s --timeout=5s --retries=8 CMD healthcheck || exit 1