Building PPA Package for ESPResSo

.github/actions/build_ubuntu_package/Dockerfile

@@ -0,0 +1,7 @@
+FROM ubuntu:jammy
+
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get update
+RUN apt-get install -y dpkg-dev build-essential
+
+COPY entrypoint.sh /entrypoint.sh

.github/actions/build_ubuntu_package/action.yml

@@ -0,0 +1,11 @@
+name: 'Ubuntu Package'
+outputs:
+  package_file:
+    description: Name of package file generated
+description: 'Build Ubuntu package'
+runs:
+  using: "docker"
+  image: "Dockerfile"
+  entrypoint: "/entrypoint.sh"
+
+

.github/actions/build_ubuntu_package/entrypoint.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+set -e -x -v
+apt build-dep -y . &&
+dpkg-buildpackage -uc -us &&
+cp ../*.deb /github/workspace &&
+package_file=`ls /github/workspace/*.deb` 
+echo "::set-output name=package_file::${package_file}" 
+

.github/actions/publish-ppa-package/Dockerfile

@@ -0,0 +1,12 @@
+FROM ubuntu:jammy
+
+ENV DEBIAN_FRONTEND noninteractive
+
+RUN apt-get update && apt-get install -y \
+    gpg debmake debhelper devscripts equivs \
+    distro-info-data distro-info
+
+COPY entrypoint.sh /entrypoint.sh
+COPY build.sh /build.sh
+
+ENTRYPOINT ["/entrypoint.sh"]

.github/actions/publish-ppa-package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Kevin Yue
+
+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.

.github/actions/publish-ppa-package/action.yml

@@ -0,0 +1,29 @@
+name: 'publish-ppa-package'
+description: 'Publish a PPA package'
+branding:
+  color: orange
+  icon: package
+inputs:
+  repository:
+    description: 'The PPA respository, e.g. ppa:yuezk/globalprotect-openconnect'
+    required: true
+  gpg_private_key:
+    description: 'GPG private key exported as an ASCII armored version or its base64 encoding'
+    required: true
+  gpg_passphrase:
+    description: 'Passphrase of the GPG private key'
+    required: false
+  pkgdir:
+    description: 'The package directory which contains the debian folder'
+    required: true
+  series:
+    description: 'The series to which the package will be published, separated by space. e.g., "bionic focal"'
+    required: false
+  is_native:
+    description: 'Indicates whether it is a native debian package or not'
+    required: false
+    default: ''
+
+runs:
+  using: docker
+  image: Dockerfile

.github/actions/publish-ppa-package/build.sh

@@ -0,0 +1,75 @@
+#!/bin/bash
+
+set -o errexit -o pipefail -o nounset
+
+REPOSITORY=$INPUT_REPOSITORY
+GPG_PRIVATE_KEY="$INPUT_GPG_PRIVATE_KEY"
+GPG_PASSPHRASE=$INPUT_GPG_PASSPHRASE
+PKGDIR=$INPUT_PKGDIR
+IS_NATIVE=$INPUT_IS_NATIVE
+SERIES=$INPUT_SERIES
+
+assert_non_empty() {
+    name=$1
+    value=$2
+    if [[ -z "$value" ]]; then
+        echo "::error::Invalid Value: $name is empty." >&2
+        exit 1
+    fi
+}
+
+assert_non_empty inputs.repository "$REPOSITORY"
+assert_non_empty inputs.gpg_private_key "$GPG_PRIVATE_KEY"
+assert_non_empty inputs.gpg_passphrase "$GPG_PASSPHRASE"
+assert_non_empty inputs.pkgdir "$PKGDIR"
+
+if [[ -z "$SERIES" ]]; then
+    SERIES=$(distro-info --supported)
+fi
+
+echo "::group::Importing GPG private key..."
+GPG_KEY_ID=$(echo "$GPG_PRIVATE_KEY" | gpg --import-options show-only --import | sed -n '2s/^\s*//p')
+echo $GPG_KEY_ID
+echo "$GPG_PRIVATE_KEY" | gpg --batch --passphrase "$GPG_PASSPHRASE" --import
+echo "::endgroup::"
+
+for s in $SERIES; do
+    ubuntu_version=$(distro-info --series $s -r)
+    version="${ubuntu_version:0:5}"
+
+    echo "::group::Building deb for: $version ($s)"
+
+    cd $PKGDIR
+    if [[ -z "$IS_NATIVE" ]]; then
+        format_file="debian/source/format"
+        if [[ ! -f "$format_file" ]] || grep -q "native" "$format_file"; then
+            IS_NATIVE="true"
+        fi
+    fi
+
+    if [[ "$IS_NATIVE" == "true" ]]; then
+        echo "Making native package..."
+        debmake -n -y
+    else
+        echo "Making non-native package..."
+        debmake -y
+    fi
+
+    mk-build-deps --install --remove --tool='apt-get -o Debug::pkgProblemResolver=yes --no-install-recommends --yes' debian/control
+
+    sed -i"" -re "s/\s\w+;/ $s;/" -re "s/\((.+)-.+\)/(\1-ppa1~ubuntu${version})/" debian/changelog 
+
+    if [[ "$IS_NATIVE" == "true" ]]; then
+        echo "y" | debuild -S -sa \
+            -k"$GPG_KEY_ID" \
+            -p"gpg --batch --passphrase "$GPG_PASSPHRASE" --pinentry-mode loopback"
+    else
+        debuild -S -sa \
+            -k"$GPG_KEY_ID" \
+            -p"gpg --batch --passphrase "$GPG_PASSPHRASE" --pinentry-mode loopback"
+    fi
+    dput $REPOSITORY ../*.changes
+
+    rm -rf ../*.{changes,build,buildinfo,deb,ddeb,dsc}
+    echo "::endgroup::"
+done

.github/actions/publish-ppa-package/entrypoint.sh

@@ -0,0 +1,5 @@
+#!/bin/bash -l
+
+set -o errexit -o pipefail -o nounset
+
+/build.sh

.github/actions/test_ubuntu_package/Dockerfile

@@ -0,0 +1,6 @@
+FROM ubuntu:focal
+
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get update && apt-get install -y python3
+
+COPY entrypoint.sh /entrypoint.sh

.github/actions/test_ubuntu_package/action.yml

@@ -0,0 +1,13 @@
+name: 'Test Ubuntu Package'
+description: 'Test Ubuntu package'
+inputs:
+  package_file:
+    description: Name of package file to install and test
+    required: true    
+runs:
+  using: "docker"
+  image: "Dockerfile"
+  entrypoint: "/entrypoint.sh"
+  args:
+    - ${{ inputs.package_file }}
+

.github/actions/test_ubuntu_package/entrypoint.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+apt-get install -y $1
+echo $1
+ls -la /github/workspace
+python3 -c 'import espressomd; system=espressomd.System(box_l=[1,1,1])'

.github/workflows/push_pull.yml → .github/workflows/mac_test.yml

@@ -55,3 +55,4 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
           title: Scheduled CI job has failed
           body: ${{ env.job_link }}
+

.github/workflows/packaging.yml

@@ -0,0 +1,40 @@
+name: Build packages
+
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 3 * * *'
+
+jobs:
+  ubuntupackage:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@main
+
+      - name: Build
+        run: |
+          mkdir -p ./artifacts/deb-build
+          git archive --prefix=espresso-espresso-4.2/ -o ./artifacts/espresso-4.2.tar.gz HEAD
+          cd ./artifacts
+          cp *.tar.gz deb-build && cd deb-build
+          tar xf *.tar.gz
+      # - name: Build package
+      #   id: build
+      #   uses: ./.github/actions/build_ubuntu_package
+      # - name: Test package
+      #   uses: ./.github/actions/test_ubuntu_package
+      #   with:
+      ##     package_file: ${{steps.build.outputs.package_file }}
+
+      - name: Publish PPA
+        uses: ./.github/actions/publish-ppa-package
+        with:
+          repository: 'ppa:bishwash369/espressoppa'
+          gpg_private_key: ${{ secrets.ESPRESSO_PPA_PRIVATE_KEY }}
+          gpg_passphrase: ${{ secrets.ESPRESSO_PPA_PASSPHRASE }}
+          pkgdir: '${{ github.workspace }}/artifacts/deb-build/espresso*/'
+
+
+

debian/changelog

@@ -0,0 +1,12 @@
+espresso (4.2.1-rc1) unstable; urgency=medium
+
+  * Initial release
+
+ -- Bishwash Krishna Parajuli <[email protected]>  Fri, 03 Feb 2023 18:57:28 +0100
+
+
+espresso (4.1.5~rc1) unstable; urgency=medium
+
+  * Initial release
+
+ -- Evangelos Ribeiro Tzaras <[email protected]>  Sun, 28 Mar 2021 17:15:36 +0200

debian/control

@@ -0,0 +1,60 @@
+Source: espresso
+Section: science
+Priority: optional
+Maintainer: Espresso Maintainers <[email protected]>
+Build-Depends:
+ cmake (>= 3.18),
+ cython3,
+ debhelper-compat (= 12),
+ fftw3-dev,
+ libblas-dev,
+ libboost-dev,
+ libboost-filesystem-dev, 
+ libboost-mpi-dev,
+ libboost-serialization-dev,
+ libboost-test-dev, 
+ libfftw3-dev,
+ libgsl-dev,
+ libhdf5-dev,
+ libhdf5-openmpi-dev,
+ libhdf5-openmpi-dev,
+ liblapack-dev,
+ python3-dev,
+ libpython3-dev,
+ openmpi-common,
+ python3,
+ python3-h5py,
+ python3-numpy,
+ python3-scipy
+Rules-Requires-Root: no
+Standards-Version: 4.5.0
+Vcs-Browser: https://github.com/espressomd/espresso
+Vcs-Git: https://github.com/espressomd/espresso.git
+Homepage: https://espressomd.org
+
+Package: espresso
+Architecture: any
+Depends:
+ python3,
+ python3-h5py,
+ python3-numpy,
+ python3-opengl,
+ python3-scipy,
+ python3-vtk7,
+ libboost-filesystem1.71.0,
+ libboost-mpi1.71.0,
+ libboost-serialization1.71.0,
+ libfftw3-3,
+ libgsl23,
+ libhdf5-openmpi-103,
+ libopenblas0-pthread,  
+ openmpi-bin,
+ libopenmpi3,
+ libstdc++6,
+ ${misc:Depends},
+Description: Molecular dynamics simulation package
+ ESPResSo is a highly versatile software package for performing
+ and analyzing scientific Molecular Dynamics many-particle
+ simulations of coarse-grained atomistic or bead-spring models
+ as they are used in soft matter research in physics, chemistry
+ and molecular biology.

debian/copyright

@@ -0,0 +1,29 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: espresso
+Upstream-Contact: Espresso mailing list <[email protected]>
+Source: https://github.com/espressomd/espresso.git
+License: GPL-3
+
+Files: *
+Copyright: 2010-2021 The ESPResSo project
+           2002-2010 Max-Planck-Institute for Polymer Research, Theory Group
+License: GPL-3
+
+
+License: GPL-3+
+ This program 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 program 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.
+ .
+ You should have received a copy of the GNU General Public License along with
+ this package; if not, write to the Free Software Foundation, Inc., 51 Franklin
+ St, Fifth Floor, Boston, MA  02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public License version 3
+ can be found in the file `/usr/share/common-licenses/GPL-3'.

debian/gbp.conf

@@ -0,0 +1,10 @@
+[DEFAULT]
+debian-branch = python
+debian-tag = v%(version)s
+debian-tag-msg = %(pkg)s v%(version)s
+
+[tag]
+sign-tags = true
+
+[dch]
+multimaint-merge = true

debian/rules

@@ -0,0 +1,10 @@
+#!/usr/bin/make -f
+
+export DEB_BUILD_MAINT_OPTIONS= hardening=+all
+
+%:
+	dh $@
+
+
+override_dh_auto_test:
+	true

debian/source/format

@@ -0,0 +1 @@
+3.0 (native)

debian/watch

@@ -0,0 +1,3 @@
+version=4
+opts=filenamemangle=s/.+\/v?(\d\S+)\.tar\.gz/espresso-$1\.tar\.gz/ \
+  https://github.com/espressomd/espresso/tags .*/v?(\d\S+)\.tar\.gz