Merge branch 'feat/gaptools' of https://github.com/cosmo-epfl/librascal…

… into feat/gaptools

.circleci/Dockerfile

@@ -1,27 +1,44 @@
 FROM ubuntu:18.04
 
 # Install generic dependencies
-RUN apt-get update && \
+RUN apt-get update
+RUN DEBIAN_FRONTEND=noninteractive \
     apt-get install -y \
         software-properties-common \
         wget \
         git \
         cmake \
-        vim \
-        python3.6 python3-pip \
         libboost-test-dev \
-        doxygen pandoc \
+        doxygen \
+        pandoc \
         valgrind
 
-# - "ppa:ubuntu-toolchain-r/test" is used for gcc-9
+# - "ppa:deadsnakes/ppa" provides other Python version
+# - "ppa:ubuntu-toolchain-r/test" is used for gcc-10
 # - "deb http://apt.llvm.org/bionic/ llvm-toolchain-bionic-9 main" is the
 #   official LLVM repository for clang-9
 RUN wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | apt-key add -  && \
+    add-apt-repository ppa:deadsnakes/ppa && \
     add-apt-repository ppa:ubuntu-toolchain-r/test && \
     add-apt-repository "deb http://apt.llvm.org/bionic/ llvm-toolchain-bionic-9 main"
+RUN apt-get update
 
-# Install compilers
-RUN apt-get update && \
+# install Python 3.8
+RUN DEBIAN_FRONTEND=noninteractive \
+    apt-get install -y \
+        python3.8 \
+        python3.8-dev \
+        python3-pip
+
+# set python 3.8 as the default so that it is picked up by cmake
+RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.6 1 && \
+    update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 2
+
+# install pip in python 3.8
+RUN python3.8 -m pip install --upgrade pip
+
+# install compilers
+RUN DEBIAN_FRONTEND=noninteractive \
     apt-get install -y \
         gcc-5 g++-5 \
         gcc-10 g++-10 \

.circleci/README.md

@@ -8,11 +8,14 @@ See the [Dockerfile] for more information.
 
 1. make your changes to the Dockerfile
 2. build the image locally
+
 ```bash
 cd .circleci
 docker build -t rascal-ci .
 ```
+
 3. tag the image (replace <VERSION> with the right value) and upload to docker hub
+
 ```bash
 docker tag rascal-ci cosmoepfl/rascal-ci:<VERSION>
 docker push cosmoepfl/rascal-ci:<VERSION>

.circleci/config.yml

@@ -5,20 +5,24 @@ version: 2
 # indicated by the CC/CXX environment variables.
 default_job: &default_job
   docker:
-    - image: cosmoepfl/rascal-ci:5
+    - image: cosmoepfl/rascal-ci:6
   steps:
     - checkout
     - run:
         name: Install Python dependencies
-        command: python3.6 -m pip install -r requirements.txt
+        command: python3.8 -m pip install -r requirements.txt
     - run:
         name: Configure
         command: |
           mkdir build
           cd build
-          cmake ${CMAKE_EXTRA} -DBUILD_BINDINGS=ON -DBUILD_TESTS=ON \
-                -DBUILD_EXAMPLES=ON -DBUILD_PROFILES=ON \
-                -DBUILD_BENCHMARKS=ON -DRUN_BENCHMARKS_FLAGS=--benchmark_min_time=0.0000001 \
+          cmake ${CMAKE_EXTRA} \
+                -DBUILD_BINDINGS=ON \
+                -DBUILD_TESTS=ON \
+                -DBUILD_EXAMPLES=ON \
+                -DBUILD_PROFILES=ON \
+                -DBUILD_BENCHMARKS=ON \
+                -DRUN_BENCHMARKS_FLAGS=--benchmark_min_time=0.0000001 \
                 -DCPPLINT=CPPLINT-NOTFOUND \
                 -DCMAKE_C_COMPILER=$CC -DCMAKE_CXX_COMPILER=$CXX ..
     - run:
@@ -80,12 +84,12 @@ jobs:
       LC_ALL: C.UTF-8
       LANG: C.UTF-8
     docker:
-    - image: cosmoepfl/rascal-ci:3
+    - image: cosmoepfl/rascal-ci:6
     steps:
       - checkout
       - run:
           name: Install Python dependencies
-          command: python3.6 -m pip install -r requirements.txt
+          command: python3.8 -m pip install -r requirements.txt
       - run:
           name: Configure
           command: |
@@ -110,12 +114,12 @@ jobs:
       LC_ALL: C.UTF-8
       LANG: C.UTF-8
     docker:
-    - image: cosmoepfl/rascal-ci:3
+    - image: cosmoepfl/rascal-ci:6
     steps:
       - checkout
       - run:
           name: Install Python dependencies
-          command: python3.6 -m pip install -r requirements.txt
+          command: python3.8 -m pip install -r requirements.txt
       - run:
           name: Configure
           command: |
@@ -129,12 +133,12 @@ jobs:
   # Special job checking that make-pretty was run
   pretty:
     docker:
-    - image: cosmoepfl/rascal-ci:3
+    - image: cosmoepfl/rascal-ci:6
     steps:
       - checkout
       - run:
           name: Install Python dependencies
-          command: python3.6 -m pip install -r requirements.txt
+          command: python3.8 -m pip install -r requirements.txt
       - run:
           name: Configure
           command: |
@@ -150,14 +154,14 @@ jobs:
   # Special job collecting code coverage
   coverage:
     docker:
-    - image: cosmoepfl/rascal-ci:3
+    - image: cosmoepfl/rascal-ci:6
     steps:
       - checkout
       - run:
           name: Install Python dependencies
           command: |
-            python3.6 -m pip install -r requirements.txt
-            python3.6 -m pip install codecov coverage
+            python3.8 -m pip install -r requirements.txt
+            python3.8 -m pip install codecov coverage
       - run:
           name: Configure
           command: |
@@ -190,22 +194,25 @@ jobs:
       CC: gcc-10
       CXX: g++-10
     docker:
-      - image: cosmoepfl/rascal-ci:5
+      - image: cosmoepfl/rascal-ci:6
     steps:
       - checkout
       - run:
           name: Install Python dependencies
-          command: python3.6 -m pip install -r requirements.txt
+          command: python3.8 -m pip install -r requirements.txt
       - run:
           name: Configure
           command: |
             mkdir build
             cd build
-            cmake ${CMAKE_EXTRA} -DBUILD_BINDINGS=ON -DBUILD_TESTS=ON \
-                  -DBUILD_EXAMPLES=ON -DBUILD_PROFILES=ON \
-                  -DBUILD_BENCHMARKS=ON -DRUN_BENCHMARKS_FLAGS=--benchmark_min_time=0.0000001 \
+            cmake ${CMAKE_EXTRA} \
+                  -DBUILD_BINDINGS=ON \
+                  -DBUILD_TESTS=OFF \
+                  -DBUILD_EXAMPLES=OFF \
+                  -DBUILD_PROFILES=OFF \
                   -DCPPLINT=CPPLINT-NOTFOUND \
-                  -DCMAKE_C_COMPILER=$CC -DCMAKE_CXX_COMPILER=$CXX ..
+                  -DCMAKE_C_COMPILER=$CC \
+                  -DCMAKE_CXX_COMPILER=$CXX ..
       - run:
           name: Build
           command: cd build && make -j2

CMakeLists.txt

@@ -1,36 +1,3 @@
-# =============================================================================
-# file   CMakeLists.txt
-#
-# @author Alexander Goscinski <[email protected]>
-# @author Till Junge <[email protected]>
-# @author Felix Musil <[email protected]>
-# @author Markus Stricker <[email protected]>
-#
-# @date   17 Jan 2019
-#
-# @brief  Main configuration file
-#
-# @section LICENSE
-#
-# Copyright © 2018 Till Junge, Felix Musil, Markus Stricker, COSMO (EPFL), LAMMM
-# (EPFL)
-#
-# Rascal is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License as
-# published by the Free Software Foundation, either version 3, or (at
-# your option) any later version.
-#
-# Rascal 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 Lesser General Public License
-# along with Rascal; see the file COPYING. If not, write to the
-# Free Software Foundation, Inc., 59 Temple Place - Suite 330,
-# Boston, MA 02111-1307, USA.
-# =============================================================================
-
 cmake_minimum_required(VERSION 3.0)
 
 # https://cmake.org/pipermail/cmake/2008-September/023808.html