Merge #3326

3326: Update maintainer and CI shell scripts r=KaiSzuttor a=jngrad

Fixes #3242

Description of changes:
- reduce number of shellcheck warnings from 238 down to 104
   - rules: `SC2002 SC2006 SC2061 SC2063 SC2086 SC2116 SC2148 SC2166 SC2196`
   - 50 of the remaining warnings are false positives from `build_cmake.sh` (`SC2086 SC2154`)
- refactor outdated maintainer shell scripts
- remove deprecated shell syntax and shell commands
- use POSIX alternatives to bashisms when the change is trivial
- quote string variables to guard against whitespace-related issues
- start unit tests before integration tests
- run unit tests for all operating systems (Debian, OpenSUSE, Fedora)

Notes:
- `shellcheck` is unsuitable for CI in its current form (e.g. no rule whitelisting capability)
- the shell scripts now have an homogeneous syntax and few linter warnings, which is desirable if we decide to port them to Python in the future

Co-authored-by: Jean-Noël Grad <jgrad@icp.uni-stuttgart.de>

.gitlab-ci.yml

@@ -132,7 +132,7 @@ debian:10:
   image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/debian-python3:10
   script:
     - export with_cuda=false
-    - export myconfig=maxset make_check=false
+    - export myconfig=maxset make_check_python=false
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -143,7 +143,7 @@ opensuse:15.1:
   stage: build
   image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/$CI_JOB_NAME
   script:
-    - export with_cuda=false myconfig=maxset make_check=false
+    - export with_cuda=false myconfig=maxset make_check_python=false
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -154,7 +154,7 @@ centos:7:
   stage: build
   image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/centos-python3:7
   script:
-    - export with_cuda=false myconfig=maxset make_check=true
+    - export with_cuda=false myconfig=maxset make_check_python=true
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -165,7 +165,7 @@ fedora:
   stage: build
   image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/centos-python3:next
   script:
-    - export with_cuda=false myconfig=maxset make_check=false
+    - export with_cuda=false myconfig=maxset make_check_python=false
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -217,7 +217,7 @@ tutorials-samples-maxset:
   stage: build
   image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   script:
-    - export myconfig=maxset with_coverage=false make_check=false
+    - export myconfig=maxset with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=true test_timeout=1200
     - bash maintainer/CI/build_cmake.sh
   tags:
@@ -230,7 +230,7 @@ tutorials-samples-default:
   stage: build
   image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   script:
-    - export myconfig=default with_coverage=false make_check=false
+    - export myconfig=default with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=true test_timeout=1200
     - bash maintainer/CI/build_cmake.sh
   tags:
@@ -245,7 +245,7 @@ tutorials-samples-empty:
   stage: build
   image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   script:
-    - export myconfig=empty with_coverage=false make_check=false
+    - export myconfig=empty with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=true test_timeout=1200 with_scafacos=false
     - bash maintainer/CI/build_cmake.sh
   tags:
@@ -260,7 +260,7 @@ tutorials-samples-no-gpu:
   stage: build
   image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   script:
-    - export myconfig=maxset with_coverage=false make_check=false
+    - export myconfig=maxset with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=true test_timeout=1200 hide_gpu=true
     - bash maintainer/CI/build_cmake.sh
   tags:
@@ -274,7 +274,7 @@ installation:
   stage: build
   image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   script:
-    - export myconfig=maxset with_coverage=false make_check=false
+    - export myconfig=maxset with_coverage=false make_check_unit_tests=false make_check_python=false
     - export srcdir=${CI_PROJECT_DIR} test_timeout=1800
     - bash maintainer/CI/build_cmake.sh
     - cd build
@@ -317,7 +317,7 @@ ubuntu:wo-dependencies:
   stage: build
   image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:wo-dependencies
   script:
-    - export myconfig=maxset make_check=false
+    - export myconfig=maxset make_check_unit_tests=false make_check_python=false
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -388,7 +388,7 @@ osx-cuda:
   <<: *global_job_definition
   stage: build
   script:
-    - export with_ccache=false myconfig=maxset with_cuda=true make_check=false
+    - export with_ccache=false myconfig=maxset with_cuda=true make_check_unit_tests=false make_check_python=false
     - bash maintainer/CI/build_cmake.sh
   tags:
     - mac

doc/doxygen/Doxyfile.in

@@ -1,6 +1,6 @@
 # Doxyfile 1.8.2
 
-@INCLUDE = @CMAKE_CURRENT_BINARY_DIR@/doxy-features
+@INCLUDE = "@CMAKE_CURRENT_BINARY_DIR@/doxy-features"
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -47,14 +47,14 @@ PROJECT_BRIEF          = "Extensible Simulation Package for Research on Soft Mat
 # exceed 55 pixels and the maximum width should not exceed 200 pixels.
 # Doxygen will copy the logo to the output directory.
 
-PROJECT_LOGO           = @CMAKE_SOURCE_DIR@/doc/logo/logo_48x48.png
+PROJECT_LOGO           = "@CMAKE_SOURCE_DIR@/doc/logo/logo_48x48.png"
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.
 # If a relative path is entered, it will be relative to the location
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = @CMAKE_CURRENT_BINARY_DIR@
+OUTPUT_DIRECTORY       = "@CMAKE_CURRENT_BINARY_DIR@"
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
 # 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -647,8 +647,8 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = @CMAKE_SOURCE_DIR@/src \
-                         @CMAKE_SOURCE_DIR@/doc/doxygen/main.dox
+INPUT                  = "@CMAKE_SOURCE_DIR@/src" \
+                         "@CMAKE_SOURCE_DIR@/doc/doxygen/main.dox"
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -686,7 +686,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = @CMAKE_SOURCE_DIR@/src/config/myconfig-default.hpp
+EXCLUDE                = "@CMAKE_SOURCE_DIR@/src/config/myconfig-default.hpp"
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -700,8 +700,8 @@ EXCLUDE_SYMLINKS       = NO
 # against the file with absolute path, so to exclude all test directories
 # for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       = @CMAKE_SOURCE_DIR@/*/unit_tests/* \
-                         @CMAKE_SOURCE_DIR@/*/tests/*
+EXCLUDE_PATTERNS       = "@CMAKE_SOURCE_DIR@/*/unit_tests/*" \
+                         "@CMAKE_SOURCE_DIR@/*/tests/*"
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -735,7 +735,7 @@ EXAMPLE_RECURSIVE      = YES
 # directories that contain image that are included in the documentation (see
 # the \image command).
 
-IMAGE_PATH             = @CMAKE_SOURCE_DIR@/doc/doxygen/figs
+IMAGE_PATH             = "@CMAKE_SOURCE_DIR@/doc/doxygen/figs"
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program

doc/sphinx/samples.py

@@ -1,3 +1,20 @@
+# Copyright (C) 2019 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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 program.  If not, see <http://www.gnu.org/licenses/>.
+
 import os
 import ast
 import textwrap