Fixes for installation (#121)

* Move around some CMake

* Simplify CMake in include/

* Fix .gitattributes for include/

* Separate Python main from library

* Fix .gitattributes

* Consolidate Python-level data

* Install YAPF on Travis

* Remove one CMake file

* Fix PYMOD_INSTALL_FULLDIR

* Fix tests

* Fix PCMSolverConfig.cmake.in

* Update Gemfile.lock

* Update default.nix

* Remove possibly useless linker flag

* Clean up tests CMakeLists.txt

* More clean-up of CMakeLists.txt

* Add PCMSolver_EXPORTS definition

* Configure go_pcm.py

* New install layout works with Psi4

* Final fixes to go_pcm.py

* Minor fixes for formatting and licensing info

* Update Pipfile.lock

* Remove one custom CMake module

Author: robertodr

.ci/Gemfile.lock

@@ -8,8 +8,8 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.5.1)
-      public_suffix (~> 2.0, >= 2.0.2)
+    addressable (2.5.2)
+      public_suffix (>= 2.0.2, < 4.0)
     claide (1.0.2)
     claide-plugins (0.9.2)
       cork
@@ -18,7 +18,7 @@ GEM
     colored2 (3.1.2)
     cork (0.3.0)
       colored2 (~> 3.1)
-    danger (5.3.4)
+    danger (5.5.10)
       claide (~> 1.0)
       claide-plugins (>= 0.9.2)
       colored2 (~> 3.1)
@@ -27,26 +27,28 @@ GEM
       faraday-http-cache (~> 1.0)
       git (~> 1)
       kramdown (~> 1.5)
+      no_proxy_fix
       octokit (~> 4.7)
       terminal-table (~> 1)
     danger-commit_lint (0.0.6)
       danger (~> 5.0)
-    danger-lgtm (0.2.0)
+    danger-lgtm (1.0.0)
       danger-plugin-api (~> 1.0)
     danger-plugin-api (1.0.0)
       danger (> 2.0)
-    faraday (0.13.0)
+    faraday (0.14.0)
       multipart-post (>= 1.2, < 3)
     faraday-http-cache (1.3.1)
       faraday (~> 0.8)
     git (1.3.0)
-    kramdown (1.14.0)
+    kramdown (1.16.2)
     multipart-post (2.0.0)
     nap (1.1.0)
-    octokit (4.7.0)
+    no_proxy_fix (0.1.2)
+    octokit (4.8.0)
       sawyer (~> 0.8.0, >= 0.5.3)
     open4 (1.3.4)
-    public_suffix (2.0.5)
+    public_suffix (3.0.2)
     sawyer (0.8.1)
       addressable (>= 2.3.5, < 2.6)
       faraday (~> 0.8, < 1.0)

.ci/ci_build.sh

@@ -2,7 +2,7 @@
 
 # The return code will capture an error from ANY of the functions in the pipe
 set -euo pipefail
-cmake --build . -- --jobs=2 VERBOSE=1 | tee build.log | grep "Building"
+cmake --build . --target install -- --jobs=2 VERBOSE=1 | tee build.log | grep "Building\|Installing"
 RESULT=$?
 
 if [ $RESULT -eq 0 ]; then

.ci/report_versions.sh

@@ -2,7 +2,7 @@
 
 echo "Report versions of whole tool stack"
 
-for tool in cmake make ${PYTHON} ${CXX_COMPILER} ${C_COMPILER} ${Fortran_COMPILER}; do
+for tool in cmake make $CXX_COMPILER $C_COMPILER $Fortran_COMPILER; do
     echo ""
     echo "Checking version of $tool:"
     $tool --version 2> /dev/null || echo "$tool not available"

.gitattributes

@@ -73,7 +73,9 @@ tests/utils/*.cpp                licensefile=.githooks/LICENSE-C++
 doc/conf.py               licensefile=.githooks/LICENSE-Python
 doc/gfx/cloc_tools.py.in  licensefile=.githooks/LICENSE-Python
 src/make_cmake_files.py   licensefile=.githooks/LICENSE-Python
-tools/codata.py.in        licensefile=.githooks/LICENSE-Python
-tools/pcmsolver.py.in     licensefile=.githooks/LICENSE-Python
+tools/codata.py           licensefile=.githooks/LICENSE-Python
 tools/plot_cavity.py      licensefile=.githooks/LICENSE-Python
+tools/init.py             licensefile=.githooks/LICENSE-Python
 tests/make_cmake_files.py licensefile=.githooks/LICENSE-Python
+tests/go_pcm.py           licensefile=.githooks/LICENSE-Python
+tests/pcmparser.py        licensefile=.githooks/LICENSE-Python

.travis.yml

@@ -37,7 +37,7 @@ matrix:
         - C_COMPILER='gcc-4.6'
         - Fortran_COMPILER='gfortran-4.6'
         - BUILD_TYPE='release'
-        - PYTHON='python2'
+        - PYTHON='--two'
         - RUN_DANGER=false
     - os: linux
       addons:
@@ -56,7 +56,7 @@ matrix:
         - C_COMPILER='gcc-6'
         - Fortran_COMPILER='gfortran-6'
         - BUILD_TYPE='release'
-        - PYTHON='python2'
+        - PYTHON='--two'
         - STATIC='--static'
         - RUN_DANGER=false
     - os: linux
@@ -74,7 +74,7 @@ matrix:
         - C_COMPILER='clang'
         - Fortran_COMPILER='gfortran-4.6'
         - BUILD_TYPE='release'
-        - PYTHON='python3'
+        - PYTHON='--three'
         - RUN_DANGER=true
     - os: linux
       addons:
@@ -92,7 +92,7 @@ matrix:
         - C_COMPILER='gcc-4.8'
         - Fortran_COMPILER='gfortran-4.8'
         - BUILD_TYPE='debug'
-        - PYTHON='python2'
+        - PYTHON='--two'
         - COVERAGE='--coverage'
         - RUN_DANGER=false
 before_install:
@@ -101,22 +101,29 @@ before_install:
   - test -n $FC && unset FC
 install:
   - pip install --user pipenv --upgrade
-  - pipenv install
+  - pipenv $PYTHON install
 before_script:
   - source $(pipenv --venv)/bin/activate
   - ./.ci/report_versions.sh
-  - cd ${TRAVIS_BUILD_DIR}
+  - cd $TRAVIS_BUILD_DIR
   - echo 'Build set up summary'
   - |
-    if [[ "${RUN_DANGER}" = true ]]; then
+    if [[ "$RUN_DANGER" = true ]]; then
       bundle install --gemfile=.ci/Gemfile
     fi
 script:
   - |
-    if [[ "${RUN_DANGER}" = true ]]; then
+    if [[ "$RUN_DANGER" = true ]]; then
       BUNDLE_GEMFILE=.ci/Gemfile bundle exec danger --dangerfile=.ci/Dangerfile
     fi
-  - python setup.py --cxx=${CXX_COMPILER} --cc=${C_COMPILER} --fc=${Fortran_COMPILER} --type=${BUILD_TYPE} ${STATIC} ${COVERAGE}
+  - |
+    python setup.py --cxx=$CXX_COMPILER \
+                    --cc=$C_COMPILER \
+                    --fc=$Fortran_COMPILER \
+                    --type=$BUILD_TYPE \
+                    $STATIC \
+                    $COVERAGE \
+                    --prefix=$HOME/Software/pcmsolver
   - cd build
   - ../.ci/ci_build.sh
   - travis_wait python ../.ci/ci_test.py ctest --output-on-failure --verbose --parallel 2

CHANGELOG.md

@@ -7,21 +7,15 @@
 - Double logarithmic scale for the integration of spherical diffuse
   interfaces: much more stable than the previous version, allowing for
   Runge-Kutta 4 integrator.
+- A new CMake module `options_wrappers.cmake` that adds new wrapper macros for
+  the CMake `option` command.
 
 ### Fixed
 
 - Bug in the diffuse interface Green's function. Contrary to the sharp
   interface case, it is wrong to remove the monopole, which becomes
   identically zero when the corresponding differential equation is
   solved in extreme cases (e.g. charge far away from the sphere).
-
-### Added
-
-- A new CMake module `options_wrappers.cmake` that adds new wrapper macros for
-  the CMake `option` command.
-
-### Fixed
-
 - Visibility of symbols in the shared library is _finally_ handled properly.
   The necessary flags to the C++ compiler were not set for the subtargets built
   as CMake `OBJECT` libraries. This results in a modest decrease in library
@@ -33,12 +27,58 @@
   `<install_prefix>/lib64` (or `<install_prefix>/lib`) as path to `libpcm.so.1`.
 - Code coverage analysis was restored. We now use
   [Codecov](https://codecov.io). Thanks @arnfinn :tada:
+- **BREAKING CHANGE** The layout of the installation for the Python scripts has
+  been changed. This addresses issue #116. Given the user-defined installation
+  prefix (`<prefix>`) one would obtain:
+  ```
+  <prefix>/pcmsolver
+           ├── bin
+           │   ├── go_pcm.py
+           │   ├── plot_cavity.py
+           │   └── run_pcm
+           ├── include
+           │   └── PCMSolver
+           │       ├── bi_operators
+           │       ├── cavity
+           │       ├── Citation.hpp
+           │       ├── Config.hpp
+           │       ├── Cxx11Workarounds.hpp
+           │       ├── ErrorHandling.hpp
+           │       ├── external
+           │       ├── GitInfo.hpp
+           │       ├── green
+           │       ├── interface
+           │       ├── LoggerInterface.hpp
+           │       ├── PCMInput.h
+           │       ├── PCMSolverExport.h
+           │       ├── pcmsolver.h
+           │       ├── PhysicalConstants.hpp
+           │       ├── solver
+           │       ├── STLUtils.hpp
+           │       ├── TimerInterface.hpp
+           │       └── utils
+           ├── lib64
+           │   ├── libpcm.a
+           │   ├── libpcm.so -> libpcm.so.1
+           │   ├── libpcm.so.1
+           │   └── python
+           │       └── pcmsolver
+           └── share
+               └── cmake
+                   └── PCMSolver
+  ```
 
 ### Changed
 
 - As a result of the visibility change, unit tests can only be linked against
   the static library, since all symbols are always visible in a static archive
   library.
+- **BREAKING CHANGE** The `pcmsolver.py` script/module **was removed** to
+  address issues #111 and #112. The `main` portion of the script has now been
+  separated into a `go_pcm.py` script which can be used in the same way as
+  `pcmsolver.py` was used before: to parse the PCMSolver input and to run the
+  module standalone. This separation greatly simplifies the use as a module
+  within the Python launcher scripts of host programs.
 
 ## [Version 1.1.12] - 2018-01-20
 

CMakeLists.txt

@@ -38,17 +38,14 @@ include(autocmake_int64)
 include(autocmake_omp)
 include(autocmake_safeguards)
 include(autocmake_python_interpreter)
+include(version)
+include(autocmake_git_info)
 include(pcmsolver)
 include(api)
-include(autocmake_git_info)
 include(autocmake_boost)
-include(version)
 include(static_library)
-include(catch)
 include(eigen)
 include(libtaylor)
 include(zlib)
-include(autogenerated)
-include(export)
 include(autocmake_src)
 include(test)