arriving into the present with the public branch

.gitmodules

@@ -5,4 +5,5 @@
 [submodule "src/f90wrap"]
 	path = src/f90wrap
 	url = https://github.com/jameskermode/f90wrap
+	branch = py3
 	fetchRecursiveSubmodules = on-demand

.travis.yml

@@ -1,7 +1,7 @@
 ---
 language: python
 python:
-  - "2.7"
+  - "3.6"
 env:
   matrix:
     - QUIP_ARCH=linux_x86_64_gfortran QUIP_INC=Makefile.nogap.inc
@@ -11,7 +11,9 @@ env:
 
 stages:
   - test
-  - documentation
+  - name: documentation
+    # freezing the python2.7 version fot this at first
+    if: branch = archived_py2
   - name: release
     if: branch = public
 
@@ -34,7 +36,12 @@ before_install:
       libhdf5-serial-dev
       python-numpy
 
-  - git clone https://${GITHUB_TOKEN}@github.com/libAtoms/GAP.git src/GAP
+  # Clone the private gap repository using deploy key
+  - echo $github_deploy_key | base64 -d > ~/.ssh/github_deploy_key
+  - chmod 0600  ~/.ssh/github_deploy_key
+  - eval $(ssh-agent -s)
+  - ssh-add ~/.ssh/github_deploy_key
+  - git clone --depth 1 git@github.com:libAtoms/GAP.git src/GAP
   # Make the build directory manually for rules
   - mkdir -p build/${QUIP_ARCH}
   # Copy the rules file (rather than make config)
@@ -59,6 +66,7 @@ script: # Compile QUIP, libquip and quippy, if a non-skipped build.
 jobs:
   include:
     - stage: documentation
+      # freezing the python2.7 version fot this at first
       python:
         - "2.7"
       env:  # serial version of QUIP
@@ -78,16 +86,21 @@ jobs:
             libgsl0-dev
             libxpm-dev
             pandoc
-
-        - git clone https://${GITHUB_TOKEN}@github.com/libAtoms/GAP.git src/GAP
+        # Clone the private gap repository using deploy key
+        - echo $github_deploy_key | base64 -d > ~/.ssh/github_deploy_key
+        - chmod 0600  ~/.ssh/github_deploy_key
+        - eval $(ssh-agent -s)
+        - ssh-add ~/.ssh/github_deploy_key
+        - git clone --depth 1 git@github.com:libAtoms/GAP.git src/GAP
         # Make the build directory manually for rules
         - mkdir -p build/${QUIP_ARCH}
         # Copy the rules file (rather than make config)
         - cp travis/${QUIP_INC} build/${QUIP_ARCH}/Makefile.inc
 
       install: # packages for building docs
         - pip install
-            ase
+            ase==3.17.0
+            docutils==0.14
             sphinx
             sphinx-rtd-theme
             nbsphinx
@@ -97,8 +110,8 @@ jobs:
         - pip install 'nbconvert[execute]' 'ipython<6'
 
         # quippy is working, install it
-        - make &> build.log
-        - make install-quippy &> build.log
+        - make &> /dev/null
+        - make install-quippy &> /dev/null
 
         # Install atomeye from src
         - export QUIP_ROOT=`pwd`

Makefile

@@ -28,7 +28,6 @@
 # H0 X
 # H0 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
 
-
 .PHONY: config doc clean deepclean distclean install test quippy doc install-structures install-dtds install-Tools install-build.QUIP_ARCH install-quippy libquip
 
 ifndef QUIP_ARCH
@@ -96,7 +95,7 @@ GAP += GAP
 GAP_PROGRAMS = gap_programs
 else
 GAP =
-GAP_PROGRAMS = 
+GAP_PROGRAMS =
 endif
 
 # now add the rest of the modules
@@ -144,7 +143,7 @@ FOX_STATIC_LIBFILE_OBJS = $(shell for i in ${FOX_STATIC_LIBFILES}; do ar -t $$i;
 
 ${MODULES}:  ${BUILDDIR}/Makefile.inc ${BUILDDIR} ${FOX}
 	@echo "********************************************"
-	@echo "" 
+	@echo ""
 	@echo " Making $@ "
 	@echo ""
 	@echo "********************************************"
@@ -159,7 +158,7 @@ ${MODULES}:  ${BUILDDIR}/Makefile.inc ${BUILDDIR} ${FOX}
 
 Programs/% src/Programs/% : ${MODULES}
 	@echo "********************************************"
-	@echo "" 
+	@echo ""
 	@echo " Making Programs "
 	@echo ""
 	@echo "********************************************"
@@ -176,7 +175,7 @@ endif
 
 gap_programs: ${MODULES}
 	@echo "********************************************"
-	@echo "" 
+	@echo ""
 	@echo " Making GAP programs "
 	@echo ""
 	@echo "********************************************"
@@ -196,18 +195,27 @@ libatoms: libAtoms
 
 libquip: libquip.a
 
-libquip.a: ${MODULES} 
+libquip.a: ${MODULES}
 	LIBQUIP_OBJS="$(shell for i in ${BUILDDIR}/libquiputils.a ${BUILDDIR}/libquip_core.a $(addprefix ${BUILDDIR}/,${GAP_LIBFILE}) ${BUILDDIR}/libatoms.a $(addprefix ${BUILDDIR}/,${THIRDPARTY_LIBS}) ${FOX_STATIC_LIBFILES}; do ar -t $$i; done | grep \.o)" && \
 		     cd ${BUILDDIR} && for i in ${FOX_STATIC_LIBFILES}; do ar -x $$i; done && ar -rcs $@ $$LIBQUIP_OBJS
 
 ${BUILDDIR}:
 	@if [ ! -d build/${QUIP_ARCH}${QUIP_ARCH_SUFFIX} ] ; then mkdir -p build/${QUIP_ARCH}${QUIP_ARCH_SUFFIX} ; fi
 
 quippy: libquip.a ${GAP_PROGRAMS}
-	${MAKE} -C quippy -I${PWD} -I${PWD}/arch build
+	@echo "********************************************"
+	@echo ""
+	@echo " Making quippy "
+	@echo ""
+	@echo "********************************************"
+	# fixme: restore the old functionality with commands like:
+	# ${MAKE} -C quippy -I${PWD} -I${PWD}/arch clean
+	rm -f ${BUILDDIR}/Makefile
+	cp ${PWD}/quippy/Makefile ${BUILDDIR}/Makefile
+	${MAKE} -C ${BUILDDIR} QUIP_ROOT=${QUIP_ROOT} -I${PWD} -I${PWD}/arch build
+	rm ${BUILDDIR}/Makefile
 
 install-quippy: quippy
-	${MAKE} -C quippy -I${PWD} -I${PWD}/arch install
 
 clean-quippy:
 	${MAKE} -C quippy -I${PWD} -I${PWD}/arch clean
@@ -242,7 +250,7 @@ ifeq (${QUIP_INSTALLDIR},)
 	@echo "'make install' needs QUIP_INSTALLDIR to be defined to install "
 	@echo "programs"
 else
-	@if [ ! -d ${QUIP_INSTALLDIR} ]; then \
+	if [ ! -d ${QUIP_INSTALLDIR} ]; then \
 	  echo "make install: QUIP_INSTALLDIR '${QUIP_INSTALLDIR}' doesn't exist or isn't a directory"; \
 	  exit 1; \
 	else	 \
@@ -256,6 +264,9 @@ else
 endif
 
 test: quippy
+	#- cd tests
+	#- make
+	#- cd ..
 	${MAKE} -C tests -I${PWD} -I${PWD}/arch -I${BUILDDIR}
 
 GIT_SUBDIRS=src/GAP src/ThirdParty
@@ -271,6 +282,3 @@ distribution:
 	bzip2 ../QUIP.distribution.`date +%Y-%m-%d`.tar
 	rm GIT_VERSION
 	@for d in ${GIT_SUBDIRS}; do if [ -d $$d ]; then pushd $$d; git archive HEAD | bzip2 > ../../$$d.distribution.`date +%Y-%m-%d`.tar.bz2; popd; fi; done
-
-
-

README.md

@@ -25,9 +25,9 @@ Silvia Cereda, Gabor Csanyi, Alessio Comisso, Tom Daff, ST John,
 Chiara Gattinoni, Gianpietro Moras, James Kermode, Letif Mones,
 Alan Nichol, David Packwood, Lars Pastewka, Giovanni Peralta, Ivan
 Solt, Oliver Strickson, Wojciech Szlachta, Csilla Varnai, Steven
-Winfield.
+Winfield, Tamas K Stenczel.
 
-Copyright 2006-2018.
+Copyright 2006-2019.
 
 Most of the publicly available version is released under the GNU
 General Public license, version 2, with some portions in the public

quippy/KIND_MAP

@@ -0,0 +1,19 @@
+# mapping from Fortran kinds to C types
+{
+        'real':     {'4': 'float',
+              '8':   'double',
+              'dp':  'double',
+	      'DP':  'double',
+              '16':  'long_double',
+              'qp':  'double',
+              'c_double':  'double'}, # qp is usually double, not quad...
+ 'complex' : {'8':   'complex_double',
+              'dp':  'complex_double'},
+ 'integer' : {'':       'int',
+ 	           '8':      'long_long',
+	           'dp':     'long_long',
+	           'c_intptr_t': 'long_long',
+			'c_int': 'long_long'}
+}
+
+

quippy/Makefile

@@ -2,7 +2,10 @@
 # HQ X
 # HQ X   quippy: Python interface to QUIP atomistic simulation library
 # HQ X
-# HQ X   Copyright James Kermode 2010
+# HQ X   Portions of this code were written by
+# HQ X     Tamas K. Stenczel, James Kermode
+# HQ X
+# HQ X   Copyright 2019
 # HQ X
 # HQ X   These portions of the source code are released under the GNU General
 # HQ X   Public License, version 2, http://www.gnu.org/copyleft/gpl.html
@@ -12,10 +15,11 @@
 # HQ X
 # HQ X   When using this software, please cite the following reference:
 # HQ X
-# HQ X   http://www.jrkermode.co.uk/quippy
+# HQ X   https://warwick.ac.uk/fac/sci/eng/staff/jrk
 # HQ X
 # HQ XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
 
+
 # include other makefiles and export env variables
 export QUIP_ARCH
 
@@ -26,27 +30,82 @@ include Makefile.${QUIP_ARCH}
 include ${BUILDDIR}/Makefile.inc
 include Makefile.rules
 
-# Test if the 'python' in the path is a Python 2, if not then
-# explicitly call python2
-# This is a workaround for old virtualenv versions that don't create the
-# 'python2' symlink.
-python_version := $(word 2, $(subst ., , $(shell python -V 2>&1)))
-ifeq (${python_version},2)
-	PYTHON := python
-else
-	PYTHON := python2
+# working on python3 only
+PYTHON := python3
+
+QUIPPY_SRC_DIR := ../../quippy
+
+FPP = gfortran -E -cpp ${QUIPPY_F90FLAGS}
+CFLAGS = -fPIC ${QUIPPY_CFLAGS}
+
+
+# The following files will be wrapped
+LIBATOMS_SOURCES =  Atoms_types.f95 Atoms.f95 System.f95 Dictionary.f95 DynamicalSystem.f95
+POT_SOURCES =  Potential.f95
+GAP_SOURCES =  descriptors.f95
+
+LIBATOMS_FILES = $(addprefix ../../src/libAtoms/,${LIBATOMS_SOURCES})
+POT_FILES = $(addprefix ../../src/Potentials/,${POT_SOURCES})
+GAP_FILES = $(addprefix ../../src/GAP/,${GAP_SOURCES})
+
+WRAP_SOURCES = ${LIBATOMS_SOURCES} ${POT_SOURCES}
+WRAP_FILES = ${LIBATOMS_FILES} ${POT_FILES}
+
+ifeq (${HAVE_GAP},1)
+	WRAP_SOURCES +=  ${GAP_SOURCES}
+	WRAP_FILES +=  ${GAP_FILES}
 endif
 
-.PHONY: build install clean test
+WRAP_FPP_FILES = $(addsuffix .fpp,$(basename ${WRAP_SOURCES}))
 
-build:
-	LD=${LINKER} CC=${CC} F90=${F90} F77=${F77} QUIP_ROOT=${QUIP_ROOT} ${PYTHON} setup.py build
+F90WRAP_FILES = $(addsuffix .f90,$(addprefix f90wrap_,$(basename ${WRAP_SOURCES}))) #f90wrap_toplevel.f90
+
+F2PY_LINK_ARGS = $(shell python -c 'import sys; print(" ".join([arg for arg in sys.argv if arg.startswith("-l") or arg.startswith("-L")]))' ${SYSLIBS} ${QUIPPY_LDFLAGS})
+
+
+#################################
+.PHONY: build clean install f90wrap
+
+install: build
+
+f90wrap:
+	@echo "********************************************"
+	@echo ""
+	@echo " Making f90wrap "
+	@echo ""
+	@echo "********************************************"
+	@echo ""
+	@echo "Attempting to automatically clone f90wrap submodule"
+	git submodule update --init ${QUIP_ROOT}/src/f90wrap || \
+            { echo "f90wrap clone failed. Download it manually" ; exit 1 ; }
+
+	cd ${QUIP_ROOT}/src/f90wrap ;  ${PYTHON} setup.py install
 
-install:
-	LD=${LINKER} CC=${CC} F90=${F90} F77=${F77} QUIP_ROOT=${QUIP_ROOT} ${PYTHON} setup.py install ${QUIPPY_INSTALL_OPTIONS}
 
 clean:
-	LD=${LINKER} CC=${CC} F90=${F90} F77=${F77} QUIP_ROOT=${QUIP_ROOT} ${PYTHON} setup.py clean
+	rm _quippy.so
+	rm _castep.so ${F90WRAP_FILES} ${WRAP_FPP_FILES}
+	rm -r castep
+	rm -r f90wrap_*.o
+	rm -rf src.*
+
+${WRAP_FPP_FILES}: ${WRAP_FILES}
+	for f in ${WRAP_FILES}; do \
+	    echo ${FPP} -D'SIZEOF_FORTRAN_T=2' $$f > $$(basename $${f%.*}).fpp ; \
+	    ${FPP} -D'SIZEOF_FORTRAN_T=2' $$f > $$(basename $${f%.*}).fpp ; \
+	done
+
+build: f90wrap ${WRAP_FPP_FILES}
+	if [ -d "quippy" ] ; then rm -r quippy; fi
+	mkdir quippy
+	cp -r ${QUIPPY_SRC_DIR}/quippy/* quippy
+	f90wrap -m quippy ${WRAP_FPP_FILES} -P -a c_error_abort \
+		--init-file ${QUIPPY_SRC_DIR}/init.py  --move-methods \
+		--shorten-routine-names -k ${QUIPPY_SRC_DIR}/KIND_MAP -s ${QUIPPY_SRC_DIR}/STRING_LENGTHS -S 10240 \
+		--skip atoms_shallowcopy atoms_initialise_ptr atoms_finalise_multi \
+		potential_initialise_inoutput \
+		cplx_2d  cplx_2d_array1_finalise --skip-types spherical_harmonics_type   --force-public set_cutoff \
+		--documentation-plugin ${QUIPPY_SRC_DIR}/doc_plugin.py
 
-test:
-	LD=${LINKER} CC=${CC} F90=${F90} F77=${F77} QUIP_ROOT=${QUIP_ROOT} ${PYTHON} setup.py test ${QUIPPY_TEST_OPTIONS}
+	f2py-f90wrap --build-dir . -c -m _quippy ${F90WRAP_FILES} ${F2PY_LINK_ARGS} \
+		-L. -lquip --link-lapack --f90flags="${QUIPPY_F90FLAGS}" -lgomp