Work on continuous integration

* Started port of the previous CI.bash
* Also fix bug in spec.f (stdout was closed so nothing appeared on screen
  at the second call to libspec)
* Work on test suite
  - utils to create clusters are tested
  - PED calculator for polar and azimutal scans are tested

.gitignore

@@ -2,3 +2,4 @@ __pycache__
 *.py[cod]
 *.so
 *.bak
+package/

CI/CI.bash

@@ -0,0 +1,176 @@
+#!/bin/bash
+
+SCRIPT_NAME=$(basename $0)
+TOPLEVEL=$(git rev-parse --show-toplevel)
+VERSION=$(git describe|sed 's/-\([[:digit:]]\+\)-.*/\.post\1/')
+(return 0 2>/dev/null) && sourced=1 || sourced=0
+
+pythonpath_prepend() {
+    if [ -d "$1" ]; then
+        PYTHONPATH=${PYTHONPATH//":$1:"/:} #delete all instances in the middle
+        PYTHONPATH=${PYTHONPATH/%":$1"/} #delete any instance at the end
+        PYTHONPATH=${PYTHONPATH/#"$1:"/} #delete any instance at the beginning
+        PYTHONPATH="$1${PYTHONPATH:+":$PYTHONPATH"}" #prepend $1 or if $PATH is empty set to $1
+	export PYTHONPATH
+    fi
+}
+
+# Setup or upgrade the Python virtual environment
+setup_virtualenv(){
+    VENV_PATH="$1"
+    virtualenv --python=python3 --system-site-packages "$VENV_PATH"
+    source "$VENV_PATH/bin/activate"
+    pip install --upgrade pip
+    pip install --upgrade numpy ase h5py lxml pint terminaltables pycairo 
+    pip install --upgrade sphinx
+    status=$?
+    deactivate
+    [ $status -eq 0 ] || exit 1
+}
+
+activate_msspec_python3_virtualenv() {
+    VENV_PATH="$1"
+    # do not activate virtualenv if already activated
+    if [ x"${VIRTUAL_ENV}" == x ]; then
+	# We are not in a virtualenv
+        if [ x"${VENV_PATH}" != x ]; then
+            # activate the specified venv
+            export MSSPEC_ROOT="${TOPLEVEL}"
+            pythonpath_prepend "$MSSPEC_ROOT/src"
+	    #PYTHONPATH="$PYTHONPATH":"$MSSPEC_ROOT"/src
+            source "$VENV_PATH/bin/activate"
+        else
+            # error
+            echo "Error: No venv specified!!"
+        fi
+    else
+        # We are in a virtualenv so load only variables
+        export MSSPEC_ROOT="${TOPLEVEL}"
+        pythonpath_prepend "$MSSPEC_ROOT/src"
+    fi
+}
+
+
+make_pymsspec_package() {
+	echo "Running setuptools for pymsspec, please wait... "
+	VERSION=$(get_package_version)
+	DEST=${TOPLEVEL}/install_resources/packages/${VERSION}
+	mkdir -p $DEST
+	cd ${TOPLEVEL}/src/python/pymsspec && python setup.py sdist 2>&1 > /dev/null
+	cp ${TOPLEVEL}/src/python/pymsspec/dist/pymsspec-${VERSION}.tar.gz ${DEST}/
+	rm -rf ${TOPLEVEL}/src/python/pymsspec/{*.egg-info,dist}
+}
+
+
+make_pybinding() {
+	echo "Creating Python library for Fortran code, please wait... "
+	activate_msspec_python3_virtualenv
+	cd ${TOPLEVEL}/src/ && make pybinding
+}
+
+
+make_selfex() {
+	echo "Creating the self-extractible setup program... "
+	VERSION=$(get_package_version)
+	DEST=${TOPLEVEL}/install_resources/packages/${VERSION}
+	LICENSE="${TOPLEVEL}/src/CI/license.txt"
+	REQUIREMENTS="${TOPLEVEL}/src/CI/requirements"
+	SETUPFILE="MsSpec-${VERSION}.setup"
+	MAKESELF=${TOPLEVEL}/src/CI/makeself/makeself.sh
+	#pip freeze > "${REQUIREMENTS}"
+	mkdir -p $DEST
+	cp "${TOPLEVEL}/src/CI/install.sh" "${DEST}"
+	chmod u+x "${DEST}/install.sh"
+	cp "${TOPLEVEL}/src/CI/uninstall.sh" "${DEST}"
+	cp "${TOPLEVEL}/src/CI/msspec" "${DEST}"
+	cp "${TOPLEVEL}/src/CI/requirements" "${DEST}"
+	cp "${TOPLEVEL}/src/CI/distro-requirements" "${DEST}"
+	get_makeself
+	cd "${DEST}/../" && ${MAKESELF} --license ${LICENSE} --quiet ${VERSION} ${SETUPFILE} "MsSpec - pymsspec"  ./install.sh
+	rm -rf ${SETUPFILE}.bak
+	rm -rf "${DEST}"
+	#rm -rf "${REQUIREMENTS}"
+}
+
+make_pdf() {
+    DEST=${TOPLEVEL}/package
+    mkdir -p ${DEST}
+    # first activate the virtual environment
+    activate_msspec_python3_virtualenv
+    # then build the documentation.
+    cd "${TOPLEVEL}/doc"
+    make --no-print-directory latexpdf || exit 1
+    # remove previous pdf
+    rm -rf "${DEST}"/*.pdf
+    # copy the produced pdf file to the final location
+    cp "build/latex/MsSpec-python.pdf" "${TOPLEVEL}/package/MsSpec-${VERSION}.pdf"
+}
+
+make_html () {
+    make_pdf
+    # first activate the virtual environment
+    activate_msspec_python3_virtualenv
+    # then build the documentation.
+    cd "${TOPLEVEL}/doc"
+    make --no-print-directory html || exit 1
+}
+
+make_tests() {
+    echo "generate results for unit tests..."
+    activate_msspec_python3_virtualenv
+    python -c "from msspec.tests import create_tests_results; create_tests_results()"
+}
+
+
+create_package() {
+    VENV_PATH="$1"
+    source "$VENV_PATH/bin/activate"
+
+    #update_version
+    #make_tests
+    #make_pdf
+    #make_pymsspec_package
+    #make_msspecgui_package
+    #make_fortran_package
+    #make_selfex
+    #cleanup
+    
+    deactivate
+}
+
+cleanup() {
+    echo "cleaning up..."
+   # remove results.txt file
+    python -c "from msspec.tests import delete_results_file; delete_results_file()"
+    VERSION=$(get_package_version)
+    rm -f ${TOPLEVEL}/guide/MsSpec-${VERSION}.pdf
+}
+
+show_help () {
+    echo "Usage: $SCRIPT_NAME [OPTIONS]"
+    echo "List of possible options:"
+    echo "    -i   Initialize a Python virtual environnment in FOLDER"
+    echo "    -d   Build the html documentation within the Python "
+    echo "         virtual environnment in FOLDER"
+}
+
+
+
+if [ "$sourced" == 0 ]; then
+
+	while getopts "hi:dt" option; do
+	    case $option in
+		i) setup_virtualenv "$OPTARG"
+		   ;;
+		d) make_html
+		   ;;
+		t) make_tests
+		   ;;
+		h) show_help
+		   ;;
+		*) show_help
+		   ;;
+	    esac
+	done
+
+fi

Makefile

@@ -8,7 +8,11 @@ SETUPFILE:=pymsspec-$(VERSION).setup
 
 
 clean:
-	@rm -rf *.setup
+	@echo "Cleaning all..."
+	@find ./src -type f -name '*.pyc' -exec rm {} +
+	@find ./src -type d -name '__pycache__' -exec rm -r {} +
+	+$(MAKE) -C src/ clean
+	+$(MAKE) -C doc/ clean
 
 version:
 	@python ./CI/update_version.py
@@ -16,9 +20,8 @@ version:
 
 purge: clean
 	@echo "Purging all..."
-	@find ./src -type f -name '*.pyc' -exec rm {} +
+	@rm -rf *.setup
-	@find ./src -type d -name '__pycache__' -exec rm -r {} +
+	+$(MAKE) -C src/ purge
-	+$(MAKE) -C src/ clean
 
 selfex: purge
 	@echo "Creating the self-extractible setup program... "

src/Makefile

@@ -16,3 +16,7 @@ clean:
 	@rm -rf dist
 	@rm -rf *.egg*
 
+purge: clean
+	+$(MAKE) -C msspec/spec/fortran purge
+	+$(MAKE) -C msspec/phagen/fortran purge
+

src/install.sh

@@ -1,6 +1,7 @@
 #!/bin/bash
 # vim: set ts=4 sw=4 sts noet mouse=a fdm=indent:
 
+SCRIPT_NAME=$(basename "$0")
 PYTHON=python3
 VERSION=$(cat ./msspec/version.py|cut -d\" -f2)
 DEFAULT_DEST="${HOME}/.local/share"

src/msspec/calculator.py

@@ -68,14 +68,14 @@ from terminaltables.ascii_table import AsciiTable
 
 
 
-try:
+#try:
-    MSSPEC_ROOT = os.environ['MSSPEC_ROOT']
+#    MSSPEC_ROOT = os.environ['MSSPEC_ROOT']
-except KeyError:
+#except KeyError:
-    cfg = Config()
+#    cfg = Config()
-    MSSPEC_ROOT = cfg.get('path')
+#    MSSPEC_ROOT = cfg.get('path')
 
-if MSSPEC_ROOT == str(None):
+#if MSSPEC_ROOT == str(None):
-    raise NameError('No path to the MsSpec distribution found !!')
+#    raise NameError('No path to the MsSpec distribution found !!')
 
 
 
@@ -185,7 +185,7 @@ class _MSCALCULATOR(Calculator):
         LOGGER.debug('    create a space dedicated to the calculation')
         ########################################################################
         self.init_folder = os.getcwd()
-        self.msspec_folder = os.path.join(MSSPEC_ROOT)
+        #self.msspec_folder = os.path.join(MSSPEC_ROOT)
         self.tmp_folder = os.path.abspath(folder)
         LOGGER.debug('    folder: \'%s\'', self.tmp_folder)
         if not os.path.exists(self.tmp_folder):
@@ -195,7 +195,7 @@ class _MSCALCULATOR(Calculator):
         #copyfile(os.path.join(self.msspec_folder, 'ase', 'Makefile'), 
         #         os.path.join(self.tmp_folder, 'Makefile'))
 
-        os.chdir(self.tmp_folder)
+        #os.chdir(self.tmp_folder)
 
         inv = cor = 'NO'
         if algorithm == 'expansion':
@@ -225,8 +225,8 @@ class _MSCALCULATOR(Calculator):
 
         calctype_spectro = self.spec_parameters.get_parameter('calctype_spectro')
         calctype_spectro = calctype_spectro.value
-        self._make_opts = (MSSPEC_ROOT, calctype_spectro, inv, cor,
+        #self._make_opts = (MSSPEC_ROOT, calctype_spectro, inv, cor,
-                           spin, sorb, self.tmp_folder)
+        #                   spin, sorb, self.tmp_folder)
 
         # Initialize the working environment
         #self._make('init')
@@ -306,6 +306,7 @@ class _MSCALCULATOR(Calculator):
             os.rename('fort.10', 'cluster.clu')
             os.rename('fort.35', 'tmatrix.tl')
             os.rename('fort.55', 'tmatrix.rad')
+            os.chdir(self.init_folder)
 	
 
     def run_spec(self):
@@ -366,6 +367,7 @@ class _MSCALCULATOR(Calculator):
 
             t1 = time.time()
             self.resources['spec_time'] = t1 - t0
+            os.chdir(self.init_folder)
 
     def get_tmatrix(self):
         LOGGER.info("Getting the TMatrix...")

src/msspec/iodata.py

@@ -67,7 +67,7 @@ from distutils.version import StrictVersion, LooseVersion
 
 import sys
 #sys.path.append('../../MsSpecGui/msspecgui/msspec/gui')
-from .msspecgui.msspec.gui.clusterviewer import ClusterViewer
+from msspec.msspecgui.msspec.gui.clusterviewer import ClusterViewer
 
 def cols2matrix(x, y, z, nx=88*1+1, ny=360*1+1):
     # mix the values of existing theta and new theta and return the 

src/msspec/phagen/fortran/Makefile

@@ -6,7 +6,7 @@ objects_src := phagen_scf.f
 objects := $(patsubst %.f,%.o, $(objects_src))
 
 
-.PHONY: clean pybinding
+.PHONY: clean purge pybinding
 
 pybinding: libphagen.so
 
@@ -24,5 +24,8 @@ $(objects): $(objects_src)
 clean:
 	@echo "cleaning..."                                               
 	rm -rf *.so *.o *.mod
+
+purge: clean
+	@echo "Purging..."                                               
 	rm -rf ../*.so
 

src/msspec/spec/fortran/Makefile

@@ -8,7 +8,7 @@ OPTS := -g -Wall -Wextra -Warray-temporaries -Wconversion -fbacktrace -ffree-lin
 EXE=prog
 
 
-.PHONY: clean pybinding
+.PHONY: clean purge pybinding
 
 pybinding: libspec.so
 
@@ -33,6 +33,9 @@ $(objects): $(objects_src)
 
 clean:
 	@echo "cleaning..."                                               
-	@rm -rf *.so *.o *.mod $(EXE)
+	@rm -rf *.so *.o *.mod
-	@rm -rf ../*.so
 
+purge: clean
+	@echo "Purging..."                                               
+	@rm -rf $(EXE)
+	@rm -rf ../*.so

src/msspec/spec/fortran/modules.f

@@ -11,6 +11,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_ADSORB()
           USE DIM_MOD
+          IF (ALLOCATED(ADS)) THEN
+            DEALLOCATE(ADS)
+          ENDIF
           ALLOCATE(ADS(3,900))
         END SUBROUTINE ALLOC_ADSORB
       END MODULE ADSORB_MOD
@@ -37,8 +40,17 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_APPROX()
           USE DIM_MOD
+          IF (ALLOCATED(RTHFWD)) THEN
+            DEALLOCATE(RTHFWD)
+          ENDIF
           ALLOCATE(RTHFWD(NATP_M))
+          IF (ALLOCATED(IBWD)) THEN
+            DEALLOCATE(IBWD)
+          ENDIF
           ALLOCATE(IBWD(NATP_M))
+          IF (ALLOCATED(RTHBWD)) THEN
+            DEALLOCATE(RTHBWD)
+          ENDIF
           ALLOCATE(RTHBWD(NATP_M))
         END SUBROUTINE ALLOC_APPROX
       END MODULE APPROX_MOD
@@ -55,8 +67,17 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_ATOMS()
           USE DIM_MOD
+          IF (ALLOCATED(VALZ)) THEN
+            DEALLOCATE(VALZ)
+          ENDIF
           ALLOCATE(VALZ(NATCLU_M))
+          IF (ALLOCATED(NZAT)) THEN
+            DEALLOCATE(NZAT)
+          ENDIF
           ALLOCATE(NZAT(NATCLU_M))
+          IF (ALLOCATED(CHEM)) THEN
+            DEALLOCATE(CHEM)
+          ENDIF
           ALLOCATE(CHEM(NATCLU_M))
         END SUBROUTINE ALLOC_ATOMS
       END MODULE ATOMS_MOD
@@ -70,7 +91,13 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_AUGER()
           USE DIM_MOD
+          IF (ALLOCATED(NLIN_A)) THEN
+            DEALLOCATE(NLIN_A)
+          ENDIF
           ALLOCATE(NLIN_A(0:20))
+          IF (ALLOCATED(L_BOUNDS)) THEN
+            DEALLOCATE(L_BOUNDS)
+          ENDIF
           ALLOCATE(L_BOUNDS(0:20,2))
         END SUBROUTINE ALLOC_AUGER
       END MODULE AUGER_MOD
@@ -83,7 +110,13 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_BASES()
           USE DIM_MOD
+          IF (ALLOCATED(ATBAS)) THEN
+            DEALLOCATE(ATBAS)
+          ENDIF
           ALLOCATE(ATBAS(3*NATP_M))
+          IF (ALLOCATED(VECBAS)) THEN
+            DEALLOCATE(VECBAS)
+          ENDIF
           ALLOCATE(VECBAS(9))
         END SUBROUTINE ALLOC_BASES
       END MODULE BASES_MOD
@@ -100,10 +133,25 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_CLUSLIM()
           USE DIM_MOD
+          IF (ALLOCATED(X_MAX)) THEN
+            DEALLOCATE(X_MAX)
+          ENDIF
           ALLOCATE(X_MAX(NATCLU_M))
+          IF (ALLOCATED(X_MIN)) THEN
+            DEALLOCATE(X_MIN)
+          ENDIF
           ALLOCATE(X_MIN(NATCLU_M))
+          IF (ALLOCATED(Y_MAX)) THEN
+            DEALLOCATE(Y_MAX)
+          ENDIF
           ALLOCATE(Y_MAX(NATCLU_M))
+          IF (ALLOCATED(Y_MIN)) THEN
+            DEALLOCATE(Y_MIN)
+          ENDIF
           ALLOCATE(Y_MIN(NATCLU_M))
+          IF (ALLOCATED(VAL)) THEN
+            DEALLOCATE(VAL)
+          ENDIF
           ALLOCATE(VAL(NATCLU_M))
         END SUBROUTINE ALLOC_CLUSLIM
       END MODULE CLUSLIM_MOD
@@ -121,10 +169,25 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_COOR()
           USE DIM_MOD
+          IF (ALLOCATED(NATYP)) THEN
+            DEALLOCATE(NATYP)
+          ENDIF
           ALLOCATE(NATYP(NATM))
+          IF (ALLOCATED(NCHTYP)) THEN
+            DEALLOCATE(NCHTYP)
+          ENDIF
           ALLOCATE(NCHTYP(NATP_M))
+          IF (ALLOCATED(NCORR)) THEN
+            DEALLOCATE(NCORR)
+          ENDIF
           ALLOCATE(NCORR(NAT_EQ_M,NATP_M))
+          IF (ALLOCATED(INEW_AT)) THEN
+            DEALLOCATE(INEW_AT)
+          ENDIF
           ALLOCATE(INEW_AT(NATCLU_M))
+          IF (ALLOCATED(SYM_AT)) THEN
+            DEALLOCATE(SYM_AT)
+          ENDIF
           ALLOCATE(SYM_AT(3,NATCLU_M))
         END SUBROUTINE ALLOC_COOR
       END MODULE COOR_MOD
@@ -142,6 +205,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_DEBWAL()
           USE DIM_MOD
+          IF (ALLOCATED(UJ2)) THEN
+            DEALLOCATE(UJ2)
+          ENDIF
           ALLOCATE(UJ2(NATM))
         END SUBROUTINE ALLOC_DEBWAL
       END MODULE DEBWAL_MOD
@@ -153,6 +219,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_INDAT()
           USE DIM_MOD
+          IF (ALLOCATED(INDATA)) THEN
+            DEALLOCATE(INDATA)
+          ENDIF
           ALLOCATE(INDATA(100))
         END SUBROUTINE ALLOC_INDAT
       END MODULE INDAT_MOD
@@ -280,6 +349,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_MASSAT()
           USE DIM_MOD
+          IF (ALLOCATED(XMT)) THEN
+            DEALLOCATE(XMT)
+          ENDIF
           ALLOCATE(XMT(NATM))
         END SUBROUTINE ALLOC_MASSAT
       END MODULE MASSAT_MOD
@@ -296,6 +368,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_MILLER()
           USE DIM_MOD
+          IF (ALLOCATED(IVN)) THEN
+            DEALLOCATE(IVN)
+          ENDIF
           ALLOCATE(IVN(3))
         END SUBROUTINE ALLOC_MILLER
       END MODULE MILLER_MOD
@@ -350,6 +425,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_RELADS()
           USE DIM_MOD
+          IF (ALLOCATED(PCRELA)) THEN
+            DEALLOCATE(PCRELA)
+          ENDIF
           ALLOCATE(PCRELA(3))
         END SUBROUTINE ALLOC_RELADS
       END MODULE RELADS_MOD
@@ -365,6 +443,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_RELAX()
           USE DIM_MOD
+          IF (ALLOCATED(PCREL)) THEN
+            DEALLOCATE(PCREL)
+          ENDIF
           ALLOCATE(PCREL(10))
         END SUBROUTINE ALLOC_RELAX
       END MODULE RELAX_MOD
@@ -429,10 +510,25 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_TRANS()
           USE DIM_MOD
+          IF (ALLOCATED(DLT)) THEN
+            DEALLOCATE(DLT)
+          ENDIF
           ALLOCATE(DLT(NE_M,NATM,0:18,2))
+          IF (ALLOCATED(TL)) THEN
+            DEALLOCATE(TL)
+          ENDIF
           ALLOCATE(TL(0:NT_M,4,NATM,NE_M))
+          IF (ALLOCATED(VK)) THEN
+            DEALLOCATE(VK)
+          ENDIF
           ALLOCATE(VK(NE_M))
+          IF (ALLOCATED(VK2)) THEN
+            DEALLOCATE(VK2)
+          ENDIF
           ALLOCATE(VK2(NE_M))
+          IF (ALLOCATED(LMAX)) THEN
+            DEALLOCATE(LMAX)
+          ENDIF
           ALLOCATE(LMAX(NATM,NE_M))
         END SUBROUTINE ALLOC_TRANS
       END MODULE TRANS_MOD
@@ -450,10 +546,25 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_TL_AED()
           USE DIM_MOD
+          IF (ALLOCATED(DLT_A)) THEN
+            DEALLOCATE(DLT_A)
+          ENDIF
           ALLOCATE(DLT_A(NE_M,NATM,0:18,2))
+          IF (ALLOCATED(TL_A)) THEN
+            DEALLOCATE(TL_A)
+          ENDIF
           ALLOCATE(TL_A(0:NT_M,4,NATM,NE_M))
+          IF (ALLOCATED(VK_A)) THEN
+            DEALLOCATE(VK_A)
+          ENDIF
           ALLOCATE(VK_A(NE_M))
+          IF (ALLOCATED(VK2_A)) THEN
+            DEALLOCATE(VK2_A)
+          ENDIF
           ALLOCATE(VK2_A(NE_M))
+          IF (ALLOCATED(LMAX_A)) THEN
+            DEALLOCATE(LMAX_A)
+          ENDIF
           ALLOCATE(LMAX_A(NATM,NE_M))
         END SUBROUTINE ALLOC_TL_AED
       END MODULE TL_AED_MOD
@@ -502,6 +613,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_TYPEM()
           USE DIM_MOD
+          IF (ALLOCATED(IEMET)) THEN
+            DEALLOCATE(IEMET)
+          ENDIF
           ALLOCATE(IEMET(NEMET_M))
         END SUBROUTINE ALLOC_TYPEM
       END MODULE TYPEM_MOD
@@ -532,6 +646,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_VALIN()
           USE DIM_MOD
+          IF (ALLOCATED(NONVOL)) THEN
+            DEALLOCATE(NONVOL)
+          ENDIF
           ALLOCATE(NONVOL(100))
         END SUBROUTINE ALLOC_VALIN
       END MODULE VALIN_MOD
@@ -544,7 +661,13 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_XMRHO()
           USE DIM_MOD
+          IF (ALLOCATED(XMAT)) THEN
+            DEALLOCATE(XMAT)
+          ENDIF
           ALLOCATE(XMAT(0:99))
+          IF (ALLOCATED(RHOAT)) THEN
+            DEALLOCATE(RHOAT)
+          ENDIF
           ALLOCATE(RHOAT(0:99))
         END SUBROUTINE ALLOC_XMRHO
       END MODULE XMRHO_MOD
@@ -570,8 +693,17 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_VECSYS()
           USE DIM_MOD
+          IF (ALLOCATED(ASYS)) THEN
+            DEALLOCATE(ASYS)
+          ENDIF
           ALLOCATE(ASYS(3))
+          IF (ALLOCATED(BSYS)) THEN
+            DEALLOCATE(BSYS)
+          ENDIF
           ALLOCATE(BSYS(3))
+          IF (ALLOCATED(CSYS)) THEN
+            DEALLOCATE(CSYS)
+          ENDIF
           ALLOCATE(CSYS(3))
         END SUBROUTINE ALLOC_VECSYS
       END MODULE VECSYS_MOD
@@ -583,6 +715,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_VIBRAT()
           USE DIM_MOD
+          IF (ALLOCATED(I_FREE)) THEN
+            DEALLOCATE(I_FREE)
+          ENDIF
           ALLOCATE(I_FREE(NATP_M))
         END SUBROUTINE ALLOC_VIBRAT
       END MODULE VIBRAT_MOD
@@ -594,6 +729,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_COEFRLM()
           USE DIM_MOD
+          IF (ALLOCATED(CF)) THEN
+            DEALLOCATE(CF)
+          ENDIF
           ALLOCATE(CF(0:2*NL_M-2,0:2*NL_M-2,0:2*NL_M-2))
         END SUBROUTINE ALLOC_COEFRLM
       END MODULE COEFRLM_MOD
@@ -605,6 +743,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_EXPROT()
           USE DIM_MOD
+          IF (ALLOCATED(EXPR)) THEN
+            DEALLOCATE(EXPR)
+          ENDIF
           ALLOCATE(EXPR(0:2*NL_M-2,0:2*NL_M-2))
         END SUBROUTINE ALLOC_EXPROT
       END MODULE EXPROT_MOD
@@ -616,6 +757,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_EXPFAC()
           USE DIM_MOD
+          IF (ALLOCATED(EXPF)) THEN
+            DEALLOCATE(EXPF)
+          ENDIF
           ALLOCATE(EXPF(0:2*NL_M-2,0:2*NL_M-2))
         END SUBROUTINE ALLOC_EXPFAC
       END MODULE EXPFAC_MOD
@@ -627,6 +771,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_LOGAMAD()
           USE DIM_MOD
+          IF (ALLOCATED(GLD)) THEN
+            DEALLOCATE(GLD)
+          ENDIF
           ALLOCATE(GLD(0:N_GAUNT,2))
         END SUBROUTINE ALLOC_LOGAMAD
       END MODULE LOGAMAD_MOD
@@ -638,6 +785,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_EXPFAC2()
           USE DIM_MOD
+          IF (ALLOCATED(EXPF2)) THEN
+            DEALLOCATE(EXPF2)
+          ENDIF
           ALLOCATE(EXPF2(0:2*NL_M-2,0:2*NL_M-2))
         END SUBROUTINE ALLOC_EXPFAC2
       END MODULE EXPFAC2_MOD
@@ -649,6 +799,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_FACTSQ()
           USE DIM_MOD
+          IF (ALLOCATED(FSQ)) THEN
+            DEALLOCATE(FSQ)
+          ENDIF
           ALLOCATE(FSQ(0:2*NL_M-2))
         END SUBROUTINE ALLOC_FACTSQ
       END MODULE FACTSQ_MOD
@@ -715,7 +868,13 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_VALIN_AV()
           USE DIM_MOD
+          IF (ALLOCATED(TH_0)) THEN
+            DEALLOCATE(TH_0)
+          ENDIF
           ALLOCATE(TH_0(NTH_M))
+          IF (ALLOCATED(PH_0)) THEN
+            DEALLOCATE(PH_0)
+          ENDIF
           ALLOCATE(PH_0(NPH_M))
         END SUBROUTINE ALLOC_VALIN_AV
       END MODULE VALIN_AV_MOD
@@ -797,6 +956,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_C_G()
           USE DIM_MOD
+          IF (ALLOCATED(CG)) THEN
+            DEALLOCATE(CG)
+          ENDIF
           ALLOCATE(CG(-LI_M:LI_M+1,2,2))
         END SUBROUTINE ALLOC_C_G
       END MODULE C_G_MOD
@@ -808,8 +970,11 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_C_G_A()
           USE DIM_MOD
-          ALLOCATE(CGA(0:NCG_M,-NCG_M:NCG_M,0:NCG_M,-NCG_M:NCG_M,0:2*NCG
+          IF (ALLOCATED(CGA)) THEN
-     &_M))
+            DEALLOCATE(CGA)
+          ENDIF
+          ALLOCATE(CGA(0:NCG_M,-NCG_M:NCG_M,0:NCG_M,-NCG_M:NCG_M,0:
+     &    2*NCG_M))
         END SUBROUTINE ALLOC_C_G_A
       END MODULE C_G_A_MOD
 
@@ -820,6 +985,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_C_G_M()
           USE DIM_MOD
+          IF (ALLOCATED(CG_S)) THEN
+            DEALLOCATE(CG_S)
+          ENDIF
           ALLOCATE(CG_S(2,2,2))
         END SUBROUTINE ALLOC_C_G_M
       END MODULE C_G_M_MOD
@@ -831,6 +999,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_DEXPFAC2()
           USE DIM_MOD
+          IF (ALLOCATED(DEXPF2)) THEN
+            DEALLOCATE(DEXPF2)
+          ENDIF
           ALLOCATE(DEXPF2(0:2*NL_M-2,0:2*NL_M-2))
         END SUBROUTINE ALLOC_DEXPFAC2
       END MODULE DEXPFAC2_MOD
@@ -842,6 +1013,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_DFACTSQ()
           USE DIM_MOD
+          IF (ALLOCATED(DFSQ)) THEN
+            DEALLOCATE(DFSQ)
+          ENDIF
           ALLOCATE(DFSQ(0:2*NL_M-2))
         END SUBROUTINE ALLOC_DFACTSQ
       END MODULE DFACTSQ_MOD
@@ -912,7 +1086,13 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_LINLBD()
           USE DIM_MOD
+          IF (ALLOCATED(LBD)) THEN
+            DEALLOCATE(LBD)
+          ENDIF
           ALLOCATE(LBD(-N_MU_M:N_MU_M,0:N_NU_M))
+          IF (ALLOCATED(NUMAX)) THEN
+            DEALLOCATE(NUMAX)
+          ENDIF
           ALLOCATE(NUMAX(NATP_M))
         END SUBROUTINE ALLOC_LINLBD
       END MODULE LINLBD_MOD
@@ -952,6 +1132,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_RA()
           USE DIM_MOD
+          IF (ALLOCATED(N_RA)) THEN
+            DEALLOCATE(N_RA)
+          ENDIF
           ALLOCATE(N_RA(NATP_M))
         END SUBROUTINE ALLOC_RA
       END MODULE RA_MOD
@@ -963,6 +1146,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_SPECTRUM()
           USE DIM_MOD
+          IF (ALLOCATED(I_SPECTRUM)) THEN
+            DEALLOCATE(I_SPECTRUM)
+          ENDIF
           ALLOCATE(I_SPECTRUM(NE_M))
         END SUBROUTINE ALLOC_SPECTRUM
       END MODULE SPECTRUM_MOD
@@ -979,9 +1165,21 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_DIRECT()
           USE DIM_MOD
+          IF (ALLOCATED(DIRANA)) THEN
+            DEALLOCATE(DIRANA)
+          ENDIF
           ALLOCATE(DIRANA(3,49))
+          IF (ALLOCATED(ANADIR)) THEN
+            DEALLOCATE(ANADIR)
+          ENDIF
           ALLOCATE(ANADIR(3,49))
+          IF (ALLOCATED(THETAR)) THEN
+            DEALLOCATE(THETAR)
+          ENDIF
           ALLOCATE(THETAR(49))
+          IF (ALLOCATED(PHIR)) THEN
+            DEALLOCATE(PHIR)
+          ENDIF
           ALLOCATE(PHIR(49))
         END SUBROUTINE ALLOC_DIRECT
       END MODULE DIRECT_MOD
@@ -998,9 +1196,21 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_DIRECT_A()
           USE DIM_MOD
+          IF (ALLOCATED(DIRANA_A)) THEN
+            DEALLOCATE(DIRANA_A)
+          ENDIF
           ALLOCATE(DIRANA_A(3,49))
+          IF (ALLOCATED(ANADIR_A)) THEN
+            DEALLOCATE(ANADIR_A)
+          ENDIF
           ALLOCATE(ANADIR_A(3,49))
+          IF (ALLOCATED(THETAR_A)) THEN
+            DEALLOCATE(THETAR_A)
+          ENDIF
           ALLOCATE(THETAR_A(49))
+          IF (ALLOCATED(PHIR_A)) THEN
+            DEALLOCATE(PHIR_A)
+          ENDIF
           ALLOCATE(PHIR_A(49))
         END SUBROUTINE ALLOC_DIRECT_A
       END MODULE DIRECT_A_MOD
@@ -1016,9 +1226,21 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_PATH()
           USE DIM_MOD
+          IF (ALLOCATED(NPATH)) THEN
+            DEALLOCATE(NPATH)
+          ENDIF
           ALLOCATE(NPATH(0:NDIF_M))
+          IF (ALLOCATED(NPATH2)) THEN
+            DEALLOCATE(NPATH2)
+          ENDIF
           ALLOCATE(NPATH2(0:NDIF_M))
+          IF (ALLOCATED(NPMA)) THEN
+            DEALLOCATE(NPMA)
+          ENDIF
           ALLOCATE(NPMA(0:NDIF_M))
+          IF (ALLOCATED(NPMI)) THEN
+            DEALLOCATE(NPMI)
+          ENDIF
           ALLOCATE(NPMI(0:NDIF_M))
         END SUBROUTINE ALLOC_PATH
       END MODULE PATH_MOD
@@ -1030,6 +1252,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_ROT()
           USE DIM_MOD
+          IF (ALLOCATED(RLM01)) THEN
+            DEALLOCATE(RLM01)
+          ENDIF
           ALLOCATE(RLM01(1-NL_M:NL_M-1,1-NL_M:NL_M-1,0:NL_M-1))
         END SUBROUTINE ALLOC_ROT
       END MODULE ROT_MOD
@@ -1043,7 +1268,13 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_TESTPA()
           USE DIM_MOD
+          IF (ALLOCATED(IT)) THEN
+            DEALLOCATE(IT)
+          ENDIF
           ALLOCATE(IT(0:NDIF_M))
+          IF (ALLOCATED(IN)) THEN
+            DEALLOCATE(IN)
+          ENDIF
           ALLOCATE(IN(0:NDIF_M))
         END SUBROUTINE ALLOC_TESTPA
       END MODULE TESTPA_MOD
@@ -1067,6 +1298,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_TLDW()
           USE DIM_MOD
+          IF (ALLOCATED(TLT)) THEN
+            DEALLOCATE(TLT)
+          ENDIF
           ALLOCATE(TLT(0:NT_M,4,NATM,NE_M))
         END SUBROUTINE ALLOC_TLDW
       END MODULE TLDW_MOD
@@ -1080,8 +1314,17 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_VARIA()
           USE DIM_MOD
+          IF (ALLOCATED(CEX)) THEN
+            DEALLOCATE(CEX)
+          ENDIF
           ALLOCATE(CEX(0:NDIF_M))
+          IF (ALLOCATED(CEXDW)) THEN
+            DEALLOCATE(CEXDW)
+          ENDIF
           ALLOCATE(CEXDW(0:NDIF_M))
+          IF (ALLOCATED(DW)) THEN
+            DEALLOCATE(DW)
+          ENDIF
           ALLOCATE(DW(0:NDIF_M))
         END SUBROUTINE ALLOC_VARIA
       END MODULE VARIA_MOD
@@ -1093,7 +1336,10 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_LBD()
           USE DIM_MOD
-          INTEGER I,J
+          INTEGER I, J
+          IF (ALLOCATED(LBDM)) THEN
+            DEALLOCATE(LBDM)
+          ENDIF
           ALLOCATE(LBDM(2,NDIF_M))
           DO I=1,NDIF_M
             DO J=1,2
@@ -1110,6 +1356,9 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_SCATMAT()
           USE DIM_MOD
+          IF (ALLOCATED(F21)) THEN
+            DEALLOCATE(F21)
+          ENDIF
           ALLOCATE(F21(NSPIN2_M,NLAMBDA_M,NLAMBDA_M,NDIF_M))
         END SUBROUTINE ALLOC_SCATMAT
       END MODULE SCATMAT_MOD
@@ -1123,7 +1372,13 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_EXTREM()
           USE DIM_MOD
+          IF (ALLOCATED(FMIN)) THEN
+            DEALLOCATE(FMIN)
+          ENDIF
           ALLOCATE(FMIN(0:NDIF_M))
+          IF (ALLOCATED(FMAX)) THEN
+            DEALLOCATE(FMAX)
+          ENDIF
           ALLOCATE(FMAX(0:NDIF_M))
         END SUBROUTINE ALLOC_EXTREM
       END MODULE EXTREM_MOD
@@ -1139,11 +1394,25 @@ C=======================================================================
       CONTAINS
         SUBROUTINE ALLOC_PRINTP()
           USE DIM_MOD
-          INTEGER I,J
+          IF (ALLOCATED(FMN)) THEN
+            DEALLOCATE(FMN)
+          ENDIF
           ALLOCATE(FMN(NPATH_M))
+          IF (ALLOCATED(PATH)) THEN
+            DEALLOCATE(PATH)
+          ENDIF
           ALLOCATE(PATH(NPATH_M))
+          IF (ALLOCATED(DMN)) THEN
+            DEALLOCATE(DMN)
+          ENDIF
           ALLOCATE(DMN(NPATH_M))
+          IF (ALLOCATED(JON)) THEN
+            DEALLOCATE(JON)
+          ENDIF
           ALLOCATE(JON(NPATH_M))
+          IF (ALLOCATED(JPON)) THEN
+            DEALLOCATE(JPON)
+          ENDIF
           ALLOCATE(JPON(NPATH_M,NDIF_M))
         END SUBROUTINE ALLOC_PRINTP
       END MODULE PRINTP_MOD

src/msspec/spec/fortran/spec.f

@@ -1285,7 +1285,7 @@ C
         WRITE(IUO1,562)
       ENDIF
       IF(ISOM.EQ.0) CLOSE(IUO2)
-      IF((ISOM.EQ.0).AND.(NFICHLEC.NE.1)) CLOSE(IUO1)
+C!      IF((ISOM.EQ.0).AND.(NFICHLEC.NE.1)) CLOSE(IUO1)
 C
 C..........  End of the loop on the data files  ..........
 C
@@ -1309,7 +1309,7 @@ c          ENDIF
         ENDIF
       ENDIF
 C
-      IF((ISOM.NE.0).OR.(NFICHLEC.EQ.1)) CLOSE(IUO1)
+C!      IF((ISOM.NE.0).OR.(NFICHLEC.EQ.1)) CLOSE(IUO1)
       IF(ISOM.NE.0) CLOSE(IUO2)
 C      STOP
       GOTO 999

src/msspec/tests.py

@@ -144,8 +144,9 @@ def create_tests_results():
     create_results(tc, 'test_cut_plane')
 
     tc = PEDCopperTestCase()
-    create_results(tc, 'test_phi_scan')
     create_results(tc, 'test_theta_scan')
+    tc = PEDCopperTestCase()
+    create_results(tc, 'test_phi_scan')
 
 def delete_results_file():
     os.remove(RESULTS_FILENAME)

src/setup.py

@@ -9,6 +9,7 @@ setup(name='msspec',
       include_package_data=True,
       packages=find_packages(include='msspec.*'),
       install_requires=[
+	'numpy',
         'ase',
         'h5py',
         'lxml',

utils/process.py

@@ -266,7 +266,7 @@ class CommonBlockInfo(BaseInfo):
                     #exit()
                 else:
                     if re.match("^[A-HO-Z].*", v.name, re.I):
-                        v.type = "DOUBLE PRECISION"
+                        v.type = "REAL"
                     else:
                         v.type = "INTEGER"
                 
@@ -808,6 +808,9 @@ def write_modules(infile):
         # for each variable with a defined dimension
         for variable in variables:
             if variable.dimension is not None:
+                s += f"    IF (ALLOCATED({variable.name})) THEN\n"
+                s += f"      DEALLOCATE({variable.name})\n"
+                s += f"    ENDIF\n"
                 s += f"    ALLOCATE({variable})\n"
         
         s += f"  END SUBROUTINE ALLOC_{cbi.name.upper()}\n"
@@ -832,10 +835,11 @@ def write_modules(infile):
 
 
 if __name__ == "__main__":
-    infile = 'spec.f'
+    infile = 'spec.f.orig'
 
     # write the modules.f file
     write_modules(infile)
+    exit()
 
     fi = FileInfo(filename=infile)