Merge branch 'staging' into 'master'

Packages update - numpy, pandas scikit learn

See merge request !116

3rdparty/quip/src/f90wrap/LICENSE

+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
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+
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+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
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+
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+
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3rdparty/quip/src/f90wrap/README.md

 f90wrap: Fortran to Python interface generator with derived type support
 ========================================================================
 
-[![Build Status](https://travis-ci.org/jameskermode/f90wrap.svg?branch=master)](https://travis-ci.org/jameskermode/f90wrap)
+![Build Status](https://github.com/jameskermode/f90wrap/actions/workflows/python-package.yml/badge.svg)
 
 f90wrap is a tool to automatically generate Python extension modules
 which interface to Fortran code that makes use of derived types. It
@@ -12,7 +12,7 @@ suitable for wrapping with f2py, together with a higher-level Pythonic
 wrapper that makes the existance of an additional layer transparent to
 the final user.
 
-Copyright (C) James Kermode 2011-2018. Released under the GNU Lesser General
+Copyright (C) James Kermode 2011-2021. Released under the GNU Lesser General
 Public License, version 3. Parts originally based on f90doc - automatic
 documentation generator for Fortran 90. Copyright (C) 2004 Ian Rutt.
 
@@ -22,37 +22,38 @@ please contact James Kermode <james.kermode@gmail.com>
 Dependencies
 ------------
 
- 1.  [Python](http://www.python.org) \>= 2.7 or 3.x (both now supported!)
+ 1.  [Python](http://www.python.org) 3.6+ (Python 2.7 no longer supported)
  2.  Recent version of [numpy](http://www.numpy.org) which includes `f2py`
  3.  Fortran compiler - tested with `gfortran` 4.6+ and recent `ifort` 12+
 
 Installation
 ------------
 
-For the latest stable release, install with either `pip` or `conda`:
+For the latest stable release, install with `pip`:
 
 ```
 pip install f90wrap
 ```
 
-f90wrap can also be installed using `conda` via the conda-forge channel:
+There is also a [conda package](https://anaconda.org/conda-forge/f90wrap) on conda-forge:
 
 ```
-conda config --add channels conda-forge
+conda install -c conda-forge f90wrap
 ```
 
-Once the conda-forge channel has been enabled, f90wrap can be installed with:
+For the development version, installation is as follows:
 
 ```
-conda install f90wrap
+pip install git+https://github.com/jameskermode/f90wrap
 ```
 
-For the development version, installation is as follows:
+Note that if your Fortran 90 compiler has a non-standard name
+(e.g. gfortran-9) then you need to set the `F90` environment variable
+prior to installing f90wrap to ensure it uses the correct one, e.g.
 
-    git clone https://github.com/jameskermode/f90wrap
-    cd f90wrap
-    python setup.py install [--prefix PREFIX]
-    
+```
+F90=gfortran-9 pip install f90wrap
+```
 
 Examples and Testing
 --------------------
@@ -60,6 +61,38 @@ Examples and Testing
 To test the installation, run `make test` from the `examples/`
 directory. You may find the code in the various examples useful.
 
+Citing f90wrap
+--------------
+
+If you find `f90wrap` useful in academic work, please cite the following
+(open access) publication:
+
+> J. R. Kermode, f90wrap: an automated tool for constructing 
+> deep Python interfaces to modern Fortran codes. 
+> J. Phys. Condens. Matter (2020) 
+>[doi:10.1088/1361-648X/ab82d2](https://dx.doi.org/10.1088/1361-648X/ab82d2)
+
+BibTeX entry:
+
+```bibtex
+
+@ARTICLE{Kermode2020-f90wrap,
+  title    = "f90wrap: an automated tool for constructing deep Python
+              interfaces to modern Fortran codes",
+  author   = "Kermode, James R",
+  journal  = "J. Phys. Condens. Matter",
+  month    =  mar,
+  year     =  2020,
+  keywords = "Fortran; Interfacing; Interoperability; Python; Wrapping codes;
+              f2py",
+  language = "en",
+  issn     = "0953-8984, 1361-648X",
+  pmid     = "32209737",
+  doi      = "10.1088/1361-648X/ab82d2"
+}
+
+```
+
 Case studies
 ------------
 
@@ -69,7 +102,8 @@ applications:
  - [QUIP](http://libatoms.github.io/QUIP/) - molecular dynamics code
  - [CASTEP](http://www.castep.org) - electronic structure code
 
-See this [IPython notebook](http://nbviewer.ipython.org/github/jameskermode/f90wrap/blob/master/docs/tutorials/kermode-csc-warwick-nov-2015.ipynb) from a recent seminar for more details.
+See this [Jupyter notebook](https://github.com/jameskermode/f90wrap/blob/master/docs/tutorials/f90wrap-demo-feb-2020.ipynb) 
+from a recent seminar for more details.
 
 Usage
 -----
@@ -142,7 +176,7 @@ allow it to be called from Python.
     type arguments replaced by integer arrays containing a
     representation of a pointer to the derived type, in the manner
     described in
-    (Pletzer2008)[https://doi.org/10.1109/MCSE.2008.94].
+    [Pletzer2008](https://doi.org/10.1109/MCSE.2008.94).
     This allows opaque references to the
     true Fortran derived type data structures to be passed back and
     forth between Python and Fortran.
@@ -164,62 +198,98 @@ Additional command line arguments can be passed to f90wrap to customize
 how the wrappers are generated. See the `examples/` directory to see how
 some of the options are used:
 
-    -h, --help            show this help message and exit
-    -v, --verbose         set verbosity level [default: None]
-    -V, --version         show program's version number and exit
-    -p PREFIX, --prefix PREFIX
-                          Prefix to prepend to arguments and subroutines.
-    -c [CALLBACK [CALLBACK ...]], --callback [CALLBACK [CALLBACK ...]]
-                          Names of permitted callback routines.
-    -C [CONSTRUCTORS [CONSTRUCTORS ...]], --constructors [CONSTRUCTORS [CONSTRUCTORS ...]]
-                          Names of constructor routines.
-    -D [DESTRUCTORS [DESTRUCTORS ...]], --destructors [DESTRUCTORS [DESTRUCTORS ...]]
-                          Names of destructor routines.
-    -k KIND_MAP, --kind-map KIND_MAP
-                          File containing Python dictionary in f2py_f2cmap
-                          format
-    -s STRING_LENGTHS, --string-lengths STRING_LENGTHS
-                          "File containing Python dictionary mapping string
-                          length names to values
-    -S DEFAULT_STRING_LENGTH, --default-string-length DEFAULT_STRING_LENGTH
-                          Default length of character strings
-    -i INIT_LINES, --init-lines INIT_LINES
-                          File containing Python dictionary mapping type names
-                          to necessary initialisation code
-    -I INIT_FILE, --init-file INIT_FILE
-                          Python source file containing code to be added to
-                          autogenerated __init__.py
-    -A ARGUMENT_NAME_MAP, --argument-name-map ARGUMENT_NAME_MAP
-                          File containing Python dictionary to rename Fortran
-                          arguments
-    --short-names SHORT_NAMES
-                          File containing Python dictionary mapping full type
-                          names to abbreviations
-    -m MOD_NAME, --mod-name MOD_NAME
-                          Name of output extension module (without .so
-                          extension).
-    -M, --move-methods    Convert routines with derived type instance as first
-                          agument into class methods
-    -P, --package         Generate a Python package instead of a single module
-    -a ABORT_FUNC, --abort-func ABORT_FUNC
-                          Name of Fortran subroutine to invoke if a fatal error
-                          occurs
-    --only [ONLY [ONLY ...]]
-                          Subroutines to include in wrapper
-    --skip [SKIP [SKIP ...]]
-                          Subroutines to exclude from wrapper         
+      -h, --help            show this help message and exit
+      -v, --verbose         set verbosity level [default: None]
+      -V, --version         show program's version number and exit
+      -p PREFIX, --prefix PREFIX
+                            Prefix to prepend to arguments and subroutines.
+      -c [CALLBACK [CALLBACK ...]], --callback [CALLBACK [CALLBACK ...]]
+                            Names of permitted callback routines.
+      -C [CONSTRUCTORS [CONSTRUCTORS ...]], --constructors [CONSTRUCTORS [CONSTRUCTORS ...]]
+                            Names of constructor routines.
+      -D [DESTRUCTORS [DESTRUCTORS ...]], --destructors [DESTRUCTORS [DESTRUCTORS ...]]
+                            Names of destructor routines.
+      -k KIND_MAP, --kind-map KIND_MAP
+                            File containting Python dictionary in f2py_f2cmap
+                            format
+      -s STRING_LENGTHS, --string-lengths STRING_LENGTHS
+                            "File containing Python dictionary mapping string
+                            length names to values
+      -S DEFAULT_STRING_LENGTH, --default-string-length DEFAULT_STRING_LENGTH
+                            Default length of character strings
+      -i INIT_LINES, --init-lines INIT_LINES
+                            File containing Python dictionary mapping type names
+                            to necessary initialisation code
+      -I INIT_FILE, --init-file INIT_FILE
+                            Python source file containing code to be added to
+                            autogenerated __init__.py
+      -A ARGUMENT_NAME_MAP, --argument-name-map ARGUMENT_NAME_MAP
+                            File containing Python dictionary to rename Fortran
+                            arguments
+      --short-names SHORT_NAMES
+                            File containing Python dictionary mapping full type
+                            names to abbreviations
+      --py-mod-names PY_MOD_NAMES
+                            File containing Python dictionary mapping Fortran
+                            module names to Python ones
+      --class-names CLASS_NAMES
+                            File containing Python dictionary mapping Fortran type
+                            names to Python classes
+      --joint-modules JOINT_MODULES
+                            File containing Python dictionary mapping modules
+                            defining times to list of additional modules defining
+                            methods
+      -m MOD_NAME, --mod-name MOD_NAME
+                            Name of output extension module (without .so
+                            extension).
+      -M, --move-methods    Convert routines with derived type instance as first
+                            agument into class methods
+      --shorten-routine-names
+                            Remove type name prefix from routine names, e.g.
+                            cell_symmetrise() -> symmetrise()
+      -P, --package         Generate a Python package instead of a single module
+      -a ABORT_FUNC, --abort-func ABORT_FUNC
+                            Name of Fortran subroutine to invoke if a fatal error
+                            occurs
+      --only [ONLY [ONLY ...]]
+                            Subroutines to include in wrapper
+      --skip [SKIP [SKIP ...]]
+                            Subroutines to exclude modules and subroutines from
+                            wrapper
+      --skip-types [SKIP_TYPES [SKIP_TYPES ...]]
+                            Subroutines to exclude types from wrapper
+      --force-public [FORCE_PUBLIC [FORCE_PUBLIC ...]]
+                            Names which are forced to be make public
+      --default-to-inout    Sets all arguments without intent to intent(inout)
+      --conf-file CONF_FILE
+                            Use Python configuration script to set options
+      --documentation-plugin DOCUMENTATION_PLUGIN
+                            Use Python script for expanding the documentation of
+                            functions and subroutines. All lines of the given tree
+                            object are passed to it with a reference to its
+                            documentation
+      --py-max-line-length PY_MAX_LINE_LENGTH
+                            Maximum length of lines in python files written.
+                            Default: 80
+      --f90-max-line-length F90_MAX_LINE_LENGTH
+                            Maximum length of lines in fortan files written.
+                            Default: 120
+         
 
 Author
 ------
 
-James Kermode: <james.kermode@gmail.com>
+James Kermode [jameskermode](https://github.com/jameskermode)
 
 Contributors
 ------------
 
+- Tamas Stenczel [stenczelt](https://github.com/stenczelt)
 - Steven Murray [steven-murray](https://github.com/steven-murray)
 - Greg Corbett  [gregcorbett](https://github.com/gregcorbett)
 - Bob Fischer [citibob](https://github.com/citibob)
 - David Verelst [davidovitch](https://github.com/davidovitch)
 - James Orr [jamesorr](https://github.com/jamesorr)
 - [yvesch](https://github.com/yvesch)
+- [Matthias Cuntz](https://github.com/mcuntz)
+- Balthasar Reuter [reuterbal](https://github.com/reuterbal)

3rdparty/quip/src/f90wrap/examples/CMakeLists.txt

+cmake_minimum_required(VERSION 3.0)
+project(test_f90wrap)
+enable_testing()
+include(CTest)
+
+list(APPEND tests
+    arrayderivedtypes
+    arrays
+    arrays_fixed
+    arrays_in_derived_types_issue50
+    cylinder
+    derivedtypes
+    elemental
+    example2
+    extends
+    interface
+    issue105_function_definition_with_empty_lines
+    issue32
+    mockderivetype
+    mod_arg_clash
+    optional_args_issue53
+    optional_derived_arrays
+    passbyreference
+    strings
+    subroutine_contains_issue101
+    type_bn
+)
+
+foreach(test ${tests})
+    message(STATUS "Adding test ${test}")
+    add_test(
+        NAME ${test}
+        COMMAND make
+        WORKING_DIRECTORY "${PROJECT_SOURCE_DIR}/${test}"
+    )
+endforeach()
+
+

3rdparty/quip/src/f90wrap/examples/Makefile

@@ -8,6 +8,7 @@ EXAMPLES = arrayderivedtypes \
 	example2 \
 	extends \
 	interface \
+	issue105_function_definition_with_empty_lines \
 	issue32 \
 	mockderivetype \
 	mod_arg_clash \
@@ -15,12 +16,21 @@ EXAMPLES = arrayderivedtypes \
 	optional_derived_arrays \
 	passbyreference \
 	strings \
+	subroutine_contains_issue101 \
 	type_bn
 
+PYTHON = python
+
+all: test
+
 test:
 	for example in ${EXAMPLES}; do \
+	  echo "" ; \
+	  echo "" ; \
+	  echo "" ; \
+	  echo "# ---------------------------------------------------" ; \
 	  echo "running make test in $$example" ; \
-	  make -C $$example test || exit ; \
+	  make -C $$example PYTHON=$(PYTHON) test || exit ; \
 	done
 
 clean:

3rdparty/quip/src/f90wrap/examples/arrayderivedtypes/Makefile

@@ -105,8 +105,9 @@ all: _${PYTHON_MODN}.so test
 
 
 clean:
-	-rm ${LIBSRC_OBJECTS} ${LIBSRC_FPP_FILES} libsrc.a _${PYTHON_MODN}.so \
-	 *.mod *.fpp f90wrap*.f90 f90wrap*.o *.o
+	-rm -f ${LIBSRC_OBJECTS} ${LIBSRC_FPP_FILES} libsrc.a _${PYTHON_MODN}*.so \
+	 *.mod *.fpp f90wrap*.f90 f90wrap*.o *.o ${PYTHON_MODN}.py
+	-rm -rf src.*/ .f2py_f2cmap .libs/ __pycache__/
 
 
 .f90.o:

3rdparty/quip/src/f90wrap/examples/arrayderivedtypes/test.f90

 module module_calcul
-type type_ptmes
-integer :: y
-end type type_ptmes
-type array_type
-type(type_ptmes) :: x(2)
-end type array_type
+  type type_ptmes
+     integer :: y
+  end type type_ptmes
+  
+  type array_type
+     type(type_ptmes) :: x(2)
+  end type array_type
+
+  type(array_type), dimension(10), target :: xarr
+  
 contains
-subroutine recup_point(x)
-type(array_type) :: x
-return
-end subroutine recup_point
-end module module_calcul
\ No newline at end of file
+  subroutine recup_point(x)
+    type(array_type) :: x
+    return
+  end subroutine recup_point
+end module module_calcul

3rdparty/quip/src/f90wrap/examples/arrays/Makefile

@@ -105,8 +105,10 @@ all: _${PYTHON_MODN}.so _${PYTHON_MODN}_pkg.so test
 
 
 clean:
-	-rm ${LIBSRC_OBJECTS} ${LIBSRC_FPP_FILES} libsrc.a _${PYTHON_MODN}.so \
-	_${PYTHON_MODN}_pkg.so *.mod *.fpp f90wrap*.f90 f90wrap*.o *.o
+	-rm -f ${LIBSRC_OBJECTS} ${LIBSRC_FPP_FILES} libsrc.a _${PYTHON_MODN}*.so \
+	_${PYTHON_MODN}_pkg.so *.mod *.fpp f90wrap*.f90 f90wrap*.o *.o ${PYTHON_MODN}.py
+	-rm -rf ${PYTHON_MODN}_pkg/
+	-rm -rf src.*/ .f2py_f2cmap .libs/ __pycache__/
 
 
 .f90.o:

3rdparty/quip/src/f90wrap/examples/arrays_fixed/Makefile

@@ -105,8 +105,10 @@ all: _${PYTHON_MODN}.so _${PYTHON_MODN}_pkg.so test
 
 
 clean:
-	-rm ${LIBSRC_OBJECTS} ${LIBSRC_FPP_FILES} libsrc.a _${PYTHON_MODN}.so \
-	_${PYTHON_MODN}_pkg.so *.mod *.fpp f90wrap*.f f90wrap*.o *.o
+	-rm -f ${LIBSRC_OBJECTS} ${LIBSRC_FPP_FILES} libsrc.a _${PYTHON_MODN}*.so \
+	_${PYTHON_MODN}_pkg.so *.mod *.fpp f90wrap*.f* f90wrap*.o *.o ${PYTHON_MODN}.py
+	-rm -rf ${PYTHON_MODN}_pkg/
+	-rm -rf src.*/ .f2py_f2cmap .libs/ __pycache__/
 
 
 .f.o:

3rdparty/quip/src/f90wrap/examples/arrays_in_derived_types_issue50/Makefile

@@ -105,8 +105,9 @@ all: _${PYTHON_MODN}.so test
 
 
 clean:
-	-rm ${LIBSRC_OBJECTS} ${LIBSRC_FPP_FILES} libsrc.a _${PYTHON_MODN}.so \
-	 *.mod *.fpp f90wrap*.f90 f90wrap*.o *.o
+	-rm -f ${LIBSRC_OBJECTS} ${LIBSRC_FPP_FILES} libsrc.a _${PYTHON_MODN}*.so \
+	 *.mod *.fpp f90wrap*.f90 f90wrap*.o *.o ${PYTHON_MODN}.py
+	-rm -rf src.*/ .f2py_f2cmap .libs/ __pycache__/
 
 
 .f90.o:

3rdparty/quip/src/f90wrap/examples/callback_print_function_issue93/Makefile

+#=======================================================================
+#                   define the compiler names
+#=======================================================================
+
+CC       = gcc
+F90      = gfortran
+#F90      = ifort
+#F90      =  /opt/intel/composer_xe_2015.3.187/bin/intel64/ifort
+PYTHON   = python
+
+#=======================================================================
+#                     additional flags
+#=======================================================================
+
+ifeq ($(F90),gfortran)
+	FPP      = gfortran -E
+	FPP_F90FLAGS = -x f95-cpp-input -fPIC
+	F90FLAGS = -fPIC
+    FCOMP    = gfortran
+    LIBS     =
+endif
+
+ifeq ($(F90),ifort)
+
+	FPP      = gfortran -E # gfortran f90wrap temp files only. not compilation
+	FPP_F90FLAGS = -x f95-cpp-input -fPIC
+	F90FLAGS = -fpscomp logicals -fPIC # use 1 and 0 for True and False
+    FCOMP    = intelem # for f2py