Removed OpenMP because I/O is not thread safe

Version:2.0.7

Bash/ezfio.sh

@@ -1,10 +1,13 @@
 #!/bin/bash
+#
+# ezfio shell command with completion
+#
 
 EZFIO_ROOT=$( cd $(dirname "${BASH_SOURCE}")/..  ; pwd -P )
 
 function _ezfio_py()
 {
-  python2 ${EZFIO_ROOT}/Python/ezfio.py "$@"
+  python3 ${EZFIO_ROOT}/Python/ezfio.py "$@"
 }
 
 

LICENSE

@@ -1,4 +1,4 @@
-    GNU GENERAL PUBLIC LICENSE
+        GNU GENERAL PUBLIC LICENSE
            Version 2, June 1991
 
  Copyright (C) 1989, 1991 Free Software Foundation, Inc.,

Makefile

@@ -35,22 +35,17 @@ clean:
 	- bash -c "[[ -f lib/libezfio.a ]] && rm $$PWD/lib/*"
 	- bash -c "[[ -f Python/ezfio.py ]] && rm $$PWD/Python/*"
 	- bash -c "[[ -f Ocaml/ezfio.ml ]] && rm $$PWD/Ocaml/*"
-	- bash -c "[[ -f Bash/ezfio.sh ]] && rm $$PWD/Bash/*"
 	- $(MAKE) -C $$PWD/src veryclean
 
-archive: distclean
+archive: veryclean
 	git archive --format=tar HEAD > EZFIO.$(VERSION).tar
 	mkdir EZFIO ; cd EZFIO ; tar -xvf ../EZFIO.$(VERSION).tar
 	rm EZFIO.$(VERSION).tar
 	tar -zcvf EZFIO.$(VERSION).tar.gz EZFIO
 	rm -rf EZFIO
 
-make.config: 
-	./configure.py
-
 veryclean:
 	$(MAKE) -C src veryclean
-	rm -f make.config
 	rm -f Ocaml/ezfio.ml
 	rm -f Python/ezfio.py
 	rm -f lib/{libezfio.a,libezfio_irp.a}

README.rst

@@ -4,13 +4,15 @@ EZFIO
 EZFIO is the Easy Fortran I/O library generator. It generates
 automatically an I/O library from a simple configuration file. The
 produced library contains Fortran subroutines to read/write the data
-from/to disk, and to check if the data exists.
-A Python and an Ocaml API are also provided.
+from/to disk, and to check if the data exists. A Python and an Ocaml API
+are also provided.
 
 With EZFIO, the data is organized in a file system inside a main
 directory. This main directory contains subdirectories, which contain
 files. Each file corresponds to a data. For atomic data the file is a
-plain text file, and for array data the file is a gzipped text file. 
+plain text file, and for array data the file is a gzipped text file.
+
+Starting with version 2.0, EZFIO produces Python3 files.
 
 Download
 ========
@@ -19,7 +21,8 @@ The following packages are needed:
 
 * `IRPF90 <http://irpf90.ups-tlse.fr>`_
 * `Python <http://www.python.org>`_
-* `GNU make <http://www.python.org>`_ or `Ninja <http://github.com/martine/ninja>`_
+* `GNU make <https://www.gnu.org/software/make>`_ 
+* `Zlib <https://www.zlib.net>`_ 
 
 
 Tutorial
@@ -32,7 +35,8 @@ the 3D space.
 Preparation of the library
 --------------------------
 
-Create an empty directory for your project and unpack the ``EZFIO.tar.gz`` file in this directory. This directory now contains:
+Create an empty directory for your project and unpack the
+``EZFIO.tar.gz`` file in this directory. This directory now contains:
 
 .. code-block:: bash
 
@@ -40,9 +44,8 @@ Create an empty directory for your project and unpack the ``EZFIO.tar.gz`` file
   EZFIO/
 
 Get into the ``EZFIO`` directory and configure the library to produce the
-desired suboutines. Get into the ``config`` directory and create a new file
-``test.config``
-containing::
+desired suboutines. Get into the ``config`` directory and create a new
+file ``test.config`` containing::
 
   molecule
     num_atoms   integer
@@ -56,14 +59,13 @@ containing::
 
 In this example, ``molecule`` and ``properties`` are containers of data.
 Those are defined in the config file by their name at the beginning of a
-new line.
-Each data contained inside a container is characterized by a triplet
-(name,type,dimension), preceded by at least one white space at the
-beginning of the line.
+new line. Each data contained inside a container is characterized by a
+triplet (name,type,dimension), preceded by at least one white space at
+the beginning of the line.
 
-If the dimension of an array is a data, the name of the data can be used
-as ``<container>_<data>`` in the definition of the dimension. For
-example, the dimension (``molecule_num_atoms``) uses the data
+If the dimension of an array is a data, the name of the data can be
+used as ``<container>_<data>`` in the definition of the dimension.
+For example, the dimension (``molecule_num_atoms``) uses the data
 ``num_atoms`` of container ``molecule``.
 
 Data can also be the result of a simple operation. In that case, the
@@ -83,16 +85,10 @@ Now, go back to the EZFIO root directory. To build with GNU make, run:
 
   $ make
 
-Or you can use Ninja to build the library:
-
-.. code-block:: bash
-
-  $ ninja
-
-
-The ``lib`` directory now contains the static library ``libezfio.a``, and a static
-library for use under the IRPF90 environment (``libezfio_irp.a``).
-The ``Python``, ``Ocaml`` and ``Bash`` directories contain the binding for these languages.
+The ``lib`` directory now contains the static library ``libezfio.a``,
+and a static library for use under the IRPF90 environment
+(``libezfio_irp.a``). The ``Python``, ``Ocaml`` and ``Bash`` directories
+contain the binding for these languages.
 
 
 Using the produced library
@@ -186,7 +182,7 @@ Create a file named ``create_input.py`` with:
 
 .. code-block:: python
 
-  #!/usr/bin/python2
+  #!/usr/bin/python3
   
   import sys
   EZFIO = "./EZFIO"  # Put here the absolute path to the EZFIO directory
@@ -201,17 +197,17 @@ Create a file named ``create_input.py`` with:
   
   Molecule = []
   for line in input.splitlines():
-    new_list = map(eval,line.split())
+    new_list = list(map(eval,line.split()))
     Molecule.append(new_list)
   
   # Create the mass array
-  mass = map( lambda x: x[0], Molecule )
-  # print mass
+  mass = [ x[0] for x in Molecule ]
+  # print(mass)
   # [16.0, 1.0, 1.0]
   
   # Create the coord array
-  coord = map( lambda x: (x[1], x[2], x[3]), Molecule )
-  # print coord
+  coord = [ (x[1], x[2], x[3]) for x in Molecule ]
+  # print(coord)
   # [(0.0, 0.222396, 0.0), (1.436494, -0.88966, 0.0), (-1.436494, -0.88966, 0.0)]
   
   # Select the EZFIO file
@@ -223,16 +219,17 @@ Create a file named ``create_input.py`` with:
   ezfio.molecule_coord = coord
   
   # Check that the total mass is correct:
-  print ezfio.properties_mass   # Should give 18.
+  print(ezfio.properties_mass)   # Should give 18.
 
 Execute the script:
 
 .. code-block:: bash
 
-  $ python2 create_input.py
+  $ python3 create_input.py
   18.0
 
-The printed mass is correct, and a new directory (``Water``) was created with our data:
+The printed mass is correct, and a new directory (``Water``) was created
+with our data:
 
 .. code-block:: bash
 
@@ -309,12 +306,12 @@ the EZFIO file.
   
   end
 
-Compile the fortran program and link it the ``libezfio.a`` library, and run the
-executable.
+Compile the fortran program and link it the ``libezfio.a`` library and
+``zlib``, and run the executable.
 
 .. code-block:: bash
 
-  $ gfortran test.f90 EZFIO/lib/libezfio.a -o test.x
+  $ gfortran test.f90 EZFIO/lib/libezfio.a -lz -o test.x
   $ ./test.x
   Data in the EZFIO file:
      16.0000000       0.00000000      0.222396001       0.00000000    
@@ -362,13 +359,14 @@ The usage of the ``ezfio`` bash command is::
   ezfio unset_verbose
 
 
-Here is the same script as the Python script, but using Bash (``create_input.sh``):
+Here is the same script as the Python script, but using Bash
+(``create_input.sh``):
 
 .. code-block:: bash
 
   #!/bin/bash
   
-  source EZFIO/Bash/ezfio.sh
+  source EZFIO/Bash/ezfio.sh  # Put correct path here
   
   # Select the EZFIO file
   ezfio set_file Water

bin/archive_ezfio.py

@@ -1,9 +1,9 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 
 import sys
 import os
 sys.path = [ os.path.dirname(__file__)+"/../Python" ]+sys.path
-import cPickle as pickle
+import pickle as pickle
 import zlib
 from ezfio import ezfio_obj, ezfio
 
@@ -20,7 +20,7 @@ def main():
     sys.argv.remove("-v")
 
   if len(sys.argv) == 1:
-    print "syntax: %s <EZFIO_Filename>"%(sys.argv[0])
+    print(("syntax: %s <EZFIO_Filename>"%(sys.argv[0])))
     sys.exit(1)
   ezfio_filename = sys.argv[1]
   while ezfio_filename[-1] == "/":
@@ -28,21 +28,19 @@ def main():
 
   ezfio.set_filename(ezfio_filename)
 
-  get_functions = filter(
-    lambda x: x.startswith("has_"),
-    ezfio_obj.__dict__.keys() )
+  get_functions = [x for x in list(ezfio_obj.__dict__.keys()) if x.startswith("has_")]
 
   d = {}
   for f in get_functions:
     f_name = f[4:]
     try:
-      exec """d['%s'] = ezfio.%s"""%(f_name,f_name)
+      exec("""d['%s'] = ezfio.%s"""%(f_name,f_name))
     except:
       if do_verbose:
-        print "%-40s [%5s]"%(f_name, "Empty")
+        print(("%-40s [%5s]"%(f_name, "Empty")))
     else:
       if do_verbose:
-        print "%-40s [%5s]"%(f_name, " OK  ")
+        print(("%-40s [%5s]"%(f_name, " OK  ")))
 
   dump = zlib.compress(pickle.dumps(d))
   file = open(ezfio_filename+".ezar","w")

bin/unarchive_ezfio.py

@@ -1,9 +1,9 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 
 import sys
 import os
 sys.path = [ os.path.dirname(__file__)+"/../Python" ]+sys.path
-import cPickle as pickle
+import pickle as pickle
 import zlib
 from ezfio import ezfio_obj, ezfio
 
@@ -15,7 +15,7 @@ ezfio.error = f
 
 def main():
   if len(sys.argv) == 1:
-    print "syntax: %s <EZFIO_Archive.ezar>"%(sys.argv[0])
+    print(("syntax: %s <EZFIO_Archive.ezar>"%(sys.argv[0])))
     sys.exit(1)
   ezfio_filename = sys.argv[1].split(".ezar")[0]
 
@@ -27,7 +27,7 @@ def main():
 
   d = pickle.loads(zlib.decompress(dump))
 
-  set_functions = d.keys()
+  set_functions = list(d.keys())
 
   nerrors_old = len(d)+1
   nerrors = nerrors_old+1
@@ -37,15 +37,15 @@ def main():
     failed = []
     for f_name in set_functions:
       try:
-        exec """ezfio.%s = d['%s']"""%(f_name,f_name)
+        exec("""ezfio.%s = d['%s']"""%(f_name,f_name))
       except:
         nerrors += 1
         failed.append(f_name)
 
   if nerrors != 0:
-    print "Unarchive failed:"
+    print("Unarchive failed:")
     for i in failed:
-      print i
+      print(i)
     sys.exit(1)
 
 if __name__ == "__main__":

build.ninja

@@ -1,31 +0,0 @@
-include version
-
-rule build_generated_ninja
-   command = python2 configure.py
-   description = Creating generated.ninja
-
-rule run_ninja
-   command = bash -c 'source .make.config.sh ; $$NINJA -f $in'
-   description = Building Fortran library
-   pool = console
-
-rule build_archive
-   command = git archive --format=tar HEAD > EZFIO.${VERSION}.tar && mkdir -p EZFIO && cd EZFIO && tar -xvf ../EZFIO.${VERSION}.tar && cd .. && rm EZFIO.${VERSION}.tar && tar -zcvf EZFIO.${VERSION}.tar.gz EZFIO && rm -rf EZFIO
-   description = Building archive
-
-rule clean_all
-   command = bash -c 'source .make.config.sh ; bash -c "$$NINJA -f $in -t clean ; $$NINJA -t clean" ; rm -rf src/IRPF90_{temp,man} src/*.pyc'
-   description = Cleaning directory
-
-
-build make.config .make.config.sh generated.ninja impossible_target: build_generated_ninja
-
-build all: run_ninja generated.ninja
-
-default all
-
-build EZFIO.${VERSION}.tar.gz: build_archive 
-
-build archive: phony EZFIO.${VERSION}.tar.gz
-
-build clean: clean_all generated.ninja

configure.py

@@ -1,146 +0,0 @@
-#!/usr/bin/env python2
-
-import os,sys
-
-def write_if_different(filename,s):
-  try:
-    with open(filename, "r") as f:
-        ref = f.read()
-  except:
-    ref = ""
-
-  if ref == s:
-      return
-  else:
-      with open(filename, "w") as f:
-        f.write(s)
-    
-  
-with open("version",'r') as f:
-    version = f.read().strip().rsplit('=')[1]
-
-d_default = {
-  "VERSION" : version,
-  "IRPF90" : 'irpf90',
-  "FC" : 'gfortran -g -ffree-line-length-none -fPIC -fopenmp',
-  "FCFLAGS" : '-O2',
-  "RANLIB" : 'ranlib',
-  "AR" : 'ar',
-  "BUILD_SYSTEM" : 'make',
-  "NINJA" : 'ninja',
-}
-
-CONFIG_FILES=' '.join([ os.path.join("config",x) for x in os.listdir('config') if x != '.empty'])
-
-def create_make_config():
-
-    try:
-        d = read_make_config()
-    except:
-        d = {}
-
-    fmt = { "make.config" :'{0}={1}\n' , 
-            ".make.config.sh": 'export {0}="{1}"\n' }
-    
-    for var,default in d_default.iteritems():
-        if var not in d:
-            try:
-                cur = os.environ[var] 
-            except KeyError:
-                cur = default
-            d[var]=cur
-        
-    for filename in fmt:
-        out = ""
-        for var,default in d_default.iteritems():
-            cur = d[var]
-            out += fmt[filename].format(var,cur)
-        write_if_different(filename,out)
-    
-    return d
-
-
-
-def read_make_config():
-    result = {}
-    with open("make.config",'r') as f:
-        for line in f.readlines():
-          try:
-            key, value = line.strip().split('=',1)
-          except:
-            print "Error in make.config:"
-            print line
-            sys.exit(1)
-          result[key] = value
-    return result
-
-
-def create_build_ninja():
-    
-    d=create_make_config()
-
-    d["irpf90_files"] = [ "src/{0}".format(x) for x in
-        """
-        IRPF90_temp/build.ninja irpf90.make irpf90_entities
-        tags libezfio_groups-gen.py libezfio_util-gen.py
-        """.split() ] 
-
-    d["irpf90_sources"] = [ "src/{0}".format(x) for x in
-        """
-        libezfio_error.irp.f create_ocaml.py groups_templates.py
-        libezfio_file.irp.f create_python.py 
-        libezfio_groups.irp.f ezfio-head.py  
-        libezfio_util.irp.f ezfio-tail.py read_config.py 
-        f_types.py test.py groups.py 
-        """.split() ] + [ "make.config" ]
-
-    d["irpf90_files"] = ' '.join(d["irpf90_files"])
-    d["irpf90_sources"] = ' '.join(d["irpf90_sources"])
-        
-
-    template = """
-
-rule compile_irpf90
-   command = bash -c 'source .make.config.sh ; cd src ; {IRPF90} --ninja'
-   description = Compiling IRPF90
-
-rule build_irpf90_a
-   command = {NINJA} -C src/IRPF90_temp && touch $out
-   description = Compiling Fortran files
-
-rule build_libezfio_a
-   command = cp src/IRPF90_temp/irpf90.a lib/libezfio.a ; {RANLIB} lib/libezfio.a
-   description = Building libezfio.a
-
-rule build_libezfio_irp_a
-   command = cp lib/libezfio.a lib/libezfio_irp.a ; {AR} dv lib/libezfio_irp.a irp_stack.irp.o > /dev/null ; {RANLIB} lib/libezfio_irp.a
-   description = Building libezfio_irp.a
-
-rule build_python
-   command = cd src ; python2 create_python.py
-   description = Building Python module
-
-rule build_ocaml
-   command = cd src ; python2 create_ocaml.py
-   description = Building Ocaml module
-
-build {irpf90_files}: compile_irpf90 | {irpf90_sources} {CONFIG_FILES}
-
-build src/IRPF90_temp/irpf90.a: build_irpf90_a | {irpf90_files}
-
-build lib/libezfio.a: build_libezfio_a | src/IRPF90_temp/irpf90.a
-
-build lib/libezfio_irp.a: build_libezfio_irp_a | lib/libezfio.a
-
-build Python/ezfio.py: build_python | lib/libezfio.a
-
-build Ocaml/ezfio.ml: build_ocaml | lib/libezfio.a
-
-"""
-    d["CONFIG_FILES"] = CONFIG_FILES
-    write_if_different('generated.ninja',template.format(**d))
-
-
-if __name__ == '__main__':
-
-    create_build_ninja()

git-tools/commit-msg

@@ -1,4 +1,4 @@
-#!/usr/bin/python2
+#!/usr/bin/python3
 
 import os,sys 
 ROOT = os.path.dirname(__file__)+'/../../'
@@ -6,7 +6,7 @@ file = open(ROOT+'version','r')
 lines = file.readlines() 
 file.close() 
 file = open(sys.argv[1],'a')
-print >>file, 'Version:'+lines[0].split('=')[1]
+print('Version:'+lines[0].split('=')[1], file=file)
 file.close()
 
 

git-tools/install_tools.sh

@@ -5,6 +5,6 @@ cd ../.git/hooks/
 
 for i in commit-msg post-commit
 do
-  rm $i
+  rm --force --  $i
   ln -s $OLD_DIR/$i $PWD/$i
 done

git-tools/post-commit

@@ -1,4 +1,4 @@
-#!/usr/bin/python2
+#!/usr/bin/python3
 
 import os
 ROOT = os.path.dirname(__file__)+'/../../'
@@ -6,7 +6,7 @@ ROOT = os.path.dirname(__file__)+'/../../'
 file = open(ROOT+'version','r') ;
 lines = file.readlines() ;
 file.close() ;
-v = map(int,lines[0].split('=')[1].split('.'));
+v = list(map(int,lines[0].split('=')[1].split('.')));
 
 v[2] += 1
 lines[0] = "VERSION=%d.%d.%d\n"%tuple(v)

make.config

@@ -0,0 +1,9 @@
+VERSION ?= 2.0.7
+RANLIB  ?= ranlib
+IRPF90  ?= irpf90
+CC      ?= gcc
+FC      ?= gfortran -g -ffree-line-length-none -fPIC
+FCFLAGS ?= -fPIC
+ARCHIVE ?= ar crs
+RANLIB  ?= ranlib
+PYTHON  ?= python3

src/Makefile

@@ -29,7 +29,7 @@ export
 
 include irpf90.make
 
-irpf90.make: $(wildcard *.irp.f) ../config/* 
+irpf90.make: $(wildcard *.irp.f) ../config/* IRPF90_temp/system.o IRPF90_temp/system_f.o 
 	$(IRPF90)
 
 include ../version
@@ -40,22 +40,29 @@ all: static ../Python/ezfio.py ../Ocaml/ezfio.ml
 
 static: ../lib/libezfio.a ../lib/libezfio_irp.a
 
+IRPF90_temp/system.o: system.c
+	mkdir -p IRPF90_temp/
+	$(CC) -c system.c -o IRPF90_temp/system.o
+
+IRPF90_temp/system_f.o: system_f.f90
+	mkdir -p IRPF90_temp/
+	$(FC) -c system_f.f90 -o IRPF90_temp/system_f.o && cp system.mod IRPF90_temp/
+
 ../lib/libezfio.a: IRPF90_temp/irpf90.a
 	rm -f ../lib/libezfio.a
-	$(AR) cru ../lib/libezfio.a $(OBJ1)
+	$(ARCHIVE) ../lib/libezfio.a IRPF90_temp/system_f.o IRPF90_temp/system.o $(OBJ1)  
 	$(RANLIB) ../lib/libezfio.a
 
 ../lib/libezfio_irp.a: ../lib/libezfio.a
 	rm -f ../lib/libezfio_irp.a
-	cp ../lib/libezfio.a ../lib/libezfio_irp.a
-	$(AR) dv ../lib/libezfio_irp.a irp_stack.irp.o
+	$(ARCHIVE) ../lib/libezfio_irp.a IRPF90_temp/system_f.o IRPF90_temp/system.o $(filter-out IRPF90_temp/irp_stack.irp.o, $(OBJ1) )
 	$(RANLIB) ../lib/libezfio_irp.a
 
 
 ../Python/ezfio.py: ../lib/libezfio.a
-	python2 create_python.py
+	$(PYTHON) create_python.py
 
 ../Ocaml/ezfio.ml: ../lib/libezfio.a
-	python2 create_ocaml.py
+	$(PYTHON) create_ocaml.py
 
 

src/create_ocaml.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 #   EZFIO is an automatic generator of I/O libraries
 #   Copyright (C) 2009 Anthony SCEMAMA, CNRS
 #
@@ -46,7 +46,7 @@ def run():
   
   for group in groups.keys():
      for var,type,dims,command in groups[group]:
-       if command is not "":
+       if command != "":
          continue
        dims_py = str(dims)
        for g in groups.keys():

src/create_python.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 #   EZFIO is an automatic generator of I/O libraries
 #   Copyright (C) 2009 Anthony SCEMAMA, CNRS
 #

src/ezfio-head.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 #   EZFIO is an automatic generator of I/O libraries
 #   Copyright (C) 2009 Anthony SCEMAMA, CNRS
 #
@@ -25,10 +25,11 @@
 
 import os, sys
 import time
-import cStringIO as StringIO
+import io as StringIO
 from gzip import GzipFile
 import tempfile
 import threading
+from functools import reduce
 
 def version(x):
   b = [int(i) for i in x.split('.')]
@@ -40,7 +41,7 @@ def size(x):
 def flatten(l):
   res = []
   for i in l:
-    if hasattr(i, "__iter__") and not isinstance(i, basestring):
+    if hasattr(i, "__iter__") and not isinstance(i, str):
       res.extend(flatten(i))
     else:
       res.append(i)
@@ -101,7 +102,7 @@ def get_conv(type):
       else:
         raise TypeError
   elif type == "ch":
-    conv = lambda x: x.strip()
+    conv = lambda x: x.decode('utf-8').strip() if isinstance(x,bytes) else x.strip()
   else:
     raise TypeError
   return conv
@@ -149,18 +150,18 @@ class ezfio_obj(object):
     except OSError:
       pass
     file = open(path.strip()+'/.version','w')
-    print >>file,self.version
+    print(self.version, file=file)
     file.close()
 
   def error(self,where,txt):
-    print '------------------------------------------------------------'
-    print 'EZFIO File     : '+self.filename
-    print 'EZFIO Error in : '+where.strip()
-    print '------------------------------------------------------------'
-    print ''
-    print txt.strip()
-    print ''
-    print '------------------------------------------------------------'
+    print('------------------------------------------------------------')
+    print('EZFIO File     : '+self.filename)
+    print('EZFIO Error in : '+where.strip())
+    print('------------------------------------------------------------')
+    print('')
+    print(txt.strip())
+    print('')
+    print('------------------------------------------------------------')
     raise IOError
 
   def get_filename(self):
@@ -233,7 +234,7 @@ echo %s > %s/ezfio/library"""%(filename,filename,self.LIBRARY,filename))
 
     indices = []
     values = []
-    for i in xrange(isize):
+    for i in range(isize):
       try:
         line = self.file.readline().split()
       except:
@@ -250,7 +251,7 @@ echo %s > %s/ezfio/library"""%(filename,filename,self.LIBRARY,filename))
     if self.buffer_rank == -1:
       self.error('write_buffer','No buffered file is open.')
 
-    for i in xrange(isize):
+    for i in range(isize):
      for j in indices[i]:
        self.file.write("%4d "%(j,))
      self.file.write("%24.15e\n"%(values[i],))

src/ezfio-tail.py

@@ -32,7 +32,7 @@ def main():
   try:
     EZFIO_FILE = os.environ["EZFIO_FILE"]
   except KeyError:
-    print "EZFIO_FILE not defined"
+    print("EZFIO_FILE not defined")
     return 1
 
   ezfio.set_file(EZFIO_FILE)
@@ -42,7 +42,7 @@ def main():
   try:
     f = getattr(ezfio,command)
   except AttributeError:
-    print "{0} not found".format(command)
+    print("{0} not found".format(command))
     return 1
 
   if command.startswith('has'):
@@ -56,12 +56,18 @@ def main():
 
   elif command.startswith('set'):
       text = sys.stdin.read()
+      true  = True
+      false = False
+      TRUE  = True
+      FALSE = False
+      T = True
+      F = False
       try:
           data = eval(text)
       except NameError:
           data = text
       except:
-          print "Syntax Error"
+          print("Syntax Error")
           return 1
       if data is None:
           data = "None"

src/ezfio.ml

@@ -1,26 +1,26 @@
 (*
     EZFIO is an automatic generator of I/O libraries
     Copyright (C) 2009 Anthony SCEMAMA, CNRS
- 
+
     This program 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 2 of the License, or
     (at your option) any later version.
- 
+
     This program 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, write to the Free Software Foundation, Inc.,
     51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- 
+
     Anthony Scemama
     LCPQ - IRSAMC - CNRS
     Universite Paul Sabatier
-    118, route de Narbonne      
-    31062 Toulouse Cedex 4      
+    118, route de Narbonne
+    31062 Toulouse Cedex 4
     scemama@irsamc.ups-tlse.fr
 *)
 
@@ -31,39 +31,39 @@ Exceptions
 ==========
 *)
 
-exception Read_only of string;;
+exception Read_only of string
 
 (*
 State variables
 ===============
 *)
-let read_only = ref false;;
-let ezfio_filename = ref "EZFIO_File";;
+let read_only = ref false
+let ezfio_filename = ref "EZFIO_File"
 
-(* 
+(*
 Helper functions
 =================
 *)
 
 let check_readonly =
   if !read_only then
-    raise (Read_only "Read only attribute is set");
-;;
+    raise (Read_only "Read only attribute is set")
+
 
 let exists path =
-  let filename = path^"/.version" in
+  let filename = Filename.concat path ".version" in
   Sys.file_exists filename
-;;
- 
+
+
 let has group name =
-  let dirname = !ezfio_filename ^ "/" ^ group in
+  let dirname = Filename.concat !ezfio_filename group in
   if (exists dirname) then
-    (Sys.file_exists (dirname ^ "/" ^ name) )
+    Sys.file_exists @@ Filename.concat dirname name
   else
     false
-;;
 
-let has_array group name = has group (name^".gz");;
+
+let has_array group name = has group (name^".gz")
 
 let mkdir path =
   check_readonly;
@@ -72,99 +72,59 @@ let mkdir path =
   Unix.mkdir path 0o777;
   let out_channel = open_out (path^"/.version") in
   Printf.fprintf out_channel "%s\n" version ;
-  close_out out_channel;
-;;
+  close_out out_channel
+
 
 let create_group group =
-  let dirname = !ezfio_filename ^ "/" ^ group in
+  let dirname = Filename.concat !ezfio_filename group in
   if not (exists dirname) then
-      mkdir dirname;
-;;
+      mkdir dirname
 
-let split line s = 
-  let rec do_work lst word = function
-  | 0 -> word::lst
-  | i -> 
-    begin
-      match line.[i-1] with
-      | a when a == s ->
-        if word <> "" then 
-           do_work (word::lst) "" (i-1) 
-        else
-           do_work lst "" (i-1) 
-      | a -> do_work lst ( (Char.escaped a)^word) (i-1)
-    end
-  in do_work [] "" (String.length line) 
-;;
 
-let ltrim s =
-  let rec do_work s l = 
-  match s.[0] with
-  | '\n' 
-  | ' ' -> do_work (String.sub s 1 (l-1)) (l-1)
-  | _ -> s
-  in
-  let l = String.length s in
-  if (l > 0) then do_work s l
-  else s
-;;
 
-let rtrim s =
-  let rec do_work s l = 
-  let newl = l-1 in
-  match s.[newl] with
-  | '\n'
-  | ' ' -> do_work (String.sub s 0 (newl)) (newl)
-  | _ -> s
-  in
-  let l = String.length s in
-  if (l > 0) then do_work s l
-  else s
-;;
-
-let trim s = ltrim (rtrim s) ;;
-
-let maxval l = 
+let maxval l =
   match l with
   | [] -> None
   | [a] -> Some a
   | hd::tail -> Some (List.fold_left max hd tail)
-;;
 
-let minval l = 
+
+let minval l =
   match l with
   | [] -> None
   | [a] -> Some a
   | hd::tail -> Some (List.fold_left min hd tail)
-;;
 
-let at arr idx = arr.(idx);;
 
-let size (_) = 0;;
+let at arr idx = arr.(idx)
+
+(*
+let size (_) = 0
+*)
 
 let n_count_ch (str,_,v) =
   let rec do_work accu = function
   | 0 -> accu
-  | i -> 
-    let newaccu = 
+  | i ->
+    let newaccu =
       if str.[i-1] == v then accu+1
-      else accu 
+      else accu
     in do_work newaccu (i-1)
   in do_work 0 (String.length str)
-;;
+
 
 let n_count (l,_,v) =
   let rec do_work accu = function
   | []  -> accu
-  | h::tail -> 
-    let newaccu = 
+  | h::tail ->
+    let newaccu =
       if h == v then accu+1
-      else accu 
+      else accu
     in do_work newaccu tail
   in do_work 0 l
-;;
 
-(* 
+
+(*
 Scalars
 =======
 *)
@@ -175,32 +135,32 @@ Read
 *)
 
 let read_scalar type_conversion group name =
-  let in_filename = !ezfio_filename ^ "/" ^ group ^ "/" ^ name in
+  let in_filename = Filename.concat !ezfio_filename @@ Filename.concat group name in
   let in_channel = open_in in_filename in
-  let trimmed_line = trim (input_line in_channel) in
+  let trimmed_line = String.trim (input_line in_channel) in
   let result = type_conversion trimmed_line in
   begin
     close_in in_channel ;
     result
   end
-;;
+
 
 let fortran_bool_of_string = function
   | "T" | "t" -> true
   | "F" | "f" -> false
   | x -> raise (Failure ("fortran_bool_of_string should be T or F: "^x))
-;;
+
 
 let fortran_string_of_bool = function
  | true -> "T\n"
  | false-> "F\n"
-;;
 
-let read_int   = read_scalar   int_of_string ;;
-let read_int64 = read_scalar Int64.of_string ;;
-let read_float = read_scalar float_of_string ;;
-let read_string= read_scalar (fun (x:string) -> x);;
-let read_bool  = read_scalar fortran_bool_of_string;;
+
+let read_int   = read_scalar   int_of_string
+let read_int64 = read_scalar Int64.of_string
+let read_float = read_scalar float_of_string
+let read_string= read_scalar (fun (x:string) -> x)
+let read_bool  = read_scalar fortran_bool_of_string
 
 (*
 Write
@@ -208,28 +168,28 @@ Write
 *)
 
 let print_int    out_channel i = Printf.fprintf out_channel "%20d\n" i
-and print_int64  out_channel i = Printf.fprintf out_channel "%20Ld\n" i
-and print_float  out_channel f = Printf.fprintf out_channel "%24.15e\n" f
-and print_string out_channel s = Printf.fprintf out_channel "%s\n" s
-and print_bool   out_channel b = Printf.fprintf out_channel "%s\n" (fortran_string_of_bool b);;
+let print_int64  out_channel i = Printf.fprintf out_channel "%20Ld\n" i
+let print_float  out_channel f = Printf.fprintf out_channel "%24.15e\n" f
+let print_string out_channel s = Printf.fprintf out_channel "%s\n" s
+let print_bool   out_channel b = Printf.fprintf out_channel "%s\n" (fortran_string_of_bool b)
 
 let write_scalar print_fun group name s =
   check_readonly;
   create_group group;
-  let out_filename = !ezfio_filename ^ "/" ^ group ^ "/" ^ name in
+  let out_filename = Filename.concat !ezfio_filename @@ Filename.concat group name in
   let out_channel = open_out out_filename in
   begin
      print_fun out_channel s;
-     close_out out_channel;
+     close_out out_channel
   end
-;;
-  
+
+
 let write_int    = write_scalar print_int
-and write_int64  = write_scalar print_int64
-and write_float  = write_scalar print_float
-and write_bool   = write_scalar print_bool
-and write_string = write_scalar print_string
-;;
+let write_int64  = write_scalar print_int64
+let write_float  = write_scalar print_float
+let write_bool   = write_scalar print_bool
+let write_string = write_scalar print_string
+
 
 
 
@@ -239,9 +199,9 @@ Arrays
 *)
 
 type 'a ezfio_data =
-| Ezfio_item of 'a array 
+| Ezfio_item of 'a array
 | Ezfio_data of ('a ezfio_data) array
-;;
+
 
 
 type 'a ezfio_array =
@@ -249,14 +209,38 @@ type 'a ezfio_array =
   dim  : int array;
   data : 'a ezfio_data ;
 }
-;;
+
+let ezfio_array_of_array ~rank ~dim ~data =
+  assert (rank > 0);
+  let read_1d data nmax =
+    (Ezfio_item (Array.sub data 0 nmax), Array.sub data nmax ((Array.length data) - nmax))
+  in
+  let rec read_nd data = function
+    | m when m<1 -> raise (Failure "dimension should not be <1")
+    | 1 -> read_1d data dim.(0)
+    | m ->
+      let rec do_work accu data = function
+      | 0 -> (Array.of_list (List.rev accu), data)
+      | n ->
+        let (newlist,rest) = read_nd data (m-1) in
+        do_work (newlist::accu) rest (n-1)
+      in
+      let (data,rest) = do_work [] data dim.(m-1) in
+      (Ezfio_data data,rest)
+  in
+  let (result,_) = read_nd data rank in
+  { rank= rank;
+    dim=  dim;
+    data=result;
+  }
+
 
 let ezfio_array_of_list ~rank ~dim ~data =
   assert (rank > 0);
   let read_1d data nmax =
     let rec do_work accu data = function
     | 0 -> (Array.of_list (List.rev accu), data)
-    | n -> 
+    | n ->
       begin
         match data with
         | x::rest -> do_work (x::accu) rest (n-1)
@@ -277,25 +261,25 @@ let ezfio_array_of_list ~rank ~dim ~data =
         do_work (newlist::accu) rest (n-1)
       in
       let (data,rest) = do_work [] data dim.(m-1) in
-      (Ezfio_data data,rest) 
-  in    
+      (Ezfio_data data,rest)
+  in
   let (result,_) = read_nd data rank in
   { rank= rank;
     dim=  dim;
     data=result;
   }
-;;
+
 
 
 let ezfio_get_element { rank=r ; dim=d ; data=data } coord =
   (*assert ((List.length coord) == r);*)
   let rec do_work buffer = function
-  | [c] -> 
+  | [c] ->
     begin match buffer with
     | Ezfio_item buffer -> buffer.(c)
     | Ezfio_data buffer -> raise (Failure "Error in ezfio_get_element")
     end
-  | c::tail -> 
+  | c::tail ->
     begin match buffer with
     | Ezfio_item buffer -> raise (Failure "Error in ezfio_get_element")
     | Ezfio_data buffer -> do_work buffer.(c) tail
@@ -303,7 +287,7 @@ let ezfio_get_element { rank=r ; dim=d ; data=data } coord =
   | [] -> raise (Failure "Error in ezfio_get_element")
   in
   do_work data coord
-;;
+
 
 
 let flattened_ezfio { rank ; dim ; data } =
@@ -327,9 +311,9 @@ let flattened_ezfio { rank ; dim ; data } =
   in
 
   match data with
-  | Ezfio_item d -> d
-  | Ezfio_data d -> flatten_n rank d
-;;
+    | Ezfio_item d -> d
+    | Ezfio_data d -> flatten_n rank d
+
 
 
 (*
@@ -337,48 +321,36 @@ Read
 ----
 *)
 
-let unzipped_filename filename =
-  if not (Sys.file_exists filename) then
-    raise (Failure ("file "^filename^" doesn't exist"));
-  let uz_filename = Filename.temp_file "" ".tmp" ~temp_dir:(Sys.getcwd ()) in
-  let command = "zcat "^filename^" > "^uz_filename
-  in
-  if (Sys.command command) == 0  then
-    uz_filename
-  else
-    begin
-     Sys.remove uz_filename ;
-     raise (Failure ("Unable to execute :\n"^command))
-    end
-;;
-
 let read_rank in_channel =
-    let trimmed_line = trim (input_line in_channel) in
-    int_of_string trimmed_line 
-;;
+    let trimmed_line = String.trim (input_line in_channel) in
+    int_of_string trimmed_line
+
 
 let read_dimensions in_channel =
-    let trimmed_line = trim (input_line in_channel) in
-    let list_of_str = split trimmed_line ' ' in
-    Array.of_list (List.map int_of_string list_of_str)
-;;
+    let line = input_line in_channel in
+    let arr_of_str  =
+      String.split_on_char ' ' line
+      |> List.filter (fun x -> x <> "")
+      |> Array.of_list
+    in
+    Array.map int_of_string arr_of_str
+
 
 
 let read_array type_conversion group name : 'a ezfio_array =
-  let in_filename = !ezfio_filename ^ "/" ^ group ^ "/" ^ name ^ ".gz" in
-  let uz_filename = unzipped_filename in_filename in
-  let in_channel = open_in uz_filename in
+  let in_filename = (Filename.concat !ezfio_filename @@ Filename.concat group name) ^ ".gz" in
+  let in_channel = Unix.open_process_in ("zcat "^in_filename) in
   (* Read rank *)
-  let rank = read_rank in_channel 
+  let rank = read_rank in_channel
   (* Read dimensions *)
-  and dimensions = read_dimensions in_channel 
+  and dimensions = read_dimensions in_channel
   in
   begin
       assert (rank == Array.length dimensions) ;
       (* Read one-dimensional arrays *)
-      let read_1d nmax = 
+      let read_1d nmax =
         Ezfio_item (Array.init nmax (fun i->
-          let buffer = trim (input_line in_channel) in
+          let buffer = String.trim (input_line in_channel) in
           try type_conversion buffer with
           | Failure s -> failwith (s^": "^buffer)))
       in
@@ -386,10 +358,10 @@ let read_array type_conversion group name : 'a ezfio_array =
       let rec read_nd = function
         | m when m<1 -> raise (Failure "dimension should not be <1")
         | 1 -> read_1d dimensions.(0)
-        | m -> 
+        | m ->
           let rec do_work accu = function
           | 0 -> Array.of_list (List.rev accu)
-          | n -> 
+          | n ->
             let newlist = read_nd (m-1) in
             do_work (newlist::accu) (n-1)
           in
@@ -399,20 +371,20 @@ let read_array type_conversion group name : 'a ezfio_array =
          rank = rank ;
          dim = dimensions ;
          data = read_nd rank ;
-      } 
+      }
       in
-      close_in in_channel ;
-      Sys.remove uz_filename ;
-      result;
+      match Unix.close_process_in in_channel with
+        | Unix.WEXITED _ -> result
+        | _ -> failwith ("Failed in reading compressed file "^in_filename)
   end
-;;
-  
+
+
 let read_int_array    = read_array          int_of_string
-and read_int64_array  = read_array        Int64.of_string
-and read_float_array  = read_array        float_of_string
-and read_bool_array   = read_array fortran_bool_of_string
-and read_string_array = read_array (fun (x:string) -> x)
-;;
+let read_int64_array  = read_array        Int64.of_string
+let read_float_array  = read_array        float_of_string
+let read_bool_array   = read_array fortran_bool_of_string
+let read_string_array = read_array (fun (x:string) -> x)
+
 
 (*
 Write
@@ -422,32 +394,29 @@ Write
 let write_array print_fun group name a =
   check_readonly;
   create_group group;
-  let out_filename = !ezfio_filename ^ "/" ^ group ^ "/" ^ name ^".gz" in
-  let uz_filename = Filename.temp_file "" ".tmp" ~temp_dir:(Sys.getcwd ()) in
-  let out_channel = open_out uz_filename in
+  let out_filename = (Filename.concat !ezfio_filename @@ Filename.concat group name)^".gz" in
+  let command = "gzip > "^out_filename in
+  let out_channel = Unix.open_process_out command in
   let { rank=rank ; dim=dimensions ; data=data } = a in
-  let data = flattened_ezfio a 
-  in
+  let data = flattened_ezfio a in
   begin
      (* Write rank *)
      Printf.fprintf out_channel "%3d\n" rank;
      (* Write dimensions *)
      Array.iter (Printf.fprintf out_channel "%20d ") dimensions;
-     Printf.fprintf out_channel "\n";
+     Printf.fprintf out_channel "\n%!";
      Array.iter (print_fun out_channel) data;
-     close_out out_channel ;
-     let command = "gzip -c < "^uz_filename^" > "^out_filename
-     in
-     if (Sys.command command == 0) then (Sys.remove uz_filename )
-     else raise (Failure ("command failed:\n"^command))
+     match Unix.close_process_out out_channel with
+      | Unix.WEXITED _ -> ()
+      | _ -> failwith ("Failed writing compressed file "^out_filename)
   end
-;;
+
 
 let write_int_array    = write_array print_int
-and write_int64_array  = write_array print_int64
-and write_float_array  = write_array print_float
-and write_string_array = write_array print_string
-and write_bool_array   = write_array print_bool;;
+let write_int64_array  = write_array print_int64
+let write_float_array  = write_array print_float
+let write_string_array = write_array print_string
+let write_bool_array   = write_array print_bool
 
 (*
 Library routines
@@ -457,7 +426,7 @@ let set_file filename =
   if not (exists filename) then
   begin
     mkdir filename;
-    mkdir (filename^"/ezfio");
+    mkdir (Filename.concat filename "ezfio");
     let command = Printf.sprintf "
       LANG= date > %s/ezfio/creation
       echo $USER > %s/ezfio/user
@@ -467,7 +436,7 @@ let set_file filename =
       raise (Failure ("Unable to create new ezfio file:\n"^filename))
   end ;
   ezfio_filename := filename
-;;
+
 
 
 (*$TAIL*)

src/f_types.py

@@ -27,7 +27,7 @@ format= {
  'integer'         : ["'(I20)'", "%20d"],
  'real'            : ["'(E24.15)'","%24.15E"],
  'double precision': ["'(E24.15)'","%24.15E"],
- 'logical'         : ["'(L)'","%c"],
+ 'logical'         : ["'(L1)'","%c"],
  'character*(*)'   : ["'(A)'","%s"]
  }
 

src/groups.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 #   EZFIO is an automatic generator of I/O libraries
 #   Copyright (C) 2009 Anthony SCEMAMA, CNRS
 #
@@ -34,26 +34,26 @@ file = open("../version","r")
 v = file.readline()
 file.close()
 v = v.split('=')[1].strip()
-print >>file_py, """
+print("""
   def get_version(self):
     return '%s'
   version = property(fset=None,fget=get_version)
-"""%(v)
+"""%(v), file=file_py)
 
 import sys
 
-for group in groups.keys():
-  print path%{ 'group' : group }
-  print >>file_py, path_py%{ 'group' : group }
+for group in list(groups.keys()):
+  print(path%{ 'group' : group })
+  print(path_py%{ 'group' : group }, file=file_py)
   for var,type,dims,command in groups[group]:
     command_py = command
     dims_py = str(dims)
-    for g in groups.keys():
-      command_py = command_py.replace(g,'self.'+g)
-      dims_py = dims_py.replace(g,'self.'+g)
+    for g in list(groups.keys()):
+      command_py = re.sub("(\W)"+g, r"\1self."+g, command_py)
+      dims_py = dims_py.replace("(\W)"+g,r'\1self.'+g)
     var = var.lower()
     group = group.lower()
-    strdims = tuple(map(lambda x: '('+str(x)+')',dims))
+    strdims = tuple(['('+str(x)+')' for x in dims])
     strdims = str(strdims).replace("'","")
     if len(dims) == 1:
       strdims = strdims[:-2]+")"
@@ -76,8 +76,8 @@ for group in groups.keys():
               'var': var,
               'group': group,
               'dims': strdims}
-        print attributes%d
-        print >>file_py, attributes_py%d
+        print(attributes%d)
+        print(attributes_py%d, file=file_py)
       else:
         d = { 'type': type,
               'var': var,
@@ -88,15 +88,15 @@ for group in groups.keys():
               'expr_py': command_py}
         buffer = calculated%d
         buffer = re.sub(r"at\((.*),(.*)\)",r'\1(\2)',buffer)
-        print buffer
-        print >>file_py, calculated_py%d
+        print(buffer)
+        print(calculated_py%d, file=file_py)
     elif type == "buffered":
       d = { 'group': group,
             'var': var,
             'dims_py': dims_py,
             'dims': dims }
-      print buffered%d
-      print >>file_py, buffered_py%d
+      print(buffered%d)
+      print(buffered_py%d, file=file_py)
     else:
       dims_loop = ''
       copy_loop = ''
@@ -107,7 +107,7 @@ for group in groups.keys():
       declar_loop = declar_loop[:-1]
       for k,d in enumerate(dims):
         dims_loop += "  dims("+str(k+1)+") = "+str(d)+"\n"
-        dims_loop_py += "    dims["+str(k)+"] = "+str(d)+"\n"
+        dims_loop_py += "    dims["+str(k)+"] = int("+str(d)+")\n"
       for k,d in enumerate(dims):
         copy_loop += k*" "+"  do i"+str(k+1)+"=1,"+str(d)+'\n'
       copy_loop += (k+1)*" "+"  %(var)s ("
@@ -119,7 +119,7 @@ for group in groups.keys():
       copy_loop = copy_loop[:-1]%{'var': var,'group': group} + ")\n"
       for k,d in enumerate(dims):
         copy_loop += (len(dims)-k-1)*" "+"  enddo\n"
-      for g in groups.keys():
+      for g in list(groups.keys()):
         dims_loop_py = dims_loop_py.replace(" "+g,' self.'+g)
         dims_loop_py = dims_loop_py.replace("*"+g,'*self.'+g)
         dims_loop_py = dims_loop_py.replace("/"+g,'/self.'+g)
@@ -140,7 +140,7 @@ for group in groups.keys():
             'dims_loop_py': dims_loop_py,
             'copy_loop': copy_loop,
             'declar_loop' : declar_loop}
-      print attributes_arr%d
-      print >>file_py, attributes_arr_py%d
+      print(attributes_arr%d)
+      print(attributes_arr_py%d, file=file_py)
 
 file_py.close()

src/groups_templates.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 #   EZFIO is an automatic generator of I/O libraries
 #   Copyright (C) 2009 Anthony SCEMAMA, CNRS
 #
@@ -58,23 +58,23 @@ BEGIN_PROVIDER [ %(type)s, %(group)s_%(var)s ]
 
 END_PROVIDER
 
-subroutine ezfio_set_%(group)s_%(var)s(%(var)s)
+subroutine ezfio_set_%(group)s_%(var)s(v)
   implicit none
   BEGIN_DOC
 ! Sets the %(group)s/%(var)s attribute
   END_DOC
-  %(type_set)s :: %(var)s
-  call ezfio_write_%(type_short)s(path_%(group)s,'%(var)s',%(var)s)
+  %(type_set)s :: v
+  call ezfio_write_%(type_short)s(path_%(group)s,'%(var)s',v)
   FREE %(group)s_%(var)s
 end subroutine
 
-subroutine ezfio_get_%(group)s_%(var)s(%(var)s)
+subroutine ezfio_get_%(group)s_%(var)s(v)
   implicit none
   BEGIN_DOC
 ! Gets the %(group)s/%(var)s attribute
   END_DOC
-  %(type)s :: %(var)s
-  %(var)s = %(group)s_%(var)s
+  %(type)s :: v
+  v = %(group)s_%(var)s
 end subroutine
 
 subroutine ezfio_has_%(group)s_%(var)s(result)
@@ -111,30 +111,30 @@ BEGIN_PROVIDER [ %(type)s, %(group)s_%(var)s, %(dims)s ]
 
 END_PROVIDER
 
-subroutine ezfio_set_%(group)s_%(var)s(%(var)s)
+subroutine ezfio_set_%(group)s_%(var)s(v)
   implicit none
   BEGIN_DOC
 ! Sets the %(group)s/%(var)s attribute
   END_DOC
-  %(type_set)s :: %(var)s (*)
+  %(type_set)s :: v (*)
   integer :: rank, dim_max, i
   integer :: dims(10)
   rank = %(rank)s
   character*(1024) :: message
 %(dims_loop)s
   call ezfio_write_array_%(type_short)s(path_%(group)s,'%(var)s', &
-   rank,dims,%(dim_max)s,%(var)s)
+   rank,dims,%(dim_max)s,v)
   FREE %(group)s_%(var)s
 end subroutine
 
-subroutine ezfio_get_%(group)s_%(var)s(%(var)s)
+subroutine ezfio_get_%(group)s_%(var)s(v)
   implicit none
   BEGIN_DOC
 ! Gets the %(group)s/%(var)s attribute
   END_DOC
-  %(type)s, intent(out) :: %(var)s (*)
+  %(type)s, intent(out) :: v (*)
   character*(1024) :: message
-  %(var)s(1: %(dim_max)s ) = reshape ( %(group)s_%(var)s, (/ %(dim_max)s /) )
+  v(1: %(dim_max)s ) = reshape ( %(group)s_%(var)s, (/ %(dim_max)s /) )
 end subroutine
 
 subroutine ezfio_has_%(group)s_%(var)s(result)
@@ -163,13 +163,13 @@ BEGIN_PROVIDER [ %(type)s, %(group)s_%(var)s ]
  %(group)s_%(var)s = %(expr)s
 END_PROVIDER
 
-subroutine ezfio_get_%(group)s_%(var)s(%(var)s)
+subroutine ezfio_get_%(group)s_%(var)s(v)
   implicit none
   BEGIN_DOC
 ! Gets the %(group)s/%(var)s attribute
   END_DOC
-  %(type)s, intent(out) :: %(var)s
-  %(var)s = %(group)s_%(var)s
+  %(type)s, intent(out) :: v
+  v = %(group)s_%(var)s
 end
 
 subroutine ezfio_free_%(group)s_%(var)s()
@@ -345,7 +345,7 @@ attributes_py = """
 attributes_arr_py = """
   def get_%(group)s_%(var)s(self):
     rank = %(rank)s
-    dims = range(rank)
+    dims = list(range(rank))
 %(dims_loop_py)s
     dim_max = 1
     for d in dims:
@@ -359,7 +359,7 @@ attributes_arr_py = """
 
   def set_%(group)s_%(var)s(self,%(var)s):
     rank = %(rank)s
-    dims = range(rank)
+    dims = list(range(rank))
 %(dims_loop_py)s
     dim_max = 1
     for d in dims:

src/libezfio_file.irp.f

@@ -147,6 +147,9 @@ subroutine ezfio_set_file(filename_in)
  END_DOC
 
   character*(*) :: filename_in
+  character(8)  :: date
+  character(73) :: time
+  character(32) :: user
 
   if (filename_in == '') then
     call ezfio_error(irp_here,'EZFIO file name is empty.')
@@ -157,16 +160,16 @@ subroutine ezfio_set_file(filename_in)
   if (.not.exists(libezfio_filename)) then
     call ezfio_mkdir(libezfio_filename)
     call ezfio_mkdir(trim(libezfio_filename)//'/ezfio')
-    call system('LANG= date > '//trim(libezfio_filename)//'/ezfio/creation')
-    call system('echo $USER > '//trim(libezfio_filename)//'/ezfio/user')
-    BEGIN_SHELL [ /usr/bin/env python2 ]
-import os
-command = "'echo %s > '//trim(libezfio_filename)//'/ezfio/library'"
-cwd = os.getcwd()
-cwd = cwd.split('src')[:-1]
-cwd = '/'.join(cwd)
-print "call system("+command%cwd+")"
-    END_SHELL
+
+    ! using keyword arguments
+    call date_and_time(DATE=date,TIME=time)
+    open (unit=73, file=trim(libezfio_filename)//'/ezfio/creation', ACTION='WRITE', STATUS='UNKNOWN')
+    write(73,*) time, ' ', date
+    close(73)
+    open (unit=73, file=trim(libezfio_filename)//'/ezfio/user', ACTION='WRITE', STATUS='UNKNOWN')
+    call getenv('USER',user)
+    write(73,*) user
+    close(73)
   endif
 
   TOUCH libezfio_filename
@@ -178,9 +181,9 @@ subroutine ezfio_finish()
 ! Close all open buffers
  END_DOC
  close(libezfio_iunit)
- BEGIN_SHELL [ /usr/bin/env python2 ]
+ BEGIN_SHELL [ /usr/bin/env python3 ]
 import os
 from zlib import crc32
-print '  call irp_finalize_%s'%(str(abs(crc32(os.getcwd()))))
+print('  call irp_finalize_%s'%(str(abs(crc32(os.getcwd().encode())))))
  END_SHELL
 end

src/libezfio_groups.irp.f

@@ -22,7 +22,7 @@
 !   31062 Toulouse Cedex 4      
 !   scemama@irsamc.ups-tlse.fr
 
-BEGIN_SHELL [ /usr/bin/env python2 ]
+BEGIN_SHELL [ /usr/bin/env python3 ]
 import groups
 END_SHELL
 

src/libezfio_util.irp.f

@@ -22,6 +22,7 @@
 !   31062 Toulouse Cedex 4      
 !   scemama@irsamc.ups-tlse.fr
 
+
  BEGIN_PROVIDER [ integer, PID ]
 &BEGIN_PROVIDER [ character*(256), PID_str ]
   implicit none
@@ -53,6 +54,7 @@ logical function ezfio_exists(path)
 end function
 
 subroutine ezfio_mkdir(path)
+  use system
   implicit none
   BEGIN_DOC
 ! Creates a directory
@@ -63,7 +65,7 @@ subroutine ezfio_mkdir(path)
     call ezfio_error(irp_here,'Read-only file.')
   endif
   if (.not.ezfio_exists(path)) then
-    call system('mkdir '//trim(path))
+    call mkdir(trim(path)//char(0))
     open(unit=libezfio_iunit,file=trim(path)//'/.version')
     write(libezfio_iunit,'(A)') libezfio_version
     close(libezfio_iunit)
@@ -72,6 +74,7 @@ end subroutine
 
 
 subroutine libezfio_openz(filename,mode,err)
+ use system
  implicit none
   BEGIN_DOC
 ! Opens a compressed file
@@ -83,7 +86,7 @@ subroutine libezfio_openz(filename,mode,err)
  err=1
  
  if (mode(1:1) == 'r') then
-   call system('zcat '//trim(filename)//' > '//trim(fifo))
+   call zcat(trim(filename)//char(0), trim(fifo)//char(0))
    open(unit=libezfio_iunit,file=trim(fifo),form='FORMATTED',action='READ')
    err=0
  else if (mode(1:1) == 'w') then
@@ -117,6 +120,7 @@ subroutine libezfio_reopenz_unformatted(filename,mode,err)
 end
 
 subroutine libezfio_closez(filename,mode)
+ use system
  implicit none
   BEGIN_DOC
 ! Closes a compressed file
@@ -126,18 +130,18 @@ subroutine libezfio_closez(filename,mode)
  fifo = trim(filename)//'.'//trim(PID_str)
  if (mode(1:1) == 'w') then
    close(unit=libezfio_iunit)
-   call system('gzip -c < '//trim(fifo)//' > '//trim(filename))
+   call gzip(trim(fifo)//char(0), trim(filename)//char(0))
    open(unit=libezfio_iunit,file=trim(fifo),form='FORMATTED',action='WRITE')
  endif
  close(unit=libezfio_iunit,status='DELETE')
 end
 
 
-BEGIN_SHELL [ /usr/bin/env python2 ]
+BEGIN_SHELL [ /usr/bin/env python3 ]
 from f_types import format, t_short
 
 
-template = """
+template_nowrite = """
 subroutine ezfio_read_%(type_short)s(dir,fil,dat)
   implicit none
   BEGIN_DOC
@@ -216,11 +220,9 @@ subroutine ezfio_read_array_%(type_short)s(dir,fil,rank,dims,dim_max,dat)
     
     allocate (buffer(dim_max))
     read(libezfio_iunit,'(A)') buffer(1:dim_max)
-    !$OMP PARALLEL DO PRIVATE(i)
     do i=1,dim_max
       read(buffer(i),%(fmt)s) dat(i)
     enddo
-    !$OMP END PARALLEL DO
     deallocate(buffer)
     call libezfio_closez(trim(l_filename),'r')
     return
@@ -228,7 +230,9 @@ subroutine ezfio_read_array_%(type_short)s(dir,fil,rank,dims,dim_max,dat)
     call ezfio_error(irp_here,'Attribute '//trim(l_filename)//' is not set')
   endif
 end
+"""
 
+template_write = """
 subroutine ezfio_write_array_%(type_short)s(dir,fil,rank,dims,dim_max,dat)
   implicit none
   BEGIN_DOC
@@ -255,14 +259,11 @@ subroutine ezfio_write_array_%(type_short)s(dir,fil,rank,dims,dim_max,dat)
     write(libezfio_iunit,'(I3)') rank
     write(libezfio_iunit,'(30(I20,X))') dims(1:rank)
     close(unit=libezfio_iunit)
-    
     allocate (buffer(dim_max))
-    !$OMP PARALLEL DO PRIVATE(i)
     do i=1,dim_max
       write(buffer(i)(1:24), %(fmt)s) dat(i)
       buffer(i)(25:25) = ACHAR(10)
     enddo
-    !$OMP END PARALLEL DO
     call libezfio_reopenz_unformatted(trim(l_filename(1)),'wb',err)
     write(libezfio_iunit) buffer
     call libezfio_closez(trim(l_filename(1)),'w')
@@ -272,6 +273,7 @@ subroutine ezfio_write_array_%(type_short)s(dir,fil,rank,dims,dim_max,dat)
 end
 """
 
+
 template_no_logical = """
 integer function n_count_%(type_short)s(array,isize,val)
   implicit none
@@ -294,9 +296,11 @@ end function
 ! Build Python functions
 """
 for t in format.keys():
-  print template%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] }
+  print(template_nowrite%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] })
+  if not t.startswith("character"):
+    print(template_write%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] })
   if t != "logical":
-    print template_no_logical%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] }
+    print(template_no_logical%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] })
 
 template_py = """
   def read_%(type_short)s(self,dir,fil):
@@ -323,7 +327,7 @@ template_py = """
     l_filename += [ dir.strip()+'/'+fil ]
     dat = conv(dat)
     file = open(l_filename[0],'w')
-    print >>file,'%(fmt)s'%%(dat,)
+    print('%(fmt)s'%%(dat,), file=file)
     file.close()
     os.rename(l_filename[0],l_filename[1])
 
@@ -363,13 +367,13 @@ template_py = """
       file.write("\\n")
 
       dat = flatten(dat)
-      for i in xrange(dim_max):
+      for i in range(dim_max):
         file.write("%(fmt)s\\n"%%(dat[i],))
       file.flush()
       buffer = file.getvalue()
       file.close()
       file = GzipFile(filename=l_filename[0],mode='wb')
-      file.write(buffer)
+      file.write(buffer.encode())
       file.close()
       os.rename(l_filename[0],l_filename[1])
     except:
@@ -379,21 +383,63 @@ template_py = """
 
 file_py = open("libezfio_util-gen.py","w")
 for t in format.keys():
-  print >>file_py, template_py%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][1] }
+  print (template_py%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][1] }, file=file_py)
 
 import os
 command = "'echo %s > '//libezfio_filename//'/ezfio/last_library'"
 cwd = os.getcwd()
 cwd = cwd.split('src')[:-1]
 cwd = '/'.join(cwd)
-print >>file_py, """
+print("""
   LIBRARY = "%s"
-"""%cwd
+"""%cwd,file=file_py)
 
 file_py.close()
 
 END_SHELL
 
+subroutine ezfio_write_array_ch(dir,fil,rank,dims,dim_max,dat)
+  implicit none
+  BEGIN_DOC
+! Writes a string array
+  END_DOC
+  character*(*), intent(in)      :: dir, fil
+  integer, intent(in)            :: rank
+  integer, intent(in)            :: dims(rank)
+  integer, intent(in)            :: dim_max
+  character*(*), intent(in)      :: dat(dim_max)
+  integer                        :: err
+  integer                        :: i
+  character*(1024)               :: l_filename(2)
+  integer                        :: length
+  character(len=:), allocatable  :: buffer
+  if (libezfio_read_only) then
+    call ezfio_error(irp_here,'Read-only file.')
+  endif
+  l_filename(1)=trim(dir)//'/.'//fil//trim(PID_str)//'.gz'
+  l_filename(2)=trim(dir)//'/'//fil//'.gz'
+  
+  err = 0
+  call libezfio_openz(trim(l_filename(1)),'wb',err)
+  if (err == 0) then
+    write(libezfio_iunit,'(I3)') rank
+    write(libezfio_iunit,'(30(I20,X))') dims(1:rank)
+    close(unit=libezfio_iunit)
+
+    length = len(dat(1))
+    allocate( character(len=(length+1)*dim_max) :: buffer )
+    do i=1,dim_max
+      write(buffer((i-1)*(length+1)+1:i*(length+1)-1), '(A)') dat(i)
+      buffer(i*(length+1):i*(length+1)) = ACHAR(10)
+    enddo
+    call libezfio_reopenz_unformatted(trim(l_filename(1)),'wb',err)
+    write(libezfio_iunit) buffer
+    call libezfio_closez(trim(l_filename(1)),'w')
+    deallocate(buffer)
+  endif
+  call rename(trim(l_filename(1)),trim(l_filename(2)) )
+end
+
 BEGIN_PROVIDER [ integer, libezfio_buffer_rank ]
  BEGIN_DOC
  ! Rank of the buffer ready for reading

src/read_config.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 #   EZFIO is an automatic generator of I/O libraries
 #   Copyright (C) 2009 Anthony SCEMAMA, CNRS
 #
@@ -31,7 +31,7 @@ import os, sys
 lines = []
 for filename in [ '../config/'+i for i in os.listdir('../config')]:
   file = open(filename,'r')
-  lines += map(lambda x: (x,filename), file.readlines())
+  lines += [(x,filename) for x in file.readlines()]
   try:
     if lines[-1] != '':
       lines.append( ('', filename) )
@@ -51,7 +51,7 @@ for line, filename in lines:
       groups[group] = my_list
     elif line[0] != ' ':  # New group
       group = line.strip()
-      if group in groups.keys():
+      if group in list(groups.keys()):
         my_list = groups[group] 
       else:
         my_list = []
@@ -76,12 +76,12 @@ for line, filename in lines:
       my_list.append(tuple(buffer))
   except:
     import sys, time
-    print >>sys.stderr, ''
-    print >>sys.stderr, '*'*80
-    print >>sys.stderr, 'Error in EZFIO config file '+filename+' :'
-    print >>sys.stderr, line
-    print >>sys.stderr, '*'*80
-    print >>sys.stderr, ''
+    print('', file=sys.stderr)
+    print('*'*80, file=sys.stderr)
+    print('Error in EZFIO config file '+filename+' :', file=sys.stderr)
+    print(line, file=sys.stderr)
+    print('*'*80, file=sys.stderr)
+    print('', file=sys.stderr)
     time.sleep(3)
     sys.exit(1)
 

src/system.c

@@ -0,0 +1,45 @@
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+#include "zlib.h"
+
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <errno.h>
+
+
+
+void fortran_mkdir(char* filename) {
+  if (mkdir (filename, S_IRWXU)) {
+     perror (strerror (errno));
+  }
+}
+
+
+#define BUFSIZE 16384
+void gzip(char* filename, char* output) {
+  FILE* in  = fopen(filename,"r");
+  gzFile out = gzopen(output,"w");
+  char buffer[BUFSIZE];
+  unsigned int size;
+  while (!feof(in)) {
+     size = (unsigned int) fread (buffer, sizeof(char), BUFSIZE, in);
+     gzwrite(out, buffer, size);
+  }
+  fclose(in);
+  gzclose(out);
+}
+
+void zcat(char* filename, char* output) {
+  gzFile in = gzopen(filename,"r");
+  FILE* out = fopen(output,"w");
+  char buffer[BUFSIZE];
+  int size;
+  while (!gzeof(in)) {
+     size = gzread (in, buffer, BUFSIZE);
+     fwrite(buffer, sizeof(char), (size_t) size, out);
+  }
+  gzclose(in);
+  fclose(out);
+}
+

src/system_f.f90

@@ -0,0 +1,24 @@
+module system
+  USE iso_c_binding
+
+  INTERFACE
+    SUBROUTINE mkdir(filename) BIND(C,name="fortran_mkdir")
+      USE iso_c_binding
+      CHARACTER(kind=C_CHAR),INTENT(in) :: filename(*)
+    END SUBROUTINE
+
+    SUBROUTINE gzip(filename,output) BIND(C,name="gzip")
+      USE iso_c_binding
+      CHARACTER(kind=C_CHAR),INTENT(in) :: filename(*)
+      CHARACTER(kind=C_CHAR),INTENT(in) :: output(*)
+    END SUBROUTINE
+
+    SUBROUTINE zcat(filename,output) BIND(C,name="zcat")
+      USE iso_c_binding
+      CHARACTER(kind=C_CHAR),INTENT(in) :: filename(*)
+      CHARACTER(kind=C_CHAR),INTENT(in) :: output(*)
+    END SUBROUTINE
+
+  END INTERFACE
+end module
+

src/test.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 #   EZFIO is an automatic generator of I/O libraries
 #   Copyright (C) 2009 Anthony SCEMAMA, CNRS
 #
@@ -44,7 +44,7 @@ values = []
 isize = 5
 EZFIO.open_read_ao_two_int()
 indices,values = EZFIO.read_buffer(isize)
-print indices
-print values
+print(indices)
+print(values)
 EZFIO.close_read_ao_two_int()
 

version

@@ -1 +1 @@
-VERSION=1.3.5
+VERSION=2.0.7