Removed Ninja

Version:1.4.0

Version:1.4.0

Bash/ezfio.sh

@@ -1,4 +1,7 @@
 #!/bin/bash
+#
+# ezfio shell command with completion
+#
 
 EZFIO_ROOT=$( cd $(dirname "${BASH_SOURCE}")/..  ; pwd -P )
 

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

@@ -38,19 +38,15 @@ clean:
 	- 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 +4,13 @@ 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.
+from/to disk, and to check if the data exists. A Python and an Ocaml API
-A Python and an Ocaml API are also provided.
+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.
 
 Download
 ========
@@ -19,7 +19,8 @@ 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 +33,8 @@ 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 +42,8 @@ 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
+desired suboutines. Get into the ``config`` directory and create a new
-``test.config``
+file ``test.config`` containing::
-containing::
 
   molecule
     num_atoms   integer
@@ -56,14 +57,13 @@ 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.
+new line. Each data contained inside a container is characterized by a
-Each data contained inside a container is characterized by a triplet
+triplet (name,type,dimension), preceded by at least one white space at
-(name,type,dimension), preceded by at least one white space at the
+the beginning of the line.
-beginning of the line.
 
-If the dimension of an array is a data, the name of the data can be used
+If the dimension of an array is a data, the name of the data can be
-as ``<container>_<data>`` in the definition of the dimension. For
+used as ``<container>_<data>`` in the definition of the dimension.
-example, the dimension (``molecule_num_atoms``) uses the data
+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 +83,10 @@ Now, go back to the EZFIO root directory. To build with GNU make, run:
 
   $ make
 
-Or you can use Ninja to build the library:
+The ``lib`` directory now contains the static library ``libezfio.a``,
-
+and a static library for use under the IRPF90 environment
-.. code-block:: bash
+(``libezfio_irp.a``). The ``Python``, ``Ocaml`` and ``Bash`` directories
-
+contain the binding for these languages.
-  $ 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.
 
 
 Using the produced library
@@ -232,7 +226,8 @@ Execute the script:
   $ python2 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 +304,12 @@ the EZFIO file.
   
   end
 
-Compile the fortran program and link it the ``libezfio.a`` library, and run the
+Compile the fortran program and link it the ``libezfio.a`` library and
-executable.
+``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    
@@ -362,7 +357,8 @@ 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
 

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/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

make.config

@@ -0,0 +1,9 @@
+VERSION ?= 1.4.0
+RANLIB  ?= ranlib
+IRPF90  ?= irpf90
+CC      ?= gcc
+FC      ?= gfortran -g -ffree-line-length-none -fPIC # -fopenmp
+FCFLAGS ?= -fPIC
+AR      ?= ar
+RANLIB  ?= ranlib
+PYTHON  ?= python2

src/Makefile

@@ -29,7 +29,7 @@ export
 
 include irpf90.make
 
-irpf90.make: $(wildcard *.irp.f) ../config/* system.c
+irpf90.make: $(wildcard *.irp.f) ../config/* IRPF90_temp/system.o IRPF90_temp/system_f.o 
 	$(IRPF90)
 
 include ../version
@@ -40,28 +40,30 @@ all: static ../Python/ezfio.py ../Ocaml/ezfio.ml
 
 static: ../lib/libezfio.a ../lib/libezfio_irp.a
 
-system_c.o: system_c.c
+IRPF90_temp/system.o: system.c
-	$(CC) -c system_c -o system_c.o
+	mkdir -p IRPF90_temp/
+	$(CC) -c system.c -o IRPF90_temp/system.o
 
-system_f.o: system_f.f90
+IRPF90_temp/system_f.o: system_f.f90
-	$(FC) -c system_f.f90 -o system_f.o
+	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 system_c.o system_f.o $(OBJ1) 
+	$(AR) cru ../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 system_c.o system_f.o
+	$(AR) dv ../lib/libezfio_irp.a irp_stack.irp.o
 	$(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/libezfio_file.irp.f

@@ -148,7 +148,7 @@ subroutine ezfio_set_file(filename_in)
 
   character*(*) :: filename_in
   character(8)  :: date
-  character(10) :: time
+  character(73) :: time
   character(32) :: user
 
   if (filename_in == '') then
@@ -163,13 +163,13 @@ subroutine ezfio_set_file(filename_in)
 
     ! using keyword arguments
     call date_and_time(DATE=date,TIME=time)
-    open (unit=10, file=trim(libezfio_filename)//'/ezfio/creation', ACTION='WRITE', STATUS='UNKNOWN')
+    open (unit=73, file=trim(libezfio_filename)//'/ezfio/creation', ACTION='WRITE', STATUS='UNKNOWN')
-    write(10,*), time, ' ', date
+    write(73,*) time, ' ', date
-    close(10)
+    close(73)
-    open (unit=10, file=trim(libezfio_filename)//'/ezfio/user', ACTION='WRITE', STATUS='UNKNOWN')
+    open (unit=73, file=trim(libezfio_filename)//'/ezfio/user', ACTION='WRITE', STATUS='UNKNOWN')
     call getenv('USER',user)
-    write(10,*) user
+    write(73,*) user
-    close(10)
+    close(73)
   endif
 
   TOUCH libezfio_filename

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
@@ -64,7 +65,7 @@ subroutine ezfio_mkdir(path)
     call ezfio_error(irp_here,'Read-only file.')
   endif
   if (.not.ezfio_exists(path)) then
-    call 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)
@@ -73,6 +74,7 @@ end subroutine
 
 
 subroutine libezfio_openz(filename,mode,err)
+ use system
  implicit none
   BEGIN_DOC
 ! Opens a compressed file
@@ -84,7 +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
@@ -118,6 +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
@@ -127,7 +130,7 @@ 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')

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_c.c

@@ -1,13 +0,0 @@
-#include <sys/stat.h>
-#include <sys/types.h>
-#include <errno.h>
-#include <string.h>
-
-
-void ezfio_mkdir(char* filename) {
-  errno = 0;
-  if (mkdir (filename, S_IRWXU)) {
-     perror (strerror (errno));
-  }
-}
-

src/system_f.f90

@@ -1,5 +1,4 @@
-MODULE system
+module system
-
   USE iso_c_binding
 
   INTERFACE
@@ -7,6 +6,19 @@ MODULE system
       USE iso_c_binding
       CHARACTER(kind=C_CHAR),INTENT(in) :: filename(*)
     END SUBROUTINE
-  END INTERFACE
 
-END MODULE
+    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
+

version

@@ -1 +1 @@
-VERSION=1.3.5
+VERSION=1.4.0