damask.Environment reads from os.environ; python module is packaging-ready

.gitignore

@@ -2,6 +2,7 @@
 *.hdf5
 *.bak
 *~
+.DS_Store
 bin
 PRIVATE
 build

Makefile

@@ -4,7 +4,7 @@ SHELL = /bin/sh
 ########################################################################################
 DAMASK_ROOT = $(shell python -c "import os,sys; print(os.path.normpath(os.path.realpath(os.path.expanduser('$(pwd)'))))")
 .PHONY: all
-all: grid mesh python processing
+all: grid mesh processing
 
 .PHONY: grid
 grid: build/grid
@@ -35,8 +35,3 @@ clean:
 .PHONY: processing
 processing:
 	@./installation/symlink_Processing.py ${MAKEFLAGS}
-
-.PHONY: python
-python:
-	@pip install --user ./python
-

PRIVATE

@@ -1 +1 @@
-Subproject commit 036faecca39b46fd2328597ca858cbb04e37f79a
+Subproject commit 12de3e01e3dfa407a724b6aeca51c78e9981b80d

env/DAMASK.csh

@@ -2,15 +2,14 @@
 # usage:  source DAMASK_env.csh
 
 set CALLED=($_)
-set DIRNAME=`dirname $CALLED[2]`
+set ENV_ROOT=`dirname $CALLED[2]`
-set DAMASK_ROOT=`python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" $DIRNAME"/../"`
+set DAMASK_ROOT=`python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" $ENV_ROOT"/../"`
 
-source $DAMASK_ROOT/CONFIG
+source $ENV_ROOT/CONFIG
 
 set path = ($DAMASK_ROOT/bin $path)
 
 set SOLVER=`which DAMASK_spectral`                                                          
-set PROCESSING=`which postResults`                                                          
 if ( "x$DAMASK_NUM_THREADS" == "x" ) then                                                                  
   set DAMASK_NUM_THREADS=1
 endif
@@ -32,7 +31,6 @@ if ( $?prompt ) then
   echo Using environment with ...
   echo "DAMASK             $DAMASK_ROOT"
   echo "Grid Solver        $SOLVER" 
-  echo "Post Processing    $PROCESSING"
   if ( $?PETSC_DIR) then
     echo "PETSc location     $PETSC_DIR"
   endif
@@ -52,3 +50,6 @@ if ( ! $?PYTHONPATH ) then
 else
   setenv PYTHONPATH $DAMASK_ROOT/python:$PYTHONPATH
 endif
+setenv MSC_ROOT
+setenv ABAQUS_VERSION
+setenv MARC_VERSION

env/DAMASK.sh

@@ -10,14 +10,14 @@ function blink {
 }
 
 if [ "$OSTYPE" == "linux-gnu" ] || [ "$OSTYPE" == 'linux' ]; then
-  DAMASK_ROOT=$(dirname $BASH_SOURCE)
+  ENV_ROOT=$(dirname $BASH_SOURCE)
 else
   [[ "${BASH_SOURCE::1}" == "/" ]] && BASE="" || BASE="$(pwd)/"
   STAT=$(stat "$(dirname $BASE$BASH_SOURCE)")
-  DAMASK_ROOT=${STAT##* }
+  ENV_ROOT=${STAT##* }
 fi
 
-DAMASK_ROOT=$(canonicalPath "$DAMASK_ROOT/../")
+DAMASK_ROOT=$(canonicalPath "$ENV_ROOT/../")
 
 
 # shorthand command to change to DAMASK_ROOT directory
@@ -27,7 +27,7 @@ eval "function DAMASK_root() { cd $DAMASK_ROOT; }"
 set() {
     export $1$2$3
  }
-source $DAMASK_ROOT/CONFIG
+source $ENV_ROOT/CONFIG
 unset -f set
 
 # add BRANCH if DAMASK_ROOT is a git repository
@@ -38,9 +38,6 @@ PATH=${DAMASK_ROOT}/bin:$PATH
 SOLVER=$(type -p DAMASK_spectral || true 2>/dev/null)
 [ "x$SOLVER" == "x" ] && SOLVER=$(blink 'Not found!')
 
-PROCESSING=$(type -p postResults || true 2>/dev/null)
-[ "x$PROCESSING" == "x" ] && PROCESSING=$(blink 'Not found!')
-
 [ "x$DAMASK_NUM_THREADS" == "x" ] && DAMASK_NUM_THREADS=1
 
 # currently, there is no information that unlimited stack size causes problems
@@ -60,7 +57,6 @@ if [ ! -z "$PS1" ]; then
   echo Using environment with ...
   echo "DAMASK             $DAMASK_ROOT $BRANCH"
   echo "Grid Solver        $SOLVER" 
-  echo "Post Processing    $PROCESSING"
   if [ "x$PETSC_DIR"   != "x" ]; then
     echo -n "PETSc location     "
     [ -d $PETSC_DIR ] && echo $PETSC_DIR || blink $PETSC_DIR
@@ -93,12 +89,8 @@ fi
 export DAMASK_NUM_THREADS
 export PYTHONPATH=$DAMASK_ROOT/python:$PYTHONPATH
 
-for var in BASE STAT SOLVER PROCESSING BRANCH; do
+for var in BASE STAT SOLVER BRANCH; do
   unset "${var}"
 done
-for var in DAMASK MSC; do
+unset "ENV_ROOT"
-  unset "${var}_ROOT"
+unset "DAMASK_ROOT"
-done
-for var in ABAQUS MARC; do
-  unset "${var}_VERSION"
-done

env/DAMASK.zsh

@@ -9,6 +9,7 @@ function blink {
   echo -e "\033[2;5m$1\033[0m"
 }
 
+ENV_ROOT=$(canonicalPath "${0:a:h}")
 DAMASK_ROOT=$(canonicalPath "${0:a:h}'/..")
 
 # shorthand command to change to DAMASK_ROOT directory
@@ -18,7 +19,7 @@ eval "function DAMASK_root() { cd $DAMASK_ROOT; }"
 set() {
     export $1$2$3
  }
-source $DAMASK_ROOT/CONFIG
+source $ENV_ROOT/CONFIG
 unset -f set
 
 # add BRANCH if DAMASK_ROOT is a git repository
@@ -29,9 +30,6 @@ PATH=${DAMASK_ROOT}/bin:$PATH
 SOLVER=$(which DAMASK_spectral || true 2>/dev/null)
 [[ "x$SOLVER" == "x" ]] && SOLVER=$(blink 'Not found!')
 
-PROCESSING=$(which postResults || true 2>/dev/null)
-[[ "x$PROCESSING" == "x" ]] && PROCESSING=$(blink 'Not found!')
-
 [[ "x$DAMASK_NUM_THREADS" == "x" ]] && DAMASK_NUM_THREADS=1
 
 # currently, there is no information that unlimited stack size causes problems
@@ -51,7 +49,6 @@ if [ ! -z "$PS1" ]; then
   echo "Using environment with ..."
   echo "DAMASK             $DAMASK_ROOT $BRANCH"
   echo "Grid Solver        $SOLVER" 
-  echo "Post Processing    $PROCESSING"
   if [ "x$PETSC_DIR" != "x" ]; then
     echo -n "PETSc location     "
     [ -d $PETSC_DIR ] && echo $PETSC_DIR || blink $PETSC_DIR
@@ -86,12 +83,8 @@ fi
 export DAMASK_NUM_THREADS
 export PYTHONPATH=$DAMASK_ROOT/python:$PYTHONPATH
 
-for var in SOLVER PROCESSING BRANCH; do
+for var in SOLVER BRANCH; do
   unset "${var}"
 done
-for var in DAMASK MSC; do
+unset "ENV_ROOT"
-  unset "${var}_ROOT"
+unset "DAMASK_ROOT"
-done
-for var in ABAQUS MARC; do
-  unset "${var}_VERSION"
-done

installation/mods_MarcMentat/apply_DAMASK_modifications.sh

@@ -2,11 +2,6 @@
 
 SCRIPTLOCATION="$( cd "$( dirname "$0" )" && pwd )"
 DAMASK_ROOT=$SCRIPTLOCATION/../../
-# defining set() allows to source the same file for tcsh and bash, with and without space around =
-set() {
-    export $1$2$3
- }
-source $DAMASK_ROOT/CONFIG
 
 if [ "x$MSC_ROOT" != "x" ]; then
  DEFAULT_DIR=$MSC_ROOT
@@ -15,7 +10,7 @@ if [ "x$MARC_VERSION" != "x" ]; then
  DEFAULT_VERSION=$MARC_VERSION
 fi
 if [ "x$DAMASK_BIN" != "x" ]; then
- BIN_DIR=$DAMASK_BIN
+ BIN_DIR=$DAMASK_ROOT/bin
 fi
 
 while [ ! -d "$SCRIPTLOCATION/$VERSION" ] || [ -z "$VERSION" ]

python/MANIFEST.in

@@ -1,3 +1,2 @@
-include damask/README
 include damask/VERSION
 include damask/LICENSE

python/damask/LICENSE

@@ -1,14 +0,0 @@
-Copyright 2011-19 Max-Planck-Institut für Eisenforschung GmbH
-
-DAMASK 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 3 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, see <http://www.gnu.org/licenses/>.

python/damask/LICENSE

@@ -0,0 +1 @@
+../../LICENSE

python/damask/README.md

@@ -1,13 +0,0 @@
-DAMASK - The Düsseldorf Advanced Material Simulation Kit
-Visit damask.mpie.de for installation and usage instructions
-
-CONTACT INFORMATION
-
-Max-Planck-Institut für Eisenforschung GmbH
-Max-Planck-Str. 1
-40237 Düsseldorf
-Germany
-
-Email: DAMASK@mpie.de
-https://damask.mpie.de
-https://magit1.mpie.de

python/damask/VERSION

@@ -1 +0,0 @@
-0.9.0

python/damask/VERSION

@@ -0,0 +1 @@
+../../VERSION

python/damask/environment.py

@@ -1,5 +1,4 @@
 import os
-import re
 
 class Environment():
     __slots__ = [ \
@@ -18,12 +17,9 @@ class Environment():
         return os.path.normpath(os.path.join(os.path.realpath(__file__),'../../../'))
 
     def get_options(self):
-        with open(self.relPath(self.rootDir()+'/CONFIG')) as configFile:
+        for item in ['DAMASK_NUM_THREADS',
-            for line in configFile:
+                     'MSC_ROOT',
-                line = line.strip()
+                     'MARC_VERSION',
-                line = line[4:] if line.startswith('set ') else line                                   # remove "set" (tcsh) when setting variables
+                     'ABAQUS_VERSION',
-                if line and not line.startswith('#'):
+                     ]:
-                    items = re.split(r'\s*=\s*',line)
+            self.options[item] = os.environ[item] if item in os.environ else None
-                    if len(items) == 2: 
-                        self.options[items[0].upper()] = \
-                          re.sub(r'\${?DAMASK_ROOT}?',self.rootDir(),os.path.expandvars(items[1]))     # expand all shell variables and DAMASK_ROOT

python/damask/solver/abaqus.py

@@ -5,29 +5,35 @@ import damask
 
 
 class Abaqus(Solver):
-  """Wrapper to run DAMASK with Abaqus."""
+    """Wrapper to run DAMASK with Abaqus."""
 
-  def __init__(self,version=int(damask.Environment().options['ABAQUS_VERSION'])):
+    def __init__(self,version=None):
-    """
+        """
-    Create a Abaqus solver object.
+        Create a Abaqus solver object.
     
-    Parameters
+        Parameters
-    ----------
+        ----------
-    version : integer
+        version : integer
-        Abaqus version
+            Abaqus version
 
-    """
+        """
-    self.solver  = 'Abaqus'
+        self.solver  = 'Abaqus'
-    self.version = int(version)
+        try:
+            self.version = int(version)
+        except TypeError:
+            try:
+                self.version = int(damask.Environment().options['ABAQUS_VERSION'])
+            except TypeError:
+                self.version = -1
 
-  def return_run_command(self,model):
+    def return_run_command(self,model):
-    try:
+        try:
-      cmd = 'abq'+self.version
+            cmd = 'abq{}'.format(self.version)
-      subprocess.check_output([cmd,'information=release'])
+            subprocess.check_output([cmd,'information=release'])
-    except OSError:                                                                                 # link to abqXXX not existing
+        except OSError:                                                                                 # link to abqXXX not existing
-      cmd = 'abaqus'
+            cmd = 'abaqus'
-      process = subprocess.Popen([cmd,'information=release'],stdout = subprocess.PIPE,stderr = subprocess.PIPE)
+            process = subprocess.Popen([cmd,'information=release'],stdout = subprocess.PIPE,stderr = subprocess.PIPE)
-      detectedVersion = int(process.stdout.readlines()[1].split()[1].decode('utf-8'))
+            detectedVersion = int(process.stdout.readlines()[1].split()[1].decode('utf-8'))
-      if self.version != detectedVersion:
+            if self.version != detectedVersion:
-        raise Exception('found Abaqus version {}, but requested {}'.format(detectedVersion,self.version))
+                raise Exception('found Abaqus version {}, but requested {}'.format(detectedVersion,self.version))
-    return '{} -job {} -user {}/src/DAMASK_abaqus interactive'.format(cmd,model,damask.Environment().rootDir())
+        return '{} -job {} -user {}/src/DAMASK_abaqus interactive'.format(cmd,model,damask.Environment().rootDir())

python/damask/solver/marc.py

@@ -1,88 +1,94 @@
 import os
 import subprocess
 import shlex
+import string
 
 from .solver import Solver
 import damask
 
 class Marc(Solver):
-  """Wrapper to run DAMASK with MSCMarc."""
+    """Wrapper to run DAMASK with MSCMarc."""
 
-  def __init__(self,version=damask.Environment().options['MARC_VERSION']):
+    def __init__(self,version=damask.Environment().options['MARC_VERSION']):
-    """
+        """
-    Create a Marc solver object.
+        Create a Marc solver object.
     
-    Parameters
+        Parameters
-    ----------
+        ----------
-    version : float
+        version : float
-        Marc version
+            Marc version
 
-    """
+        """
-    self.solver  = 'Marc'
+        self.solver  = 'Marc'
-    self.version = damask.Environment().options['MARC_VERSION']
+        try:
+            self.version = int(version)
+        except TypeError:
+            try:
+                self.version = int(damask.Environment().options['MARC_VERSION'])
+            except TypeError:
+                self.version = -1
 
 
 #--------------------------
-  def libraryPath(self):
+    def libraryPath(self):
 
-    path_MSC = damask.Environment().options['MSC_ROOT']   
+        path_MSC = damask.Environment().options['MSC_ROOT']   
-    path_lib = '{}/mentat{}/shlib/linux64'.format(path_MSC,self.version)
+        path_lib = '{}/mentat{}/shlib/linux64'.format(path_MSC,self.version)
 
-    return path_lib if os.path.exists(path_lib) else ''
+        return path_lib if os.path.exists(path_lib) else ''
 
 
 #--------------------------
-  def toolsPath(self):
+    def toolsPath(self):
 
-    path_MSC   = damask.Environment().options['MSC_ROOT']
+        path_MSC   = damask.Environment().options['MSC_ROOT']
-    path_tools = '{}/marc{}/tools'.format(path_MSC,self.version)
+        path_tools = '{}/marc{}/tools'.format(path_MSC,self.version)
 
-    return path_tools if os.path.exists(path_tools) else ''
+        return path_tools if os.path.exists(path_tools) else ''
 
 
 #--------------------------
-  def submit_job(self,
+    def submit_job(self,
-                 model,
+                   model,
-                 job          = 'job1',
+                   job          = 'job1',
-                 logfile      = False,
+                   logfile      = False,
-                 compile      = False,
+                   compile      = False,
-                 optimization = '',
+                   optimization = '',
-                ):
+                  ):
 
 
-    damaskEnv = damask.Environment()
+        damaskEnv = damask.Environment()
    
-    user = os.path.join(damaskEnv.relPath('src'),'DAMASK_marc{}.{}'.format(self.version,'f90' if compile else 'marc'))
+        user = os.path.join(damaskEnv.relPath('src'),'DAMASK_marc{}.{}'.format(self.version,'f90' if compile else 'marc'))
-    if not os.path.isfile(user):
+        if not os.path.isfile(user):
-      raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),user))
+            raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),user))
 
-    # Define options [see Marc Installation and Operation Guide, pp 23]
+        # Define options [see Marc Installation and Operation Guide, pp 23]
-    script = 'run_damask_{}mp'.format(optimization)
+        script = 'run_damask_{}mp'.format(optimization)
     
-    cmd = os.path.join(self.toolsPath(),script) + \
+        cmd = os.path.join(self.toolsPath(),script) + \
-          ' -jid ' + model + '_' + job + \
+              ' -jid ' + model + '_' + job + \
-          ' -nprocd 1  -autorst 0 -ci n  -cr n  -dcoup 0 -b no -v no'
+              ' -nprocd 1  -autorst 0 -ci n  -cr n  -dcoup 0 -b no -v no'
 
-    if compile: cmd += ' -u ' + user + ' -save y'
+        if compile: cmd += ' -u ' + user + ' -save y'
-    else:       cmd += ' -prog ' + os.path.splitext(user)[0]
+        else:       cmd += ' -prog ' + os.path.splitext(user)[0]
 
-    print('job submission {} compilation: {}'.format('with' if compile else 'without',user))
+        print('job submission {} compilation: {}'.format('with' if compile else 'without',user))
-    if logfile: log = open(logfile, 'w')
+        if logfile: log = open(logfile, 'w')
-    print(cmd)
+        print(cmd)
-    process = subprocess.Popen(shlex.split(cmd),stdout = log,stderr = subprocess.STDOUT)
+        process = subprocess.Popen(shlex.split(cmd),stdout = log,stderr = subprocess.STDOUT)
-    log.close()
+        log.close()
-    process.wait()
+        process.wait()
       
 #--------------------------
-  def exit_number_from_outFile(self,outFile=None):
+    def exit_number_from_outFile(self,outFile=None):
-    import string
+        exitnumber = -1
-    exitnumber = -1
+        with open(outFile,'r') as fid_out:
-    with open(outFile,'r') as fid_out:
+            for line in fid_out:
-      for line in fid_out:
+                if (string.find(line,'tress iteration') != -1):
-        if (string.find(line,'tress iteration') != -1):
+                    print(line)
-          print(line)
+                elif (string.find(line,'Exit number')   != -1):
-        elif (string.find(line,'Exit number')   != -1):
+                    substr = line[string.find(line,'Exit number'):len(line)]
-          substr = line[string.find(line,'Exit number'):len(line)]
+                    exitnumber = int(substr[12:16])
-          exitnumber = int(substr[12:16])
 
-    return exitnumber
+        return exitnumber

python/makeDistribution.sh

@@ -1,12 +0,0 @@
-#!/bin/bash
-
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-cd $DIR
-
-VERSION=$(head -n1 damask/VERSION)
-read -p "updated version [${VERSION}]: " UP
-echo ${UP:-$VERSION} > damask/VERSION
-
-rm -rf dist/
-python3 setup.py sdist bdist_wheel
-python3 -m twine upload dist/*

python/setup.py

@@ -3,7 +3,7 @@ import os
 import re
 
 with open(os.path.join(os.path.dirname(__file__),'damask/VERSION')) as f:
-  version = re.sub(r'^v','',f.readline().strip())
+  version = re.sub(r'(-([^-]*)).*$',r'.\2',re.sub(r'^v(\d+\.\d+(\.\d+)?)',r'\1',f.readline().strip()))
 
 setuptools.setup(
     name="damask",