.gitignore

-# use glob syntax.
-syntax: glob
-*.ser
-*.class
-*~
-*.bak
-#*.off
-*.old
+# python
+__pycache__
+.mypy_cache
 *.pyc
-*.bk
-*.swp
-.DS_Store
-**/__pycache__
-
-# logging files
-detailed.log
-
-# eclipse conf file
-.settings
-.classpath
-.project
-.manager
-.scala_dependencies
-
-# idea
-.idea
-*.iml
-
-# building
-target
-build
-null
-tmp*
-temp*
-dist
-test-output
-build.log
-
-# other scm
-.svn
-.CVS
-.hg*
-
-# switch to regexp syntax.
-#  syntax: regexp
-#  ^\.pc/
-
-#SHITTY output not in target directory
-build.log
-
-#emacs TAGS
-TAGS
-
-lib/
-env/
-
-# Egg
-parser/parser-big-dft/bigdftparser.egg-info/
+*.egg-info/
\ No newline at end of file

molcasparser/__init__.py

+from .main import MolcasParser

parser/parser-molcas/functionals.py → molcasparser/functionals.py

-# Copyright 2016-2018 The NOMAD Developers Group
+# Copyright 2016-2018 Ask Hjorth Larsen, Fawzi Mohamed
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

parser/parser-molcas/main.py → molcasparser/main.py

-# Copyright 2016-2018 The NOMAD Developers Group
+# Copyright 2016-2018 Ask Hjorth Larsen, Fawzi Mohamed
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -17,8 +17,8 @@
 from __future__ import print_function
 import os
 import sys
-import setup_paths
 import re
+import logging
 
 import numpy as np
 from ase import Atoms
@@ -29,10 +29,11 @@ from nomadcore.simple_parser import mainFunction, SimpleMatcher as SM
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
 from nomadcore.unit_conversion.unit_conversion \
     import register_userdefined_quantity, convert_unit
+import nomad_meta_info
 
-from functionals import functionals
+from .functionals import functionals
 
-metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/molcas.nomadmetainfo.json"))
+metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)), "molcas.nomadmetainfo.json"))
 metaInfoEnv, warnings = loadJsonFile(filePath=metaInfoPath,
                                      dependencyLoader=None,
                                      extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
@@ -640,29 +641,53 @@ def molcas_main_loop_sm():
            ] + get_anymodule_sms())
     return m
 
-mainFileDescription = SM(
-    name='root',
-    weak=True,
-    startReStr='',
-    fixedStartValues={'program_name': 'Molcas',
-                      'program_basis_set_type': 'gaussians'},
-    sections=['section_run'],
-    subMatchers=[
-        get_header_sm(),
-        #get_inputfile_echo_sm(),
-        molcas_main_loop_sm(),
-        SM(r'x^',  # force parser to parse the whole file
-           name='impossible')
-    ])
-
-
-def main(**kwargs):
-    mainFunction(mainFileDescription=mainFileDescription,
-                 metaInfoEnv=metaInfoEnv,
-                 parserInfo=parser_info,
-                 cachingLevelForMetaName={},
-                 superContext=context,
-                 **kwargs)
+def main_file_description():
+    return SM(
+        name='root',
+        weak=True,
+        startReStr='',
+        fixedStartValues={'program_name': 'Molcas',
+                        'program_basis_set_type': 'gaussians'},
+        sections=['section_run'],
+        subMatchers=[
+            get_header_sm(),
+            #get_inputfile_echo_sm(),
+            molcas_main_loop_sm(),
+            SM(r'x^',  # force parser to parse the whole file
+            name='impossible')
+        ])
+
+
+class MolcasParser():
+    """ A proper class envolop for running this parser from within python. """
+    def __init__(self, backend, **kwargs):
+        self.backend_factory = backend
+
+    def parse(self, mainfile):
+        global context
+        context = MolcasContext()
+
+        from unittest.mock import patch
+        logging.debug('molcas parser started')
+        logging.getLogger('nomadcore').setLevel(logging.WARNING)
+        backend = self.backend_factory(metaInfoEnv)
+        with patch.object(sys, 'argv', ['<exe>', '--uri', 'nmd://uri', mainfile]):
+            mainFunction(
+                mainFileDescription=main_file_description(),
+                metaInfoEnv=metaInfoEnv,
+                parserInfo=parser_info,
+                cachingLevelForMetaName={},
+                superContext=context,
+                superBackend=backend)
+
+        return backend
+
 
 if __name__ == '__main__':
-    main()
+    mainFunction(
+        mainFileDescription=main_file_description(),
+        metaInfoEnv=metaInfoEnv,
+        parserInfo=parser_info,
+        cachingLevelForMetaName={},
+        superContext=context,
+        **kwargs)

parser/parser-molcas/generate_scala_testcode.py

-# Copyright 2016-2018 The NOMAD Developers Group
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-# Main author and maintainer: Ask Hjorth Larsen <asklarsen@gmail.com>
-
-from __future__ import print_function
-import os
-from glob import glob
-
-scala_imports = """package eu.nomad_lab.parsers
-
-import eu.nomad_lab.{ parsers, DefaultPythonInterpreter }
-import org.scalacheck.Properties
-import org.specs2.mutable.Specification
-import org.{ json4s => jn }
-
-"""
-
-test_template = """\
-    "test %(name)s " >> {
-      "test with json-events" >> {
-        ParserRun.parse(MolcasParser, "parsers/molcas/test/examples/%(name)s", "json-events") must_== ParseResult.ParseSuccess
-      }
-      "test with json" >> {
-        ParserRun.parse(MolcasParser, "parsers/molcas/test/examples/%(name)s", "json") must_== ParseResult.ParseSuccess
-      }
-    }"""
-
-fd = open('out.scala', 'w')
-
-fd.write(scala_imports)
-
-print('object MolcasParserSpec extends Specification {', file=fd)
-print('  "MolcasParserTest" >> {', file=fd)
-
-fnames = glob('test/test???.input.out')
-fnames.sort()
-for fname in fnames:
-    fname = os.path.basename(fname)
-    print(test_template % dict(name=fname), file=fd)
-
-print('  }', file=fd)
-print('}', file=fd)

parser/parser-molcas/nomad_meta_info

-../../../../nomad-meta-info/meta_info/nomad_meta_info
\ No newline at end of file

parser/parser-molcas/runtests.py

-# Copyright 2016-2018 The NOMAD Developers Group
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-# Main author and maintainer: Ask Hjorth Larsen <asklarsen@gmail.com>
-
-from __future__ import print_function
-from glob import glob
-import re
-from optparse import OptionParser
-from subprocess import Popen, PIPE
-import os
-from ase.parallel import world
-import platform
-
-p = OptionParser()
-opts, args = p.parse_args()
-
-if len(args) == 0:
-    testfiles = glob('test/test???.input.out')
-    testfiles.sort()
-else:
-    testfiles = argv
-
-for i, testfile in enumerate(testfiles):
-    if i % world.size != world.rank:
-        continue
-    dirname, basename = os.path.split(testfile)
-    py = 'python'
-    if platform.node() == 'labdev-nomad':
-        py = '/labEnv3/bin/python'
-    args = [py, 'main.py', '--annotate']
-    args.append(testfile)
-    print(' '.join(args))
-    proc = Popen(args, stdout=PIPE)
-    txt = proc.stdout.read()
-    with open('%s.json' % testfile, 'w') as fd:
-        fd.write(txt.decode('ascii'))

parser/parser-molcas/setup_paths.py

-# Copyright 2016-2018 The NOMAD Developers Group
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-# Main author and maintainer: Ask Hjorth Larsen <asklarsen@gmail.com>
-
-import sys, os, os.path
-baseDir = os.path.dirname(os.path.abspath(__file__))
-commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/common/python"))
-
-if not commonDir in sys.path:
-    sys.path.insert(0, commonDir)

parser/parser-molcas/test

-../../test/examples
\ No newline at end of file

pysrc

-parser/parser-molcas
\ No newline at end of file

setup.py

+# Copyright 2016-2018 Ask Hjorth Larsen, Fawzi Mohamed
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+
+from setuptools import setup, find_packages
+
+
+def main():
+    setup(
+        name='molcasparser',
+        version='0.1',
+        description='NOMAD parser implementation for Molcas.',
+        author='Ask Hjorth Larsen, Fawzi Mohamed',
+        license='APACHE 2.0',
+        packages=find_packages(),
+        install_requires=[
+            'nomadcore'
+        ],
+    )
+
+
+if __name__ == '__main__':
+    main()

src/main/scala/eu/nomad_lab/parsers/MolcasParser.scala

-/*
-   Copyright 2016-2017 The NOMAD Developers Group
-
-   Licensed under the Apache License, Version 2.0 (the "License");
-   you may not use this file except in compliance with the License.
-   You may obtain a copy of the License at
-
-       http://www.apache.org/licenses/LICENSE-2.0
-
-   Unless required by applicable law or agreed to in writing, software
-   distributed under the License is distributed on an "AS IS" BASIS,
-   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-   See the License for the specific language governing permissions and
-   limitations under the License.
- */
-package eu.nomad_lab.parsers
-
-import eu.{ nomad_lab => lab }
-import eu.nomad_lab.DefaultPythonInterpreter
-import org.{ json4s => jn }
-import scala.collection.breakOut
-
-object MolcasParser extends SimpleExternalParserGenerator(
-  name = "MolcasParser",
-  parserInfo = jn.JObject(
-    ("name" -> jn.JString("MolcasParser")) ::
-      ("parserId" -> jn.JString("MolcasParser" + lab.MolcasVersionInfo.version)) ::
-      ("versionInfo" -> jn.JObject(
-        ("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map {
-          case (k, v) => k -> jn.JString(v.toString)
-        }(breakOut): List[(String, jn.JString)])) ::
-          (lab.MolcasVersionInfo.toMap.map {
-            case (key, value) =>
-              (key -> jn.JString(value.toString))
-          }(breakOut): List[(String, jn.JString)])
-      )) :: Nil
-  ),
-  mainFileTypes = Seq("text/.*"),
-  mainFileRe = """
-    \s*\^[\s\^]*M O L C A S\s*
-    \s*\^[\s\^]*version \S+ patchlevel \S+\s*
-""".r,
-  cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/molcas/parser/parser-molcas/main.py",
-    "--uri", "${mainFileUri}", "${mainFilePath}"),
-  resList = Seq(
-    "parser-molcas/main.py",
-    "parser-molcas/functionals.py",
-    "parser-molcas/setup_paths.py",
-    "nomad_meta_info/public.nomadmetainfo.json",
-    "nomad_meta_info/common.nomadmetainfo.json",
-    "nomad_meta_info/meta_types.nomadmetainfo.json",
-    "nomad_meta_info/molcas.nomadmetainfo.json"
-  ) ++ DefaultPythonInterpreter.commonFiles(),
-  dirMap = Map(
-    "parser-molcas" -> "parsers/molcas/parser/parser-molcas",
-    "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info",
-    "python" -> "python-common/common/python/nomadcore"
-  ) ++ DefaultPythonInterpreter.commonDirMapping(),
-  metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.molcas)
-)