initial commit: skeleton for parser using the simple parser infrastructure

.gitignore

+# use glob syntax.
+syntax: glob
+*.ser
+*.class
+*~
+*.bak
+#*.off
+*.old
+*.pyc
+*.bk
+*.swp
+.DS_Store
+
+# 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/

README.md

+# Octopus Parser
+
+This is the parser for [octopus](http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page).
+It is part of the [NOMAD Laboratory](http://nomad-lab.eu).
+The official version lives at
+
+    git@gitlab.mpcdf.mpg.de:nomad-lab/parser-octopus.git
+
+you can browse it at
+
+    https://gitlab.mpcdf.mpg.de/nomad-lab/parser-octopus
+
+It relies on having the nomad-meta-info and the python common repositories one level higher.
+The simplest way to have this is to check out nomad-lab-base recursively:
+
+    git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
+
+then this will be in parsers/octopus.

parser/parser-octopus/parser_octopus.py

+import setup_paths
+from nomadcore.simple_parser import mainFunction, SimpleMatcher as SM
+from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
+import os, sys, json
+
+# description of the input
+mainFileDescription = SM(
+    name = 'root',
+    weak = True,
+    startReStr = "",
+    subMatchers = [
+        SM(name = 'newRun',
+           startReStr = r"\s*# SampleParser #\s*",
+           repeats = True,
+           required = True,
+           forwardMatch = True,
+           sections   = ['section_run'],
+           subMatchers = [
+               SM(name = 'header',
+                  startReStr = r"\s*# SampleParser #\s*")
+           ])
+])
+
+# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/octopus.nomadmetainfo.json
+metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/octopus.nomadmetainfo.json"))
+metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
+
+parserInfo = {
+  "name": "parser_octopus",
+  "version": "1.0"
+}
+
+class OctopusParserContext(object):
+    """main place to keep the parser status, open ancillary files,..."""
+    def __init__(self):
+        self.scfIterNr = 0
+
+    # just examples, you probably want to remove the following two triggers
+
+    def onClose_section_single_point_evaluation(self, backend, gIndex, section):
+        """trigger called when section_single_point_evaluation is closed"""
+        #backend.addValue("", self.scfIterNr)
+        logging.getLogger("nomadcore.parsing").info("closing section_single_point_evaluation gIndex %d %s", gIndex, section.simpleValues)
+        self.scfIterNr = 0
+
+    def onClose_section_scf_iteration(self, backend, gIndex, section):
+        """trigger called when section_scf_iteration is closed"""
+        logging.getLogger("nomadcore.parsing").info("closing section_scf_iteration bla gIndex %d %s", gIndex, section.simpleValues)
+        self.scfIterNr += 1
+
+# which values to cache or forward (mapping meta name -> CachingLevel)
+cachingLevelForMetaName = {}
+
+if __name__ == "__main__":
+    mainFunction(mainFileDescription, metaInfoEnv, parserInfo,
+                 cachingLevelForMetaName = cachingLevelForMetaName,
+                 superContext = OctopusParserContext())

parser/parser-octopus/setup_paths.py

+import sys, os, os.path
+baseDir = os.path.dirname(os.path.abspath(__file__))
+commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/python"))
+
+if not commonDir in sys.path:
+    sys.path.insert(0, commonDir)

test/examples/README.md

+sample files to test the parser