Quantum espresso mapping parser (#10)

* Revisions from review

* Add initial fhiaims parser

* Initial workflow parser classes

* Refactor

* Use workflow defs

* Parse workflow

* Parse workflow

* Add phononpy

* Initial quantum espresso parser

* Linting fix

* Refactor exciting schema

* Linting fix

* Remove unnecessary change

* Fix commit

* Fix structlog error

* Add qe tests

Author: ladinesa

pyproject.toml

@@ -130,6 +130,8 @@ fhiaims_parser_entry_point = "nomad_simulation_parsers.parsers:fhiaims_parser_en
 fhiaims_schema_package_entry_point = "nomad_simulation_parsers.schema_packages:fhiaims_schema_package_entry_point"
 phonopy_parser_entry_point = "nomad_simulation_parsers.parsers:phonopy_parser_entry_point"
 phonopy_schema_package_entry_point = "nomad_simulation_parsers.schema_packages:phonopy_schema_package_entry_point"
+quantumespresso_parser_entry_point = "nomad_simulation_parsers.parsers:quantumespresso_parser_entry_point"
+quantumespresso_schema_package_entry_point = "nomad_simulation_parsers.schema_packages:quantumespresso_schema_package_entry_point"
 vasp_parser_entry_point = "nomad_simulation_parsers.parsers:vasp_parser_entry_point"
 vasp_schema_package_entry_point = "nomad_simulation_parsers.schema_packages:vasp_schema_package_entry_point"
 wannier90_parser_entry_point = "nomad_simulation_parsers.parsers:wannier90_parser_entry_point"

src/nomad_simulation_parsers/parsers/__init__.py

@@ -69,6 +69,21 @@ class Wannier90ParserEntryPoint(EntryPoint):
     code_homepage='https://phonopy.github.io/phonopy/',
 )
 
+quantumespresso_parser_entry_point = EntryPoint(
+    name='parsers/quantumespresso',
+    aliases=['parsers/quantumespresso'],
+    description='NOMAD parser for QUANTUMESPRESSO.',
+    python_package='nomad_simulation_parsers',
+    mainfile_contents_re=(
+        r'(Program [A-Z]+.*starts)|(Current dimensions of program [A-Z]+ are)'
+    ),
+    supported_compressions=['gz', 'bz2', 'xz'],
+    parser_class_name='nomad_simulation_parsers.parsers.quantumespresso.parser.QuantumEspressoParser',
+    code_name='QuantumESPRESSO',
+    code_homepage='http://www.quantum-espresso.org/',
+    code_category='Atomistic code',
+)
+
 vasp_parser_entry_point = EntryPoint(
     name='parsers/vasp',
     description='Parser for VASP XML and OUTCAR outputs',

src/nomad_simulation_parsers/parsers/exciting/parser.py

@@ -193,7 +193,7 @@ def write_to_archive(self) -> None:
 
         # read xc functionals from input.xml
         input_xml_files = (
-            search_files('input.xml', maindir, mainbase)
+            search_files('input.xml', maindir, re_pattern=mainbase)
             if not self.archive.m_xpath('data.model_method[0].xc_functionals')
             else []
         )
@@ -204,7 +204,7 @@ def write_to_archive(self) -> None:
             input_xml_parser.close()
 
         # eigenvalues from eigval.out
-        eigval_files = search_files('EIGVAL.OUT', maindir, mainbase)
+        eigval_files = search_files('EIGVAL.OUT', maindir, re_pattern=mainbase)
         if eigval_files:
             eigval_parser = EigvalParser(
                 filepath=eigval_files[0], text_parser=EigvalFileParser()
@@ -214,7 +214,9 @@ def write_to_archive(self) -> None:
             eigval_parser.close()
 
         # bandstructure from bandstructure.xml
-        bandstructure_files = search_files('bandstructure.xml', maindir, mainbase)
+        bandstructure_files = search_files(
+            'bandstructure.xml', maindir, re_pattern=mainbase
+        )
         if bandstructure_files:
             bandstructure_parser = BandstructureXMLParser(
                 filepath=bandstructure_files[0]
@@ -225,7 +227,7 @@ def write_to_archive(self) -> None:
             bandstructure_parser.close()
 
         # dos from dos.xml
-        dos_files = search_files('dos.xml', maindir, mainbase)
+        dos_files = search_files('dos.xml', maindir, re_pattern=mainbase)
         if dos_files:
             dos_parser = DosXMLParser(filepath=dos_files[0])
             data_parser.annotation_key = 'dos_xml'