♻️ REFACTOR: move basic parsing into BaseParser class

docs/source/conf.py

@@ -84,7 +84,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-# language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -151,6 +151,10 @@
     (r'.*', r'Tuple.*'),
 ]
 nitpick_ignore = [
+    ('py:class', 'AttributeDict'),
+    ('py:class', 'ExitCode'),
+    ('py:class', 'StructureData'),
+    ('py:class', 'PseudoPotentialFamily'),
     ('py:exc', 'ArithmeticError'),
     ('py:exc', 'AssertionError'),
     ('py:exc', 'AttributeError'),
@@ -209,6 +213,4 @@
     ('py:obj', 'Mapping'),
     ('py:obj', 'qe_tools.parsers.CpInputFile'),
     ('py:obj', 'qe_tools.parsers.PwInputFile'),
-    ('py:class', 'StructureData'),
-    ('py:class', 'PseudoPotentialFamily'),
 ]

src/aiida_quantumespresso/calculations/__init__.py

@@ -143,6 +143,22 @@ def define(cls, spec):
         )
         spec.inputs.validator = cls.validate_inputs
 
+        spec.exit_code(
+            302,
+            'ERROR_OUTPUT_STDOUT_MISSING',
+            message='The retrieved folder did not contain the required stdout output file.'
+        )
+        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ', message='The stdout output file could not be read.')
+        spec.exit_code(311, 'ERROR_OUTPUT_STDOUT_PARSE', message='The stdout output file could not be parsed.')
+        spec.exit_code(
+            312,
+            'ERROR_OUTPUT_STDOUT_INCOMPLETE',
+            message='The stdout output file was incomplete probably because the calculation got interrupted.'
+        )
+        spec.exit_code(
+            400, 'ERROR_OUT_OF_WALLTIME', message='The calculation stopped prematurely because it ran out of walltime.'
+        )
+
     @classmethod
     def validate_inputs(cls, value, port_namespace):
         """Validate the entire inputs namespace."""

src/aiida_quantumespresso/calculations/cp.py

@@ -131,12 +131,6 @@ def define(cls, spec):
             message='The required XML file is not present in the retrieved folder.')
         spec.exit_code(304, 'ERROR_OUTPUT_XML_MULTIPLE',
             message='The retrieved folder contains multiple XML files.')
-        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
-            message='The stdout output file could not be read.')
-        spec.exit_code(311, 'ERROR_OUTPUT_STDOUT_PARSE',
-            message='The output file contains invalid output.')
-        spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
-            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(320, 'ERROR_OUTPUT_XML_READ',
             message='The required XML file could not be read.')
         spec.exit_code(330, 'ERROR_READING_POS_FILE',

src/aiida_quantumespresso/calculations/dos.py

@@ -27,10 +27,6 @@ def define(cls, spec):
         spec.output('output_parameters', valid_type=orm.Dict)
         spec.output('output_dos', valid_type=orm.XyData)
         spec.default_output_node = 'output_parameters'
-        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
-            message='The stdout output file could not be read.')
-        spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
-            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(330, 'ERROR_READING_DOS_FILE',
             message='The dos file could not be read from the retrieved folder.')
         # yapf: enable

src/aiida_quantumespresso/calculations/matdyn.py

@@ -37,10 +37,6 @@ def define(cls, spec):
         spec.output('output_phonon_bands', valid_type=orm.BandsData)
         spec.default_output_node = 'output_parameters'
 
-        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
-            message='The stdout output file could not be read.')
-        spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
-            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(330, 'ERROR_OUTPUT_FREQUENCIES',
             message='The output frequencies file could not be read from the retrieved folder.')
         spec.exit_code(410, 'ERROR_OUTPUT_KPOINTS_MISSING',

src/aiida_quantumespresso/calculations/namelists.py

@@ -58,6 +58,14 @@ def define(cls, spec):
             help='Use an additional node for special settings')
         spec.input('parent_folder', valid_type=(RemoteData, FolderData, SinglefileData), required=False,
             help='Use a local or remote folder as parent folder (for restarts and similar)')
+        spec.exit_code(302, 'ERROR_OUTPUT_STDOUT_MISSING',
+            message='The retrieved folder did not contain the required stdout output file.')
+        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
+            message='An exception was raised while reading the `stdout` file: {exception}')
+        spec.exit_code(311, 'ERROR_OUTPUT_STDOUT_PARSE',
+            message='An exception was raised while parsing the `stdout` file: {exception}')
+        spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
+            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         # yapf: enable
 
     @classmethod

src/aiida_quantumespresso/calculations/neb.py

@@ -78,12 +78,6 @@ def define(cls, spec):
         spec.default_output_node = 'output_parameters'
         spec.exit_code(303, 'ERROR_MISSING_XML_FILE',
             message='The required XML file is not present in the retrieved folder.')
-        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
-            message='The stdout output file could not be read.')
-        spec.exit_code(311, 'ERROR_OUTPUT_STDOUT_PARSE',
-            message='The output file contains invalid output.')
-        spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
-            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(320, 'ERROR_OUTPUT_XML_READ',
             message='The XML output file could not be read.')
         spec.exit_code(321, 'ERROR_OUTPUT_XML_PARSE',

src/aiida_quantumespresso/calculations/open_grid.py

@@ -28,13 +28,7 @@ def define(cls, spec):
 
         spec.exit_code(300, 'ERROR_NO_RETRIEVED_FOLDER',
             message='The retrieved folder data node could not be accessed.')
-        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
-            message='The stdout output file could not be read.')
-        spec.exit_code(311, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
-            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(312, 'ERROR_INCOMPATIBLE_FFT_GRID',
             message='Found rotation or fractional translation not compatible with FFT grid.')
-        spec.exit_code(340, 'ERROR_GENERIC_QE_ERROR',
-            message='Encountered a generic error message.')
         spec.exit_code(350, 'ERROR_OUTPUT_KPOINTS_MISMATCH',
             message='Mismatch between kmesh dimensions and number of kpoints.')

src/aiida_quantumespresso/calculations/pp.py

@@ -98,6 +98,8 @@ def define(cls, spec):
             message='The parent folder did not contain the required XML output file.')
         spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
             message='The stdout output file could not be read.')
+        spec.exit_code(311, 'ERROR_OUTPUT_STDOUT_PARSE',
+            message='The stdout output file could not be parsed.')
         spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
             message='The stdout output file was incomplete.')
         spec.exit_code(340, 'ERROR_OUT_OF_WALLTIME_INTERRUPTED',

src/aiida_quantumespresso/calculations/projwfc.py

@@ -62,10 +62,6 @@ def define(cls, spec):
             message='The retrieved temporary folder could not be accessed.')
         spec.exit_code(303, 'ERROR_OUTPUT_XML_MISSING',
             message='The retrieved folder did not contain the required XML file.')
-        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
-            message='The stdout output file could not be read.')
-        spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
-            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(320, 'ERROR_OUTPUT_XML_READ',
             message='The XML output file could not be read.')
         spec.exit_code(321, 'ERROR_OUTPUT_XML_PARSE',

src/aiida_quantumespresso/calculations/pw.py

@@ -87,20 +87,12 @@ def define(cls, spec):
         # Unrecoverable errors: required retrieved files could not be read, parsed or are otherwise incomplete
         spec.exit_code(301, 'ERROR_NO_RETRIEVED_TEMPORARY_FOLDER',
             message='The retrieved temporary folder could not be accessed.')
-        spec.exit_code(302, 'ERROR_OUTPUT_STDOUT_MISSING',
-            message='The retrieved folder did not contain the required stdout output file.')
         spec.exit_code(303, 'ERROR_OUTPUT_XML_MISSING',
             message='The retrieved folder did not contain the required XML file.')
         spec.exit_code(304, 'ERROR_OUTPUT_XML_MULTIPLE',
             message='The retrieved folder contained multiple XML files.')
         spec.exit_code(305, 'ERROR_OUTPUT_FILES',
             message='Both the stdout and XML output files could not be read or parsed.')
-        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
-            message='The stdout output file could not be read.')
-        spec.exit_code(311, 'ERROR_OUTPUT_STDOUT_PARSE',
-            message='The stdout output file could not be parsed.')
-        spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
-            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(320, 'ERROR_OUTPUT_XML_READ',
             message='The XML output file could not be read.')
         spec.exit_code(321, 'ERROR_OUTPUT_XML_PARSE',
@@ -116,8 +108,6 @@ def define(cls, spec):
             message='The code failed in finding a valid reciprocal lattice vector.')
 
         # Significant errors but calculation can be used to restart
-        spec.exit_code(400, 'ERROR_OUT_OF_WALLTIME',
-            message='The calculation stopped prematurely because it ran out of walltime.')
         spec.exit_code(410, 'ERROR_ELECTRONIC_CONVERGENCE_NOT_REACHED',
             message='The electronic minimization cycle did not reach self-consistency.')
 

src/aiida_quantumespresso/calculations/pw2gw.py

@@ -38,16 +38,8 @@ def define(cls, spec):
         spec.output('eps', valid_type=orm.ArrayData,
             help='The `eps` output node containing 5 arrays `energy`, `epsX`, `epsY`, `epsZ`, `epsTOT`')
 
-        spec.exit_code(302, 'ERROR_OUTPUT_STDOUT_MISSING',
-            message='The retrieved folder did not contain the required stdout output file.')
         spec.exit_code(305, 'ERROR_OUTPUT_FILES',
             message='The eps*.dat output files could not be read or parsed.')
-        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
-            message='The stdout output file could not be read.')
-        spec.exit_code(311, 'ERROR_OUTPUT_STDOUT_PARSE',
-            message='The stdout output file could not be parsed.')
-        spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
-            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(330, 'ERROR_OUTPUT_FILES_INVALID_FORMAT',
             message='The eps*.dat output files do not have the expected shape (N, 2).')
         spec.exit_code(331, 'ERROR_OUTPUT_FILES_ENERGY_MISMATCH',

src/aiida_quantumespresso/calculations/pw2wannier90.py

@@ -31,10 +31,6 @@ def define(cls, spec):
                    help='The output folder of a pw.x calculation')
         spec.output('output_parameters', valid_type=Dict)
         spec.default_output_node = 'output_parameters'
-        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
-            message='The stdout output file could not be read.')
-        spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
-            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(340, 'ERROR_GENERIC_QE_ERROR',
             message='Encountered a generic error message')
         spec.exit_code(350, 'ERROR_UNEXPECTED_PARSER_EXCEPTION',

src/aiida_quantumespresso/calculations/q2r.py

@@ -32,10 +32,6 @@ def define(cls, spec):
         super().define(spec)
         spec.input('parent_folder', valid_type=(orm.RemoteData, orm.FolderData), required=True)
         spec.output('force_constants', valid_type=ForceConstantsData)
-        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
-            message='The stdout output file could not be read.')
-        spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
-            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(330, 'ERROR_READING_FORCE_CONSTANTS_FILE',
             message='The force constants file could not be read.')
         # yapf: enable

src/aiida_quantumespresso/calculations/xspectra.py

@@ -61,12 +61,6 @@ def define(cls, spec):
         spec.output('spectra', valid_type=XyData)
         spec.default_output_node = 'output_parameters'
 
-        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ', message='The stdout output file could not be read.')
-        spec.exit_code(
-            312,
-            'ERROR_OUTPUT_STDOUT_INCOMPLETE',
-            message='The stdout output file was incomplete probably because the calculation got interrupted.'
-        )
         spec.exit_code(
             313,
             'ERROR_OUTPUT_ABSORBING_SPECIES_WRONG',