Add GULP calculations (#4)

- update aiida-core to v1.0.0b3
- added GULP calculations, tests and documentation
- add dependencies for reading CIF files
- implement calculation submission tests (using process.prepare_for_submission)
- implement new calculation immigration method
- re-number calculation exit codes
- update readthedocs build

.condarc

@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+  - defaults
+
+# Show channel URLs when displaying what is going to be downloaded
+# and in 'conda list'. The default is False.
+show_channel_urls: True
+
+# For more information about this file see:
+# https://conda.io/docs/user-guide/configuration/use-condarc.html

.readthedocs.yml

@@ -8,8 +8,8 @@ python:
   install:
     - method: pip
       path: .
-      extra_requirements:
-          - docs
+      # extra_requirements:
+      #     - docs
 
 # default
 # sphinx:

.vscode/settings.json

@@ -18,12 +18,12 @@
     "python.linting.pylintEnabled": false,
     "python.linting.flake8Enabled": true,
     "python.linting.enabled": true,
-    "python.unitTest.pyTestArgs": [
+    "python.testing.pyTestArgs": [
         "aiida_crystal17"
     ],
-    "python.unitTest.unittestEnabled": false,
-    "python.unitTest.nosetestsEnabled": false,
-    "python.unitTest.pyTestEnabled": true,
+    "python.testing.unittestEnabled": false,
+    "python.testing.nosetestsEnabled": false,
+    "python.testing.pyTestEnabled": true,
     "restructuredtext.preview.sphinx.disabled": true,
     "restructuredtext.confPath": "${workspaceFolder}/docs/source"
 }

aiida_crystal17/__init__.py

@@ -4,4 +4,4 @@
 AiiDA plugin for running the CRYSTAL17 code
 """
 
-__version__ = "0.5.0b2"
+__version__ = "0.5.0b3"

aiida_crystal17/calculations/cry_abstract.py

@@ -32,24 +32,31 @@ def define(cls, spec):
         spec.input('metadata.options.parser_name',
                    valid_type=six.string_types, default='crystal17.main')
 
+        # TODO review aiidateam/aiida_core#2997, when closed, for exit code formalization
+
+        # Unrecoverable errors: resources like the retrieved folder or its expected contents are missing
         spec.exit_code(
-            130, 'ERROR_NO_RETRIEVED_FOLDER',
+            200, 'ERROR_NO_RETRIEVED_FOLDER',
             message='The retrieved folder data node could not be accessed.')
         spec.exit_code(
-            140, 'ERROR_OUTPUT_FILE_MISSING',
+            210, 'ERROR_OUTPUT_FILE_MISSING',
             message='the main output file was not found')
+
+        # Unrecoverable errors: required retrieved files could not be read, parsed or are otherwise incomplete
         spec.exit_code(
-            200, 'ERROR_CRYSTAL_RUN',
-            message='The main crystal output file flagged an error')
-        spec.exit_code(
-            210, 'ERROR_OUTPUT_PARSING',
+            300, 'ERROR_OUTPUT_PARSING',
             message=('An error was flagged trying to parse the '
                      'main crystal output file'))
+
+        # Significant errors but calculation can be used to restart
+        spec.exit_code(
+            400, 'ERROR_CRYSTAL_RUN',
+            message='The main crystal output file flagged an error')
         spec.exit_code(
-            220, 'ERROR_SYMMETRY_INCONSISTENCY',
+            410, 'ERROR_SYMMETRY_INCONSISTENCY',
             message=('inconsistency in the input and output symmetry'))
         spec.exit_code(
-            230, 'ERROR_SYMMETRY_NOT_FOUND',
+            420, 'ERROR_SYMMETRY_NOT_FOUND',
             message=('primitive symmops were not found in the output file'))
 
         spec.output(cls.link_output_results,

aiida_crystal17/calculations/cry_main.py

@@ -7,7 +7,9 @@
 import six
 from aiida.common.datastructures import (CalcInfo, CodeInfo)
 from aiida.common.exceptions import InputValidationError
+from aiida.orm import Code
 from aiida.plugins import DataFactory
+
 from aiida_crystal17.calculations.cry_abstract import CryAbstractCalculation
 from aiida_crystal17.parsers.gui_parse import gui_file_write
 from aiida_crystal17.parsers.inputd12_write import (
@@ -57,7 +59,7 @@ def define(cls, spec):
     @classmethod
     def create_builder(cls, parameters, structure, bases,
                        symmetry=None, kinds=None,
-                       code=None, options=None, unflatten=False):
+                       code=None, metadata=None, unflatten=False):
         """ prepare and validate the inputs to the calculation,
         and return a builder pre-populated with the calculation inputs
 
@@ -72,9 +74,9 @@ def create_builder(cls, parameters, structure, bases,
             or dict mapping {<symbol>: <BasisSetData>}
         symmetry: SymmetryData or None
             giving symmetry operations, etc
-        options: dict
-            the computation option, e.g.
-            {"resources": {"num_machines": 1, "num_mpiprocs_per_machine": 1}}
+        metadata: dict
+            the computation metadata, e.g.
+            {"options": {"resources": {"num_machines": 1, "num_mpiprocs_per_machine": 1}}}
         unflatten: bool
             whether to unflatten the input parameters dictionary
 
@@ -94,9 +96,11 @@ def create_builder(cls, parameters, structure, bases,
         if kinds is not None:
             builder.kinds = kinds
         if code is not None:
+            if isinstance(code, six.string_types):
+                code = Code.get_from_string(code)
             builder.code = code
-        if options is not None:
-            builder.metadata.options = options
+        if metadata is not None:
+            builder.metadata = metadata
 
         # validate parameters
         atom_props = create_atom_properties(structure, kinds)

aiida_crystal17/calculations/tests/test_cry_basic.py

@@ -3,23 +3,24 @@
 """
 import os
 
-import aiida_crystal17
-from aiida_crystal17.tests import TEST_DIR
 import ejplugins
 from jsonextended import edict
 import pytest
 
+import aiida_crystal17
+from aiida_crystal17.tests import TEST_DIR
+from aiida_crystal17.tests.utils import AiidaTestApp  # noqa: F401
 
-@pytest.mark.skip(reason="dry run implemented after v1.0.0b2")
-def test_dry_run(db_test_app):
+
+def test_calcjob_submission(db_test_app):
+    # type: (AiidaTestApp) -> None
     """Test submitting a calculation"""
-    from aiida.engine import run_get_node
     from aiida.plugins import DataFactory
-    SinglefileData = DataFactory('singlefile')
+    singlefile_data_cls = DataFactory('singlefile')
 
     # Prepare input parameters
     code = db_test_app.get_or_create_code('crystal17.basic')
-    infile = SinglefileData(
+    infile = singlefile_data_cls(
         file=os.path.join(TEST_DIR, "input_files",
                           'mgo_sto3g_scf.crystal.d12'))
     infile.store()
@@ -29,15 +30,21 @@ def test_dry_run(db_test_app):
     builder.metadata.options.withmpi = False
     builder.metadata.options.resources = {
         "num_machines": 1, "num_mpiprocs_per_machine": 1}
-    builder.metadata.store_provenance = True
     builder.input_file = infile
 
-    builder.metadata.dry_run = True
+    with db_test_app.sandbox_folder() as folder:
+        calc_info = db_test_app.generate_calcinfo(
+            'crystal17.basic', folder, builder)
 
-    outcome = run_get_node(builder)
+        cmdline_params = ['main']
+        local_copy_list = [[infile.uuid, infile.filename, u'main.d12']]
+        retrieve_list = ['main.out', 'main.gui']
 
-    incoming = outcome.node.get_incoming()
-    assert set(incoming.all_link_labels()) == set(['code', 'input_file'])
+        # Check the attributes of the returned `CalcInfo`
+        assert calc_info.codes_info[0].cmdline_params == cmdline_params
+        assert sorted(calc_info.local_copy_list) == sorted(local_copy_list)
+        assert sorted(calc_info.retrieve_list) == sorted(retrieve_list)
+        assert sorted(calc_info.retrieve_temporary_list) == sorted([])
 
 
 @pytest.mark.parametrize("inpath_main,inpath_gui", (
@@ -47,11 +54,12 @@ def test_dry_run(db_test_app):
 ))
 @pytest.mark.timeout(60)
 @pytest.mark.process_execution
-def test_full_runs(db_test_app, inpath_main, inpath_gui):
+def test_calcjob_run(db_test_app, inpath_main, inpath_gui):
+    # type: (AiidaTestApp, str, str) -> None
     """Test running an optimisation calculation"""
     from aiida.engine import run_get_node
     from aiida.plugins import DataFactory
-    SinglefileData = DataFactory('singlefile')
+    singlefile_data_cls = DataFactory('singlefile')
 
     code = db_test_app.get_or_create_code('crystal17.basic')
 
@@ -69,11 +77,11 @@ def test_full_runs(db_test_app, inpath_main, inpath_gui):
     }
 
     # Prepare input parameters
-    infile = SinglefileData(
+    infile = singlefile_data_cls(
         file=os.path.join(TEST_DIR, "input_files", inpath_main))
     builder.input_file = infile
     if inpath_gui is not None:
-        ingui = SinglefileData(
+        ingui = singlefile_data_cls(
             file=os.path.join(TEST_DIR, "input_files", inpath_gui))
         builder.input_external = ingui