CHANGELOG.md

@@ -6,6 +6,26 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/)
 
 ## [Unreleased]
 
+## [0.5.6] - 2025-02-05
+
+### Added
+- **docs**: add a section on resource configuration ([#411](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/411))
+- **amml**: apply constraints optionally in view structure ([#405](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/405))
+- **amml**: add periodic boundary conditions (PBC) to input structure automatically with Vasp calculator ([#401](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/401))
+
+### Fixed
+- **interpreter**: fix warnings not being suppressed by `-w` flag ([#412](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/412))
+- **cli**: fix cases with empty search results to avoid crash of `%find ... load one` ([#410](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/410))
+- **interpreter**: fix printing the type in case of evaluation error ([#408](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/408))
+- **grammar**: fix a semantic version grammar rule ([#404](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/404))
+
+### Changed
+- **setup**: adapt package dependencies for the new fireworks release ([#413](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/413))
+- **amml**: change default value of an environment variable to the vendor default ([#411](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/411))
+- **interpreter**: do not show Python exception traceback of evaluation errors ([#402](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/402))
+- **docs**: make several corrections in docs ([#400](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/400))
+- **grammar**: make parse rule version requirement more precise ([#354](https://gitlab.kit.edu/kit/virtmat-tools/vre-language/-/issues/354))
+
 ## [0.5.5] - 2025-01-13
 
 ### Added

docs/installation.md

@@ -34,17 +34,17 @@ The project can be installed into a Python virtual environment using the `pip` p
     python -m pip install vre-language
     ```
 
-**NOTE: Broken install due to an open issue in FireWorks**
+**NOTE: Warnings due to an open issue in FireWorks**
 
-Fresh installations of VRE Language will currently *sometimes* not work. When running `texts` this error may occur
+Fresh installations of VRE Language will currently *sometimes* print many warnings containing this line when running `texts`:
 
 ```
 ModuleNotFoundError: No module named 'pytest'
 ```
 
-The error is documented in this [issue](https://github.com/materialsproject/fireworks/issues/535).
+The issue is documented [here](https://github.com/materialsproject/fireworks/issues/535).
 
-As a work-around, the `pytest` package can be installed via this command:
+The warning can be ignored or muted by installing the `pytest` package via this command:
 
 ```
 python -m pip install pytest

docs/tools.md

@@ -14,15 +14,15 @@ In all evaluation modes, the model is first parsed using a grammar. The grammar
 
 #### Instant and deferred modes
 
-In the *instant* mode the evaluation is performed *immediately* and *locally*. In *deferred* mode the evaluation is deferred but still performed *locally*. In *instant* and *deferred* modes the model does not persist after the interpreter has finished, i.e. the `texts script` has returned. Only parameters of `print` statements in the program will be evaluated.
+In the *instant* mode the evaluation is performed *immediately* and *locally*. In *deferred* mode the evaluation is deferred but still performed *locally*. In *instant* and *deferred* modes the model does not persist after the interpreter has finished, i.e. the `texts script` has returned. Only parameters of `print` and `view` statements in the program will be evaluated.
 
 #### Workflow mode
 
 In the *workflow* mode the intepreter creates a workflow from the model and stores the workflow in a database. Therefore, the model is *persistent* after the interpreter returns, i.e. the *model instance* continues existing on the database. A model instance can be retrieved via a *universally unique identifier* (UUID) that is generated at the time when the model instance is created. A model instance can only be evaluated and extended but not otherwise modified.
 
-If no additional flags are specified the model is not evaluated after interpretation except for parameters in `print` statements that contain no references to variables. Otherwise `n.c.` will be printed instead of the not yet computed values. Optionally, a model can be evaluated locally after the intepreter finishes by specifying the `-r | --autorun` flag. In this case all variables will be evaluated but only those in print statements will be printed. Additionally, the `-d | --on-demand` flag restricts the evaluation to only those variables that are referenced in `print` and `view` statements.
+If no additional flags are specified, the model is not evaluated after interpretation except for parameters in `print` and `view` statements that contain no references to variables. Otherwise `n.c.` will be printed instead of the not yet computed values and `view` statements will produce warnings. Optionally, a model can be evaluated locally after the intepreter finishes by specifying the `-r | --autorun` flag. In this case all variables will be evaluated but only those in `print`/`view` statements will be printed/displayed. Additionally, the `-d | --on-demand` flag restricts the evaluation to only those variables that are referenced in `print` and `view` statements.
 
-In order to work in workflow mode, a launchpad describing a connection to a MongoDB database must be configured. Using the flag `-l LAUNCHPAD_FILE, --launchpad-file LAUNCHPAD_FILE` the launchpad data (such as hostname, database name and credentials) can be optionally specified. Otherwise the script looks up the current working directory and then the folder `$HOME/.fireworks` for a launchpad configuration. More information about configuring a launchpad can be found [here](https://vre-middleware.readthedocs.io/en/latest/launchpad.html).
+In order to work in workflow mode, a launchpad describing a connection to a MongoDB database must be configured. Using the flag `-l LAUNCHPAD_FILE, --launchpad-file LAUNCHPAD_FILE` the launchpad data (such as hostname, database name and credentials) can be optionally specified. Otherwise `texts` looks up the current working directory and then the folder `$HOME/.fireworks` for a launchpad configuration. More information about configuring a launchpad can be found [here](https://vre-middleware.readthedocs.io/en/latest/installation.html#setting-up-fireworks-with-a-mongodb-instance).
 
 By using the `-h, --help` flag a summarized help can be obtained:
 
@@ -204,7 +204,7 @@ Repeated initialization error is issued by the interpreter when it applies seman
 
 ### Runtime errors
 
-Some errors occur only during the evaluation. These are called *runtime errors*. Runtime errors have the same format as the static errors. Runtime errors only occur if the evaluation is requested, e.g. by `print` statements. For example, this input:
+Some errors occur only during the evaluation. These are called *runtime errors*. Runtime errors have the same format as the static errors. Runtime errors only occur if the evaluation is requested, e.g. by `print` or `view` statements. For example, this input:
 
 ```
 length = 1 [m]

setup.cfg

 [metadata]
 name = vre-language
-version = 0.5.5
+version = 0.5.6
 author = The Virtmat Tools Team
 author_email = virtmat-tools@lists.kit.edu
 description = VRE Language

src/virtmat/language/constraints/chem.py

@@ -2,8 +2,7 @@
 from textx import get_children_of_type, textx_isinstance
 from virtmat.language.utilities.textx import get_reference
 from virtmat.language.utilities.errors import StaticValueError, raise_exception
-from virtmat.language.utilities.errors import issue_warning
-from virtmat.language.utilities.warnings import TextSUserWarning
+from virtmat.language.utilities.warnings import warnings, TextSUserWarning
 from virtmat.language.utilities.chemistry import is_equation_balanced
 
 
@@ -25,7 +24,7 @@ def check_chem_reaction_balance(react, metamodel):
     if len(lcomps+rcomps) != len(react.educts+react.products):
         msg = ('reaction balance check skipped due to missing '
                'composition in some terms')
-        issue_warning(react, TextSUserWarning, msg)
+        warnings.warn(TextSUserWarning(msg, obj=react))
         return
     if not is_equation_balanced(lcomps, lcoeff, rcomps, rcoeff):
         msg = ('Reaction equation is not balanced. Check '

src/virtmat/language/metamodel/processors.py

@@ -17,8 +17,8 @@ from virtmat.language.constraints.processors import add_constraints_processors
 from virtmat.language.constraints.processors import check_variable_update_processor
 from virtmat.language.interpreter.workflow_executor import workflow_model_processor
 from virtmat.language.utilities.textx import isinstance_m
-from virtmat.language.utilities.errors import raise_exception, StaticTypeError, error_handler
-from virtmat.language.utilities.warnings import TextSUserWarning
+from virtmat.language.utilities.errors import raise_exception, StaticTypeError
+from virtmat.language.utilities.warnings import warnings, TextSUserWarning
 from .function import function_call_processor
 from .workflow import source_code_statement_processor, qadapter_processor
 from .workflow import default_worker_name_processor, resources_processor
@@ -84,17 +84,15 @@ def print_parameter_processor(obj):
         setattr(obj, 'inp_units', getattr(obj, 'units', None))
 
 
-@error_handler
 def tag_processor(obj):
     """warn if tag is found in instant or in deferred evaluation modes"""
     msg = 'tags are interpreted only in workflow evaluation mode'
-    raise_exception(obj, TextSUserWarning, msg)
+    warnings.warn(TextSUserWarning(msg, obj=obj))
 
 
-@error_handler
 def vary_processor(obj):
     """warn if vary is found in instant or in deferred evaluation modes"""
-    raise_exception(obj, TextSUserWarning, 'vary statement has no effect')
+    warnings.warn(TextSUserWarning('vary statement has no effect', obj=obj))
 
 
 def add_obj_processors(metamodel, wflow_processors=False):

src/virtmat/language/metamodel/view.py

@@ -6,7 +6,7 @@ from matplotlib import pyplot
 from virtmat.language.utilities.types import is_array_type, is_array, is_numeric, NC
 from virtmat.language.utilities.errors import RuntimeTypeError, RuntimeValueError
 from virtmat.language.utilities.errors import textxerror_wrap, raise_exception, error_handler
-from virtmat.language.utilities.warnings import TextSUserWarning
+from virtmat.language.utilities.warnings import warnings, TextSUserWarning
 from virtmat.language.utilities.units import get_units, get_df_units
 from virtmat.language.utilities.units import convert_df_units, strip_units, ureg
 from virtmat.language.utilities.arrays import get_nested_array
@@ -165,7 +165,9 @@ def display(self, show=True):
     """define display() method in View metamodel class"""
     if any(get_par_value(par) is NC for par in self.params):
         par = next(p for p in self.params if get_par_value(p) is NC)
-        raise_exception(par, TextSUserWarning, 'parameter value is not computed yet')
+        msg = 'parameter value is not computed yet'
+        warnings.warn(TextSUserWarning(msg, obj=par))
+        return
     if self.mode in ('lineplot', 'scatterplot'):
         display_seaborn(self, show=show)
     elif self.mode == 'bs':

src/virtmat/language/utilities/ase_params.py

@@ -19,7 +19,7 @@ from virtmat.language.utilities.lists import list_apply
 
 spec = {
   'vasp': {
-    'module': 'ase.calculators.vasp',
+    'module': 'virtmat.language.utilities.ase_wrappers',
     'class': 'Vasp',
     'modulefile': {'name': 'vasp', 'verspec': '>=5.0.0'},
     'envvars': {'VASP_COMMAND': 'vasp_std'},

src/virtmat/language/utilities/ase_wrappers.py

@@ -15,9 +15,11 @@ from ase.dft.dos import DOS
 from ase.mep import NEBTools, DimerControl, MinModeAtoms, MinModeTranslate
 from ase.vibrations import Vibrations
 from ase.calculators.singlepoint import SinglePointCalculator
+from ase.calculators.vasp import Vasp
 from ase.md import velocitydistribution
 from virtmat.language.utilities.errors import RuntimeValueError
 from virtmat.language.utilities.ase_params import spec
+from virtmat.language.utilities.warnings import warnings, TextSUserWarning
 
 
 @contextmanager
@@ -287,3 +289,16 @@ class VibrationsWrapper(IOContext):
                         'eigen_imag': enes.imag, 'eigen_modes': modes,
                         'transition_state': imag == 1, 'energy_minimum': imag == 0}
         return True
+
+
+def vasp_calculate_decorator(func):
+    """perform modifications of Vasp.calculate's arguments"""
+    def calculate_wrapper(self, atoms, *args, **kwargs):
+        if not all(p for p in atoms.pbc):
+            warnings.warn('setting PBC for structure in Vasp', TextSUserWarning)
+            atoms.pbc = True
+        return func(self, atoms, *args, **kwargs)
+    return calculate_wrapper
+
+
+Vasp.calculate = vasp_calculate_decorator(vars(Vasp)['calculate'])

src/virtmat/language/utilities/errors.py

@@ -6,7 +6,6 @@ from pint.errors import PintError, DimensionalityError, UndefinedUnitError
 from pint.errors import OffsetUnitCalculusError
 from ase.calculators.calculator import CalculatorSetupError
 from virtmat.middleware.exceptions import ResourceConfigurationError
-from virtmat.language.utilities.warnings import TextSUserWarning
 from virtmat.language.utilities.compatibility import CompatibilityError
 from virtmat.language.utilities.textx import get_location_context
 
@@ -290,8 +289,6 @@ def process_error(err):
             err_type = 'File exists error'
         elif isinstance(err.__cause__, OSError):
             err_type = 'Operating system error'
-        elif isinstance(err.__cause__, TextSUserWarning):
-            err_type = 'Warning'
         else:
             raise err.__cause__
     else:
@@ -340,9 +337,3 @@ def error_handler(func):
         except Exception as err:
             raise RuntimeError('non-handled exception') from err
     return wrapper
-
-
-@error_handler
-def issue_warning(*args, **kwargs):
-    """issue a user warning or any other exception as a warning"""
-    raise_exception(*args, **kwargs)

src/virtmat/language/utilities/warnings.py

 """handling domain-specific warnings"""
 import warnings
+from virtmat.language.utilities.textx import get_location_context
+from virtmat.language.utilities.errors import format_textxerr_msg
 
 
 class TextSUserWarning(UserWarning):
     """warning to use within the processors"""
+    def __init__(self, *args, obj=None, **kwargs):
+        self.obj = obj
+        super().__init__(*args, **kwargs)
+        if obj:
+            for key, val in get_location_context(obj).items():
+                setattr(self, key, val)
+            self.message = str(self)
 
 
 def format_warning_wrapper(func):
@@ -13,6 +22,8 @@ def format_warning_wrapper(func):
         warning_cls = args[1]
         if isinstance(warning, TextSUserWarning):
             assert warning_cls is TextSUserWarning
+            if warning.obj:
+                return 'Warning: ' + format_textxerr_msg(warning) + '\n'
             return 'Warning: ' + str(warning) + '\n'
         return func(*args, **kwargs)
     return wrapper

tests/test_amml.py

@@ -5,6 +5,7 @@ import os
 import pytest
 from textx import get_children_of_type
 from textx.exceptions import TextXError
+from ase.calculators.calculator import CalculatorSetupError
 from virtmat.language.utilities.typemap import typemap
 from virtmat.language.utilities.amml import AMMLStructure
 from virtmat.language.utilities.errors import StaticValueError, RuntimeValueError
@@ -182,7 +183,7 @@ def test_amml_property_literal(meta_model, model_kwargs):
            "                )"
            "        ),"
            "        (cell: [[10., 0., 0.], [0., 10., 0.], [0., 0., 10.]] [angstrom]),"
-           "        (pbc: [true, true, true])"
+           "        (pbc: [true, true, false])"
            "      );"
            "calc = Calculator vasp >= 5.4.4 ("
            "          (algo: 'Fast'),"
@@ -207,7 +208,14 @@ def test_amml_property_literal(meta_model, model_kwargs):
            "          (xc: 'PBE')"
            "       );"
            "props = Property energy, forces ((structure: h2o), (calculator: calc))")
-    meta_model.model_from_str(inp, **model_kwargs)
+    prog = meta_model.model_from_str(inp, **model_kwargs)
+    var_list = get_children_of_type('Variable', prog)
+    msg = (r'Please set either command in calculator or one of the following '
+           r'environment variables \(prioritized as follows\): ASE_VASP_COMMAND, '
+           r'VASP_COMMAND, VASP_SCRIPT')
+    with pytest.raises(TextXError, match=msg) as err:
+        _ = next(v for v in var_list if v.name == 'props').value
+    assert isinstance(err.value.__cause__, CalculatorSetupError)
 
 
 def test_amml_property_access_properties(meta_model, model_kwargs):

tests/test_builtins.py

@@ -6,6 +6,7 @@ from textx import get_children_of_type
 from textx.exceptions import TextXError, TextXSyntaxError, TextXSemanticError
 from virtmat.language.utilities.typemap import typemap
 from virtmat.language.utilities.errors import VaryError
+from virtmat.language.utilities.warnings import TextSUserWarning
 
 
 def test_empty_program(meta_model, model_kwargs):
@@ -516,12 +517,13 @@ def test_scalar_complex_real_imag_parts(meta_model, model_kwargs):
     assert next(v for v in var_list if v.name == 'h').value is True
 
 
-def test_pointless_use_of_vary_statement(meta_model, model_kwargs, capsys):
+def test_pointless_use_of_vary_statement(meta_model, model_kwargs):
     """test pointless use of vary statement"""
-    warn_msg = 'vary statement has no effect'
-    meta_model.model_from_str('vary ((a: 1, 2))', **model_kwargs)
-    if not model_kwargs.get('model_instance'):
-        assert warn_msg in capsys.readouterr().err
+    if model_kwargs.get('model_instance'):
+        meta_model.model_from_str('vary ((a: 1, 2))', **model_kwargs)
+    else:
+        with pytest.warns(TextSUserWarning, match='vary statement has no effect'):
+            meta_model.model_from_str('vary ((a: 1, 2))', **model_kwargs)
 
 
 def test_invalid_reference_to_vary_statement(meta_model, model_kwargs):

tests/test_chemistry.py

@@ -6,6 +6,7 @@ from textx import get_children_of_type
 from textx.exceptions import TextXError
 from virtmat.language.utilities.errors import StaticTypeError, StaticValueError
 from virtmat.language.utilities.errors import RuntimeValueError
+from virtmat.language.utilities.warnings import TextSUserWarning
 from virtmat.language.utilities.formatters import formatter
 
 
@@ -110,13 +111,13 @@ def test_reaction_not_balanced_composition_ref(meta_model, model_kwargs):
     assert isinstance(err.value.__cause__, RuntimeValueError)
 
 
-def test_reaction_balance_check_skipped(meta_model, model_kwargs, capsys):
+def test_reaction_balance_check_skipped(meta_model, model_kwargs):
     """test when the reaction equation balance check is skipped"""
     inp = ("r = Reaction 2 H2 + O2 -> 2 H2O; H2O = Species H2O;"
            "H2 = Species H2, composition: 'H2'; O2 = Species O2, composition: 'O2'")
-    meta_model.model_from_str(inp, **model_kwargs)
-    std_err = capsys.readouterr().err
-    assert 'reaction balance check skipped due to missing composition' in std_err
+    msg = 'reaction balance check skipped due to missing composition'
+    with pytest.warns(TextSUserWarning, match=msg):
+        meta_model.model_from_str(inp, **model_kwargs)
 
 
 def test_chem_species_iterable(meta_model, model_kwargs):

tests/test_session.py

@@ -13,6 +13,7 @@ from virtmat.language.interpreter.workflow_executor import NonCompletedException
 from virtmat.language.utilities.errors import error_handler, ModelNotFoundError
 from virtmat.language.utilities.errors import VaryError, ReuseError, TagError
 from virtmat.language.utilities.errors import ConfigurationError, StaticValueError
+from virtmat.language.utilities.warnings import TextSUserWarning
 from virtmat.language.utilities.textx import GRAMMAR_LOC
 from virtmat.language.utilities.formatters import formatter
 
@@ -204,7 +205,7 @@ def test_session_model_with_uuid_and_grammar(lpad):
     old_session = Session(lpad, grammar_path=GRAMMAR_LOC, model_str='a = 1')
     assert old_session.uuid is not None
     msg = 'provided grammar ignored in favor of grammar from provided uuid'
-    with pytest.warns(UserWarning, match=msg):
+    with pytest.warns(TextSUserWarning, match=msg):
         Session(lpad, uuid=old_session.uuid, grammar_path=GRAMMAR_LOC)