docs/installation.md

@@ -34,30 +34,20 @@ 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: Broken install due to an 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* not work. When running `texts` this error may occur
 
 ```
-AttributeError:
-"safe_load()" has been removed, use
-
-  yaml = YAML(typ='safe', pure=True)
-  yaml.load(...)
-
-instead of file "jupyter-base-2024-05-14/lib64/python3.9/site-packages/fireworks/utilities/fw_serializers.py", line 256
-
-            dct = yaml.safe_load(f_str)
+ModuleNotFoundError: No module named 'pytest'
 ```
 
-This [issue](https://github.com/materialsproject/fireworks/issues/516) has been solved in FireWorks main branch but not yet released. See more discussions in this [issue](https://github.com/materialsproject/fireworks/issues/531).
+The error is documented in this [issue](https://github.com/materialsproject/fireworks/issues/535).
 
-As a work-around, VRE Language tries to downgrade `ruamel.yaml` automatically. If downgrade of `ruamel.yaml <0.18.0` is not possible, for example when the `ruamel.yaml` package is installed system-wide, then the error above occurs when running `texts`. In this case, another non-automatic workaround has to be performed by the user. A fresh virtual environment has to be created (without fireworks, vre-language and vre-middleware). Then VRE Language is installed by the following two commands:
+As a work-around, the `pytest` package can be installed via this command:
 
 ```
-python -m pip install git+https://github.com/materialsproject/fireworks.git
-python -m pip install vre-language
+python -m pip install pytest
 ```
 
 ## Installation in developer (editable) mode

docs/quickstart.md

@@ -14,7 +14,6 @@ The instructions for the quick installation and local database setup are:
 1. Install the VRE Language with the `mongomock` extra:
     ```bash
     python -m pip install --upgrade pip
-    python -m pip install git+https://github.com/materialsproject/fireworks.git
     python -m pip install "vre-language[mongomock]"
     ```
 

docs/resources.md

@@ -8,7 +8,7 @@ In the [*workflow* evaluation mode](tools.md#workflow-mode) it is possible to sp
 
 ## Granularity
 
-Currently the evaluation's granularity of the workflow executor is determined by the amount of computations in the individial [variables](scl.md#variables) in the model source. The reason for this is that the interpreter maps variables to the *tasks* within a task graph which is used to construct a workflow.
+Currently the evaluation's granularity of the workflow executor is determined by the amount of computations in individual [variables](scl.md#variables). The reason for this is that the interpreter maps variables to *tasks* within a task graph which is used to construct a workflow.
 
 **Rationale:** If a variable has several parameters, different from references to other variables, these will be executed on the same resources. This is beneficial only if no parameter or only one parameter requires a large amount of computation. If two or more parameters require high and different amounts of computation the granularity has to be decreased by splitting the statement into two or more statements such that in every statement maximum one parameter requires large computing resources (for example >95%).
 
@@ -87,6 +87,15 @@ In this example, `b` (which must be of [Series](scl.md#series) type) is split in
 
 The interpreter will split the input data as much as possible into equally sized chunks. Nevertheless, if the number of data elements is not divisible by the number of chunks some of the chunks may have different number of elements.
 
+## Resource configuration
+
+[Resource annotation](#resource-annotation) enables constructing a *qadapter* object fully automatically by the interpreter. For this the interpreter uses the resource configuration created by the [VRE Middleware](https://vre-middleware.readthedocs.io/en/latest/resconfig.html). The configurations of computing resources and environment modules are captured fully automatically by running the [resconfig tool](https://vre-middleware.readthedocs.io/en/latest/resconfig_cli.html) but some settings specific for the *run-time environment* are not. These are:
+* environment variables
+* shell commands
+* launch directory
+
+These and all other configurations can be set or modified (using Python) as described [here](https://vre-middleware.readthedocs.io/en/latest/resconfig.html).
+
 ## Glossary
 
 * [**Computing resource**](https://en.wikipedia.org/wiki/System_resource) requirement can be, for example, the number of processors, the size of memory and an estimate of the job running time.

requirements.txt

@@ -3,13 +3,12 @@ numpy
 pandas >=2.2.0
 pint >=0.24.3
 pint-pandas ==0.6.2
-fireworks >=2.0.3
+fireworks >=2.0.4
 pyyaml
 dill
 ase >=3.23.0
 seaborn
-vre-middleware >=1.2.1
+vre-middleware >=1.2.2
 jupyter_client
 ipykernel
-ruamel.yaml <0.18.0
 pympler

setup.cfg

@@ -39,15 +39,14 @@ install_requires =
     pandas >=2.2.0
     pint >=0.24.3
     pint-pandas ==0.7.1
-    fireworks >=2.0.3
+    fireworks >=2.0.4
     pyyaml
     dill
     ase >=3.23.0
     seaborn
-    vre-middleware >=1.2.1
+    vre-middleware >=1.2.2
     jupyter_client
     ipykernel
-    ruamel.yaml <0.18.0
     pympler
 
 [options.extras_require]

src/virtmat/language/interpreter/deferred_executor.py

@@ -23,7 +23,7 @@ from virtmat.language.utilities.formatters import formatter
 from virtmat.language.utilities.errors import textxerror_wrap, error_handler
 from virtmat.language.utilities.errors import SubscriptingError, PropertyError
 from virtmat.language.utilities.errors import InvalidUnitError, RuntimeValueError
-from virtmat.language.utilities.errors import RuntimeTypeError
+from virtmat.language.utilities.errors import RuntimeTypeError, TEXTX_WRAPPED_EXCEPTIONS
 from virtmat.language.utilities.typemap import typemap, checktype, checktype_
 from virtmat.language.utilities.typemap import is_table_like_type, is_table_like
 from virtmat.language.utilities.types import is_array, is_scalar, settype
@@ -110,13 +110,17 @@ def type_func(self):
        and callable(get_object_import(par.ref)) or not numeric):
         return (lambda: typemap['Table']([dct]), tuple())
     assert numeric
+    func, pars = par.func
 
-    def retfunc(val):
-        dct['dimensionality'] = str(get_dimensionality(val))
-        dct['units'] = str(get_units(val))
+    def retfunc(*args):
+        try:
+            val = func(*args)
+            dct['dimensionality'] = str(get_dimensionality(val))
+            dct['units'] = str(get_units(val))
+        except TEXTX_WRAPPED_EXCEPTIONS:
+            pass
         return typemap['Table']([dct])
-    func, pars = par.func
-    return (lambda *x: retfunc(func(*x)), pars)
+    return retfunc, pars
 
 
 def variable_func(self):

src/virtmat/language/interpreter/instant_executor.py

@@ -10,6 +10,7 @@ import numpy
 import pint_pandas
 from pint.errors import PintError
 from textx import get_children_of_type, get_parent_of_type
+from textx.exceptions import TextXError
 from virtmat.language.constraints.imports import get_object_import
 from virtmat.language.metamodel.function import subst
 from virtmat.language.utilities.textx import isinstance_m
@@ -158,8 +159,11 @@ def type_value(self):
            'numeric': numeric,
            'datatype': get_datatype_name(datatype)}
     if numeric:
-        dct['dimensionality'] = str(get_dimensionality(par.value))
-        dct['units'] = str(get_units(par.value))
+        try:
+            dct['dimensionality'] = str(get_dimensionality(par.value))
+            dct['units'] = str(get_units(par.value))
+        except TextXError:
+            pass
     return typemap['Table']([dct])
 
 

src/virtmat/language/interpreter/session_manager.py

@@ -241,10 +241,10 @@ class SessionManager(InteractiveConsole):
             wfs = self.get_wflows_from_user_query(q_dict)
             if model.load_one:
                 wf_uuids = [wf['metadata']['uuid'] for wf in wfs]
-                if self.uuid not in wf_uuids:
+                if wf_uuids and self.uuid not in wf_uuids:
                     self.switch_model(wf_uuids[0])
-                print('uuids:', formatter(self.uuid), formatter(self.session.uuids))
-            else:
+                    print('uuids:', formatter(self.uuid), formatter(self.session.uuids))
+            elif wfs:
                 lines = []
                 for wf in wfs:
                     lines.append(' '.join((f'{wf["state"]:10}',

src/virtmat/language/interpreter/workflow_executor.py

@@ -309,10 +309,14 @@ def type_value(self):
     if (isinstance_m(par, ['GeneralReference']) and isinstance_m(par.ref, ['ObjectImport'])
        and callable(get_object_import(par.ref))):
         return pandas.DataFrame([dct])
-    parval = get_par_value(par)
-    if parval is not NC and is_numeric(parval):
-        dct['dimensionality'] = str(get_dimensionality(parval))
-        dct['units'] = str(get_units(parval))
+    try:
+        parval = get_par_value(par)
+    except TextXError:
+        pass
+    else:
+        if parval is not NC and is_numeric(parval):
+            dct['dimensionality'] = str(get_dimensionality(parval))
+            dct['units'] = str(get_units(parval))
     if (isinstance_m(par, ['GeneralReference'])
        and not isinstance_m(par.ref, ['ObjectImport'])):
         model = get_model(self)

src/virtmat/language/utilities/ase_params.py

@@ -22,7 +22,7 @@ spec = {
     'module': 'ase.calculators.vasp',
     'class': 'Vasp',
     'modulefile': {'name': 'vasp', 'verspec': '>=5.0.0'},
-    'envvars': {'VASP_COMMAND': '"$DO_PARALLEL $VASP_MPI"'},
+    'envvars': {'VASP_COMMAND': 'vasp_std'},
     'properties': ['energy', 'dipole', 'forces', 'stress', 'vibrational_energies',
                    'energy_minimum', 'transition_state', 'trajectory', 'magmom',
                    'magmoms']

src/virtmat/language/utilities/fireworks.py

@@ -21,15 +21,24 @@ def launchdir(tmp_dir):
 
 def run_fireworks(lpad, fw_ids, worker_name=None, create_subdirs=False):
     """launch fireworks with the provided fw_ids"""
-    worker = FWorker(name=worker_name, query={'fw_id': {'$in': fw_ids}})
+    fw_query = {'fw_id': {'$in': fw_ids}}
+    launch_kwargs = {'strm_lvl': lpad.strm_lvl}
+    launch_kwargs['fworker'] = FWorker(name=worker_name, query=fw_query)
     cfg = get_default_resconfig()
-    default_launchdir = cfg and cfg.default_worker.default_launchdir
-    with launchdir(default_launchdir or os.getcwd()):
+    if cfg:
+        if worker_name:
+            wcfg = next(w for w in cfg.workers if w.name == worker_name)
+        else:
+            wcfg = cfg.default_worker
+        default_launchdir = wcfg.default_launchdir or os.getcwd()
+    else:
+        default_launchdir = os.getcwd()
+    with launchdir(default_launchdir):
         if create_subdirs:
-            rapidfire(lpad, fworker=worker, nlaunches=0, strm_lvl=lpad.strm_lvl)
+            rapidfire(lpad, nlaunches=0, local_redirect=True, **launch_kwargs)
         else:
             for _ in fw_ids:
-                launch_rocket(lpad, fworker=worker, strm_lvl=lpad.strm_lvl)
+                launch_rocket(lpad, **launch_kwargs)
 
 
 def get_nodes_providing(lpad, uuid, name):

tests/test_amml.py

@@ -398,7 +398,7 @@ def test_amml_property_resources(meta_model_wf, model_kwargs_wf, _res_config_loc
            "prop = Property energy, forces ((structure: h2o), (calculator: calc))"
            "       on 4 cores for 0.1 [hour]")
     pre_rocket = ('module purge; module use null; module load chem/vasp/5.4.4.pl2; '
-                  'export VASP_COMMAND="$DO_PARALLEL $VASP_MPI"')
+                  'export VASP_COMMAND=vasp_std')
     prog = meta_model_wf.model_from_str(inp, **model_kwargs_wf)
     var_list = get_children_of_type('Variable', prog)
     var = next(v for v in var_list if v.name == 'prop')

tests/test_builtins.py

@@ -548,6 +548,17 @@ def test_builtin_type_function(meta_model, model_kwargs):
     assert typ.value.units.tolist() == ['meter']
 
 
+def test_builtin_type_function_with_eval_error(meta_model, model_kwargs, test_config):
+    """test the built-in type function with evaluation error"""
+    prog_inp = "a = 2 / 0; print(type(a))"
+    prog = meta_model.model_from_str(prog_inp, **model_kwargs)
+    ref = ("((name: 'a'), (type: 'Quantity'), (scalar: true), (numeric: true),"
+           " (datatype: 'float')")
+    if test_config[1] or not test_config[0]:
+        # fixme: deferred will work only with non-strict eval
+        assert ref in prog.value
+
+
 def test_builtin_type_function_callable_import(meta_model, model_kwargs):
     """test the built-in type function with callable import"""
     prog_inp = "use random from numpy.random; print(type(random))"