aiida-chemshell 0.2.2__tar.gz → 0.3.0__tar.gz

{aiida_chemshell-0.2.2/src/aiida_chemshell.egg-info → aiida_chemshell-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiida-chemshell
-Version: 0.2.2
+Version: 0.3.0
 Summary: AiiDA workflow plugin for the ChemShell chemical modelling software package
 Author-email: "Dr. Benjamin T. Speake" <benjamin.speake@stfc.ac.uk>
 License: BSD 3-Clause License
@@ -46,6 +46,7 @@ Provides-Extra: dev
 Requires-Dist: aiida-core>=2.8; extra == "dev"
 Requires-Dist: pytest>=8.0; extra == "dev"
 Requires-Dist: pytest-cov>=6.0; extra == "dev"
+Requires-Dist: pytest-xdist>=3.0; extra == "dev"
 Requires-Dist: ruff>=0.11.0; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
@@ -64,30 +65,28 @@ Dynamic: license-file
 
 [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.18392782-blue.svg)](https://doi.org/10.5281/zenodo.18392782)
 
-
 # AiiDA ChemShell
 
-An [AiiDA](https://www.aiida.net) plugin for the [ChemShell](https://chemshell.org/) multiscale 
-computational chemistry software package. 
+An [AiiDA](https://www.aiida.net) plugin for the [ChemShell](https://chemshell.org/) multiscale
+computational chemistry software package.
 
-## Installation 
+## Installation
 
-This plugin is available through PyPI and should be installed using [`pip`](https://pip.pypa.io/en/stable/) python package manager. 
+This plugin is available through PyPI and should be installed using [`pip`](https://pip.pypa.io/en/stable/) python package manager.
 
-```
+``` bash
 pip install aiida-chemshell 
 ```
 
-## Requirements 
-
-To use this plugin a configured AiiDA profile and computer configuration are required, see the 
-[AiiDa documentation](https://aiida.readthedocs.io/projects/aiida-core/en/latest/intro/get_started.html) 
-for instructions on how to install and configure AiiDA. 
+## Requirements
 
+To use this plugin a configured AiiDA profile and computer configuration are required, see the
+[AiiDa documentation](https://aiida.readthedocs.io/projects/aiida-core/en/latest/intro/get_started.html)
+for instructions on how to install and configure AiiDA.
 
-## Setup 
+## Setup
 
-To configure the ChemShell plugin an AiiDA code instance needs to be configured for the ChemShell executable. 
+To configure the ChemShell plugin an AiiDA code instance needs to be configured for the ChemShell executable.
 The following is an example of a basic YAML configuration file:
 
 ```yaml
@@ -109,30 +108,31 @@ step. The code can then be configured by running:
 verdi code create core.code.installed --config chemshell.yml -n 
 ```
 
-If successful this will have created a code with the label `chemsh` which can then be used to run ChemShell jobs within the AiiDA workflow. 
+If successful this will have created a code with the label `chemsh` which can then be used to run ChemShell jobs within the AiiDA workflow.
 
 ### ChemShell with MPI
 
-It is important to note that the configuration of an MPI enabled ChemShell code differs slightly depending on whether the code instance uses 
+It is important to note that the configuration of an MPI enabled ChemShell code differs slightly depending on whether the code instance uses
 the `chemsh` or `chemsh.x` executable. If you have a parallel (MPI enabled) build of ChemShell but are using the `chemsh` wrapper executable
 please set `with_mpi: false` as the underlying plugin will handle how to call the mpi runtime. If you are calling the `chemsh.x` executable
-directly then `with_mpi: true` is required to run parallel jobs. 
+directly then `with_mpi: true` is required to run parallel jobs.
 
-## Examples 
+## Examples
 
-### QM Based Single Point Energy 
+### QM Based Single Point Energy
 
-The following is a python script that will run a Quantum Mechanics based single point energy calculation using the NWChem ChemShell interface. 
-The associated structure file can be found in the `tests/data/` folder. 
+The following is a python script that will run a Quantum Mechanics based single point energy calculation using the NWChem ChemShell interface.
+The associated structure file can be found in the `tests/data/` folder.
 
-```python 
-from aiida.engine import run 
+```python
+from aiida.engine import run
 from aiida.orm import load_code, SinglefileData, Dict
-from aiida import load_profile 
+from aiida import load_profile
 
-load_profile("user_profile")  # This is not required if running in a verdi shell environment 
+# This is not required if running in a verdi shell environment
+load_profile("user_profile")
 
-builder = load_code("chemsh").get_builder() 
+builder = load_code("chemsh").get_builder()
 builder.structure = SinglefileData(file="/absolute/path/to/water.cjson")
 builder.qm_parameters = Dict({"theory": "NWChem", "method": "HF", "basis": "3-21G"})
 builder.calculation_parameters = Dict({"gradients": False, "hessian": False})
@@ -142,19 +142,20 @@ results, node = run.get_node(builder)
 print("Final Energy = ", results.get("energy"))
 ```
 
-This can either be run as a script or as directly within a verdi shell python environment. 
+This can either be run as a script or as directly within a verdi shell python environment.
 
-### QM/MM Based Geometry Optimisation 
+### QM/MM Based Geometry Optimisation
 
 The following is a python script that will run a combined QM/MM based geometry optimisation using the NWChem and DL_POLY ChemShell interfaces.
-The associated structure and force field files can be found in the `tests/data/` folder. 
+The associated structure and force field files can be found in the `tests/data/` folder.
 
-```python 
-from aiida.engine import run 
+```python
+from aiida.engine import run
 from aiida.orm import load_code, SinglefileData, Dict
-from aiida import load_profile 
+from aiida import load_profile
 
-load_profile("user_profile")  # This is not required if running in a verdi shell environment 
+# This is not required if running in a verdi shell environment
+load_profile("user_profile")
 
 builder = load_code("chemsh").get_builder()
 builder.structure = SinglefileData(file="/absolute/path/to/h2o_dimer.cjson")

{aiida_chemshell-0.2.2 → aiida_chemshell-0.3.0}/README.md

@@ -7,30 +7,28 @@
 
 [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.18392782-blue.svg)](https://doi.org/10.5281/zenodo.18392782)
 
-
 # AiiDA ChemShell
 
-An [AiiDA](https://www.aiida.net) plugin for the [ChemShell](https://chemshell.org/) multiscale 
-computational chemistry software package. 
+An [AiiDA](https://www.aiida.net) plugin for the [ChemShell](https://chemshell.org/) multiscale
+computational chemistry software package.
 
-## Installation 
+## Installation
 
-This plugin is available through PyPI and should be installed using [`pip`](https://pip.pypa.io/en/stable/) python package manager. 
+This plugin is available through PyPI and should be installed using [`pip`](https://pip.pypa.io/en/stable/) python package manager.
 
-```
+``` bash
 pip install aiida-chemshell 
 ```
 
-## Requirements 
-
-To use this plugin a configured AiiDA profile and computer configuration are required, see the 
-[AiiDa documentation](https://aiida.readthedocs.io/projects/aiida-core/en/latest/intro/get_started.html) 
-for instructions on how to install and configure AiiDA. 
+## Requirements
 
+To use this plugin a configured AiiDA profile and computer configuration are required, see the
+[AiiDa documentation](https://aiida.readthedocs.io/projects/aiida-core/en/latest/intro/get_started.html)
+for instructions on how to install and configure AiiDA.
 
-## Setup 
+## Setup
 
-To configure the ChemShell plugin an AiiDA code instance needs to be configured for the ChemShell executable. 
+To configure the ChemShell plugin an AiiDA code instance needs to be configured for the ChemShell executable.
 The following is an example of a basic YAML configuration file:
 
 ```yaml
@@ -52,30 +50,31 @@ step. The code can then be configured by running:
 verdi code create core.code.installed --config chemshell.yml -n 
 ```
 
-If successful this will have created a code with the label `chemsh` which can then be used to run ChemShell jobs within the AiiDA workflow. 
+If successful this will have created a code with the label `chemsh` which can then be used to run ChemShell jobs within the AiiDA workflow.
 
 ### ChemShell with MPI
 
-It is important to note that the configuration of an MPI enabled ChemShell code differs slightly depending on whether the code instance uses 
+It is important to note that the configuration of an MPI enabled ChemShell code differs slightly depending on whether the code instance uses
 the `chemsh` or `chemsh.x` executable. If you have a parallel (MPI enabled) build of ChemShell but are using the `chemsh` wrapper executable
 please set `with_mpi: false` as the underlying plugin will handle how to call the mpi runtime. If you are calling the `chemsh.x` executable
-directly then `with_mpi: true` is required to run parallel jobs. 
+directly then `with_mpi: true` is required to run parallel jobs.
 
-## Examples 
+## Examples
 
-### QM Based Single Point Energy 
+### QM Based Single Point Energy
 
-The following is a python script that will run a Quantum Mechanics based single point energy calculation using the NWChem ChemShell interface. 
-The associated structure file can be found in the `tests/data/` folder. 
+The following is a python script that will run a Quantum Mechanics based single point energy calculation using the NWChem ChemShell interface.
+The associated structure file can be found in the `tests/data/` folder.
 
-```python 
-from aiida.engine import run 
+```python
+from aiida.engine import run
 from aiida.orm import load_code, SinglefileData, Dict
-from aiida import load_profile 
+from aiida import load_profile
 
-load_profile("user_profile")  # This is not required if running in a verdi shell environment 
+# This is not required if running in a verdi shell environment
+load_profile("user_profile")
 
-builder = load_code("chemsh").get_builder() 
+builder = load_code("chemsh").get_builder()
 builder.structure = SinglefileData(file="/absolute/path/to/water.cjson")
 builder.qm_parameters = Dict({"theory": "NWChem", "method": "HF", "basis": "3-21G"})
 builder.calculation_parameters = Dict({"gradients": False, "hessian": False})
@@ -85,19 +84,20 @@ results, node = run.get_node(builder)
 print("Final Energy = ", results.get("energy"))
 ```
 
-This can either be run as a script or as directly within a verdi shell python environment. 
+This can either be run as a script or as directly within a verdi shell python environment.
 
-### QM/MM Based Geometry Optimisation 
+### QM/MM Based Geometry Optimisation
 
 The following is a python script that will run a combined QM/MM based geometry optimisation using the NWChem and DL_POLY ChemShell interfaces.
-The associated structure and force field files can be found in the `tests/data/` folder. 
+The associated structure and force field files can be found in the `tests/data/` folder.
 
-```python 
-from aiida.engine import run 
+```python
+from aiida.engine import run
 from aiida.orm import load_code, SinglefileData, Dict
-from aiida import load_profile 
+from aiida import load_profile
 
-load_profile("user_profile")  # This is not required if running in a verdi shell environment 
+# This is not required if running in a verdi shell environment
+load_profile("user_profile")
 
 builder = load_code("chemsh").get_builder()
 builder.structure = SinglefileData(file="/absolute/path/to/h2o_dimer.cjson")

{aiida_chemshell-0.2.2 → aiida_chemshell-0.3.0}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
 [project]
-version = "0.2.2"
+version = "0.3.0"
 name = "aiida-chemshell"
 description = "AiiDA workflow plugin for the ChemShell chemical modelling software package"
 authors = [
@@ -46,11 +46,23 @@ dev = [
     "aiida-core>=2.8",
     "pytest>=8.0",
     "pytest-cov>=6.0",
+    "pytest-xdist>=3.0",
     "ruff>=0.11.0",
     "pre-commit",
 ]
 docs = ["sphinx>=8.0.2", "piccolo-theme>=0.14.0", "sphinx-toolbox", "numpydoc"]
 
+[tool.pytest.ini_options]
+filterwarnings = [
+    # Third-party warnings we cannot act on and that only add noise:
+    # plumpy still calls the deprecated asyncio.get_event_loop().
+    "ignore:There is no current event loop:DeprecationWarning",
+    # AiiDA's SQLAlchemy storage backend emits autoflush session warnings.
+    "ignore::sqlalchemy.exc.SAWarning",
+    # AiiDA reports creating its config folder inside the temp test profile.
+    "ignore:Creating AiiDA configuration folder:UserWarning",
+]
+
 [tool.ruff]
 target-version = "py310"
 line-length = 88

{aiida_chemshell-0.2.2 → aiida_chemshell-0.3.0}/src/aiida_chemshell/workflows/batch_calculation.py

@@ -1,9 +1,17 @@
 """Workflow for processing a series of structures from a single input."""
 
 import re
+from io import BytesIO
 
 from aiida.engine import ProcessSpec, ToContext, WorkChain, calcfunction
-from aiida.orm import ProcessNode, SinglefileData, StructureData, TrajectoryData
+from aiida.orm import (
+    ArrayData,
+    Float,
+    ProcessNode,
+    SinglefileData,
+    StructureData,
+    TrajectoryData,
+)
 from aiida.plugins.factories import CalculationFactory
 
 ChemShellCalculation = CalculationFactory("chemshell")
@@ -49,6 +57,30 @@ class BatchProcessWorkChain(WorkChain):
             ),
         )
 
+        # Results combination key
+        spec.input(
+            "combine_results",
+            valid_type=bool,
+            required=False,
+            non_db=True,
+            help=(
+                "A key which tells the workchain to combine all the results from the "
+                "individual batch processing tasks into one final results object which "
+                'is an extended xyz file (key="xyz").'
+            ),
+            # validator=cls.validate_combination_input_key,
+        )
+        # Results combination output node
+        spec.output(
+            "combined_results",
+            valid_type=SinglefileData,
+            required=False,
+            help=(
+                "An extended XYZ file with all the ChemShell results from the batch "
+                "processed input structures."
+            ),
+        )
+
         spec.exit_code(
             350,
             "ERROR_NO_INPUTS",
@@ -65,6 +97,16 @@ class BatchProcessWorkChain(WorkChain):
             cls.collate_results,
         )
 
+    # @classmethod
+    # def validate_combination_input_key(cls, key: str | None, _) -> str | None:
+    #     """Validate the combine_results input key."""
+    #     if key in ["xyz", "trajectory"]:
+    #         return None
+    #     return (
+    #         f"Invalid input for 'combine_results'. {key} must be either 'xyz' or "
+    #         "'trajectory'"
+    #     )
+
     def validate_inputs(self):
         """Validate the inputs provided to the WorkChain."""
         has_trajectory = "trajectory" in self.inputs
@@ -130,6 +172,46 @@ class BatchProcessWorkChain(WorkChain):
 
     def collate_results(self) -> None:
         """Collect the WorkChain's results."""
+        if self.inputs.get("combine_results", None):
+            if "optimisation_parameters" in self.inputs:
+                self.logger.warning(
+                    "Output combination is not currently supported for optimisation "
+                    "jobs."
+                )
+                return
+            inputs = {}
+            include_forces = self.inputs.get("calculation_parameters", {}).get(
+                "gradients", False
+            )
+            if "trajectory" in self.inputs:
+                inputs["structure_trajectory"] = self.inputs.trajectory
+                for i in range(self.inputs.trajectory.numsteps):
+                    inputs[f"energy_trajectory_frame_{i}"] = self.ctx[
+                        f"trajectory_frame_{i}"
+                    ].outputs.energy
+                    if include_forces:
+                        inputs[f"array_trajectory_frame_{i}"] = self.ctx[
+                            f"trajectory_frame_{i}"
+                        ].outputs.gradients
+            if "structures" in self.inputs:
+                for key, structure in self.inputs.structures.items():
+                    inputs[f"structure_{key}"] = structure
+                    inputs[f"energy_{key}"] = self.ctx[key].outputs.energy
+                    if include_forces:
+                        inputs[f"array_{key}"] = self.ctx[key].outputs.gradients
+            if "structure_files" in self.inputs:
+                for key, structure in self.structures_from_files.items():
+                    inputs[f"structure_{key}"] = structure
+                    inputs[f"energy_{key}"] = self.ctx[key].outputs.energy
+                    if include_forces:
+                        inputs[f"array_{key}"] = self.ctx[key].outputs.gradients
+            combined_output_node = combine_into_extended_xyz(**inputs)
+            combined_output_node.label = "ChemShell Batch Processed Structures"
+            combined_output_node.description = (
+                "Collection of structures processed by ChemShell from WorkChain: "
+                f" {self.node.pk}"
+            )
+            self.out("combined_results", combined_output_node)
         return
 
 
@@ -203,3 +285,73 @@ def extract_structures_from_xyz(file: SinglefileData):
         i += natoms
 
     return structures
+
+
+@calcfunction
+def combine_into_extended_xyz(**kwargs) -> SinglefileData:
+    """Combine a set of batch results into a single extxyz file."""
+    structures: list[StructureData] = []
+    energies: list[Float] = []
+    arrays: list[ArrayData] = []
+
+    # Extract individual structures and SP calculation results.
+    for _key, node in kwargs.items():
+        if isinstance(node, TrajectoryData):
+            for tindex in range(node.numsteps):
+                structures.append(node.get_step_structure(tindex))
+        elif isinstance(node, StructureData):
+            structures.append(node)
+        elif isinstance(node, Float):
+            energies.append(node)
+        elif isinstance(node, ArrayData):  # Ensure after TrajectoryData !!
+            arrays.append(node)
+        else:
+            raise ValueError(
+                f"Invalid input of type {node} to 'combine_into_extended_xyz' "
+                "calcfunction."
+            )
+    if not structures:
+        raise ValueError("No StructureData nodes were provided.")
+    if len(structures) != len(energies):
+        raise ValueError(
+            f"Mismatched input lengths: received {len(structures)} structures and "
+            f"{len(energies)} energies."
+        )
+    if arrays:
+        if len(arrays) != len(energies):
+            raise ValueError(
+                f"Mismatched input lengths: received {len(arrays)} arrays and "
+                f"{len(energies)} energies."
+            )
+
+    xyz_lines = []
+
+    for i in range(len(structures)):
+        structure = structures[i]
+        energy = energies[i]
+
+        xyz_lines.append(str(len(structure.sites)))
+
+        header_line = f"Energy={energy.value}"
+        if arrays:
+            forces = arrays[i].get_array("gradients")
+            header_line += " Properties=species:S:1:pos:R:3:force:R:3"
+        else:
+            forces = None
+            header_line += " Properties=species:S:1:pos:R:3"
+        xyz_lines.append(header_line)
+
+        for j, site in enumerate(structure.sites):
+            kind = structure.get_kind(site.kind_name)
+            symbol = kind.symbols[0]
+            x, y, z = site.position
+            site_line = f"{symbol:<4} {x:15.8f} {y:15.8f} {z:15.8f}"
+            if forces is not None:
+                fx, fy, fz = forces[j]
+                site_line += f" {fx:15.8f} {fy:15.8f} {fz:15.8f}"
+            xyz_lines.append(site_line)
+
+    content = "\n".join(xyz_lines)
+    stream = BytesIO(content.encode("utf-8"))
+
+    return SinglefileData(file=stream, filename="chemshell_batch_workchain.extxyz")

{aiida_chemshell-0.2.2 → aiida_chemshell-0.3.0}/src/aiida_chemshell/workflows/isolated_atoms.py

@@ -22,7 +22,7 @@ class IsolatedAtomicEnergiesWorkChain(WorkChain):
             ChemShellCalculation, include=("structure", "qm_parameters", "code")
         )
         spec.expose_inputs(
-            ChemShellCalculation, include=("metadata"), namespace="chemsh"
+            ChemShellCalculation, include=("metadata",), namespace="chemsh"
         )
 
         spec.output(

{aiida_chemshell-0.2.2 → aiida_chemshell-0.3.0/src/aiida_chemshell.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiida-chemshell
-Version: 0.2.2
+Version: 0.3.0
 Summary: AiiDA workflow plugin for the ChemShell chemical modelling software package
 Author-email: "Dr. Benjamin T. Speake" <benjamin.speake@stfc.ac.uk>
 License: BSD 3-Clause License
@@ -46,6 +46,7 @@ Provides-Extra: dev
 Requires-Dist: aiida-core>=2.8; extra == "dev"
 Requires-Dist: pytest>=8.0; extra == "dev"
 Requires-Dist: pytest-cov>=6.0; extra == "dev"
+Requires-Dist: pytest-xdist>=3.0; extra == "dev"
 Requires-Dist: ruff>=0.11.0; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
@@ -64,30 +65,28 @@ Dynamic: license-file
 
 [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.18392782-blue.svg)](https://doi.org/10.5281/zenodo.18392782)
 
-
 # AiiDA ChemShell
 
-An [AiiDA](https://www.aiida.net) plugin for the [ChemShell](https://chemshell.org/) multiscale 
-computational chemistry software package. 
+An [AiiDA](https://www.aiida.net) plugin for the [ChemShell](https://chemshell.org/) multiscale
+computational chemistry software package.
 
-## Installation 
+## Installation
 
-This plugin is available through PyPI and should be installed using [`pip`](https://pip.pypa.io/en/stable/) python package manager. 
+This plugin is available through PyPI and should be installed using [`pip`](https://pip.pypa.io/en/stable/) python package manager.
 
-```
+``` bash
 pip install aiida-chemshell 
 ```
 
-## Requirements 
-
-To use this plugin a configured AiiDA profile and computer configuration are required, see the 
-[AiiDa documentation](https://aiida.readthedocs.io/projects/aiida-core/en/latest/intro/get_started.html) 
-for instructions on how to install and configure AiiDA. 
+## Requirements
 
+To use this plugin a configured AiiDA profile and computer configuration are required, see the
+[AiiDa documentation](https://aiida.readthedocs.io/projects/aiida-core/en/latest/intro/get_started.html)
+for instructions on how to install and configure AiiDA.
 
-## Setup 
+## Setup
 
-To configure the ChemShell plugin an AiiDA code instance needs to be configured for the ChemShell executable. 
+To configure the ChemShell plugin an AiiDA code instance needs to be configured for the ChemShell executable.
 The following is an example of a basic YAML configuration file:
 
 ```yaml
@@ -109,30 +108,31 @@ step. The code can then be configured by running:
 verdi code create core.code.installed --config chemshell.yml -n 
 ```
 
-If successful this will have created a code with the label `chemsh` which can then be used to run ChemShell jobs within the AiiDA workflow. 
+If successful this will have created a code with the label `chemsh` which can then be used to run ChemShell jobs within the AiiDA workflow.
 
 ### ChemShell with MPI
 
-It is important to note that the configuration of an MPI enabled ChemShell code differs slightly depending on whether the code instance uses 
+It is important to note that the configuration of an MPI enabled ChemShell code differs slightly depending on whether the code instance uses
 the `chemsh` or `chemsh.x` executable. If you have a parallel (MPI enabled) build of ChemShell but are using the `chemsh` wrapper executable
 please set `with_mpi: false` as the underlying plugin will handle how to call the mpi runtime. If you are calling the `chemsh.x` executable
-directly then `with_mpi: true` is required to run parallel jobs. 
+directly then `with_mpi: true` is required to run parallel jobs.
 
-## Examples 
+## Examples
 
-### QM Based Single Point Energy 
+### QM Based Single Point Energy
 
-The following is a python script that will run a Quantum Mechanics based single point energy calculation using the NWChem ChemShell interface. 
-The associated structure file can be found in the `tests/data/` folder. 
+The following is a python script that will run a Quantum Mechanics based single point energy calculation using the NWChem ChemShell interface.
+The associated structure file can be found in the `tests/data/` folder.
 
-```python 
-from aiida.engine import run 
+```python
+from aiida.engine import run
 from aiida.orm import load_code, SinglefileData, Dict
-from aiida import load_profile 
+from aiida import load_profile
 
-load_profile("user_profile")  # This is not required if running in a verdi shell environment 
+# This is not required if running in a verdi shell environment
+load_profile("user_profile")
 
-builder = load_code("chemsh").get_builder() 
+builder = load_code("chemsh").get_builder()
 builder.structure = SinglefileData(file="/absolute/path/to/water.cjson")
 builder.qm_parameters = Dict({"theory": "NWChem", "method": "HF", "basis": "3-21G"})
 builder.calculation_parameters = Dict({"gradients": False, "hessian": False})
@@ -142,19 +142,20 @@ results, node = run.get_node(builder)
 print("Final Energy = ", results.get("energy"))
 ```
 
-This can either be run as a script or as directly within a verdi shell python environment. 
+This can either be run as a script or as directly within a verdi shell python environment.
 
-### QM/MM Based Geometry Optimisation 
+### QM/MM Based Geometry Optimisation
 
 The following is a python script that will run a combined QM/MM based geometry optimisation using the NWChem and DL_POLY ChemShell interfaces.
-The associated structure and force field files can be found in the `tests/data/` folder. 
+The associated structure and force field files can be found in the `tests/data/` folder.
 
-```python 
-from aiida.engine import run 
+```python
+from aiida.engine import run
 from aiida.orm import load_code, SinglefileData, Dict
-from aiida import load_profile 
+from aiida import load_profile
 
-load_profile("user_profile")  # This is not required if running in a verdi shell environment 
+# This is not required if running in a verdi shell environment
+load_profile("user_profile")
 
 builder = load_code("chemsh").get_builder()
 builder.structure = SinglefileData(file="/absolute/path/to/h2o_dimer.cjson")

{aiida_chemshell-0.2.2 → aiida_chemshell-0.3.0}/src/aiida_chemshell.egg-info/requires.txt

@@ -4,6 +4,7 @@ aiida-core>=2.5
 aiida-core>=2.8
 pytest>=8.0
 pytest-cov>=6.0
+pytest-xdist>=3.0
 ruff>=0.11.0
 pre-commit