Merge pull request #48 from JPchico/workchains

aiida-core 2.x compatibility changes

.github/workflows/cd.yml

@@ -86,7 +86,6 @@ jobs:
     - name: Installation
       run: |
         pip install -e .[testing,pre-commit]
-        reentry scan
 
     - name: Run pytest
       run: |

.github/workflows/ci.yml

@@ -2,7 +2,7 @@ name: CI
 
 on:
   push:
-    branches: [master, develop]
+    branches: [master, develop, workchains]
   pull_request:
 
 jobs:
@@ -32,25 +32,23 @@ jobs:
       matrix:
         include:
         - python-version: "3.8"
-          lammps-version: "2020.12.24"
-          backend: django
+          lammps-version: "2020.03.03"
         - python-version: "3.8"
           lammps-version: "2020.12.24"
-          backend: sqlalchemy
         - python-version: "3.9"
           lammps-version: "2020.12.24"
-          backend: django
+        - python-version: "3.9"
+          lammps-version: "2020.03.03"
         - python-version: "3.10"
           lammps-version: "2021.09.29"
-          backend: django
 
     runs-on: ubuntu-latest
 
     services:
       postgres:
         image: postgres:10
         env:
-          POSTGRES_DB: test_${{ matrix.backend }}
+          POSTGRES_DB: test_lammps
           POSTGRES_PASSWORD: ''
           POSTGRES_HOST_AUTH_METHOD: trust
         options: >-
@@ -86,7 +84,6 @@ jobs:
     - name: Installation
       run: |
         pip install -e .[testing,pre-commit]
-        reentry scan
 
     - name: Run pytest
       run: |

README.md

@@ -447,8 +447,7 @@ the test suite can be run in an isolated, virtual environment using `tox` (see `
 or directly:
 
 ```shell
->> pip install -e .[testing]
->> reentry scan -r aiida
+>> pip install .[testing]
 >> pytest -v
 ```
 

aiida_lammps/calculations/lammps/__init__.py

@@ -6,8 +6,6 @@
 from aiida.common import CalcInfo, CodeInfo
 from aiida.common.exceptions import ValidationError
 from aiida.engine import CalcJob
-from aiida.orm import Dict, StructureData
-from aiida.plugins import DataFactory
 import numpy as np
 
 from aiida_lammps.common.generate_structure import generate_lammps_structure
@@ -34,7 +32,7 @@ def get_supercell(
 
     supercell_array = np.dot(cell, np.diag(supercell_shape))
 
-    supercell = StructureData(cell=supercell_array)
+    supercell = orm.StructureData(cell=supercell_array)
     for k in range(positions.shape[0]):
         for entry in itertools.product(*[range(i) for i in supercell_shape[::-1]]):
             position = positions[k, :] + np.dot(np.array(entry[::-1]), cell)
@@ -118,7 +116,7 @@ def define(cls, spec):
         super().define(spec)
         spec.input(
             "structure",
-            valid_type=StructureData,
+            valid_type=orm.StructureData,
             help="the structure",
         )
         spec.input(
@@ -128,7 +126,7 @@ def define(cls, spec):
         )
         spec.input(
             "parameters",
-            valid_type=Dict,
+            valid_type=orm.Dict,
             help="the parameters",
             required=False,
         )
@@ -160,7 +158,7 @@ def define(cls, spec):
 
         spec.output(
             "results",
-            valid_type=DataFactory("dict"),
+            valid_type=orm.Dict,
             required=True,
             help="the data extracted from the main output file",
         )
@@ -331,7 +329,7 @@ def prepare_for_submission(self, tempfolder):  # pylint: disable=arguments-diffe
         if "parameters" in self.inputs:
             parameters = self.inputs.parameters
         else:
-            parameters = Dict()
+            parameters = orm.Dict()
 
         # Setup input parameters
         input_txt = self.create_main_input_content(

aiida_lammps/calculations/lammps/force.py

@@ -1,6 +1,6 @@
 """Single point calculation of the energy in LAMMPS."""
 # pylint: disable=fixme, duplicate-code, useless-super-delegation
-from aiida.plugins import DataFactory
+from aiida import orm
 
 from aiida_lammps.calculations.lammps import BaseLammpsCalculation
 from aiida_lammps.common.utils import convert_date_string
@@ -22,7 +22,7 @@ def define(cls, spec):
 
         spec.output(
             "arrays",
-            valid_type=DataFactory("array"),
+            valid_type=orm.ArrayData,
             required=True,
             help="force data per atom",
         )
@@ -39,7 +39,7 @@ def create_main_input_content(
     ):
         # pylint: disable=too-many-arguments, too-many-locals
         version_date = convert_date_string(
-            parameter_data.get_attribute("lammps_version", "11 Aug 2017")
+            parameter_data.base.attributes.get("lammps_version", "11 Aug 2017")
         )
 
         lammps_input_file = f"units          {potential_data.default_units}\n"
@@ -55,7 +55,7 @@ def create_main_input_content(
         lammps_input_file += "neigh_modify    every 1 delay 0 check no\n"
 
         thermo_keywords = ["step", "temp", "epair", "emol", "etotal", "press"]
-        for kwd in parameter_data.get_attribute("thermo_keywords", []):
+        for kwd in parameter_data.base.attributes.get("thermo_keywords", []):
             if kwd not in thermo_keywords:
                 thermo_keywords.append(kwd)
         lammps_input_file += f'thermo_style custom {" ".join(thermo_keywords)}\n'
@@ -85,7 +85,7 @@ def create_main_input_content(
 
         lammps_input_file += "run             0\n"
 
-        variables = parameter_data.get_attribute("output_variables", [])
+        variables = parameter_data.base.attributes.get("output_variables", [])
         for var in variables:
             var_alias = var.replace("[", "_").replace("]", "_")
             lammps_input_file += f"variable {var_alias} equal {var}\n"

aiida_lammps/calculations/lammps/md.py

@@ -1,11 +1,12 @@
 """Single stage MD calculation in LAMMPS."""
 # pylint: disable=fixme, useless-super-delegation, duplicate-code
+from aiida import orm
 from aiida.common.exceptions import InputValidationError
-from aiida.plugins import DataFactory
 import numpy as np
 
 from aiida_lammps.calculations.lammps import BaseLammpsCalculation
 from aiida_lammps.common.utils import convert_date_string, get_path, join_keywords
+from aiida_lammps.data.trajectory import LammpsTrajectory
 from aiida_lammps.validation import validate_against_schema
 
 
@@ -25,13 +26,13 @@ def define(cls, spec):
 
         spec.output(
             "trajectory_data",
-            valid_type=DataFactory("lammps.trajectory"),
+            valid_type=LammpsTrajectory,
             required=True,
             help="atomic configuration data per dump step",
         )
         spec.output(
             "system_data",
-            valid_type=DataFactory("array"),
+            valid_type=orm.ArrayData,
             required=False,
             help="selected system data per dump step",
         )

aiida_lammps/calculations/lammps/md_multi.py

@@ -1,10 +1,11 @@
 """Run a multi-stage molecular dynamic simulation."""
 # pylint: disable=fixme
+from aiida import orm
 from aiida.common.exceptions import InputValidationError
-from aiida.plugins import DataFactory
 
 from aiida_lammps.calculations.lammps import BaseLammpsCalculation
 from aiida_lammps.common.utils import convert_date_string, get_path, join_keywords
+from aiida_lammps.data.trajectory import LammpsTrajectory
 from aiida_lammps.validation import validate_against_schema
 
 
@@ -25,14 +26,14 @@ def define(cls, spec):
         spec.output_namespace(
             "system",
             dynamic=True,
-            valid_type=DataFactory("array"),
+            valid_type=orm.ArrayData,
             help="selected system data per dump step of a stage",
         )
 
         spec.output_namespace(
             "trajectory",
             dynamic=True,
-            valid_type=DataFactory("lammps.trajectory"),
+            valid_type=LammpsTrajectory,
             help="atomic configuration data per dump step of a stage",
         )
 

aiida_lammps/calculations/lammps/optimize.py

@@ -1,12 +1,14 @@
 """Class describing the calculation of the optimization of a structure
 using LAMMPS (minimize method).
 """
+from aiida import orm
+
 # pylint: disable=fixme, duplicate-code, useless-super-delegation
 from aiida.common.exceptions import InputValidationError
-from aiida.plugins import DataFactory
 
 from aiida_lammps.calculations.lammps import BaseLammpsCalculation
 from aiida_lammps.common.utils import convert_date_string, join_keywords
+from aiida_lammps.data.trajectory import LammpsTrajectory
 from aiida_lammps.validation import validate_against_schema
 
 
@@ -25,13 +27,13 @@ def define(cls, spec):
 
         spec.output(
             "structure",
-            valid_type=DataFactory("structure"),
+            valid_type=orm.StructureData,
             required=True,
             help="the structure output from the calculation",
         )
         spec.output(
             "trajectory_data",
-            valid_type=DataFactory("lammps.trajectory"),
+            valid_type=LammpsTrajectory,
             required=True,
             help="forces, stresses and positions data per step",
         )
@@ -160,7 +162,7 @@ def validate_parameters(param_data, potential_object) -> bool:
             raise InputValidationError("parameter data not set")
         validate_against_schema(param_data.get_dict(), "optimize.schema.json")
 
-        # ensure the potential and paramters are in the same unit systems
+        # ensure the potential and parameters are in the same unit systems
         # TODO convert between unit systems (e.g. using https://pint.readthedocs.io)
         if "units" in param_data.get_dict():
             punits = param_data.get_dict()["units"]

aiida_lammps/common/input_generator.py

@@ -319,7 +319,7 @@ def write_structure_block(
     structure_block += f'dimension {structure.get_dimensionality()["dim"]}\n'
     structure_block += "boundary "
     for _bound in ["pbc1", "pbc2", "pbc3"]:
-        structure_block += f'{"p" if structure.attributes[_bound] else "f"} '
+        structure_block += f'{"p" if structure.base.attributes.all[_bound] else "f"} '
     structure_block += "\n"
     structure_block += f'atom_style {parameters_structure["atom_style"]}\n'
     structure_block += f"read_data {structure_filename}\n"

aiida_lammps/common/utils.py

@@ -36,6 +36,7 @@ def convert_date_string(string):
     """converts date string e.g. '10 Nov 2017' to datetime object
     if None, return todays date
     '"""
+
     if string is None:
         date = datetime.today()
     else: