Fixing formatting errors to conform with ruff.

.github/workflows/ci.yml

@@ -14,12 +14,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4.1.1
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.8"
-    - uses: pre-commit/action@v3.0.0
+      - uses: actions/checkout@v3.3.0
+      - name: Set up Python
+        uses: actions/setup-python@v4.5.0
+        with:
+          python-version: "3.9"
+      - name: Make sure virtualevn>20 is installed, which will yield newer pip and possibility to pin pip version.
+        run: pip install "virtualenv>20"
+      - name: Install Tox
+        run: pip install tox
+      - name: Run pre-commit in Tox
+        run: tox -e pre-commit
+
 
   tests:
 
@@ -31,16 +37,14 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - python-version: "3.8"
-            lammps-version: "2020.03.03"
-          - python-version: "3.8"
-            lammps-version: "2020.12.24"
           - python-version: "3.9"
             lammps-version: "2020.12.24"
           - python-version: "3.9"
-            lammps-version: "2020.03.03"
+            lammps-version: "2022.06.23"
           - python-version: "3.10"
-            lammps-version: "2021.09.29"
+            lammps-version: "2022.06.23"
+          - python-version: "3.11"
+            lammps-version: "2022.06.23"
 
     runs-on: ubuntu-latest
 
@@ -87,10 +91,10 @@ jobs:
 
       - name: Run pytest
         run: |
-          tox -e ${{ matrix.python-version }}-aiida_lammps -- tests/ --cov=./aiida_lammps --cov-append --cov-report=xml --cov-report=term-missing
+          tox -e ${{ matrix.python-version }}-aiida_lammps -- tests/ --cov=aiida_lammps --cov-append --cov-report=xml --cov-report=term-missing
 
       - name: Upload to Codecov
-        if: matrix.python-version == 3.8
+        if: matrix.python-version == 3.10
         uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

conftest.py

@@ -1,6 +1,7 @@
 """
 initialise a test database and profile
 """
+
 # pylint: disable=redefined-outer-name
 from __future__ import annotations
 
@@ -14,18 +15,18 @@
 
 from aiida import orm
 from aiida.common import AttributeDict, CalcInfo, LinkType, exceptions
-from aiida.engine import CalcJob
+from aiida.engine import Process
 from aiida.engine.utils import instantiate_process
 from aiida.manage.manager import get_manager
 from aiida.plugins import WorkflowFactory
 from aiida.plugins.entry_point import format_entry_point_string
+from aiida_lammps.calculations.base import LammpsBaseCalculation
+from aiida_lammps.data.potential import LammpsPotentialData
+from aiida_lammps.data.trajectory import LammpsTrajectory
 import numpy as np
 import pytest
 import yaml
 
-from aiida_lammps.calculations.base import LammpsBaseCalculation
-from aiida_lammps.data.potential import LammpsPotentialData
-from aiida_lammps.data.trajectory import LammpsTrajectory
 from tests.utils import TEST_DIR, AiidaTestApp
 
 pytest_plugins = ["aiida.manage.tests.pytest_fixtures"]
@@ -68,6 +69,12 @@ def pytest_report_header(config):
     ]
 
 
+@pytest.fixture
+def structure_parameters() -> AttributeDict:
+    parameteters = AttributeDict({"dimension": 2, "boundary": ["p", "p", "f"]})
+    return parameteters
+
+
 @pytest.fixture
 def filepath_tests() -> pathlib.Path:
     """Return the path to the tests folder."""
@@ -119,6 +126,15 @@ def parameters_minimize() -> AttributeDict:
         "ke/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
         "stress/atom": [{"type": ["NULL"], "group": "all"}],
         "pressure": [{"type": ["thermo_temp"], "group": "all"}],
+        "property/atom": [
+            {
+                "type": [
+                    {"keyword": " ", "value": "fx"},
+                    {"keyword": " ", "value": "fy"},
+                ],
+                "group": "all",
+            }
+        ],
     }
 
     parameters.minimize = {
@@ -171,6 +187,15 @@ def parameters_minimize_groups() -> AttributeDict:
         "stress/atom": [{"type": ["NULL"], "group": "all"}],
         "pressure": [{"type": ["thermo_temp"], "group": "all"}],
         "ke": [{"type": [{"keyword": " ", "value": " "}], "group": "test"}],
+        "property/atom": [
+            {
+                "type": [
+                    {"keyword": " ", "value": "fx"},
+                    {"keyword": " ", "value": "fy"},
+                ],
+                "group": "all",
+            }
+        ],
     }
 
     parameters.minimize = {
@@ -218,6 +243,15 @@ def parameters_md_nve() -> AttributeDict:
         "ke/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
         "stress/atom": [{"type": ["NULL"], "group": "all"}],
         "pressure": [{"type": ["thermo_temp"], "group": "all"}],
+        "property/atom": [
+            {
+                "type": [
+                    {"keyword": " ", "value": "fx"},
+                    {"keyword": " ", "value": "fy"},
+                ],
+                "group": "all",
+            }
+        ],
     }
     parameters.md = {
         "integration": {
@@ -262,6 +296,15 @@ def parameters_md_nvt() -> AttributeDict:
         "ke/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
         "stress/atom": [{"type": ["NULL"], "group": "all"}],
         "pressure": [{"type": ["thermo_temp"], "group": "all"}],
+        "property/atom": [
+            {
+                "type": [
+                    {"keyword": " ", "value": "fx"},
+                    {"keyword": " ", "value": "fy"},
+                ],
+                "group": "all",
+            }
+        ],
     }
     parameters.md = {
         "integration": {
@@ -309,6 +352,15 @@ def parameters_md_npt() -> AttributeDict:
         "ke/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
         "stress/atom": [{"type": ["NULL"], "group": "all"}],
         "pressure": [{"type": ["thermo_temp"], "group": "all"}],
+        "property/atom": [
+            {
+                "type": [
+                    {"keyword": " ", "value": "fx"},
+                    {"keyword": " ", "value": "fy"},
+                ],
+                "group": "all",
+            }
+        ],
     }
     parameters.md = {
         "integration": {
@@ -565,7 +617,7 @@ def factory(
         entry_point_name: str,
         inputs: dict[str, Any] | None = None,
         return_process: bool = False,
-    ) -> tuple[pathlib.Path, CalcInfo] | CalcJob:
+    ) -> tuple[pathlib.Path, CalcInfo] | Process:
         """Create a :class:`aiida.engine.CalcJob` instance with the given inputs.
 
         :param entry_point_name: The entry point name of the calculation job plugin to run.

docs/source/conf.py

@@ -4,19 +4,19 @@
 `tox -e docs-clean` and `tox -e docs-update`,
 or directly: `sphinx-build -n -W --keep-going docs/source docs/_build`
 """
+
 import pathlib
 import time
 
-from aiida.manage.configuration import load_documentation_profile
-
+from aiida.manage.configuration import Profile, load_profile
 from aiida_lammps import __version__
 
 # -- AiiDA-related setup --------------------------------------------------
 
 # Load the dummy profile even if we are running locally, this way the
 # documentation will succeed even if the current
 # default profile of the AiiDA installation does not use a Django backend.
-load_documentation_profile()
+load_profile(Profile("docs", {"process_control": {}, "storage": {}}))
 
 project = "AiiDA LAMMPS"
 copyright = f"2021-{time.localtime().tm_year}, AiiDA Team. All rights reserved"
@@ -45,7 +45,7 @@
 
 # Settings for the `autoapi.extenstion` automatically generating API docs
 filepath_docs = pathlib.Path(__file__).parent.parent
-filepath_src = filepath_docs.parent / "aiida_lammps"
+filepath_src = filepath_docs.parent / "src/aiida_lammps"
 autoapi_type = "python"
 autoapi_dirs = [filepath_src]
 autoapi_ignore = [filepath_src / "*cli*"]

docs/source/developers/index.md

@@ -32,7 +32,7 @@ The test suite can be run in an isolated, virtual environment using `tox` (see `
 
 ```console
 pip install tox
-tox -e 3.8-aiida_lammps
+tox -e 3.9-aiida_lammps
 ```
 
 or directly:
@@ -57,7 +57,7 @@ conda install lammps==2019.06.05
 You can specify a different executable name for LAMMPS with:
 
 ```console
-tox -e 3.8-aiida_lammps -- --lammps-exec lmp_exec
+tox -e 3.9-aiida_lammps -- --lammps-exec lmp_exec
 ```
 
 To output the results of calcjob executions to a specific directory:

docs/source/topics/data/parameters.md

@@ -58,6 +58,8 @@ The dictionary is separated into several nested dictionaries that control differ
     * ``box_tilt``: determines how [skewed the cell](https://docs.lammps.org/box.html) is, of great importance for triclinic systems (default: ``small``).
     * ``groups``: list with the names of the groups to be added. The names of the possible groups are generated by the list of possible kind names generated by the structure (default: skip parameter).
     * ``atom_style``: how the [atoms](https://docs.lammps.org/atom_style.html) are treated by the ``LAMMPS`` simulation.
+    * ``boundary``: allows to override the [boundary](https://docs.lammps.org/boundary.html) conditions as set by the AiiDA structure as they can be incompatible with what ``LAMMPS`` expects.
+    * ``dimension``: allows to override the [dimension](https://docs.lammps.org/dimension.html) as determined by the AiiDA structure as it is determined by the boundary conditions and this is not what ``LAMMPS`` expects.
 - ``potential``: parameters related to the potential describing the system:
     * ``potential_style_options``: extra parameters related to each of the possible pair styles (default: skip parameter).
     * ``neighbor``: sets the parameters affecting the construction of the [neighbor list](https://docs.lammps.org/neighbor.html) (default: skip parameter).

docs/source/tutorials/include/scripts/run_md_basic.py

@@ -3,11 +3,10 @@
 
 from aiida.engine import run
 from aiida.orm import Dict, StructureData, load_code
+from aiida_lammps.data.potential import LammpsPotentialData
 from ase.build import bulk
 import requests
 
-from aiida_lammps.data.potential import LammpsPotentialData
-
 # Load the code configured for ``lmp``. Make sure to replace
 # this string with the label used in the code setup.
 code = load_code("lammps@localhost")

docs/source/tutorials/include/scripts/run_minimization_basic.py

@@ -3,11 +3,10 @@
 
 from aiida.engine import run
 from aiida.orm import Dict, StructureData, load_code
+from aiida_lammps.data.potential import LammpsPotentialData
 from ase.build import bulk
 import requests
 
-from aiida_lammps.data.potential import LammpsPotentialData
-
 # Load the code configured for ``lmp``. Make sure to replace
 # this string with the label used in the code setup.
 code = load_code("lammps@localhost")

examples/calculations/launch_lammps_md.py

@@ -5,9 +5,8 @@
 from aiida.common.extendeddicts import AttributeDict
 from aiida.engine import run_get_node
 from aiida.plugins import CalculationFactory
-import numpy as np
-
 from aiida_lammps.data.potential import LammpsPotentialData
+import numpy as np
 
 
 def generate_structure() -> orm.StructureData:

examples/calculations/launch_lammps_minimize.py

@@ -5,9 +5,8 @@
 from aiida.common.extendeddicts import AttributeDict
 from aiida.engine import run_get_node
 from aiida.plugins import CalculationFactory
-import numpy as np
-
 from aiida_lammps.data.potential import LammpsPotentialData
+import numpy as np
 
 
 def generate_structure() -> orm.StructureData:

examples/launch_lammps_base_restart_file.py

@@ -5,9 +5,8 @@
 from aiida.common.extendeddicts import AttributeDict
 from aiida.engine import run_get_node
 from aiida.plugins import CalculationFactory
-import numpy as np
-
 from aiida_lammps.data.potential import LammpsPotentialData
+import numpy as np
 
 
 def generate_structure() -> orm.StructureData:

examples/launch_lammps_base_restart_folder.py

@@ -5,9 +5,8 @@
 from aiida.common.extendeddicts import AttributeDict
 from aiida.engine import run_get_node
 from aiida.plugins import CalculationFactory
-import numpy as np
-
 from aiida_lammps.data.potential import LammpsPotentialData
+import numpy as np
 
 
 def generate_structure() -> orm.StructureData: