Deps/aiida29

.github/workflows/cd.yml

@@ -52,7 +52,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.14']
 
     services:
       rabbitmq:

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Install Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.11'
         cache: pip
         cache-dependency-path: pyproject.toml
 
@@ -31,7 +31,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.14']
 
     services:
       rabbitmq:

.github/workflows/validate_release_tag.py

@@ -1,4 +1,5 @@
 """Validate that the version in the tag label matches the version of the package."""
+
 import argparse
 import ast
 from pathlib import Path
@@ -12,7 +13,7 @@ def get_version_from_module(content: str) -> str:
     try:
         module = ast.parse(content)
     except SyntaxError as exception:
-        raise IOError('Unable to parse module.') from exception
+        raise OSError('Unable to parse module.') from exception
 
     try:
         return next(
@@ -23,7 +24,7 @@ def get_version_from_module(content: str) -> str:
             if isinstance(target, ast.Name) and target.id == '__version__'
         )
     except StopIteration as exception:
-        raise IOError('Unable to find the `__version__` attribute in the module.') from exception
+        raise OSError('Unable to find the `__version__` attribute in the module.') from exception
 
 
 if __name__ == '__main__':

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
   - id: flynt
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.3
+  rev: v0.8.6
   hooks:
   - id: ruff-format
   - id: ruff

docs/source/conf.py

@@ -3,6 +3,7 @@
 This file only contains a selection of the most common options. For a full list see the documentation:
 https://www.sphinx-doc.org/en/master/usage/configuration.html
 """
+
 import aiida_shell
 
 project = 'aiida-shell'

docs/source/examples/include/scripts/gromacs.py

@@ -1,8 +1,10 @@
 #!/usr/bin/env runaiida
 """Simulation of lysozyme protein dynamics using GROMACS."""
+
 import urllib.request
 
 from aiida import engine, orm
+
 from aiida_shell import launch_shell_job
 
 # Download the lysozyme protein structure.

docs/source/examples/include/scripts/lammps.py

@@ -1,6 +1,8 @@
 #!/usr/bin/env runaiida
 """Simulation of Lennard-Jones fluid using LAMMPS."""
+
 from aiida import orm
+
 from aiida_shell import launch_shell_job
 
 script = """

docs/source/examples/include/scripts/qe.py

@@ -1,8 +1,10 @@
 #!/usr/bin/env runaiida
 """Simulation of electronic band structure of GaAs using Quantum ESPRESSO."""
+
 import urllib.request
 
 from aiida import engine, orm
+
 from aiida_shell import launch_shell_job
 
 # Generate a folder with the required pseudopotentials

pyproject.toml

@@ -13,22 +13,23 @@ classifiers = [
   'Operating System :: POSIX :: Linux',
   'Operating System :: MacOS :: MacOS X',
   'Programming Language :: Python',
-  'Programming Language :: Python :: 3.9',
   'Programming Language :: Python :: 3.10',
   'Programming Language :: Python :: 3.11',
   'Programming Language :: Python :: 3.12',
+  'Programming Language :: Python :: 3.13',
+  'Programming Language :: Python :: 3.14',
   'Topic :: Scientific/Engineering'
 ]
 dependencies = [
-  'aiida-core~=2.6,>=2.6.1',
+  "aiida-core==2.9.0rc0",
   'dill'
 ]
 dynamic = ['description', 'version']
 keywords = ['aiida', 'workflows']
 license = {file = 'LICENSE.txt'}
 name = 'aiida-shell'
 readme = 'README.md'
-requires-python = '>=3.9'
+requires-python = '>=3.10'
 
 [project.entry-points.'aiida.calculations']
 'core.shell' = 'aiida_shell.calculations.shell:ShellJob'
@@ -43,9 +44,9 @@ requires-python = '>=3.9'
 
 [project.optional-dependencies]
 dev = [
-  'mypy==1.6.1',
+  'mypy~=2.3.0',
   'pre-commit',
-  'pytest~=6.2',
+  'pytest~=8.4',
   'pytest-regressions'
 ]
 docs = [

src/aiida_shell/__init__.py

@@ -1,4 +1,5 @@
 """AiiDA plugin that makes running shell commands easy."""
+
 __version__ = '0.8.2'
 
 from .calculations import ShellJob
@@ -7,10 +8,10 @@
 from .parsers import ShellParser
 
 __all__ = (
-    'ShellJob',
     'EntryPointData',
     'PickledData',
     'ShellCode',
-    'launch_shell_job',
+    'ShellJob',
     'ShellParser',
+    'launch_shell_job',
 )

src/aiida_shell/calculations/__init__.py

@@ -1,4 +1,5 @@
 """Module for :mod:`aiida_shell.calculations`."""
+
 from .shell import ShellJob
 
 __all__ = ('ShellJob',)

src/aiida_shell/calculations/shell.py

@@ -1,4 +1,5 @@
 """Implementation of :class:`aiida.engine.CalcJob` to make it easy to run an arbitrary shell command on a computer."""
+
 from __future__ import annotations
 
 import inspect

src/aiida_shell/data/__init__.py

@@ -1,4 +1,5 @@
 """Module for :mod:`aiida_shell.data`."""
+
 from .code import ShellCode
 from .entry_point import EntryPointData
 from .pickled import PickledData

src/aiida_shell/data/code.py

@@ -1,4 +1,5 @@
 """Code that represents a shell command."""
+
 from __future__ import annotations
 
 import typing as t

src/aiida_shell/data/entry_point.py

@@ -1,15 +1,16 @@
 """Data plugin to store a reference to an entry point."""
+
 from __future__ import annotations
 
 import typing as t
+from importlib.metadata import EntryPoint
 
 from aiida.common.exceptions import EntryPointError
 from aiida.common.lang import type_check
 from aiida.common.log import AIIDA_LOGGER
 from aiida.orm import Data
 from aiida.plugins.entry_point import get_entry_point
 from aiida.plugins.utils import PluginVersionProvider
-from importlib_metadata import EntryPoint
 
 __all__ = ('EntryPointData',)
 

src/aiida_shell/data/pickled.py

@@ -1,4 +1,5 @@
 """Data plugin to store (almost) any Python object by pickling it."""
+
 from __future__ import annotations
 
 import importlib.metadata

src/aiida_shell/launch.py

@@ -1,4 +1,5 @@
 """Convenience wrapper function to simplify the interface to launch a :class:`aiida_shell.ShellJob` job."""
+
 from __future__ import annotations
 
 import logging

src/aiida_shell/parsers/__init__.py

@@ -1,4 +1,5 @@
 """Module for :mod:`aiida_shell.parsers`."""
+
 from .shell import ShellParser
 
 __all__ = ('ShellParser',)

src/aiida_shell/parsers/shell.py

@@ -7,6 +7,7 @@
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
 """Parser for a :class:`aiida_shell.ShellJob` job."""
+
 from __future__ import annotations
 
 import pathlib

tests/calculations/test_shell.py

@@ -1,11 +1,13 @@
 """Tests for the :mod:`aiida_shell.calculations.shell` module."""
+
 import pathlib
 import shlex
 
 import pytest
 from aiida.common.datastructures import CodeInfo
 from aiida.engine import run_get_node
-from aiida.orm import Data, Float, FolderData, Int, List, RemoteData, SinglefileData, Str
+from aiida.orm import Data, Float, FolderData, Int, List, Log, RemoteData, SinglefileData, Str
+
 from aiida_shell.calculations.shell import ShellJob
 from aiida_shell.data import EntryPointData, PickledData
 
@@ -90,7 +92,7 @@ def test_nodes_folder_data(generate_calc_job, generate_code, tmp_path):
 def test_nodes_remote_data(generate_calc_job, generate_code, tmp_path, aiida_localhost, use_symlinks):
     """Test the ``nodes`` input with ``RemoteData`` nodes."""
     inputs = {
-        'code': generate_code(),
+        'code': generate_code(computer_label=aiida_localhost.label),
         'arguments': [],
         'nodes': {
             'remote': RemoteData(remote_path=str(tmp_path.absolute()), computer=aiida_localhost),
@@ -119,7 +121,7 @@ def test_nodes_remote_data_filename(generate_calc_job, generate_code, tmp_path,
     remote_data_b = RemoteData(remote_path=str(remote_path_b.absolute()), computer=aiida_localhost)
 
     inputs = {
-        'code': generate_code(),
+        'code': generate_code(computer_label=aiida_localhost.label),
         'arguments': ['{remote_a}'],
         'nodes': {
             'remote_a': remote_data_a,
@@ -451,7 +453,7 @@ def parser(dirpath):
     assert node.outputs.string == value
 
 
-def test_input_output_filename_overlap(generate_calc_job, generate_code, tmp_path, caplog):
+def test_input_output_filename_overlap(generate_calc_job, generate_code, tmp_path):
     """Test functionality when input and output filenames overlap."""
     code = generate_code()
 
@@ -479,18 +481,22 @@ def test_input_output_filename_overlap(generate_calc_job, generate_code, tmp_pat
 
     # If the filename clash is due to an "implicit" filename, instead of raising, the filename of the node should be
     # automatically made unique and a warning logged to make the user aware.
-    dirpath, calc_info = generate_calc_job(
-        'core.shell',
-        inputs={
+    def generate_inputs():
+        return {
             'code': code,
             'nodes': {'file': SinglefileData.from_string('content', filename='stdout')},
-        },
-    )
+        }
+
+    dirpath, calc_info = generate_calc_job('core.shell', inputs=generate_inputs())
+    process = generate_calc_job('core.shell', inputs=generate_inputs(), return_process=True)
+
     code_info = calc_info.codes_info[0]
     filenames = [p.name for p in dirpath.iterdir()]
     assert code_info.stdout_name not in filenames
     assert code_info.stderr_name not in filenames
-    assert 'filename `stdout` for node `file` overlaps' in caplog.records[0].message
+
+    message = 'filename `stdout` for node `file` overlaps'
+    assert any(message in entry.message for entry in Log.collection.get_logs_for(process.node))
 
     # If the contents of a ``FolderData`` overlap with a reserved filename, an exception is raised. This is done because
     # not doing everything will most likely fail the calculation as some input files will be overwritten. The plugin can

tests/conftest.py

@@ -1,4 +1,5 @@
 """Module with test fixtures."""
+
 from __future__ import annotations
 
 import collections
@@ -18,6 +19,7 @@
 from aiida.manage.manager import get_manager
 from aiida.orm import CalcJobNode, Computer, FolderData
 from aiida.plugins import CalculationFactory, ParserFactory
+
 from aiida_shell import ShellCode
 
 pytest_plugins = 'aiida.tools.pytest_fixtures'
@@ -86,7 +88,7 @@ def factory(
         manager = get_manager()
         runner = manager.get_runner()
 
-        process_class: t.Type['CalcJob'] = CalculationFactory(entry_point_name)  # type: ignore[assignment]
+        process_class: t.Type[CalcJob] = CalculationFactory(entry_point_name)  # type: ignore[assignment]
         process: CalcJob = instantiate_process(runner, process_class, **inputs or {})  # type: ignore[assignment]
 
         if presubmit:

tests/data/test_code.py

@@ -1,5 +1,7 @@
 """Tests for :mod:`aiida_shell.data.code`."""
+
 import pytest
+
 from aiida_shell.data.code import ShellCode
 
 

tests/data/test_entry_point.py

@@ -1,9 +1,12 @@
 """Tests for the :mod:`aiida_shell.data.entry_point` module."""
+
+from importlib.metadata import EntryPoint
+
 import pytest
 from aiida.orm import load_node
 from aiida.plugins.entry_point import get_entry_point
+
 from aiida_shell.data.entry_point import EntryPointData
-from importlib_metadata import EntryPoint
 
 InvalidEntryPoint = EntryPoint('b', 'a', group='c')
 InconsistentEntryPoint = EntryPoint('b', 'aiida_shell.data.pickled:PickledData', group='c')

tests/data/test_pickled.py

@@ -1,7 +1,9 @@
 """Tests for the :mod:`aiida_shell.data.pickled` module."""
+
 import dill
 import pytest
 from aiida.orm import Node, load_node
+
 from aiida_shell.data.pickled import PickledData
 
 

tests/parsers/test_shell.py

@@ -1,9 +1,11 @@
 """Tests for the :mod:`aiida_shell.parsers.shell` module."""
+
 import copy
 import pathlib
 
 import pytest
 from aiida.orm import FolderData, List, SinglefileData
+
 from aiida_shell.calculations.shell import ShellJob
 
 

tests/test_launch.py

@@ -1,4 +1,5 @@
 """Tests for the :mod:`aiida_shell.launch` module."""
+
 import datetime
 import json
 import pathlib
@@ -7,6 +8,7 @@
 import pytest
 from aiida.engine import WorkChain, run_get_node, workfunction
 from aiida.orm import AbstractCode, Computer, Float, Int, RemoteData, SinglefileData, Str
+
 from aiida_shell.calculations.shell import ShellJob
 from aiida_shell.launch import launch_shell_job, prepare_computer
 

tests/test_version.py

@@ -1,7 +1,9 @@
 """Tests for the :mod:`aiida_shell` module."""
-import aiida_shell
+
 from packaging.version import Version, parse
 
+import aiida_shell
+
 
 def test_version():
     """Test that :attr:`aiida_shell.__version__` is a PEP-440 compatible version identifier."""