Devops: Move the source directory into src/ (#329)

This package directory structure is fast becoming the standard in the
Python packaging community. Even though the PyPA is not yet officially
recommending it as the standard, there are various articles out there
outlining the advantages of this structure over having the source folder
at the root of the repository.

.github/workflows/validate_release_tag.py

@@ -34,6 +34,8 @@ def get_version_from_module(content: str) -> str:
     TAG_PREFIX = 'refs/tags/v'
     assert args.GITHUB_REF.startswith(TAG_PREFIX), f'GITHUB_REF should start with "{TAG_PREFIX}": {args.GITHUB_REF}'
     tag_version = args.GITHUB_REF[len(TAG_PREFIX) :]
-    package_version = get_version_from_module(Path('aiida_common_workflows/__init__.py').read_text(encoding='utf-8'))
+    package_version = get_version_from_module(
+        Path('src/aiida_common_workflows/__init__.py').read_text(encoding='utf-8')
+    )
     error_message = f'The tag version `{tag_version}` is different from the package version `{package_version}`'
     assert tag_version == package_version, error_message

pyproject.toml

@@ -130,6 +130,9 @@ select = [
 [tool.ruff.format]
 quote-style = 'single'
 
+[tool.ruff.lint.isort]
+known-first-party = ['src']
+
 [tool.pytest.ini_options]
 testpaths = [
     'tests',

tests/cli/test_launch.py

@@ -4,7 +4,6 @@
 
 import click
 import pytest
-
 from aiida_common_workflows.cli import launch, utils
 
 

tests/cli/test_options.py

@@ -7,15 +7,14 @@
 import click
 import pytest
 from aiida import orm
-
 from aiida_common_workflows.cli import options
 
 
 @pytest.fixture
 def filepath_cif():
     """Return a path to a valid CIF file."""
     basepath = pathlib.Path(__file__).parent.parent.parent
-    filepath = basepath.joinpath('aiida_common_workflows', 'common', 'data', 'Si.cif')
+    filepath = basepath.joinpath('src', 'aiida_common_workflows', 'common', 'data', 'Si.cif')
     return filepath
 
 

tests/cli/test_plot.py

@@ -4,7 +4,6 @@
 
 import matplotlib.pyplot as plt
 import pytest
-
 from aiida_common_workflows.cli import plot
 
 

tests/cli/test_utils.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 """Tests for the :mod:`aiida_common_workflows.cli.utils` module."""
 import pytest
-
 from aiida_common_workflows.cli.utils import get_code_from_list_or_database
 
 

tests/generators/test_generator.py

@@ -3,7 +3,6 @@
 import pytest
 from aiida import orm
 from aiida.plugins import WorkflowFactory
-
 from aiida_common_workflows.generators import InputGenerator
 
 

tests/protocol/test_registry.py

@@ -3,7 +3,6 @@
 import typing as t
 
 import pytest
-
 from aiida_common_workflows.protocol import ProtocolRegistry
 
 

tests/workflows/bands/test_implementations.py

@@ -3,7 +3,6 @@
 
 import pytest
 from aiida import engine, orm, plugins
-
 from aiida_common_workflows.generators.ports import InputGeneratorPort
 from aiida_common_workflows.plugins import get_workflow_entry_point_names
 from aiida_common_workflows.workflows.bands.workchain import CommonBandsWorkChain

tests/workflows/bands/test_workchain.py

@@ -3,7 +3,6 @@
 """Tests for the :mod:`aiida_common_workflows.workflows.bands.workchain` module."""
 import pytest
 from aiida.plugins import WorkflowFactory
-
 from aiida_common_workflows.plugins import get_workflow_entry_point_names
 from aiida_common_workflows.workflows.bands import CommonBandsInputGenerator
 from aiida_common_workflows.workflows.bands.workchain import CommonBandsWorkChain

tests/workflows/dissociation_curve/test_workchain_diss_curve.py

@@ -7,7 +7,6 @@
 from aiida import orm
 from aiida.engine import WorkChain
 from aiida.plugins import WorkflowFactory
-
 from aiida_common_workflows.plugins import get_workflow_entry_point_names
 from aiida_common_workflows.workflows import dissociation
 from aiida_common_workflows.workflows.relax.workchain import CommonRelaxWorkChain

tests/workflows/eos/test_workchain_eos.py

@@ -7,7 +7,6 @@
 from aiida import orm
 from aiida.engine import WorkChain
 from aiida.plugins import WorkflowFactory
-
 from aiida_common_workflows.plugins import get_workflow_entry_point_names
 from aiida_common_workflows.workflows import eos
 from aiida_common_workflows.workflows.relax.generator import RelaxType

tests/workflows/relax/test_castep.py

@@ -8,8 +8,6 @@
 from aiida.orm import StructureData
 from aiida.plugins import WorkflowFactory
 from aiida_castep.data.otfg import OTFGGroup
-from ase.build.bulk import bulk
-
 from aiida_common_workflows.workflows.relax.castep.generator import (
     CastepCommonRelaxInputGenerator,
     ElectronicType,
@@ -22,6 +20,7 @@
     generate_inputs_relax,
 )
 from aiida_common_workflows.workflows.relax.castep.workchain import CastepCommonRelaxWorkChain
+from ase.build.bulk import bulk
 
 WORKCHAIN = plugins.WorkflowFactory('common_workflows.relax.castep')
 GENERATOR = WORKCHAIN.get_input_generator()

tests/workflows/relax/test_implementations.py

@@ -3,7 +3,6 @@
 
 import pytest
 from aiida import engine, orm, plugins
-
 from aiida_common_workflows.common.types import ElectronicType, RelaxType, SpinType
 from aiida_common_workflows.generators.ports import InputGeneratorPort
 from aiida_common_workflows.plugins import get_workflow_entry_point_names

tests/workflows/relax/test_quantum_espresso.py

@@ -3,9 +3,8 @@
 
 import pytest
 from aiida import engine, plugins
-from qe_tools import CONSTANTS
-
 from aiida_common_workflows.workflows.relax.generator import ElectronicType, RelaxType, SpinType
+from qe_tools import CONSTANTS
 
 WORKCHAIN = plugins.WorkflowFactory('common_workflows.relax.quantum_espresso')
 GENERATOR = WORKCHAIN.get_input_generator()

tests/workflows/relax/test_workchain.py

@@ -3,7 +3,6 @@
 """Tests for the :mod:`aiida_common_workflows.workflows.relax.workchain` module."""
 import pytest
 from aiida.plugins import WorkflowFactory
-
 from aiida_common_workflows.plugins import get_workflow_entry_point_names
 from aiida_common_workflows.workflows.relax import CommonRelaxInputGenerator
 from aiida_common_workflows.workflows.relax.workchain import CommonRelaxWorkChain