[DATALAD RUNCMD] run isort

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "isort docs neurodocker && black docs neurodocker",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

docs/conf.py

@@ -6,12 +6,13 @@
 
 # -- Path setup --------------------------------------------------------------
 
+import sys
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 from pathlib import Path
-import sys
 
 _here = Path(__file__).parent.absolute()
 sys.path.insert(0, str(_here / ".."))

docs/sphinxext/github_link.py

@@ -2,12 +2,12 @@
 https://github.com/scikit-learn/scikit-learn/blob/master/doc/sphinxext/github_link.py
 """
 
-from operator import attrgetter
 import inspect
-import subprocess
 import os
+import subprocess
 import sys
 from functools import partial
+from operator import attrgetter
 
 REVISION_CMD = "git rev-parse --short HEAD"
 

neurodocker/__init__.py

@@ -5,8 +5,8 @@
 
 from pathlib import Path
 
-from neurodocker._version import get_versions
 from neurodocker import reproenv  # noqa: F401
+from neurodocker._version import get_versions
 
 __version__ = get_versions()["version"]
 del get_versions

neurodocker/cli/cli.py

@@ -1,8 +1,7 @@
 import click
 
 from neurodocker import __version__
-from neurodocker.cli.generate import generate
-from neurodocker.cli.generate import genfromjson
+from neurodocker.cli.generate import generate, genfromjson
 
 
 @click.group()

neurodocker/cli/generate.py

@@ -6,19 +6,23 @@
 # TODO: add a dedicated class for key=value in the eat-all class.
 
 import json as json_lib
-from pathlib import Path
 import sys
 import typing as ty
+from pathlib import Path
 
 import click
 
-from neurodocker.reproenv.renderers import _Renderer
-from neurodocker.reproenv.renderers import DockerRenderer
-from neurodocker.reproenv.renderers import SingularityRenderer
-from neurodocker.reproenv.state import get_template
-from neurodocker.reproenv.state import register_template
-from neurodocker.reproenv.state import registered_templates
-from neurodocker.reproenv.state import registered_templates_items
+from neurodocker.reproenv.renderers import (
+    DockerRenderer,
+    SingularityRenderer,
+    _Renderer,
+)
+from neurodocker.reproenv.state import (
+    get_template,
+    register_template,
+    registered_templates,
+    registered_templates_items,
+)
 from neurodocker.reproenv.template import Template
 from neurodocker.reproenv.types import allowed_pkg_managers
 

neurodocker/cli/minify/_prune.py

@@ -1,7 +1,7 @@
 """Remove all files under a directory but not caught by `reprozip trace`."""
 
-from pathlib import Path
 import typing as ty
+from pathlib import Path
 
 import yaml
 

neurodocker/cli/minify/tests/test_minify.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
-from click.testing import CliRunner
 import pytest
+from click.testing import CliRunner
 
 from neurodocker.cli.cli import _arm_on_mac
 from neurodocker.cli.minify.trace import minify

neurodocker/cli/minify/trace.py

@@ -9,9 +9,9 @@
 
 import io
 import logging
-from pathlib import Path
 import tarfile
 import typing as ty
+from pathlib import Path
 
 import click
 

neurodocker/cli/tests/test_build_images_with_cli.py

@@ -1,14 +1,15 @@
 from pathlib import Path
 
-from click.testing import CliRunner
 import pytest
+from click.testing import CliRunner
 
-from neurodocker.cli.cli import generate
-from neurodocker.cli.cli import genfromjson
+from neurodocker.cli.cli import generate, genfromjson
 from neurodocker.reproenv.state import _TemplateRegistry
-from neurodocker.reproenv.tests.utils import get_build_and_run_fns
-from neurodocker.reproenv.tests.utils import skip_if_no_docker
-from neurodocker.reproenv.tests.utils import skip_if_no_singularity
+from neurodocker.reproenv.tests.utils import (
+    get_build_and_run_fns,
+    skip_if_no_docker,
+    skip_if_no_singularity,
+)
 
 # Test that a template can be rendered
 # We need to use `reproenv generate` as the entrypoint here because the generate command

neurodocker/cli/tests/test_cli.py

@@ -2,8 +2,8 @@
 
 from pathlib import Path
 
-from click.testing import CliRunner
 import pytest
+from click.testing import CliRunner
 
 from neurodocker.cli.cli import generate
 from neurodocker.cli.generate import OptionEatAll

neurodocker/reproenv/__init__.py

@@ -4,7 +4,7 @@
 
 from neurodocker.reproenv.renderers import DockerRenderer  # noqa: F401
 from neurodocker.reproenv.renderers import SingularityRenderer  # noqa: F401
+from neurodocker.reproenv.state import get_template  # noqa: F401
 from neurodocker.reproenv.state import register_template  # noqa: F401
 from neurodocker.reproenv.state import registered_templates  # noqa: F401
-from neurodocker.reproenv.state import get_template  # noqa: F401
 from neurodocker.reproenv.template import Template  # noqa: F401

neurodocker/reproenv/renderers.py

@@ -12,18 +12,17 @@
 
 import jinja2
 
-from neurodocker.reproenv.exceptions import RendererError
-from neurodocker.reproenv.exceptions import TemplateError
-from neurodocker.reproenv.state import _TemplateRegistry
-from neurodocker.reproenv.state import _validate_renderer
-from neurodocker.reproenv.template import _BaseInstallationTemplate
-from neurodocker.reproenv.template import Template
-from neurodocker.reproenv.types import _SingularityHeaderType
-from neurodocker.reproenv.types import REPROENV_SPEC_FILE_IN_CONTAINER
-from neurodocker.reproenv.types import allowed_pkg_managers
-from neurodocker.reproenv.types import allowed_installation_methods
-from neurodocker.reproenv.types import installation_methods_type
-from neurodocker.reproenv.types import pkg_managers_type
+from neurodocker.reproenv.exceptions import RendererError, TemplateError
+from neurodocker.reproenv.state import _TemplateRegistry, _validate_renderer
+from neurodocker.reproenv.template import Template, _BaseInstallationTemplate
+from neurodocker.reproenv.types import (
+    REPROENV_SPEC_FILE_IN_CONTAINER,
+    _SingularityHeaderType,
+    allowed_installation_methods,
+    allowed_pkg_managers,
+    installation_methods_type,
+    pkg_managers_type,
+)
 
 # All jinja2 templates are instantiated from this environment object. It is
 # configured to dislike undefined attributes. For example, if a template is

neurodocker/reproenv/state.py

@@ -3,8 +3,8 @@
 import copy
 import json
 import os
-from pathlib import Path
 import typing as ty
+from pathlib import Path
 
 import jsonschema
 import yaml
@@ -16,9 +16,11 @@
 except ImportError:  # pragma: no cover
     from yaml import SafeLoader  # type: ignore  # pragma: no cover
 
-from neurodocker.reproenv.exceptions import RendererError
-from neurodocker.reproenv.exceptions import TemplateError
-from neurodocker.reproenv.exceptions import TemplateNotFound
+from neurodocker.reproenv.exceptions import (
+    RendererError,
+    TemplateError,
+    TemplateNotFound,
+)
 from neurodocker.reproenv.types import TemplateType
 
 _schemas_path = Path(__file__).parent / "schemas"

neurodocker/reproenv/template.py

@@ -7,9 +7,11 @@
 
 from neurodocker.reproenv.exceptions import TemplateKeywordArgumentError
 from neurodocker.reproenv.state import _validate_template
-from neurodocker.reproenv.types import _BinariesTemplateType
-from neurodocker.reproenv.types import _SourceTemplateType
-from neurodocker.reproenv.types import TemplateType
+from neurodocker.reproenv.types import (
+    TemplateType,
+    _BinariesTemplateType,
+    _SourceTemplateType,
+)
 
 
 class Template:

neurodocker/reproenv/tests/test_build_images_from_registered_templates.py

@@ -1,18 +1,18 @@
 # TODO: add more tests for `from_dict` method.
 
-from pathlib import Path
 import typing as ty
+from pathlib import Path
 
 import pytest
 
-from neurodocker.reproenv.renderers import DockerRenderer
-from neurodocker.reproenv.renderers import SingularityRenderer
+from neurodocker.reproenv.renderers import DockerRenderer, SingularityRenderer
 from neurodocker.reproenv.state import _TemplateRegistry
-from neurodocker.reproenv.tests.utils import get_build_and_run_fns
-from neurodocker.reproenv.tests.utils import skip_if_no_docker
-from neurodocker.reproenv.tests.utils import skip_if_no_singularity
-from neurodocker.reproenv.types import installation_methods_type
-from neurodocker.reproenv.types import pkg_managers_type
+from neurodocker.reproenv.tests.utils import (
+    get_build_and_run_fns,
+    skip_if_no_docker,
+    skip_if_no_singularity,
+)
+from neurodocker.reproenv.types import installation_methods_type, pkg_managers_type
 
 _template_filepath = Path(__file__).parent / "sample-template-jq.yaml"
 

neurodocker/reproenv/tests/test_build_images_simple.py

@@ -1,10 +1,11 @@
 import pytest
 
-from neurodocker.reproenv.renderers import DockerRenderer
-from neurodocker.reproenv.renderers import SingularityRenderer
-from neurodocker.reproenv.tests.utils import get_build_and_run_fns
-from neurodocker.reproenv.tests.utils import skip_if_no_docker
-from neurodocker.reproenv.tests.utils import skip_if_no_singularity
+from neurodocker.reproenv.renderers import DockerRenderer, SingularityRenderer
+from neurodocker.reproenv.tests.utils import (
+    get_build_and_run_fns,
+    skip_if_no_docker,
+    skip_if_no_singularity,
+)
 
 
 @pytest.mark.parametrize(

neurodocker/reproenv/tests/test_renderers.py

@@ -1,9 +1,11 @@
 import pytest
 
 from neurodocker.reproenv.exceptions import RendererError
-from neurodocker.reproenv.renderers import _Renderer
-from neurodocker.reproenv.renderers import DockerRenderer
-from neurodocker.reproenv.renderers import SingularityRenderer
+from neurodocker.reproenv.renderers import (
+    DockerRenderer,
+    SingularityRenderer,
+    _Renderer,
+)
 
 
 def test_renderer():

neurodocker/reproenv/tests/test_state.py

@@ -3,9 +3,8 @@
 import pytest
 import yaml
 
-from neurodocker.reproenv import exceptions
+from neurodocker.reproenv import exceptions, types
 from neurodocker.reproenv.state import _TemplateRegistry, _validate_template
-from neurodocker.reproenv import types
 
 
 def test_validate_template_invalid_templates():

neurodocker/reproenv/tests/test_template.py

@@ -1,8 +1,6 @@
 import pytest
 
-from neurodocker.reproenv import exceptions
-from neurodocker.reproenv import template
-from neurodocker.reproenv import types
+from neurodocker.reproenv import exceptions, template, types
 
 
 def test_template():

neurodocker/reproenv/tests/utils.py

@@ -1,10 +1,10 @@
 import contextlib
 import getpass
 import os
-from pathlib import Path
 import subprocess
 import typing as ty
 import uuid
+from pathlib import Path
 
 import pytest