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Remove all files from the pre-commit exclude list (#4196)
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Except for the documentation of course, which should remain excluded.

Also move the `pylint` pre-commit hook back under `local`. The idea by
putting it under the remote repos was to profit from the separate
virtual environment that is created with the exact version specified in
order to prevent clashes with requirements of other projects being
developed in the same virtual environment. However, this approach leads
to many spurious false positive import-errors because `pylint` cannot
find all other third party dependencies. This can be fixed by specifying
`language: system`, but this just forces the normal virtual environment
to be used, rendering the whole point of using the remote repos moot.
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@sphuber
sphuber authored Jul 1, 2020
1 parent 52bd5ad commit 855ae82
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Showing 118 changed files with 3,613 additions and 3,357 deletions.
45 changes: 25 additions & 20 deletions .ci/workchains.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,14 +8,14 @@
# For further information please visit http://www.aiida.net #
###########################################################################
# pylint: disable=invalid-name
"""Work chain implementations for testing purposes."""
from aiida.common import AttributeDict
from aiida.engine import calcfunction, workfunction, WorkChain, ToContext, append_, while_, ExitCode
from aiida.engine import BaseRestartWorkChain, process_handler, ProcessHandlerReport
from aiida.engine.persistence import ObjectLoader
from aiida.orm import Int, List, Str
from aiida.plugins import CalculationFactory


ArithmeticAddCalculation = CalculationFactory('arithmetic.add')


Expand Down Expand Up @@ -54,15 +54,15 @@ def setup(self):
def sanity_check_not_too_big(self, node):
"""My puny brain cannot deal with numbers that I cannot count on my hand."""
if node.is_finished_ok and node.outputs.sum > 10:
return ProcessHandlerReport(True, self.exit_codes.ERROR_TOO_BIG)
return ProcessHandlerReport(True, self.exit_codes.ERROR_TOO_BIG) # pylint: disable=no-member

@process_handler(priority=460, enabled=False)
def disabled_handler(self, node):
def disabled_handler(self, node): # pylint: disable=unused-argument
"""By default this is not enabled and so should never be called, irrespective of exit codes of sub process."""
return ProcessHandlerReport(True, self.exit_codes.ERROR_ENABLED_DOOM)
return ProcessHandlerReport(True, self.exit_codes.ERROR_ENABLED_DOOM) # pylint: disable=no-member

@process_handler(priority=450, exit_codes=ExitCode(1000, 'Unicorn encountered'))
def a_magic_unicorn_appeared(self, node):
def a_magic_unicorn_appeared(self, node): # pylint: disable=no-self-argument,no-self-use
"""As we all know unicorns do not exist so we should never have to deal with it."""
raise RuntimeError('this handler should never even have been called')

Expand All @@ -78,30 +78,24 @@ class NestedWorkChain(WorkChain):
"""
Nested workchain which creates a workflow where the nesting level is equal to its input.
"""

@classmethod
def define(cls, spec):
super().define(spec)
spec.input('inp', valid_type=Int)
spec.outline(
cls.do_submit,
cls.finalize
)
spec.outline(cls.do_submit, cls.finalize)
spec.output('output', valid_type=Int, required=True)

def do_submit(self):
if self.should_submit():
self.report('Submitting nested workchain.')
return ToContext(
workchain=append_(self.submit(
NestedWorkChain,
inp=self.inputs.inp - 1
))
)
return ToContext(workchain=append_(self.submit(NestedWorkChain, inp=self.inputs.inp - 1)))

def should_submit(self):
return int(self.inputs.inp) > 0

def finalize(self):
"""Attach the outputs."""
if self.should_submit():
self.report('Getting sub-workchain output.')
sub_workchain = self.ctx.workchain[0]
Expand All @@ -112,15 +106,13 @@ def finalize(self):


class SerializeWorkChain(WorkChain):
"""Work chain that serializes inputs."""

@classmethod
def define(cls, spec):
super().define(spec)

spec.input(
'test',
valid_type=Str,
serializer=lambda x: Str(ObjectLoader().identify_object(x))
)
spec.input('test', valid_type=Str, serializer=lambda x: Str(ObjectLoader().identify_object(x)))

spec.outline(cls.echo)
spec.outputs.dynamic = True
Expand All @@ -130,6 +122,8 @@ def echo(self):


class NestedInputNamespace(WorkChain):
"""Work chain with nested namespace."""

@classmethod
def define(cls, spec):
super().define(spec)
Expand All @@ -143,6 +137,8 @@ def do_echo(self):


class ListEcho(WorkChain):
"""Work chain that simply echos a `List` input."""

@classmethod
def define(cls, spec):
super().define(spec)
Expand All @@ -157,6 +153,8 @@ def do_echo(self):


class DynamicNonDbInput(WorkChain):
"""Work chain with dynamic non_db inputs."""

@classmethod
def define(cls, spec):
super().define(spec)
Expand All @@ -172,6 +170,8 @@ def do_test(self):


class DynamicDbInput(WorkChain):
"""Work chain with dynamic input namespace."""

@classmethod
def define(cls, spec):
super().define(spec)
Expand All @@ -186,6 +186,8 @@ def do_test(self):


class DynamicMixedInput(WorkChain):
"""Work chain with dynamic mixed input."""

@classmethod
def define(cls, spec):
super().define(spec)
Expand All @@ -194,6 +196,7 @@ def define(cls, spec):
spec.outline(cls.do_test)

def do_test(self):
"""Run the test."""
input_non_db = self.inputs.namespace.inputs['input_non_db']
input_db = self.inputs.namespace.inputs['input_db']
assert isinstance(input_non_db, int)
Expand All @@ -206,6 +209,7 @@ class CalcFunctionRunnerWorkChain(WorkChain):
"""
WorkChain which calls an InlineCalculation in its step.
"""

@classmethod
def define(cls, spec):
super().define(spec)
Expand All @@ -223,6 +227,7 @@ class WorkFunctionRunnerWorkChain(WorkChain):
"""
WorkChain which calls a workfunction in its step
"""

@classmethod
def define(cls, spec):
super().define(spec)
Expand Down
103 changes: 11 additions & 92 deletions .pre-commit-config.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,104 +8,16 @@ repos:
- id: mixed-line-ending
- id: trailing-whitespace

- repo: https://github.com/PyCQA/pylint
rev: pylint-2.5.2
hooks:
- id: pylint
language: system
exclude: &exclude_files >
(?x)^(
.ci/workchains.py|
aiida/backends/djsite/queries.py|
aiida/backends/djsite/db/models.py|
aiida/backends/djsite/db/migrations/0001_initial.py|
aiida/backends/djsite/db/migrations/0002_db_state_change.py|
aiida/backends/djsite/db/migrations/0003_add_link_type.py|
aiida/backends/djsite/db/migrations/0004_add_daemon_and_uuid_indices.py|
aiida/backends/djsite/db/migrations/0005_add_cmtime_indices.py|
aiida/backends/djsite/db/migrations/0006_delete_dbpath.py|
aiida/backends/djsite/db/migrations/0007_update_linktypes.py|
aiida/backends/djsite/db/migrations/0008_code_hidden_to_extra.py|
aiida/backends/djsite/db/migrations/0009_base_data_plugin_type_string.py|
aiida/backends/djsite/db/migrations/0010_process_type.py|
aiida/backends/djsite/db/migrations/0011_delete_kombu_tables.py|
aiida/backends/djsite/db/migrations/0012_drop_dblock.py|
aiida/backends/djsite/db/migrations/0013_django_1_8.py|
aiida/backends/djsite/db/migrations/0014_add_node_uuid_unique_constraint.py|
aiida/backends/djsite/db/migrations/0016_code_sub_class_of_data.py|
aiida/backends/djsite/db/migrations/0017_drop_dbcalcstate.py|
aiida/backends/sqlalchemy/migrations/versions/0aebbeab274d_base_data_plugin_type_string.py|
aiida/backends/sqlalchemy/migrations/versions/35d4ee9a1b0e_code_hidden_attr_to_extra.py|
aiida/backends/sqlalchemy/migrations/versions/59edaf8a8b79_adding_indexes_and_constraints_to_the_.py|
aiida/backends/sqlalchemy/migrations/versions/6c629c886f84_process_type.py|
aiida/backends/sqlalchemy/migrations/versions/70c7d732f1b2_delete_dbpath.py|
aiida/backends/sqlalchemy/migrations/versions/89176227b25_add_indexes_to_dbworkflowdata_table.py|
aiida/backends/sqlalchemy/migrations/versions/a514d673c163_drop_dblock.py|
aiida/backends/sqlalchemy/migrations/versions/a6048f0ffca8_update_linktypes.py|
aiida/backends/sqlalchemy/migrations/versions/e15ef2630a1b_initial_schema.py|
aiida/backends/sqlalchemy/migrations/versions/f9a69de76a9a_delete_kombu_tables.py|
aiida/backends/sqlalchemy/migrations/versions/62fe0d36de90_add_node_uuid_unique_constraint.py|
aiida/backends/sqlalchemy/migrations/versions/a603da2cc809_code_sub_class_of_data.py|
aiida/backends/sqlalchemy/migrations/versions/162b99bca4a2_drop_dbcalcstate.py|
aiida/backends/sqlalchemy/models/computer.py|
aiida/backends/sqlalchemy/models/settings.py|
aiida/backends/sqlalchemy/models/node.py|
aiida/backends/utils.py|
aiida/common/datastructures.py|
aiida/engine/daemon/execmanager.py|
aiida/engine/processes/calcjobs/tasks.py|
aiida/orm/querybuilder.py|
aiida/orm/nodes/data/array/bands.py|
aiida/orm/nodes/data/array/projection.py|
aiida/orm/nodes/data/array/xy.py|
aiida/orm/nodes/data/code.py|
aiida/orm/nodes/data/orbital.py|
aiida/orm/nodes/data/remote.py|
aiida/orm/nodes/data/structure.py|
aiida/orm/utils/remote.py|
aiida/parsers/plugins/arithmetic/add.py|
aiida/parsers/plugins/templatereplacer/doubler.py|
aiida/parsers/plugins/templatereplacer/__init__.py|
aiida/plugins/entry.py|
aiida/plugins/info.py|
aiida/plugins/registry.py|
aiida/tools/data/array/kpoints/legacy.py|
aiida/tools/data/array/kpoints/seekpath.py|
aiida/tools/data/__init__.py|
aiida/tools/dbexporters/__init__.py|
aiida/tools/dbimporters/baseclasses.py|
aiida/tools/dbimporters/__init__.py|
aiida/tools/dbimporters/plugins/cod.py|
aiida/tools/dbimporters/plugins/icsd.py|
aiida/tools/dbimporters/plugins/__init__.py|
aiida/tools/dbimporters/plugins/mpds.py|
aiida/tools/dbimporters/plugins/mpod.py|
aiida/tools/dbimporters/plugins/nninc.py|
aiida/tools/dbimporters/plugins/oqmd.py|
aiida/tools/dbimporters/plugins/pcod.py|
docs/.*|
examples/.*|
tests/engine/test_work_chain.py|
tests/schedulers/test_direct.py|
tests/schedulers/test_lsf.py|
tests/schedulers/test_pbspro.py|
tests/schedulers/test_sge.py|
tests/schedulers/test_torque.py|
tests/sphinxext/workchain_source/conf.py|
tests/sphinxext/workchain_source_broken/conf.py|
tests/transports/test_all_plugins.py|
tests/transports/test_local.py|
tests/transports/test_ssh.py|
tests/test_dataclasses.py|
)$

- repo: https://github.com/pre-commit/mirrors-yapf
rev: v0.30.0
hooks:
- id: yapf
name: yapf
types: [python]
exclude: *exclude_files
exclude: &exclude_files >
(?x)^(
docs/.*|
)$
args: ['-i']

- repo: https://github.com/pre-commit/mirrors-mypy
Expand All @@ -120,6 +32,13 @@ repos:
)$
- repo: local

hooks:
- id: pylint
name: pylint
language: system
exclude: *exclude_files

hooks:
- id: dm-generate-all
name: Update all requirements files
Expand Down
3 changes: 2 additions & 1 deletion .pylintrc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,8 @@ disable=bad-continuation,
import-outside-toplevel,
cyclic-import,
duplicate-code,
too-few-public-methods
too-few-public-methods,
inconsistent-return-statements

# Enable the message, report, category or checker with the given id(s). You can
# either give multiple identifier separated by comma (,) or put this option
Expand Down
12 changes: 7 additions & 5 deletions aiida/backends/djsite/db/migrations/0001_initial.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,8 @@
# For further information on the license, see the LICENSE.txt file #
# For further information please visit http://www.aiida.net #
###########################################################################

# pylint: disable=invalid-name
"""Database migration."""
from django.db import models, migrations
import django.db.models.deletion
import django.utils.timezone
Expand All @@ -19,6 +20,7 @@


class Migration(migrations.Migration):
"""Database migration."""

dependencies = [
('auth', '0001_initial'),
Expand Down Expand Up @@ -53,8 +55,8 @@ class Migration(migrations.Migration):
'is_active',
models.BooleanField(
default=True,
help_text=
'Designates whether this user should be treated as active. Unselect this instead of deleting accounts.'
help_text='Designates whether this user should be treated as active. Unselect this instead of '
'deleting accounts.'
)
),
('date_joined', models.DateTimeField(default=django.utils.timezone.now)),
Expand All @@ -65,8 +67,8 @@ class Migration(migrations.Migration):
related_name='user_set',
to='auth.Group',
blank=True,
help_text=
'The groups this user belongs to. A user will get all permissions granted to each of his/her group.',
help_text='The groups this user belongs to. A user will get all permissions granted to each of '
'his/her group.',
verbose_name='groups'
)
),
Expand Down
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