Merge branch 'imports_cleanup' into 'master'

Imports cleanup

This merge request mainly separates the cleanup introduced by isort from future work.

See merge request !126

.flake8

 [flake8]
-max-line-length = 80
+max-line-length = 88
 select = B,C,E,F,W,T4,B9,B950
 ignore = E501, W503, E203

.isort.cfg

+[settings]
+line_length=88
+order_by_type=true
+lines_between_types=1

.pre-commit-config.yaml

 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
+  - repo: https://github.com/timothycrosley/isort
+    rev: 4.3.21-2
+    hooks:
+    - id: isort
+      args: [-sl]
   - repo: https://github.com/ambv/black
     rev: stable
     hooks:
@@ -9,6 +14,8 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.0.0
     hooks:
+      - id: check-ast
+      - id: check-case-conflict
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: debug-statements

MANIFEST.in

 include COPYING README.rst version.txt requirements.txt buildout.cfg
 recursive-include doc conf.py *.rst *.png *.ico *.md
-recursive-include beat/editor/templates *.jinja2

beat/editor/backend/asset.py

@@ -24,15 +24,17 @@
 ###############################################################################
 
 import importlib
+
+from enum import Enum
+from enum import unique
+
 import simplejson as json
 
 import beat.core
 
-from enum import Enum, unique
-
 from beat.backend.python import utils
-from beat.core.schema import validate
 from beat.cmdline import common
+from beat.core.schema import validate
 
 
 @unique

beat/editor/backend/assetmodel.py

@@ -25,15 +25,14 @@
 
 import os
 
+from PyQt5.QtCore import QStringListModel
+from PyQt5.QtCore import pyqtProperty
 from PyQt5.QtCore import pyqtSignal
 from PyQt5.QtCore import pyqtSlot
-from PyQt5.QtCore import pyqtProperty
-from PyQt5.QtCore import QStringListModel
 
 from ..utils import dataformat_basetypes
-
-from .asset import AssetType
 from .asset import Asset
+from .asset import AssetType
 
 
 class AssetModel(QStringListModel):

beat/editor/backend/eventfilters.py

@@ -23,10 +23,9 @@
 #                                                                             #
 ###############################################################################
 
-from PyQt5.QtCore import Qt
 from PyQt5.QtCore import QEvent
 from PyQt5.QtCore import QObject
-
+from PyQt5.QtCore import Qt
 from PyQt5.QtWidgets import QAbstractSpinBox
 from PyQt5.QtWidgets import QComboBox
 

beat/editor/backend/resourcemodels.py

@@ -35,7 +35,6 @@ from .asset import Asset
 from .asset import AssetType
 from .assetmodel import AssetModel
 
-
 PARAMETER_TYPE_KEY = "parameter_type"
 DEFAULT_VALUE_KEY = "default_value"
 EDITED_KEY = "edited"
@@ -80,10 +79,13 @@ class ExperimentResources:
         DATASET_TABLE = "CREATE TABLE datasets(name varchar, outputs integer)"
         INSERT_DATASET = "INSERT INTO datasets(name, outputs) VALUES(?, ?)"
 
-
         query = QSqlQuery()
 
-        for query_str in [ALGORITHM_TABLE_CLEANUP, QUEUE_TABLE_CLEANUP, DATASET_TABLE_CLEANUP]:
+        for query_str in [
+            ALGORITHM_TABLE_CLEANUP,
+            QUEUE_TABLE_CLEANUP,
+            DATASET_TABLE_CLEANUP,
+        ]:
             if not query.exec_(query_str):
                 raise RuntimeError(f"Failed to drop table: {query.lastError().text()}")
 

beat/editor/scripts/editor_cli.py

@@ -35,27 +35,23 @@ import click
 import pkg_resources
 
 from click_plugins import with_plugins
-
-from PyQt5.QtWidgets import QApplication
 from PyQt5.QtCore import QCoreApplication
+from PyQt5.QtWidgets import QApplication
 
+from beat.cmdline import environments
 from beat.cmdline.click_helper import AliasedGroup
 from beat.cmdline.decorators import raise_on_error
 from beat.cmdline.decorators import verbosity_option
-from beat.cmdline import environments
-
-from ..utils import setup_logger
-from ..utils import check_prefix_folders
-from ..utils import check_prefix_dataformats
-
-from ..widgets.mainwindow import MainWindow
-from ..widgets.assetwidget import AssetWidget
 
-from ..backend.asset import AssetType
+from .. import version
 from ..backend.asset import Asset
+from ..backend.asset import AssetType
 from ..backend.eventfilters import MouseWheelFilter
-
-from .. import version
+from ..utils import check_prefix_dataformats
+from ..utils import check_prefix_folders
+from ..utils import setup_logger
+from ..widgets.assetwidget import AssetWidget
+from ..widgets.mainwindow import MainWindow
 
 global logger
 logger = None

beat/editor/templates/algorithm.jinja2

-# You may import any python packages that will be available in the environment
-# you will run this algorithm in Environments can change based on the
-# experiment's settings
-{% for ref, lib in contents.uses.items() %}# Library "{{ lib }}" is available under "{{ ref }}"
-{% endfor %}
-
-class Algorithm:
-    # initialise fields to store cross-input data (e.g. machines,
-    # aggregations, etc.)
-    def __init__(self):
-        pass
-{% if contents.parameters %}
-
-    # do initial setup work with the given parameters for the algorithm
-    def setup(self, parameters):
-        # Parameters available:
-        {% for p_name, param in contents.parameters.items() %}# Parameter "{{ p_name }}" with type "{{ param.type }}"
-        {% endfor %}
-        # get a parameter like:
-        #       param1_value = parameters.get('param_1', self.param1_default)
-        return True
-
-{% endif %}
-    # this will be called each time the sync'd input has more data available to
-    # be processed
-    def process(self, inputs, outputs):
-        # Groups available:
-{% for group in contents.groups %}        # Group {{ loop.index - 1 }}:
-        {% for iName, input in group.inputs.items() %}#   Input "{{ iName }}" with type  "{{ input.type }}"
-        {% endfor %}{% if 'outputs' in group %}{% for oName, output in group.outputs.items() %}#   Output "{{ oName }}" with type  "{{ output.type }}"
-        {% endfor %}{% endif %}{% endfor %}{% if 'splittable' not in contents %}
-        # Results available:
-        {% for rName, result in contents.results.items() %}#   Result "{{ rName }}" with type "{{ result.type }}"
-        {% endfor %}{% endif %}
-        # to check if there is more data waiting in the inputs
-        # (if it is False, you have processed all the inputs and this "process"
-        # function won't be called again):
-        #       if inputs.hasMoreData():
-
-        # to check if a specific input is done:
-        #       if inputs["input1"].isDataUnitDone():
-
-        # to manually fetch the next input of a specific input
-        # (e.g. the block is not sync'd to the input but you want the input
-        # immediately)
-        #       inputs['input1'].next()
-        # you can then access that input value as normal:
-        #       self.val1 = inputs['input1'].data
-
-        # to get the data for an input (note that the value will be of the type
-        # specified in the metadata!):
-        #       data_value = inputs['input1'].data
-
-        # to write to an output:
-        #       outputs['output1'].write({
-        #           'output_field_1': 1,
-        #           'output_field_2': 'output'
-        #       })
-
-        # always return True, it signals BEAT to continue processing
-        return True

beat/editor/templates/database.jinja2

-# You may import any python packages that will be available in the environment
-# you will run this database in Environments can change based on the
-# experiment's settings
-from beat.backend.python.database import View
-
-{% for view in views %}
-class {{ view }}(View):
-    # build the data for your view
-    # split the raw data into (homogenous) bits and return a keyed iterable
-    # (something with `.keys()` available to it, like a dict)
-    # the key names must be the same as the output names for sets that use this
-    # view.
-    #    root_folder: the path to the root folder of the database's files (not
-    #                 always applicable)
-    #    parameters: parameters passed to the view, defined in the metadata
-    def index(self, root_folder, parameters):
-        pass
-
-    # returns a value at a specific index in the iterable for this view
-    #   output: the specific output value requested
-    #   index: the current index of the iterable
-    def get(self, output, index):
-        # to get the current object referenced by the given index:
-        #       obj = self.objs[index]
-        # note that this object is a named tuple, with fields equivalent to
-        # your keys from the objects returned from the index function
-        pass
-{% endfor -%}

beat/editor/templates/library.jinja2

-# You may import any python packages that will be available in the environment
-# you will run this library in Environments can change based on the
-# experiment's settings
-{% for ref, lib in uses.items() %}# Library "{{ lib }}" is available under "{{ ref }}"
-{% endfor -%}

beat/editor/templates/plotter.jinja2

-# You may import any python packages that will be available in the environment you will run this plotter in
-# Environments can change based on the experiment's settings
-{% for ref, lib in uses.uses.items() %}# Library "{{ lib }}" is available under "{{ ref }}"
-{% endfor %}
-
-# Makes sure we won't require an X11 connection
-import matplotlib
-matplotlib.use('Agg')
-
-import numpy
-import itertools
-
-class Plotter(baselib.Plotter):
-{% if uses.parameters %}
-    # do initial setup work with the given parameters for the plotter
-    def setup(self, parameters):
-        super(Plotter, self).setup(parameters)
-        # Parameters available:
-        {% for p_name, param in uses.parameters.items() %}# Parameter "{{ p_name }}" with type "{{ param.type }}"
-        {% endfor %}
-        # get a parameter like:
-        #       param1_value = parameters.get('param_1', self.param1_default)
-        return True
-{% endif %}
-    # this will be called each time the sync'd input has more data available to be processed
-    def process(self, inputs):
-        fig, ax = super(Plotter, self).prepare_canvas()
-        # apply at the beginning of this function or before returning for needed modifications
-        super(Plotter, self).apply_parameters(ax)
-        # ax.set_title(self.title, fontdict={'fontsize':self.title_fontsize})
-
-        # ax.set_xlabel(self.xlabel, fontdict={'fontsize':self.axis_fontsize})
-        # ax.set_ylabel(self.ylabel, fontdict={'fontsize':self.axis_fontsize})
-        # ax.set_xlim((self.xlim_left,self.xlim_right))
-        # ax.set_ylim((self.ylim_bottom,self.ylim_top))
-        return super(Plotter, self).encode_figure(fig)

beat/editor/test/conftest.py

@@ -23,18 +23,19 @@
 #                                                                             #
 ###############################################################################
 
+import importlib
 import os
+import shutil
+import subprocess
 import sys
 import tempfile
-import pytest
-import pkg_resources
-import simplejson as json
-import subprocess
-import shutil
-import importlib
 
 from collections import namedtuple
 
+import pkg_resources
+import pytest
+import simplejson as json
+
 from beat.cmdline.config import Configuration
 
 from ..backend.asset import AssetType

beat/editor/test/test_algorithmeditor.py

@@ -32,20 +32,19 @@ from beat.backend.python.algorithm import Algorithm
 from ..backend.asset import Asset
 from ..backend.asset import AssetType
 from ..backend.assetmodel import AssetModel
-from ..widgets.algorithmeditor import PropertyEditor
-from ..widgets.algorithmeditor import ParameterEditor
-from ..widgets.algorithmeditor import ResultEditor
-from ..widgets.algorithmeditor import IOWidget
-from ..widgets.algorithmeditor import GroupEditor
-from ..widgets.algorithmeditor import AlgorithmEditor
 from ..widgets.algorithmeditor import ALGORITHM_TYPE
-from ..widgets.algorithmeditor import DEFAULT_SCHEMA_VERSION
 from ..widgets.algorithmeditor import DEFAULT_API_VERSION
+from ..widgets.algorithmeditor import DEFAULT_SCHEMA_VERSION
+from ..widgets.algorithmeditor import AlgorithmEditor
+from ..widgets.algorithmeditor import GroupEditor
+from ..widgets.algorithmeditor import IOWidget
+from ..widgets.algorithmeditor import ParameterEditor
+from ..widgets.algorithmeditor import PropertyEditor
+from ..widgets.algorithmeditor import ResultEditor
 from ..widgets.algorithmeditor import migrate_to_api_v2
 from ..widgets.algorithmeditor import update_code
-
-from .conftest import sync_prefix
 from .conftest import prefix
+from .conftest import sync_prefix
 
 
 def get_algorithm_declaration(prefix_path, algorithm_name):

beat/editor/test/test_asset.py

@@ -24,11 +24,12 @@
 ###############################################################################
 
 import os
-import pytest
 import shutil
-import simplejson as json
 import tempfile
 
+import pytest
+import simplejson as json
+
 from ..backend.asset import Asset
 from ..backend.asset import AssetType
 

beat/editor/test/test_assetbrowser.py

@@ -25,8 +25,8 @@
 
 from PyQt5.QtCore import Qt
 
-from ..backend.asset import AssetType
 from ..backend.asset import Asset
+from ..backend.asset import AssetType
 from ..widgets.assetbrowser import AssetBrowser
 
 

beat/editor/test/test_assetmodel.py

@@ -24,10 +24,11 @@
 ###############################################################################
 
 import os
+
 import pytest
 
-from ..backend.assetmodel import AssetModel
 from ..backend.asset import AssetType
+from ..backend.assetmodel import AssetModel
 from ..utils import dataformat_basetypes
 
 

beat/editor/test/test_assetwidget.py

@@ -24,32 +24,29 @@
 ###############################################################################
 
 import os
-import pytest
 import random
 
-from PyQt5 import QtCore
+import pytest
 
+from PyQt5 import QtCore
 from PyQt5.QtWidgets import QMessageBox
 
+from ..backend.asset import Asset
+from ..backend.asset import AssetType
+from ..backend.assetmodel import AssetModel
+from ..widgets.algorithmeditor import AlgorithmEditor
 from ..widgets.assetwidget import AssetWidget
 from ..widgets.assetwidget import widget_for_asset_type
-from ..widgets.dialogs import AssetCreationDialog
-
-from ..widgets.editor import PlaceholderEditor
-from ..widgets.algorithmeditor import AlgorithmEditor
 from ..widgets.databaseeditor import DatabaseEditor
 from ..widgets.dataformateditor import DataformatEditor
+from ..widgets.dialogs import AssetCreationDialog
+from ..widgets.editor import PlaceholderEditor
 from ..widgets.experimenteditor import ExperimentEditor
 from ..widgets.libraryeditor import LibraryEditor
 from ..widgets.plottereditor import PlotterEditor
 from ..widgets.plotterparameterseditor import PlotterParametersEditor
 from ..widgets.protocoltemplateeditor import ProtocolTemplateEditor
 from ..widgets.toolchaineditor import ToolchainEditor
-
-from ..backend.asset import AssetType
-from ..backend.asset import Asset
-from ..backend.assetmodel import AssetModel
-
 from .conftest import sync_prefix
 
 

beat/editor/test/test_databaseeditor.py

@@ -24,22 +24,22 @@
 ###############################################################################
 
 import copy
+
 import pytest
 
 from PyQt5 import QtCore
-
 from PyQt5.QtWidgets import QComboBox
 from PyQt5.QtWidgets import QInputDialog
 
-from ..backend.asset import AssetType
 from ..backend.asset import Asset
+from ..backend.asset import AssetType
 from ..widgets.databaseeditor import DatabaseEditor
-from ..widgets.databaseeditor import ViewEditor
-from ..widgets.databaseeditor import ViewsEditor
-from ..widgets.databaseeditor import ProtocolEditor
 from ..widgets.databaseeditor import DatabaseWidget
 from ..widgets.databaseeditor import ParameterTypeDelegate
 from ..widgets.databaseeditor import ProtocolDialog
+from ..widgets.databaseeditor import ProtocolEditor
+from ..widgets.databaseeditor import ViewEditor
+from ..widgets.databaseeditor import ViewsEditor
 
 
 @pytest.yield_fixture(params=[i for i in range(1, 3)])