Add lint

.github/workflows/test.yaml

@@ -12,8 +12,14 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: pre-commit/[email protected]
   unit_test_suite:
     name: Unit tests on ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    needs: [pre-commit]
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false

.gitignore

@@ -3,4 +3,4 @@ __pycache__/
 .ipynb_checkpoints/
 .pytest_cache
 dist
-scratch/
+scratch/

.pre-commit-config.yaml

@@ -0,0 +1,33 @@
+# This is the configuration for pre-commit, a local framework for managing pre-commit hooks
+#   Check out the docs at: https://pre-commit.com/
+
+exclude: (\.min\.js$|\.svg$|\.html$)
+default_stages: [commit]
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-builtin-literals
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-toml
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.285
+    hooks:
+      - id: ruff
+        args: [holonote]
+        files: holonote/
+  - repo: https://github.com/hoxbro/clean_notebook
+    rev: v0.1.10
+    hooks:
+      - id: clean-notebook
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.5
+    hooks:
+    - id: codespell
+      additional_dependencies:
+        - tomli

README.md

@@ -64,4 +64,4 @@ have different types:
 data, containing information that is not to be visualized by
 `holonote`. These are defined by the user or application and can have
 arbitrary types and contents. A complete set of fields together with one
-or more regions constitutes an annotation.
+or more regions constitutes an annotation.

examples/Basics.ipynb

@@ -105,7 +105,7 @@
    "id": "616fd061-fffd-4f1a-94ce-dc8bc6b9d5bd",
    "metadata": {},
    "source": [
-    "**Note**: The tools made available by the region editor are appropriate to both the enable region types as well as the dimensionality of the elemnt (here, a single key dimension along the x-axis)\n"
+    "**Note**: The tools made available by the region editor are appropriate to both the enable region types as well as the dimensionality of the element (here, a single key dimension along the x-axis)\n"
    ]
   },
   {
@@ -141,7 +141,7 @@
    "id": "c0fd9b3f-8827-4e02-bb03-8edfbde88eb1",
    "metadata": {},
    "source": [
-    "You can set the range of interest programatically as well:"
+    "You can set the range of interest programmatically as well:"
    ]
   },
   {
@@ -227,7 +227,7 @@
    "id": "18335801-7230-40b9-a5b1-ed4d7050deec",
    "metadata": {},
    "source": [
-    "Note that uuid values are randomly generated (by default) which means we do not know what these values will be ahead of time. As a result we need a programatic way to access them. Using the dataframe index directly is awkard, so annotators offer a more natural, interactive way to select annotations - simply click on them in the plot to select them.\n",
+    "Note that uuid values are randomly generated (by default) which means we do not know what these values will be ahead of time. As a result we need a programmatic way to access them. Using the dataframe index directly is awkward, so annotators offer a more natural, interactive way to select annotations - simply click on them in the plot to select them.\n",
     "\n",
     "Click on a range region in the plot above and run the following cell to see it's uuid:"
    ]
@@ -702,7 +702,7 @@
     "\n",
     "### Styling the annotator\n",
     "\n",
-    "You can set the style either throught the `_style` keywords in `.overlay`:"
+    "You can set the style either through the `_style` keywords in `.overlay`:"
    ]
   },
   {
@@ -737,22 +737,9 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
    "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.16"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

examples/Basics_2D.ipynb

@@ -144,7 +144,7 @@
    "id": "c0fd9b3f-8827-4e02-bb03-8edfbde88eb1",
    "metadata": {},
    "source": [
-    "You can set the range of interest programatically as well:"
+    "You can set the range of interest programmatically as well:"
    ]
   },
   {
@@ -220,7 +220,7 @@
    "id": "18335801-7230-40b9-a5b1-ed4d7050deec",
    "metadata": {},
    "source": [
-    "Note that uuid values are randomly generated (by default) which means we do not know what these values will be ahead of time. As a result we need a programatic way to access them. Using the dataframe index directly is awkard, so annotators offer a more natural, interactive way to select annotations - simply click on them in the plot to select them.\n",
+    "Note that uuid values are randomly generated (by default) which means we do not know what these values will be ahead of time. As a result we need a programmatic way to access them. Using the dataframe index directly is awkward, so annotators offer a more natural, interactive way to select annotations - simply click on them in the plot to select them.\n",
     "\n",
     "Click on a range region in the plot above and run the following cell to see it's uuid:"
    ]
@@ -678,7 +678,7 @@
     "\n",
     "### Styling the annotator\n",
     "\n",
-    "You can set the style either throught the `_style` keywords in `.overlay`:"
+    "You can set the style either through the `_style` keywords in `.overlay`:"
    ]
   },
   {
@@ -713,22 +713,9 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
    "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.16"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

holonote/__init__.py

@@ -1,2 +1,3 @@
-from . import annotate
-from . import editor
+from __future__ import annotations
+
+from . import annotate, editor  # noqa: F401

holonote/annotate/__init__.py

@@ -1,3 +1,11 @@
-from .annotator import Annotator
-from .connector import Connector, SQLiteDB,  AutoIncrementKey, UUIDHexStringKey, UUIDBinaryKey
+from __future__ import annotations
+
+from .annotator import Annotator  # noqa: F401
+from .connector import (  # noqa: F401
+    AutoIncrementKey,
+    Connector,
+    SQLiteDB,
+    UUIDBinaryKey,
+    UUIDHexStringKey,
+)
 from .table import *

holonote/annotate/annotator.py

@@ -1,13 +1,14 @@
-import sys
-import weakref
+from __future__ import annotations
+
 import holoviews as hv
 import numpy as np
 import pandas as pd
 import param
 from bokeh.models.tools import BoxSelectTool, HoverTool
 from holoviews.element.selection import Selection1DExpr
-from .connector import Connector, SQLiteDB, AnnotationTable
 
+from .connector import Connector, SQLiteDB
+from .table import AnnotationTable
 
 
 class Indicator:
@@ -17,11 +18,11 @@ class Indicator:
     """
 
     range_style = dict(color='red', alpha=0.4, apply_ranges=False)
-    point_style = dict()
+    point_style = {}
     indicator_highlight = {'alpha':(0.7,0.2)}
 
     edit_range_style = dict(alpha=0.4, line_alpha=1, line_width=1, line_color='black')
-    edit_point_style = dict()
+    edit_point_style = {}
 
     @classmethod
     def indicator_style(cls, range_style, point_style, highlighters):
@@ -167,13 +168,12 @@ def df(self):
             region_column_names.extend(point_column_names)
         view = pd.concat(views)
         view = view.rename(columns={'_id':field_name})
-        column_ordering = [field_name] + region_column_names + fields_columns
+        column_ordering = [field_name, *region_column_names, *fields_columns]
         return view[column_ordering].set_index(field_name)
 
 
     def refresh(self, clear=False):
         "Method to update display state of the annotator and optionally clear stale visual state"
-        pass
 
     def set_annotation_table(self, annotation_table): # FIXME! Won't work anymore, set_connector??
         self._region = {}
@@ -430,7 +430,7 @@ def clear_indicated_region(self):
     def selection_element(self):
         if self.element is None:
             kdims = list(self.kdim_dtypes.keys())
-            kdim_dtype = list(self.kdim_dtypes.values())[0]
+            kdim_dtype = next(iter(self.kdim_dtypes.values()))
             return hv.Curve(([kdim_dtype(), kdim_dtype()],
                              [0,1]), kdims=kdims) # Note: Any concrete Selection1dExpr will do...
 
@@ -596,7 +596,7 @@ def _build_hover_tool(self):
         extra_cols = [(col, '@{%s}' % col.replace(' ','_')) for col in self.annotation_table._field_df.columns]
         region_tooltips = []
         region_formatters = {}
-        for direction, kdim, dtype in zip(['x','y'], self.kdim_dtypes.keys(), self.kdim_dtypes.values()):
+        for direction, kdim in zip(['x','y'], self.kdim_dtypes.keys()):
             if self.kdim_dtypes[kdim] is np.datetime64:
                 region_tooltips.append((f'start {kdim}', f'@{direction}0{{%F}}'))
                 region_tooltips.append((f'end {kdim}', f'@{direction}1{{%F}}'))

holonote/annotate/connector.py

@@ -1,32 +1,31 @@
-import os
-import uuid
-import sqlite3
+from __future__ import annotations
+
 import datetime as dt
+import sqlite3
+import uuid
 
-import param
-import pandas as pd
 import numpy as np
+import pandas as pd
+import param
 
 try:
     import sqlalchemy
-except:
+except ModuleNotFoundError:
     sqlalchemy = None
 
-from .table import AnnotationTable
-
 
 class PrimaryKey(param.Parameterized):
     """
     Generator of the primary key used to keep track of annotations in
     HoloViews.
 
     The generated key is used to reference annotations until they are
-    comitted, at which point they may 1) be inserted in the database as
+    committed, at which point they may 1) be inserted in the database as
     the primary key value (policy='insert') 2) are checked against the
     primary key value chosen by the database which is expected to match
     in most cases.
 
-    In real situations where the key is chosen by the databse, the key
+    In real situations where the key is chosen by the database, the key
     generated will *not* always match the actual key assigned. The
     policy parameter decides the resulting behavior in these cases.
     """
@@ -44,7 +43,7 @@ class PrimaryKey(param.Parameterized):
     def __call__(self, connector, key_list=None):
         """
         The key list is the current list of index values that are
-        outstanding (i.e. have not been comitted).
+        outstanding (i.e. have not been committed).
         """
         raise NotImplementedError
 
@@ -133,7 +132,6 @@ class WidgetKey(PrimaryKey):
     Placeholder for a concept where the user can insert a primary key
     value via a widget.
     """
-    pass
 
 
 
@@ -186,7 +184,7 @@ def field_value_to_type(cls, value):
         elif isinstance(value, param.Parameter) and value.default is not None:
             return type(value.default)
         else:
-            raise Exception(f'Connector cannot handle type {str(type(value))}')
+            raise Exception(f'Connector cannot handle type {type(value)!s}')
 
     @classmethod
     def schema_from_field_values(cls, fields):
@@ -231,7 +229,7 @@ def _incompatible_schema_check(self, expected_keys, columns, fields, region_type
         missing_region_columns = set(expected_keys) - non_field_columns
         if missing_region_columns:
             raise Exception(msg_prefix
-                            + f'Missing {repr(region_type)} region columns {missing_region_columns}. '
+                            + f'Missing {region_type!r} region columns {missing_region_columns}. '
                             + msg_suffix)
 
 
@@ -315,7 +313,7 @@ def get_tables(self):
 
     def create_table(self, column_schema=None):
         column_schema = column_schema if column_schema else self.column_schema
-        column_spec = ',\n'.join(['{name} {spec}'.format(name=name, spec=spec)
+        column_spec = ',\n'.join([f'{name} {spec}'
                                   for name, spec in column_schema.items()])
         create_table_sql = f'CREATE TABLE IF NOT EXISTS {self.table_name} (' + column_spec +  ');'
         self.cursor.execute(create_table_sql)
@@ -340,7 +338,7 @@ def add_row(self, **fields):
            columns = columns[1:]
 
         placeholders = ', '.join(['?'] * len(field_values))
-        self.cursor.execute(f"INSERT INTO {self.table_name} {str(columns)} VALUES({placeholders});", field_values)
+        self.cursor.execute(f"INSERT INTO {self.table_name} {columns!s} VALUES({placeholders});", field_values)
         self.primary_key.validate(self.cursor.lastrowid, fields[self.primary_key.field_name])
         self.con.commit()
 
@@ -359,7 +357,7 @@ def update_row(self, **updates): # updates as a dictionary OR remove posarg?
         id_val = updates.pop(self.primary_key.field_name)
         set_updates = ', '.join('\"' + k + '\"' + " = ?" for k in updates.keys())
         query = f"UPDATE {self.table_name} SET " + set_updates + f" WHERE \"{self.primary_key.field_name}\" = ?;"
-        self.cursor.execute(query, list(updates.values()) + [id_val])
+        self.cursor.execute(query, [*updates.values(), id_val])
         self.con.commit()
 
     def add_schema(self, schema):