Solve merge conflict

Author: Sarah Krebs

.flake8

@@ -9,4 +9,4 @@ extend-ignore =
     # No whitespace before ':' in [x : y]
     E203,
     # No lambdas — too strict
-    E731,  
+    E731,

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
         files: tests
 
   - repo: https://github.com/ambv/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
       - id: black
         name: black formatter deepcave
@@ -33,14 +33,38 @@ repos:
     hooks:
       - id: pydocstyle
         files: deepcave
-        additional_dependencies: ["toml"] # Needed to parse pyproject.toml
+        additional_dependencies: ["tomli"] # Needed to parse pyproject.toml
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.930
+    rev: v1.5.1
     hooks:
       - id: mypy
         name: mypy deepcave
         files: deepcave
+        args: [--install-types, --non-interactive]
+        additional_dependencies: [
+            'wheel>=0.41.2',
+            'setuptools==68.2.2',
+            'absl-py>=1.0.0',
+            'jsonlines>=3.0.0',
+            'pandas>=1.3.4',
+            'numpy>=1.22.2',
+            'matplotlib>=3.5.1',
+            'pyyaml>=6.0.1',
+            'kaleido>=0.2.1',
+            'gplearn>=0.4.2',
+            'sympy>=1.12',
+            'ConfigSpace==0.6.1',
+            'pyrfr>=0.9.0',
+            'hpbandster==0.7.4',
+            'dash==2.0.0',
+            'dash-extensions==0.0.71',
+            'dash-bootstrap-components==1.0.3',
+            'redis>=4.1.4',
+            'rq>=1.10.1',
+            'werkzeug==2.0.3',
+            'pyPDPPartitioner>=0.1.8'
+        ] # Needed for mypy, so that it knows the types to check
 
   - repo: https://github.com/PyCQA/flake8
     rev: 6.0.0

CHANGELOG.md

@@ -1,15 +1,48 @@
-# Version 1.1.4
+# Version 1.2
 
-## General
-- It is now possible to view multiple unequal runs at once.
+## Plugins
+- Add symbolic explanations plugin (#46).
+- It is now possible to view multiple unequal runs at once in Cost over Time and Pareto (#93).
 - Added an enum for displaying according warning messages.
-- Updated the Cost over Time documentation accordingly.
+
+## Enhancements
+- Fix lower bounds of dependency versions.
+- Allow to load multi-objective SMAC3v2 and add example (#69)
+- Do not disable existing loggers.
+- Update author email.
+- Add exit button which first deletes running jobs and then terminates DeepCave.
+- Nicer handling of Keyboard Interrupt.
+- Disable debug mode.
 
 ## Bug-Fixes
+- Fix missing objective specification in LPI evaluator (#71).
+- Don't convert BOHB runs with status 'running' (consistent with SMAC).
+- Fix api examples (#68).
+- Reset inputs to fix error when subsequently selecting runs with different configspaces, objectives or budgets (#106).
+- Fix errors due to changing inputs before runselection (#64).
+- For fANOVA, remove constant hyperparameters from configspace (#9).
 - When getting budget, objectives etc from multiple runs in Cost over Time and Pareto Front:
     - Instead of taking the first run as comparative value,
     - take the one with the lowest budget, else the index for the budgets could be out of bounds.
 
+## Version-Updates
+- Black version from 23.1.0 to 23.3.0
+- Mypy from 0.930 to 1.5.1
+
+## Mypy
+- Updated args so there are no missing imports
+- Updated additional dependencies, so mypy can check all types
+- Note: If the installs in requirements change, it has to be adapted in additional dependencies
+- Added many type annotations
+- In some cases internal refactoring for variables, due to typing
+
+## Pydocstyle and Linter
+- Major overhaul of docstrings in various files
+- Removed unused imports and variables
+
+## Additional Changes
+- Added a "make install examples" in Makefile
+
 # Version 1.1.3
 
 ## Bug-Fixes

Makefile

@@ -2,7 +2,7 @@
 # are usually completed in github actions.
 
 SHELL := /bin/bash
-VERSION := 1.1.3
+VERSION := 1.2
 
 NAME := DeepCAVE
 PACKAGE_NAME := deepcave
@@ -42,13 +42,16 @@ MYPY ?= mypy
 PRECOMMIT ?= pre-commit
 FLAKE8 ?= flake8
 
-install: 
+install:
 	$(PIP) install -e .
 
 install-dev:
 	$(PIP) install -e ".[dev]"
 	pre-commit install
-
+	
+install-examples:
+	$(PIP) install -e ".[examples]"
+	
 check-black:
 	$(BLACK) ${SOURCE_DIR} --check || :
 	$(BLACK) ${EXAMPLES_DIR} --check || :
@@ -62,7 +65,7 @@ check-pydocstyle:
 	$(PYDOCSTYLE) ${SOURCE_DIR} || :
 
 check-mypy:
-	$(MYPY) ${SOURCE_DIR} || :
+	$(MYPY) --check-untyped-defs --install-types --non-interactive --ignore-missing-imports ${SOURCE_DIR} || :
 
 check-flake8:
 	$(FLAKE8) ${SOURCE_DIR} || :
@@ -115,7 +118,7 @@ build:
 # This is done to prevent accidental publishing but provide the same conveniences
 publish: clean build
 	read -p "Did you update the version number in Makefile and deepcave/__init__.py?"
-	
+
 	$(PIP) install twine
 	$(PYTHON) -m twine upload --repository testpypi ${DIST}/*
 	@echo

README.md

@@ -47,6 +47,11 @@ conda install -c anaconda swig
 make install-dev
 ```
 
+If you want to use the given examples, run this after installing:
+```bash
+make install-examples
+```
+
 Please visit the [documentation](https://automl.github.io/DeepCAVE/main/installation.html) to get
 further help (e.g. if you can not install redis server or you are on a mac).
 

deepcave/__init__.py

@@ -1,3 +1,12 @@
+#  noqa: D400
+"""
+# DeepCAVE
+
+This module is used to initialize and set up the configuration for the DeepCAVE framework.
+
+The Dash application gets created.
+"""
+
 from typing import Any, Callable, TypeVar, cast
 
 import datetime
@@ -9,23 +18,36 @@
 name = "DeepCAVE"
 package_name = "deepcave"
 author = "R. Sass and E. Bergman and A. Biedenkapp and F. Hutter and M. Lindauer"
-author_email = "sass@tnt.uni-hannover.de"
+author_email = "s.segel@ai.uni-hannover.de"
 description = "An interactive framework to visualize and analyze your AutoML process in real-time."
 url = "automl.org"
 project_urls = {
     "Documentation": "https://automl.github.io/DeepCAVE/main",
     "Source Code": "https://github.com/automl/deepcave",
 }
 copyright = f"Copyright {datetime.date.today().strftime('%Y')}, {author}"
-version = "1.1.3"
+version = "1.2"
 
 _exec_file = sys.argv[0]
 _exec_files = ["server.py", "worker.py", "sphinx-build"]
 
 ROOT_DIR = Path(__file__).parent
 
 
-def get_app(title: str):
+def get_app(title: str) -> Any:
+    """
+    Get the Dash Proxy.
+
+    Parameters
+    ----------
+    title : str
+        The title of the application.
+
+    Returns
+    -------
+    DashProxy
+        The dash proxy.
+    """
     import dash_bootstrap_components as dbc
     from dash_extensions.enrich import (
         DashProxy,
@@ -61,8 +83,8 @@ def get_app(title: str):
 if any(file in _exec_file for file in _exec_files):
     from deepcave.custom_queue import Queue
     from deepcave.runs.handler import RunHandler
-    from deepcave.runs.objective import Objective  # noqa
-    from deepcave.runs.recorder import Recorder  # noqa
+    from deepcave.runs.objective import Objective
+    from deepcave.runs.recorder import Recorder
     from deepcave.utils.cache import Cache
     from deepcave.utils.configs import parse_config
     from deepcave.utils.notification import Notification
@@ -129,8 +151,37 @@ def get_app(title: str):
 
 
 def interactive(func: F) -> F:
+    """
+    Define the interactive decorator.
+
+    Parameters
+    ----------
+    func : F
+        The function to be decorated.
+
+    Returns
+    -------
+    F
+        The decorated function.
+    """
+
     @wraps(func)
     def inner(*args: Any, **kwargs: Any) -> Any:
+        """
+        Inner function of the decorator.
+
+        Parameters
+        ----------
+        *args : Any
+            Arguments to be passed to the wrap function.
+        **kwargs : Any
+            Keyword arguments to be passed to the wrap function.
+
+        Returns
+        -------
+        Any
+            The result of the function.
+        """
         if _api_mode:
             return
 

deepcave/cli.py

@@ -1,4 +1,13 @@
-from typing import Any, List
+#  noqa: D400
+"""
+# CLI
+
+This module defines command-line options using flags.
+
+This includes the entry point for the programs execution.
+"""
+
+from typing import Any
 
 import multiprocessing
 import subprocess
@@ -23,7 +32,8 @@
 )
 
 
-def execute(_) -> None:
+def execute(_: Any) -> None:
+    """Entry point for the programs execution."""
     if (config_key := FLAGS.get_config_value) is not None:
         config = FLAGS.config
         if config is not None:
@@ -49,4 +59,8 @@ def execute(_) -> None:
 
 
 def main() -> None:
-    app.run(execute)
+    """Call the execute function."""
+    try:
+        app.run(execute)
+    except KeyboardInterrupt:
+        exit("KeyboardInterrupt.")