Modernize ProjectQ (isort, PEP 257 docstrings, drop Python 2 code, more flake8 plugins) and fix phase estimation unit tests (#408)

* Fix tests for the phase estimation decomposition

* Fix docstrings according to PEP257

* Modernize code by removing some Python 2 compatibility code

* Update CHANGELOG

* Add isort to pre-commit-config.yaml and run it on the project

* Move common exception classes to their own files

* Fix changes from the latest on develop

* Update CHANGELOG

* Update Python code in documentation folder

* Add `meta` repository to pre-commit configuration

* Re-indent and cleanup .pre-commit-config.yaml

* Add some more flake8 plugins to pre-commit config file

- flake8-breakpoint
- flake8-comprehensions
- flake8-eradicate
- flake8-mutable

* Fix small bug with drawing using matplotlib

* Address review comments

* Better comment in docs/conf.py

Author: Takishima

.pre-commit-config.yaml

@@ -12,56 +12,77 @@
 #
 # See https://github.com/pre-commit/pre-commit
 
+---
+
 ci:
-    skip: [check-manifest]
+  skip: [check-manifest]
 
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
-  hooks:
-  - id: check-added-large-files
-  - id: check-case-conflict
-  - id: check-merge-conflict
-  - id: check-symlinks
-  - id: check-yaml
-  - id: check-toml
-  - id: debug-statements
-  - id: end-of-file-fixer
-  - id: mixed-line-ending
-  - id: trailing-whitespace
-  - id: fix-encoding-pragma
+  - repo: meta
+    hooks:
+      - id: check-useless-excludes
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: check-toml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+      - id: fix-encoding-pragma
+
+  # Changes tabs to spaces
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.1.10
+    hooks:
+      - id: remove-tabs
 
-# Changes tabs to spaces
-- repo: https://github.com/Lucas-C/pre-commit-hooks
-  rev: v1.1.10
-  hooks:
-  - id: remove-tabs
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.9.1
+    hooks:
+      - id: isort
+        name: isort (python)
 
-- repo: https://github.com/psf/black
-  rev: 21.5b1
-  hooks:
-  - id: black
-    language_version: python3
-    # This is a slow hook, so only run this if --hook-stage manual is passed
-    stages: [manual]
+  - repo: https://github.com/psf/black
+    rev: 21.5b1
+    hooks:
+      - id: black
+        language_version: python3
+        # This is a slow hook, so only run this if --hook-stage manual is passed
+        stages: [manual]
 
-- repo: https://gitlab.com/pycqa/flake8
-  rev: 3.9.2
-  hooks:
-  - id: flake8
-    exclude: ^(docs/.*|tools/.*)$
+  - repo: https://gitlab.com/PyCQA/flake8
+    rev: 3.9.2
+    hooks:
+      - id: flake8
+        name: flake8-strict
+        exclude: ^(.*_test\.py)$
+        additional_dependencies: [flake8-comprehensions, flake8-breakpoint,
+                                  flake8-eradicate, flake8-mutable,
+                                  flake8-docstrings]
+      - id: flake8
+        name: flake8-test-files
+        additional_dependencies: [flake8-comprehensions, flake8-breakpoint,
+                                  flake8-eradicate, flake8-mutable]
+        files: ^(.*_test\.py)$
 
-- repo: https://github.com/pre-commit/mirrors-pylint
-  rev: 'v3.0.0a3'
-  hooks:
-  - id: pylint
-    args: ['--score=n']
-    # This is a slow hook, so only run this if --hook-stage manual is passed
-    stages: [manual]
-    additional_dependencies: ['pybind11>=2.6', 'numpy', 'requests', 'boto3', 'matplotlib', 'networkx']
+  - repo: https://github.com/pre-commit/mirrors-pylint
+    rev: 'v3.0.0a3'
+    hooks:
+      - id: pylint
+        args: ['--score=n']
+        # This is a slow hook, so only run this if --hook-stage manual is passed
+        stages: [manual]
+        additional_dependencies: [pybind11>=2.6, numpy, requests, boto3, matplotlib, networkx, sympy]
 
-- repo: https://github.com/mgedmin/check-manifest
-  rev: "0.46"
-  hooks:
-  - id: check-manifest
-    additional_dependencies: ['setuptools-scm', 'pybind11>=2.6']
+  - repo: https://github.com/mgedmin/check-manifest
+    rev: '0.46'
+    hooks:
+      - id: check-manifest
+        additional_dependencies: ['setuptools-scm', 'pybind11>=2.6']

CHANGELOG.md

@@ -16,10 +16,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 -   Prevent infinite recursion errors when too many compiler engines are added to the MainEngine
+-   Error in testing the decomposition for the phase estimation gate
+-   Make all docstrings PEP257 compliant
 
 ### Removed
+
+-   Some compatibility code for Python 2.x
+
 ### Repository
 
+-   Added `isort` to the list of pre-commit hooks
+-   Added `flake8-docstrings` to the flake8 checks to ensure PEP257 compliance for docstrings
+
 ## [0.6.1] - 2021-06-23
 
 ### Repository