Update package installation files and development environment

.bumpversion.cfg

@@ -10,3 +10,7 @@ replace = version = {new_version}
 [bumpversion:file:src/murfey/__init__.py]
 search = __version__ = "{current_version}"
 replace = __version__ = "{new_version}"
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"

.pre-commit-config.yaml

@@ -1,7 +1,10 @@
+# YAML formatting specifications: https://yaml.org/spec/1.2.2/
+
 repos:
 # Syntax validation and some basic sanity checks
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  #rev: v4.0.1
+  rev: v4.5.0  # Format depends entirely on how version tag is formatted on the repo (with 'v', without it, etc.)
   hooks:
   - id: check-merge-conflict
   - id: check-ast
@@ -12,9 +15,30 @@ repos:
   - id: check-yaml
     args: [--allow-multiple-documents]
 
-# Automatically sort imports
+# Automatic source code formatting
+- repo: https://github.com/psf/black
+  #rev: 22.3.0
+  rev: 24.3.0
+  hooks:
+  - id: black
+    args: [--safe, --quiet]
+
+# Ruff for linting and formatting
+# Ruff can replace isort and flake8 (https://docs.astral.sh/ruff/linter/)
+# - repo: https://github.com/astral-sh/ruff-pre-commit
+#   rev: v0.3.5
+#   hooks:
+#   # Ruff linter
+#   - id: ruff
+#     args: [--fix]
+#   # Ruff formatter
+#   - id: ruff-format
+#     types_or: [python]
+
+# # Automatically sort imports
 - repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+  #rev: 5.12.0
+  rev: 5.13.2
   hooks:
   - id: isort
     args: [
@@ -29,24 +53,26 @@ repos:
            '--rm', 'from __future__ import with_statement',   # -2.6
           ]
 
-# Automatic source code formatting
-- repo: https://github.com/psf/black
-  rev: 22.3.0
-  hooks:
-  - id: black
-    args: [--safe, --quiet]
-
-# Linting
+# # Linting
 - repo: https://github.com/PyCQA/flake8
-  rev: 4.0.1
+  # Release history: https://flake8.pycqa.org/en/latest/release-notes/index.html
+  #rev: 4.0.1
+  rev: 7.0.0
   hooks:
   - id: flake8
-    additional_dependencies: ['flake8-comprehensions==3.8.0']
+    # Added Flake8-pyproject plugin for .toml compatibility
+    # flake8-comprehensions URL: https://github.com/adamchainz/flake8-comprehensions
+    #additional_dependencies: ['flake8-comprehensions==3.8.0']
+    additional_dependencies: [
+      "Flake8-pyproject==1.2.3",
+      'flake8-comprehensions==3.14.0'
+      ]
 
 # Type checking
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.910
+  #rev: v0.910
+  rev: v1.9.0
   hooks:
   - id: mypy
-    files: 'src/.*\.py$'
-    additional_dependencies: [ types-requests ]
+    files: '(src|tests)/.*\.py$'  # Single quote critical due to escape character '\' used in RegEx search string (see YAML - 7.3 Flow Scalar Styles)
+    additional_dependencies: [types-requests]

pyproject.toml

@@ -2,6 +2,156 @@
 requires = ["setuptools >= 40.6.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
+# TEP 2024-04-03
+[project]
+name = "murfey"
+authors = []
+maintainers = []
+description = "Client-Server architecture hauling Cryo-EM data"
+readme = "README.md"
+requires-python = ">=3.9"
+keywords = [""]
+license = {file = "LICENSE"}
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "pydantic",
+    "requests",
+    "rich",
+]
+version = "0.11.5"
+#dynamic = ["version"]  # Clashes with version variable immediately above
+
+[project.urls]
+Bug-Tracker = "https://github.com/DiamondLightSource/python-murfey/issues"
+Documentation = "https://github.com/DiamondLightSource/python-murfey"
+GitHub = "https://github.com/DiamondLightSource/python-murfey"
+
+
+# TEP 2024-04-03
+[project.optional-dependencies]
+client = [
+    "procrunner",
+    "textual==0.42.0",
+    "websocket-client",
+    "werkzeug",
+    "xmltodict",
+]
+server = [
+    "mysql-connector-python<=8.0.29",
+    "fastapi>=0.101",
+    "cryptography",
+    "importlib_resources; python_version<'3.9'",
+    "ispyb",
+    "jinja2",
+    "packaging",
+    "numpy",
+    "sqlmodel",
+    "pillow",
+    "prometheus_client",
+    "uvicorn[standard]",
+    "werkzeug",
+    "zocalo",
+]
+developer = [
+    "pytest",
+    "pre-commit",
+    "bump2version",
+]
+
+# TEP 2024-04-03
+[project.scripts]
+# Where there are "." in the variable name, enclose with inverted commas
+murfey = "murfey.client:run"
+"murfey.server" = "murfey.server:run"
+"murfey.simulate" = "murfey.cli.dummy:run"
+"murfey.transfer" = "murfey.cli.transfer:run"
+"murfey.db_sql" = "murfey.cli.murfey_db_sql:run"
+"murfey.sessions" = "murfey.cli.db_sessions:run"
+"murfey.generate_password" = "murfey.cli.generate_db_password:run" 
+"murfey.generate_key" = "murfey.cli.generate_crypto_key:run"
+"murfey.decrypt_password" = "murfey.cli.decrypt_db_password:run"
+"murfey.create_db" = "murfey.cli.create_db:run"
+"murfey.spa_inject" = "murfey.cli.inject_spa_processing:run"
+"murfey.spa_ispyb_entries" = "murfey.cli.spa_ispyb_messages:run"
+
+# TEP 2024-04-03
+[tool.setuptools]
+package-dir = {"" = "src"}
+include-package-data = true
+zip-safe = false
+
+# TEP 2024-04-03
+#[tool.setuptools.packages]
+#find = {}  # This option leads to pip searching for stuff in "tests"
+
+# TEP 2024-04-03
+[tool.setuptools.packages.find]
+where = ["src"]
+
+# TEP 2024-04-03
+[tool.setuptools.package-data]
+"murfey.client.tui" = ["*.css"]
+
+# TEP 2024-04-04
+# Flake8-pyproject allows .toml settings to be read into Flake8
+# Flake8-pyproject: https://pypi.org/project/Flake8-pyproject/
+[tool.flake8]
+select = [
+    "C4",
+    "E401",
+    "E711",
+    "E712",
+    "E713",
+    "E714",
+    "E721",
+    "E722",
+    "E901",
+    "F401",
+    "F402",
+    "F403",
+    "F405",
+    "F541",
+    "F631",
+    "F632",
+    "F633",
+    "F811",
+    "F812",
+    "F821",
+    "F822",
+    "F841",
+    "F901",
+    "W191",
+    "W291",
+    "W292",
+    "W293",
+    "W602",
+    "W603",
+    "W604",
+    "W605",
+    "W606",
+]
+ignore = [
+    # "E203", 
+    # "E266",
+    # "E501", 
+    "W503"
+]
+max-line-length = "88"
+# Also worth investigating Ruff's compatibility with Flake8 for use with pyproject.toml
+# Suggested by VSCode's auto-fill, so should be pretty popular
+# Ruff: https://github.com/astral-sh/ruff
+
 [tool.isort]
 profile = "black"
 
@@ -10,3 +160,108 @@ addopts = "-ra"
 
 [tool.mypy]
 mypy_path = "src"
+disable_error_code = "annotation-unchecked"  # Disables non-error messages thrown up by mypy
+
+[tool.ruff]
+include = [
+    "pyproject.toml",
+    "setup.cfg",
+    "setup.py",
+    "src/**/*.py",
+    "tests/**/*.py"
+]
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+# Assume Python 3.8
+target-version = "py38"
+
+[tool.ruff.lint]
+# Currently, not all Flake8 rule coes are implemented in Ruff
+# A mix of the two need to be used for the rule codes currently desired
+select = [
+    "C4",
+    "E401",
+    "E711",
+    "E712",
+    "E713",
+    "E714",
+    "E721",
+    "E722",
+    # "E901",
+    "F401",
+    "F402",
+    "F403",
+    "F405",
+    "F541",
+    "F631",
+    "F632",
+    "F633",
+    "F811",
+    # "F812",
+    "F821",
+    "F822",
+    "F841",
+    "F901",
+    "W191",
+    "W291",
+    "W292",
+    "W293",
+    # "W602",
+    # "W603",
+    # "W604",
+    "W605",
+    # "W606",
+]
+ignore = [
+    "E203", 
+    "E266",
+    "E501", 
+    # "W503"
+]
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+docstring-code-format = false
+docstring-code-line-length = "dynamic"