Switched to using pyproject.toml to build environment for CI tests instead

.azure-pipelines/ci.yml

@@ -44,8 +44,7 @@ steps:
 
   - script: |
       set -eux
-      pip install --disable-pip-version-check -r "$(Pipeline.Workspace)/src/requirements_dev.txt"
-      pip install --no-deps --disable-pip-version-check -e "$(Pipeline.Workspace)/src"
+      pip install --disable-pip-version-check -e "$(Pipeline.Workspace)/src"[cicd,clem,client,server,developer]
     displayName: Install package
 
   - script: |

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 repos:
   # Syntax validation and some basic sanity checks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0 # Released 2023-10-09 # Prev: v4.0.1
+    rev: v4.5.0 # Released 2023-10-09
     # rev input based on version tag format in repo (e.g. with or without 'v')
     hooks:
       - id: check-added-large-files
@@ -32,31 +32,17 @@ repos:
         name: Formatting the pyproject.toml file
         additional_dependencies: ["tox>=4.9"]
 
-  # Ruff for linting and formatting
-  # Possible replacement for isort and flake8 (https://docs.astral.sh/ruff/linter/)
-  # - repo: https://github.com/astral-sh/ruff-pre-commit
-  #   rev: v0.3.5 # Released 2024-04-01
-  #   hooks:
-  #   # Ruff linter
-  #   - id: ruff
-  #     name: Running Ruff linter
-  #     args: [--fix]
-  #   # Ruff formatter
-  #   - id: ruff-format
-  #     name: Running Ruff formatter
-  #     types_or: [python]
-
   # Automatic source code formatting
   - repo: https://github.com/psf/black
-    rev: 24.3.0 # Released 2024-03-15 # Prev: 22.3.0
+    rev: 24.3.0 # Released 2024-03-15
     hooks:
       - id: black
         name: Formatting Python scripts according to Black
         args: [--safe, --quiet]
 
   # Automatically sort imports
   - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2 # Released 2023-12-13 # Prev: 5.12.0
+    rev: 5.13.2 # Released 2023-12-13
     hooks:
       - id: isort
         name: Tidying Python imports via Isort
@@ -83,20 +69,20 @@ repos:
   # Linting
   - repo: https://github.com/PyCQA/flake8
     # Release history: https://flake8.pycqa.org/en/latest/release-notes/index.html
-    rev: 7.0.0 # Released 2024-01-05 # Prev: 4.0.1
+    rev: 7.0.0 # Released 2024-01-05
     hooks:
       - id: flake8
         name: Running Flake8 linter on Python files
         additional_dependencies: [
             # Added Flake8-pyproject plugin for .toml compatibility
-            "Flake8-pyproject==1.2.3",
+            "Flake8-pyproject==1.2.3", # Released 2023-03-21
             # flake8-comprehensions URL: https://github.com/adamchainz/flake8-comprehensions
-            "flake8-comprehensions==3.14.0", # prev: 3.8.0
+            "flake8-comprehensions==3.14.0", # Released 2023-07-10
           ]
 
   # Type checking
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0 # Released 2024-03-09 # Prev: v0.910
+    rev: v1.9.0 # Released 2024-03-09
     hooks:
       - id: mypy
         name: Checking types in Python scripts using MyPy
@@ -113,7 +99,7 @@ repos:
 
   # Use Prettier to format other files
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.1.0 # Latest stable version (Released 2023-11-13)
+    rev: v3.1.0 # Released 2023-11-13 | Latest stable version
     hooks:
       - id: prettier
         name: Formatting other file types according to Prettier

pyproject.toml

@@ -36,6 +36,9 @@ dependencies = [
     "werkzeug",
 ]
 [project.optional-dependencies]
+cicd = [
+    "pytest-cov", # Used by Azure Pipelines for PyTest coverage reports
+]
 clem = [
     # "matplotlib", # For visual statistical analysis of images
     "readlif", # cryo-CLEM; open LIF files; part of bioio-lif
@@ -56,7 +59,6 @@ developer = [
 server = [
     "cryptography",
     "fastapi",
-    "importlib_resources; python_version<'3.9'", # Not needed anymore, since dropping support for Python 3.8
     "ispyb",
     "jinja2",
     "mysql-connector-python<=8.0.29", # ispyb 8.0.0 requires ==8.0.29
@@ -98,104 +100,11 @@ zip-safe = false
 [tool.setuptools.packages.find]
 where = ["src", "tests"]
 
-[tool.ruff]
-# Copied Ruff default recommended settings
-# Files and dirs to format
-include = [
-    "pyproject.toml",
-    # "setup.cfg",
-    "setup.py",
-    "src/**/*.py",
-    "tests/**/*.py",
-]
-# Exclude 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",
-]
-indent-width = 4  # Format same as Black.
-line-length = 88  # Format same as Black.
-target-version = "py39"  # Assume Python 3.9 and above
-
-[tool.ruff.format]
-docstring-code-format = false
-docstring-code-line-length = "dynamic"
-indent-style = "space"
-line-ending = "auto"
-quote-style = "double"
-skip-magic-trailing-comma = false
-
-[tool.ruff.lint]
-# Currently, not all Flake8 rule codes appear to be implemented in Ruff. VSCode throws up errors for them.
-# select: E901, F812, W602, W603, W604, W606
-# ignore: W503
-# A mix of the two need to be used for the rule codes currently desired.
-select = [
-    "C4",
-    "E401",
-    "E711",
-    "E712",
-    "E713",
-    "E714",
-    "E721",
-    "E722",
-    "F401",
-    "F402",
-    "F403",
-    "F405",
-    "F541",
-    "F631",
-    "F632",
-    "F633",
-    "F811",
-    "F821",
-    "F822",
-    "F841",
-    "F901",
-    "W191",
-    "W291",
-    "W292",
-    "W293",
-    "W605",
-]
-ignore = [
-    "E203",
-    "E266",
-    "E501",
-]
-fixable = ["ALL"]  # Allow fix for all enabled rules (when `--fix`) is provided in pre-commit.
-unfixable = []
-dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"  # Allow unused variables when underscore-prefixed.
-
 [tool.isort]
 profile = "black"
 
 [tool.flake8]
-# Flake8-pyproject allows .toml settings to be read into Flake8
+# Flake8-pyproject allows TOML file settings to be read into Flake8
 # URL: https://pypi.org/project/Flake8-pyproject/
 select = [
     "C4",