switch to Potry for build, pin Napari at 0.4.19.post1, and prep version 0.3.4 release

vreuter · vreuter · commit 94bbab763ab1 · 2025-04-01T12:59:02.000+02:00
diff --git a/.github/workflows/format.yaml b/.github/workflows/format.yaml
@@ -17,9 +17,20 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Set up Poetry
+        uses: snok/install-poetry@v1    # v1.3.4 at time of adoption
+        with:
+          poetry-version: "1.7.1"
+      - uses: actions/cache@v3
+        with:
+          path: |
+            ~/.cache/pypoetry/virtualenvs
+            ~/.cache/pytest
+          key: ${{ runner.os }}-poetry-tests-${{ hashFiles('poetry.lock') }}
       - name: Install project
-        run: pip install .[formatting]
+        run: poetry sync --no-interaction --with formatting
       - name: Run codespell
-        run: codespell --enable-colors
+        run: poetry run codespell --enable-colors
       - name: Run ruff
-        run: ruff format --diff .
+        run: poetry run ruff format --diff .
+
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -17,9 +17,20 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Set up Poetry
+        uses: snok/install-poetry@v1    # v1.3.4 at time of adoption
+        with:
+          poetry-version: "1.7.1"
+      - uses: actions/cache@v3
+        with:
+          path: |
+            ~/.cache/pypoetry/virtualenvs
+            ~/.cache/pytest
+          key: ${{ runner.os }}-poetry-tests-${{ hashFiles('poetry.lock') }}
       - name: Install project
-        run: pip install .[linting]
+        run: poetry sync --no-interaction --with linting
       - name: Run mypy on Python ${{ matrix.python-version }} on ${{ matrix.os }}
-        run: mypy
+        run: poetry run mypy
       - name: Run ruff on Python ${{ matrix.python-version }} on ${{ matrix.os }}
-        run: ruff check .
+        run: poetry run ruff check .
+
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -10,14 +10,27 @@ jobs:
         python-version: [ "3.10", "3.11", "3.12" ]
         os: [  ubuntu-latest, macos-latest, windows-latest, ubuntu-20.04 ]
     runs-on: ${{ matrix.os }}
-
+    defaults:
+      run:
+        shell: bash
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
+      - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Set up Poetry
+        uses: snok/install-poetry@v1    # v1.3.4 at time of adoption
+        with:
+          poetry-version: "1.7.1"
+      - uses: actions/cache@v3
+        with:
+          path: |
+            ~/.cache/pypoetry/virtualenvs
+            ~/.cache/pytest
+          key: ${{ runner.os }}-poetry-tests-${{ hashFiles('poetry.lock') }}
       - name: Install project
-        run: python -m pip install .[testsuite]
+        run: poetry sync --no-interaction --with testsuite
       - name: Run unit tests on Python ${{ matrix.python-version }} on ${{ matrix.os }}
-        run: pytest
+        run: poetry run pytest -v
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.3.4] - 2025-04-01
+
+### Changed
+* Pin Napari at 0.4.19.post1
+* Switch build to Poetry
+
 ## [v0.3.3] - 2025-03-28
 
 ### Changed
diff --git a/looptrace_loci_vis/__init__.py b/looptrace_loci_vis/__init__.py
@@ -1,3 +1,3 @@
 """Napari plugin for visualising locus-specific points from looptrace"""
 
-__version__ = "0.3.3"
+__version__ = "0.3.4"
diff --git a/looptrace_loci_vis/points_parser.py b/looptrace_loci_vis/points_parser.py
@@ -12,7 +12,7 @@
 from ._types import PathLike, QCFailReasons
 from .point_record import PointRecord
 
-Input = TypeVar("Input", contravariant=True)
+Input = TypeVar("Input", contravariant=True)  # noqa: PLC0105
 I1 = TypeVar("I1")
 I2 = TypeVar("I2", bound=Sized)
 
diff --git a/looptrace_loci_vis/reader.py b/looptrace_loci_vis/reader.py
@@ -55,7 +55,7 @@ def filename_extension(self) -> str:  # noqa: D102
     raises=dict(RuntimeError="If collection of QC statuses inferred from files doesn't make sense"),
     returns="A function to create layers from folder path, if folder path is parsable",
 )
-def get_reader(path: PathOrPaths) -> Optional[Reader]:  # noqa: D103
+def get_reader(path: PathOrPaths) -> Optional[Reader]:  # noqa: D103, C901, PLR0911, PLR0912
     if isinstance(path, str):
         path: Path = Path(path)  # type: ignore[no-redef]
     if not isinstance(path, Path):
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,86 +1,87 @@
-[project]
+[tool.poetry]
 name = "looptrace-loci-vis"
-dynamic = ["version"]
-requires-python = ">= 3.10, < 3.13"
-authors = [
-    {name = "Vince Reuter"}
-]
+version = "0.3.4"
 description = "This project facilitates viewing, in `napari`, locus-specific spots from `looptrace`."
+authors = ["Vince Reuter"]
+license = "MIT"
 readme = "README.md"
-license = {file = "LICENSE"}
+repository = "https://github.com/gerlichlab/looptrace-loci-vis.git"
 keywords = ["visualisation", "bioinformatics", "chromatin", "napari", "FISH"]
 classifiers = [
-    "Development Status :: 1 - Planning",
-    "License :: OSI Approved :: MIT License",
-    "Operating System :: POSIX :: Linux",
-    "Operating System :: MacOS",
-    "Operating System :: Microsoft :: Windows",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-    "Typing :: Typed",
-]
-dependencies = [
-    "expression >= 5.0.2",
-    "gertils @ git+https://github.com/gerlichlab/gertils.git@v0.6.0",
-    "napari >= 0.4.19; sys_platform == 'darwin'",
-    "napari[all] >= 0.4.19; sys_platform != 'darwin'",
-    "numpy",
-    "numpydoc_decorator >= 2.2.1",
-    "pandas",
-    "pyqt6 >= 6.5.0; sys_platform == 'darwin'",
-    "zarr >= 2.4.12",
+  "Development Status :: 1 - Planning",
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: POSIX :: Linux",
+  "Operating System :: MacOS",
+  "Operating System :: Microsoft :: Windows",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Typing :: Typed",
 ]
 
 [build-system]
-requires = ["setuptools", "wheel"]
-build-backend = "setuptools.build_meta"
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
 
-[project.urls]
-Homepage = "https://github.com/gerlichlab/looptrace-loci-vis"
-Repository = "https://github.com/gerlichlab/looptrace-loci-vis.git"
-Issues = "https://github.com/gerlichlab/looptrace-loci-vis/issues"
+[tool.poetry.plugins."napari.manifest"]
+looptrace-loci-vis = "looptrace_loci_vis:napari.yaml"
 
-[tool.setuptools.dynamic]
-version = { attr = "looptrace_loci_vis.__version__" }
+[tool.poetry.dependencies]
+python = ">=3.10,<3.13"
+expression = ">=5.0.2"
+gertils = { git = "https://github.com/gerlichlab/gertils.git", tag = "v0.6.0" }
+numpy = "*"
+numpydoc_decorator = ">=2.2.1"
+pandas = "*"
+zarr = ">=2.4.12"
 
-[tool.setuptools.package-data]
-looptrace_loci_vis = [ "napari.yaml", "examples/*.csv" ]
+# OS-specific dependency declarations
+napari = { version = "==0.4.19.post1", markers = "sys_platform == 'darwin'" }
+pyqt6 = { version = ">=6.5.0", markers = "sys_platform == 'darwin'" }
 
-[project.entry-points."napari.manifest"]
-looptrace-loci-vis = "looptrace_loci_vis:napari.yaml"
+[tool.poetry.group.dev]
+optional = true
 
-[project.optional-dependencies]
-formatting = [
-    "codespell >= 2.2.4",
-    "ruff == 0.7.4", # https://github.com/astral-sh/ruff/issues/14681
-]
-linting = [
-    "mypy >= 1.0.1",
-    "pandas-stubs",
-    "ruff == 0.7.4", # https://github.com/astral-sh/ruff/issues/14681
-]
-testsuite = [
-    "npe2",
-    "pytest >= 7.1.0",
-    "pytest-cov >= 5.0.0",
-    "typer",
-]
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.2.0"
+
+[tool.poetry.group.formatting]
+optional = true
+
+[tool.poetry.group.formatting.dependencies]
+codespell = ">=2.2.4"
+ruff = "==0.7.4"  # https://github.com/astral-sh/ruff/issues/14681
+
+[tool.poetry.group.linting]
+optional = true
+
+[tool.poetry.group.linting.dependencies]
+mypy = ">=1.0.1"
+pandas-stubs = "*"
+ruff = "==0.7.4"  # https://github.com/astral-sh/ruff/issues/14681
+
+[tool.poetry.group.testsuite.dependencies]
+npe2 = "*"
+pytest = ">=7.1.0"
+pytest-cov = ">=5.0.0"
+typer = "*"
 
 [tool.codespell]
-skip = ".git,.mypy_cache,.nox,.vscode,__pycache__,poetry.lock"
+skip = ".git,.mypy_cache,.nox,.vscode,__pycache__,pyproject.toml,poetry.lock"
 builtin = "clear,rare,informal,usage,code,names"
-ignore-words-list = "jupyter,iff"
+ignore-words-list = "jupyter,iff"  # prevent jupyter -> jupiter, iff -> if
 check-filenames = true
-uri-ignore-words-list = "*"
+uri-ignore-words-list = "*" # prevent spelling correction in URL-like values.
 
 [tool.mypy]
-files = ['looptrace_loci_vis/*.py']
+files = ['looptrace_loci_vis/*.py', 'tests/*.py']
+plugins = ["pydantic.mypy"]
 warn_redundant_casts = true
 warn_unused_ignores = true
 warn_return_any = true
 warn_unreachable = true
+enable_error_code = ["ignore-without-code"]
 
 [[tool.mypy.overrides]]
 module = "looptrace_loci_vis.*"
@@ -95,15 +96,19 @@ disallow_subclassing_any = true
 implicit_optional = false
 strict_optional = true
 
-[tool.pytest.ini_options]
-addopts = "-vv --cov looptrace_loci_vis --cov-report term-missing"
-
 [tool.ruff]
 # Black uses line-length = 88, but allows exceptions when breaking the line
 # would lead to other rule violations. Use 100 as a maximum hard limit:
 line-length = 100
 target-version = "py310"
 
+[tool.ruff.lint.per-file-ignores]
+"tests/*.py" = [
+    "INP001", # part of an implicit namespace package
+    "D103", # Missing docstring in public function
+    "ANN201", # Missing return type annotation for public function
+]
+
 [tool.ruff.lint]
 select = ["ALL"]
 ignore = [
@@ -115,19 +120,16 @@ ignore = [
     # Opinionated syntax
     "D203", # Ignore this to instead opt for class body or docstring to possibly start right away under class.
     "D213", # Ignore this to instead opt for summary part of docstring to be on first physical line.
+    "D401", # First line of docstring should be in imperative mood
     "TRY003", # Avoid specifying long messages outside the exception class
     "C408",  # Unnecessary `dict` call (rewrite as a literal)
     "EM",  # Exception must not use a (f-)string literal, assign to variable first
     "FIX002",  # Line contains TODO, consider resolving the issue
     "D400",  # First line should end with a period
     "D415",  # First line should end with a period, question mark, or exclamation point
     "N818",  # Exception should be named with an Error suffix
-    "PLR0913", # Too many arguments in function definition
-    "D401", # First line of docstring should be in imperative mood
-    "PLC0105", # This suggests suffixing a type variable with variance type (e.g., co/contra)
 
     # Imports and type annotations
-    "ANN003",  # Missing type annotation for kwargs
     "FA100",  # Missing `from __future__ import annotations`, but uses `typing.*`
     "TCH002",  # Move third-party import `...` into a type-checking block
     "TCH003",  # Move standard library import `...` into a type-checking block
@@ -152,25 +154,5 @@ ignore = [
     "ISC001",  # single-line-implicit-string-concatenation
     "ISC002",  # multi-line-implicit-string-concatenation
     "E501",  # line-too-long
-
-    # Other
-    "PLR0912",  # too many branches (of a conditional)
-    "TD002",  # missing author in TODO
-    "C901", # function too complex
-    "PLR0911", # too many return statements
-    "LOG015", # Use own logger instead
-]
-
-[tool.ruff.lint.per-file-ignores]
-"tests/*" = [
-    # Ignore some groups of checks in our test code.
-    "ANN",  # Type annotations
-    "D10",  # Missing docstrings
-    "INP001", # File `...` is part of an implicit namespace package. Add an `__init__.py`.
-
-    # Ignore some more specific checks in our test code.
-    "D401",  # First line of docstring should be in imperative mood
-    "N802",  # Function name `...` should be lowercase
-    "S101",  # Use of `assert` detected
 ]
 
diff --git a/shell.nix b/shell.nix
@@ -5,18 +5,26 @@
   }) {}, 
   dev ? true,
 }:
-let 
-  pyenv = pkgs.python311.withPackages (pp: with pp; [ pip wheel ]);
-  pipInstallExtras = if dev then "\"[formatting,linting,testsuite]\"" else "";
+let py311 = pkgs.python311.withPackages (ps: with ps; [ numpy pandas ]);
+    poetryExtras = if dev then [ "formatting" "linting" "testsuite" ] else [ ];
+    poetryInstallExtras = (
+      if poetryExtras == [] then ""
+      else pkgs.lib.concatStrings [ " --with " (pkgs.lib.concatStringsSep "," poetryExtras) ]
+    );
 in
 pkgs.mkShell {
   name = "looptrace-loci-vis-env";
-  buildInputs = [ pyenv ];
+  buildInputs = [ pkgs.poetry ];
   shellHook = ''
-    [[ -d .venv ]] || python3.11 -m venv .venv
-    source .venv/bin/activate
-    installcmd='pip install -e .${pipInstallExtras}'
+    # To get this working on the lab machine, we need to modify Poetry's keyring interaction:
+    # https://stackoverflow.com/questions/74438817/poetry-failed-to-unlock-the-collection
+    # https://github.com/python-poetry/poetry/issues/1917
+    export PYTHON_KEYRING_BACKEND=keyring.backends.null.Keyring
+    poetry env use "${py311}/bin/python"
+    installcmd="poetry install -vvvv --sync${poetryInstallExtras}"
     echo "Running installation command: $installcmd"
     eval "$installcmd"
+    source "$(poetry env info --path)/bin/activate"
   '';
 }
+

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,3 @@`
`1`	`1`	`"""Napari plugin for visualising locus-specific points from looptrace"""`
`2`	`2`
`3`		`-__version__ = "0.3.3"`
	`3`	`+__version__ = "0.3.4"`
Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@ def filename_extension(self) -> str: # noqa: D102`
`55`	`55`	`raises=dict(RuntimeError="If collection of QC statuses inferred from files doesn't make sense"),`
`56`	`56`	`returns="A function to create layers from folder path, if folder path is parsable",`
`57`	`57`	`)`
`58`		`-def get_reader(path: PathOrPaths) -> Optional[Reader]: # noqa: D103`
	`58`	`+def get_reader(path: PathOrPaths) -> Optional[Reader]: # noqa: D103, C901, PLR0911, PLR0912`
`59`	`59`	`if isinstance(path, str):`
`60`	`60`	`path: Path = Path(path) # type: ignore[no-redef]`
`61`	`61`	`if not isinstance(path, Path):`