update deps and readme

.github/workflows/ci.yml

@@ -2,14 +2,18 @@ name: CI
 
 on:
   push:
-    branches:
-      - main
-    tags:
-      - "v*"
+    branches: [main]
+    tags: [v*]
   pull_request:
   workflow_dispatch:
 
 jobs:
+  check-manifest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - run: pipx run check-manifest
+
   test:
     name: ${{ matrix.platform }} (${{ matrix.python-version }})
     runs-on: ${{ matrix.platform }}
@@ -19,34 +23,38 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10']
-        platform: [ubuntu-latest]
+        python-version: [3.7, 3.8, 3.9, "3.10", "3.11"]
+        platform: [ubuntu-latest, windows-latest]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: tlambert03/setup-qt-libs@v1
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
           mamba-version: "*"
           channels: conda-forge,defaults
           channel-priority: true
 
+      - name: Install OpenCL
+        if: matrix.platform == 'ubuntu-latest'
+        run: mamba install pyopencl pocl
+
       - name: Install dependencies
         run: |
-          mamba install pyopencl pocl
-          sudo apt-get install -y xvfb
-          pip install -U pip wheel
-          pip install -e .[tests]
+          python -m pip install -U pip
+          python -m pip install -e .[test,pyqt5]
 
-      - name: Test with xvfb
-        if: runner.os == 'Linux'
-        run: xvfb-run --auto-servernum pytest --cov llspy
+      - name: Test
+        uses: aganders3/headless-gui@v2
+        with:
+          shell: bash -el {0}
+          run: python -m pytest --cov llspy
 
       - name: Coverage
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
 
   deploy:
     name: Deploy
@@ -55,7 +63,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v2
@@ -70,9 +78,7 @@ jobs:
           python -m build .
 
       - name: twine check
-        run: |
-          twine check dist/*
-          ls -lh dist
+        run: twine check dist/*
 
       - name: Build and publish
         run: twine upload dist/*

.gitignore

@@ -119,4 +119,4 @@ tests/testdata/sample/MIPs/
 tests/testdata/sample/sample_ProcessingLog.txt
 tests/testdata/sample/GPUdecon/
 
-llspy/_version.py
+src/llspy/_version.py

.pre-commit-config.yaml

@@ -1,38 +1,33 @@
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.5.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
-  - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v1.20.1
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.16
     hooks:
-      - id: setup-cfg-fmt
-  - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+      - id: validate-pyproject
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.3.4
     hooks:
-      - id: flake8
-        additional_dependencies: [flake8-typing-imports==1.7.0]
-  - repo: https://github.com/myint/autoflake
-    rev: v1.4
-    hooks:
-      - id: autoflake
-        args: ["--in-place", "--remove-all-unused-imports"]
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
-    hooks:
-      - id: isort
-  - repo: https://github.com/psf/black
-    rev: 22.6.0
-    hooks:
-      - id: black
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v2.37.1
-    hooks:
-      - id: pyupgrade
-        args: [--py37-plus, --keep-runtime-typing]
+      - id: ruff
+        args: [--fix, --unsafe-fixes]
+      - id: ruff-format
+
   # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v0.812
+  #   rev: v1.9.0
   #   hooks:
   #     - id: mypy
+  #       files: "^src/"
+  #       # # you have to add the things you want to type check against here
+  #       # additional_dependencies:
+  #       #   - numpy

MANIFEST.in

@@ -1,10 +1,10 @@
 include README.rst
 include CHANGELOG.rst
 
-recursive-include llspy *.py
-recursive-include llspy *.ui
-recursive-include llspy *.ini
-recursive-include llspy *.png
+recursive-include src/llspy *.py
+recursive-include src/llspy *.ui
+recursive-include src/llspy *.ini
+recursive-include src/llspy *.png
 recursive-include img *
 
 recursive-exclude tests *

README.rst

@@ -170,24 +170,15 @@ Requirements
 Installation
 ============
 
-**Note**: *As of version 0.4.2 cudaDecon is now included in the LLSpy conda package and requires no additional steps for installation.  Horray for open source!*
-
-
-#. Install `Anaconda <https://www.anaconda.com/download/>`_ or `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_
-#. Launch a ``terminal`` window (OS X, Linux), or ``Anaconda Prompt`` (Windows)
-#. Add the "conda-forge" and "talley" channels to your conda config
-
-    .. code:: bash
-
-        $ conda config --add channels conda-forge
-        $ conda config --add channels talley
-
+#. Install `conda <https://github.com/conda-forge/miniforge>`_
+#. Launch a ``terminal`` window (Linux), or ``Anaconda Prompt`` (Windows)
 #. Install LLSpy into a new conda environment
 
     .. code:: bash
 
-        $ conda create -n llsenv python=3.6 llspy
+        $ conda create -n llsenv python=3.11 cudadecon
         $ conda activate llsenv
+        $ pip install llspy
 
     The ``create -n llsenv`` line creates a virtual environment.  This is optional, but recommended as it easier to uninstall cleanly and prevents conflicts with any other python environments.  If installing into a virtual environment, you must source the environment before proceeding, and each time before using llspy.
 

pyproject.toml

@@ -3,7 +3,93 @@ requires = ["setuptools>=45", "wheel", "setuptools_scm>=6.2"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-write_to = "llspy/_version.py"
+write_to = "src/llspy/_version.py"
+
+# https://peps.python.org/pep-0621/
+[project]
+name = "llspy"
+dynamic = ["version"]
+description = "Lattice Light Sheet Processing Tools."
+readme = "README.rst"
+requires-python = ">=3.7"
+license = { text = "BSD-3-Clause" }
+authors = [{ name = "Talley Lambert", email = "[email protected]" }]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering :: Visualization",
+]
+dependencies = [
+    "click ~=8.1",
+    "llspy-slm>=0.2.1",
+    "matplotlib",
+    "numpy",
+    "parse ~=1.20",
+    "qtpy >=2.4",
+    "scipy <=1.12",
+    "sentry-sdk ~=1.38",
+    "tifffile",
+    "voluptuous ~=0.14",
+    "watchdog ~=3.0",
+    "numba;python_version < '3.13'",
+    "importlib_metadata; python_version < '3.8'",
+]
+
+# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
+[project.optional-dependencies]
+napari = ["napari"]
+pyqt5 = ["PyQt5"]
+pyside2 = ["PySide2"]
+spimagine = ["spimagine"]
+test = ["pytest", "pytest-cov", "pytest-qt"]
+dev = ["ipython", "mypy", "pdbpp", "pre-commit", "rich", "ruff"]
+
+[project.urls]
+homepage = "https://github.com/tlambert03/LLSpy"
+repository = "https://github.com/tlambert03/LLSpy"
+
+[project.scripts]
+lls = "llspy.bin.llspy_cli:cli"
+lls-gui = "llspy.bin.llspy_gui:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+# https://docs.astral.sh/ruff
+[tool.ruff]
+line-length = 88
+target-version = "py37"
+src = ["src"]
+
+[tool.ruff.lint]
+# https://docs.astral.sh/ruff/rules
+select = [
+    "E",    # style errors
+    "W",    # style warnings
+    "F",    # flakes
+    "I",    # isort
+    "UP",   # pyupgrade
+    "C4",   # flake8-comprehensions
+    "A001", # flake8-builtins
+    "RUF",  # ruff-specific rules
+    "TCH",  # flake8-type-checking
+    "TID",  # flake8-tidy-imports
+]
+ignore = [
+    "E501", # line length
+]
+exclude = ["docs/*"]
 
 [tool.check-manifest]
-ignore = ["llspy/_version.py", ".pre-commit-config.yaml"]
+ignore = ["llspy/_version.py", ".pre-commit-config.yaml", "tests/*"]