Update packaging (#62)

* update packaging

* update usage tips

* fix github runner images

* bump min python

* update tox

Author: kevinyamauchi

.github/workflows/test_and_deploy.yml

@@ -22,8 +22,8 @@ jobs:
     runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
-        platform: [ubuntu-latest, windows-latest, macos-13]
-        python-version: [3.8, 3.9, '3.10']
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v2

.gitignore

@@ -2,6 +2,9 @@
 
 .idea
 
+# uv virtual environment
+.venv/
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

MANIFEST.in

@@ -0,0 +1,9 @@
+# Tips for using surforama
+
+Here are some tips for using `surforama`:
+
+- We recommend denoising your tomograms before visualizing them in `surforama`. In our experience [cryocare](https://github.com/juglab/cryoCARE_pip) and [Isonet2](https://github.com/IsoNet-cryoET/IsoNet2) are a good starting point.
+- If you are visualizing large, remote datasets, a low latency connection is essential for a good experience. Using a hard-wired connection and choosing a server that is geographically close to you can help with this.
+- We find that using "light mode" in napari can help with visual contrast. See the [napari documentation](https://napari.org/stable/tutorials/fundamentals/viewer.html#changing-the-viewer-theme) for instructions how to change the theme.
+
+If you have other tips for using `surforama`, please make changes to the `/docs/usage_tips.md` file and then submit a pull request.

docs/usage_tips.md

@@ -85,48 +85,16 @@ nav:
   - 'Overview': index.md
   - 'Getting started': getting_started.md
   - 'Installation': installation.md
-  - 'CZ cryoET Data Portal': surforama_for_data_portal.md
+  - 'CZ cryoET Data Portal example': surforama_for_data_portal.md
+  - 'Tips and tricks': usage_tips.md
   - 'Contributing': contributing.md
 
 plugins:
   - search
-  - mkdocstrings:
-      handlers:
-        python:
-          import:
-            - https://docs.python.org/3/objects.inv
-          selection:
-            docstring_style: numpy
-            filters: [ "!^_" ]
-          rendering:
-            show_root_heading: true
-            show_root_toc_entry: true
-            show_root_full_path: true
-            show_object_full_path: false
-            # show_root_members_full_path: false
-            # show_category_heading: false
-            show_if_no_docstring: false
-            # show_signature: true
-            show_signature_annotations: true
-            show_source: true
-            # show_bases: true
-            # group_by_category: true
-            # heading_level: 2
-            members_order: source  # alphabetical/source
-
-            ## experimental
-            docstring_section_style: spacy  # or table/list/spacy
   - mkdocs-video:
       is_video: True
       video_autoplay: True
       video_loop: True
-#  - gallery:
-#      conf_script: docs/gallery_conf.py
-#      examples_dirs: [docs/examples]
-#      gallery_dirs: [docs/generated/gallery]
-#      filename_pattern: /*.py  # which scripts will be executed for the docs
-#      ignore_pattern: /__init__.py  # ignore these example files completely
-#      run_stale_examples: True
 
 extra_css:
   - stylesheets/extra.css

mkdocs.yml

@@ -1,7 +1,84 @@
 [build-system]
-requires = ["setuptools>=42.0.0", "wheel"]
+requires = ["setuptools>=64", "setuptools_scm[toml]>=8"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "surforama"
+dynamic = ["version"]
+description = "a tool for using surfaces to explore volumetric data in napari"
+readme = "README.md"
+license = { file = "LICENSE" }
+authors = [
+    { name = "Kyle Harrington", email = "surforama@kyleharrington.com" },
+]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Framework :: napari",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering :: Image Processing",
+]
+requires-python = ">=3.10"
+dependencies = [
+    "magicgui",
+    "mrcfile",
+    "numpy",
+    "pooch",
+    "qtpy",
+    "pyacvd",
+    "pyvista",
+    "rich",
+    "scikit-image",
+    "starfile",
+    "trimesh",
+    "typer",
+]
+
+[project.urls]
+"Bug Tracker"   = "https://github.com/cellcanvas/surforama/issues"
+"Documentation" = "https://github.com/cellcanvas/surforama#README.md"
+"Source Code"   = "https://github.com/cellcanvas/surforama"
+"User Support"  = "https://github.com/cellcanvas/surforama/issues"
+
+[project.scripts]
+surforama = "surforama._cli:app"
+
+[project.entry-points."napari.manifest"]
+surforama = "surforama:napari.yaml"
+
+[project.optional-dependencies]
+testing = [
+    "napari",
+    "pyqt5",
+    "pytest",
+    "pytest-cov",
+    "pytest-qt",
+    "tox",
+]
+docs = [
+    "mkdocs<2",
+    "mkdocs-material",
+    "mkdocstrings[python]",
+    "mkdocs-video",
+]
+napari = ["napari[all]"]
+dev = [
+    "surforama[testing,docs]",
+    "pre-commit",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"*" = ["*.yaml"]
 
 [tool.setuptools_scm]
 write_to = "src/surforama/_version.py"

pyproject.toml

@@ -1,3 +1,8 @@
 from .app import QtSurforama
 
+try:
+    from surforama._version import __version__
+except ImportError:
+    __version__ = "unknown"
+
 __all__ = ("QtSurforama",)

setup.cfg

@@ -1,13 +1,13 @@
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{38,39,310}-{linux,macos,windows}
+envlist = py{310,311,312}-{linux,macos,windows}
 isolated_build=true
 
 [gh-actions]
 python =
-    3.8: py38
-    3.9: py39
     3.10: py310
+    3.11: py311
+    3.12: py312
 
 [gh-actions:env]
 PLATFORM =