pyproject.toml

[build-system]
requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]

[project]
name = "ChimeraX-copick"
version = "0.5.0"
dynamic = ["classifiers", "requires-python"]
dependencies = [
    "ChimeraX-Core>=1.7",
    "ChimeraX-ArtiaX>=0.5.0",
    "ChimeraX-OME-Zarr>=0.5.4",
    "pydantic",
    "hatchling",
    "s3fs>=2024.3.1",
    "copick[all]>=0.6.0",
]
authors = [
  {name = "Utz H. Ermel", email = "utz@ermel.me"},
]
description = "ChimeraX extension for collaborative annotation of cryo-electron tomograms."
readme = "README.md"
license = {file = "LICENSE"}
keywords = ["cryoet", "cryo-et", "tomography", "annotation", "segmentation", "collaborative", "copick"]

[project.urls]
Repository = "https://github.com/copick/chimerax-copick.git"
Issues = "https://github.com/copick/chimerax-copick/issues"

[project.optional-dependencies]
dev = [
    "black",
    "ipython",
    "pre-commit",
    "ruff",
]

[chimerax]
categories = ["Volume Data", "General"]
package = "chimerax.copick"
min-session-version="1"
max-session-version="1"
classifiers = [
    "Development Status :: 3 - Alpha",
    "License :: OSI Approved :: MIT License",
]

[chimerax.tool."Copick"]
tool_name = "Copick"
category = ["Volume Data", "General"]
synopsis = "Collaborative annotation of cryo-electron tomograms."

[chimerax.command."copick start"]
category = "General"
synopsis = "Start a copick session or load a new config file."


[chimerax.package-data]
"src/icons/" = ["*.png"]

### TOOLBAR ###
# Copick tab, Visualization
[chimerax.provider."Tilted Slab"]
manager = "toolbar"
tab = "Copick"
section = "Visualization"
display_name = "Slab"
icon = "slab.png"

[chimerax.provider."Volume Rendering"]
manager = "toolbar"
tab = "Copick"
section = "Visualization"
display_name = "Volume"
icon = "fullvolume.png"

[chimerax.provider."Orthoplanes"]
manager = "toolbar"
tab = "Copick"
section = "Visualization"
display_name = "Orthoplanes"
icon = "orthoplanes.png"

[chimerax.provider."Surface"]
manager = "toolbar"
tab = "Copick"
section = "Visualization"
display_name = "Surface"
icon = "view_surface.png"

# Copick tab, Resolution
[chimerax.provider."1x"]
manager = "toolbar"
tab = "Copick"
section = "Binning"
display_name = "1x"
icon = "step_1.png"

[chimerax.provider."2x"]
manager = "toolbar"
tab = "Copick"
section = "Binning"
display_name = "2x"
icon = "step_2.png"

[chimerax.provider."4x"]
manager = "toolbar"
tab = "Copick"
section = "Binning"
display_name = "4x"
icon = "step_4.png"

# Copick tab, Markers
[chimerax.provider."layout-markers"]
manager = "toolbar"
tab="Copick"
section="Markers"
compact="true"

[chimerax.provider."Show Markers"]
manager = "toolbar"
tab = "Copick"
section = "Markers"
display_name= "Show"
icon="show_markers.png"
description= "Show particles as spheres."

[chimerax.provider."Hide Markers"]
manager = "toolbar"
tab="Copick"
section="Markers"
display_name="Hide"
icon="hide_markers.png"
description="Hide spheres."

# Copick tab, Axes
[chimerax.provider."Show Axes"]
manager = "toolbar"
tab = "Copick"
section = "Axes"
display_name = "Show"
icon = "show_axes.png"
description = "Show principle axes of particles."

[chimerax.provider."Hide Axes"]
manager = "toolbar"
tab = "Copick"
section = "Axes"
display_name = "Hide"
icon = "hide_axes.png"
description = "Hide axes."

[chimerax.provider."layout-axes"]
manager = "toolbar"
tab = "Copick"
section = "Axes"
compact = true

# Copick tab, Surfaces
[chimerax.provider."Show Surfaces"]
manager = "toolbar"
tab = "Copick"
section = "Surfaces"
display_name = "Show"
icon = "show_surfaces.png"
description = "Show particle surfaces."

[chimerax.provider."Hide Surfaces"]
manager = "toolbar"
tab = "Copick"
section = "Surfaces"
display_name = "Hide"
icon = "hide_surfaces.png"
description = "Hide surfaces."

[chimerax.provider."layout-surfaces"]
manager = "toolbar"
tab = "Copick"
section = "Surfaces"
compact = true

# Copick tab, View
[chimerax.provider."XY"]
manager = "toolbar"
tab = "Copick"
section = "View"
icon = "view_xy.png"
description = "Set viewing direction to XY planes."

[chimerax.provider."XZ"]
manager = "toolbar"
tab = "Copick"
section = "View"
icon = "view_xz.png"
description = "Set viewing direction to XZ planes."

[chimerax.provider."YZ"]
manager = "toolbar"
tab = "Copick"
section = "View"
icon = "view_yz.png"
description = "Set viewing direction to YZ planes."


[chimerax.provider."Clip"]
manager = "toolbar"
tab = "Copick"
section = "View"
icon = "clip.png"
description = "Turn slab-clipping on or off for all tomograms."

[chimerax.provider."Invert Contrast"]
manager = "toolbar"
tab = "Copick"
section = "View"
icon = "invert_contrast.png"
description = "Invert the contrast of displayed tomogram."

# Copick tab, Standard Mouse Modes
#[chimerax.provider."Rotate"]
#manager = "toolbar"
#tab = "Copick"
#section = "Movement"
#mouse_mode = "rotate"
#display_name = "Rotate"
##icon = "rotate.png"
#description = "Rotate models."

#[chimerax.provider."Translate"]
#manager = "toolbar"
#tab = "Copick"
#section = "Movement"
#mouse_mode = "translate"
#display_name = "Translate"
##icon = "translate.png"
#description = "Translate models."

#[chimerax.provider."Pivot"]
#manager = "toolbar"
#tab = "Copick"
#section = "Movement"
#mouse_mode = "pivot"
#display_name = "Center On"
##icon = "crosshairs.png"
#description = "Set center of rotation on particle."

# Copick tab, Place Markers mirrored
[chimerax.provider."mark maximum"]
manager = "toolbar"
tab = "Copick"
section = "Place Particles"
mouse_mode = "mark maximum"
display_name = "Maximum"
icon = "maximum.png"
description = "Mark maximum."

[chimerax.provider."mark plane"]
manager = "toolbar"
tab = "Copick"
section = "Place Particles"
mouse_mode = "mark plane"
display_name = "Plane"
icon = "plane.png"
description = "Mark volume plane."

[chimerax.provider."mark surface"]
manager = "toolbar"
tab = "Copick"
section = "Place Particles"
mouse_mode = "mark surface"
display_name = "Surface"
icon = "surface.png"
description = "Mark surface."

[chimerax.provider."mark center"]
manager = "toolbar"
tab = "Copick"
section = "Place Particles"
mouse_mode = "mark center"
display_name = "Center"
icon = "center.png"
description = "Mark center."

[chimerax.provider."mark point"]
manager = "toolbar"
tab = "Copick"
section = "Place Particles"
mouse_mode = "mark point"
display_name = "Point"
icon = "point.png"
description = "Mark point."

# Copick tab, Manipulate Particles
[chimerax.provider."Select"]
manager = "toolbar"
tab = "Copick"
section = "Manipulate Particles"
mouse_mode = "select"
display_name = "Select"
icon = "select.png"
description = "Select models."

[chimerax.provider."Translate Selected Particles"]
manager = "toolbar"
tab = "Copick"
section = "Manipulate Particles"
mouse_mode = "translate selected particles"
display_name = "Translate Selected"
icon = "translate_selected.png"
description = "Shift selected particles (hold SHIFT to rotate)."

[chimerax.provider."Rotate Selected Particles"]
manager = "toolbar"
tab = "Copick"
section = "Manipulate Particles"
mouse_mode = "rotate selected particles"
display_name = "Rotate Selected"
icon = "rotate_selected.png"
description = "Rotate selected particles (hold SHIFT to translate)."

[chimerax.provider."Translate Picked Particle"]
manager = "toolbar"
tab = "Copick"
section = "Manipulate Particles"
mouse_mode = "translate picked particle"
display_name = "Translate Picked"
icon = "translate_picked.png"
description = "Shift picked particle (hold SHIFT to rotate)."

[chimerax.provider."Rotate Picked Particle"]
manager = "toolbar"
tab = "Copick"
section = "Manipulate Particles"
mouse_mode = "rotate picked particle"
display_name = "Rotate Picked"
icon = "rotate_picked.png"
description = "Rotate picked particle (hold SHIFT to translate)."

# Copick tab, Delete Particles
[chimerax.provider."Delete Selected Particles"]
manager = "toolbar"
tab = "Copick"
section = "Delete Particles"
display_name = "Delete Selected"
icon = "delete_selected.png"
description = "Delete picked particle."

[chimerax.provider."Delete Picked Particle"]
manager = "toolbar"
tab = "Copick"
section = "Delete Particles"
mouse_mode = "delete picked particle"
display_name = "Delete Picked"
icon = "delete.png"
description = "Delete picked particle."

[tool.black]
line-length = 120
target_version = ['py311']

[tool.ruff]
select = [
    "E", "W",  # pycodestyle
    "F",  # pyflakes
    "B",  # bugbear
    "I",  # isort
    "N",  # pep8-naming
    "ASYNC",  # async
    "COM",  # commas
    "C4",  # comprehensions
    "DTZ",  # datetimez
    "ISC",  # implicit-str-concat
    "G",  # logging-format
    "T20",  # print
    "SIM",  # simplify
]
ignore = [
    "N815",  # Variable in class scope should not be mixedCase
    "N802",  # Function name should be lowercase
    "N806",  # Variable in function should be lowercase
    "B008",  # Do not perform calls in argument defaults
    "N999",  # Invalid module name
    "E501",  # line too long
    "C408",  # rewrite empty built-ins as literals
    "T201",  # print statements.
    "DTZ007", # Datetime objects without timezones.
    "DTZ005", # More datetimes without timezones.
]
line-length = 120
target-version = "py311"

[tool.ruff.isort]
known-first-party =["common"]

[tool.ruff.flake8-quotes]
docstring-quotes = "double"

[tool.mypy]
show_error_codes = true
ignore_missing_imports = true
warn_unreachable = true
strict = true