Merge branch 'main' into kaiming-weight-init

.github/workflows/docs.yaml

@@ -1,9 +1,6 @@
 name: Generate Pages
 
 on:
-  pull_request:
-    branches:
-      - main
   push:
     branches:
       - main

.pre-commit-config.yaml

@@ -3,14 +3,9 @@ ci:
   autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
   autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
 
-default_install_hook_types: [pre-commit, commit-msg]
+default_install_hook_types: [pre-commit]
 
 repos:
-  # - repo: https://github.com/compilerla/conventional-pre-commit
-  #   rev: v2.1.1
-  #   hooks:
-  #     - id: conventional-pre-commit
-  #       stages: [commit-msg]
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: v0.2.1
@@ -32,7 +27,7 @@ repos:
     rev: v1.8.0
     hooks:
       - id: mypy
-        files: "^src/"
+        files: "^dacapo/"
         # # you have to add the things you want to type check against here
         # additional_dependencies:
         #   - numpy

CONTRIBUTOR.md

@@ -1,22 +1,27 @@
 # Contributor Guide
 
 ## Development Installation
-- currently, pip install -r requirements-dev.txt
-and then pip install -e .
-TODO: set up pip install -e .[dev]
+`pip install -e .[dev,test]`
 
 ## Style and Pre-Commit
-- TODO: pre-commit with black mypy
-- do use ruff and black
-- do have typing, developers should supply types
+To set up pre-commit:
+```
+pre-commit autoupdate
+pre-commit install
+```
+Then any time you write a commit, it will run ruff, black, mypy, and validate the pyproject.toml. 
+To skip the pre-commit step, use:
+`git commit --no-verify`
+
+Ruff, black, and mypy settings are specified in the pyproject.toml. Currently they are not very strict, but this may change in the future.
 
 ## Testing
-- Unittest your functions
-- Pytest run automatically on PR, and so is codcov (maybe)
-TODO: codecov
+To run tests with coverage locally:
+`pytest tests --color=yes --cov --cov-report=term-missing`
+This will also be run automatically when a PR is made to master and a codecov report will be generated telling you if your PR increased or decreased coverage.
 
 
 ## Branching and PRs
 - Users that have been added to the CellMap organization and the DaCapo project should be able to develop directly into the CellMap fork of DaCapo. Other users will need to create a fork.
 - For a completely new feature, make a branch off of the `main` branch of CellMap's fork of DaCapo with a name describing the feature. If you are collaborating on a feature that already has a branch, you can branch off that feature branch.
-- Currently, you should make your PRs into the main branch of CellMap's fork, or the feature branch you branched off of. Once the PR is merged, the feature branch should be deleted. 
+- Currently, you should make your PRs into the main branch of CellMap's fork, or the feature branch you branched off of. PRs currently require one maintainer's approval before merging. Once the PR is merged, the feature branch should be deleted. 

Makefile

@@ -2,8 +2,7 @@ default:
 	pip install .
 
 install-dev:
-	pip install -e .
-	pip install --upgrade -r requirements-dev.txt
+	pip install -e ".[dev]"
 
 .PHONY: tests
 tests:

README.md

@@ -19,7 +19,7 @@ framework, but currently only supports [`torch`](https://pytorch.org/) with
 plans to support [`tensorflow`](https://www.tensorflow.org/).
 
 ## Installation and Setup
-Currently, only python 3.10 is supported. We recommend creating a new conda environment for dacapo with python 3.10.
+Currently, python>=3.10 is supported. We recommend creating a new conda environment for dacapo with python 3.10.
 ```
 conda create -n dacapo python=3.10
 ```
@@ -30,12 +30,16 @@ git clone git@github.com:janelia-cellmap/dacapo.git
 cd dacapo
 pip install .
 ```
-This will install the minimum required dependencies. However, having acess to a MongoDB server for storing outputs is strongly recommended for smoothest performance.
+This will install the minimum required dependencies. However, having access to a MongoDB server for storing outputs is strongly recommended for smoothest performance.
 
 To install and run MongoDB locally, refer to the MongoDB documentation [here](https://www.mongodb.com/docs/manual/installation/).
 
 ## Functionality Overview
 
-Tasks we support
-
-Networks we have for those tasks
+Tasks we support and approaches for those tasks:
+ - Instance Segmentation
+    - Affinities
+    - Local Shape Descriptors
+ - Semantic segmentation
+    - Signed distances
+    - One-hot encoding of different types of objects

pyproject.toml

@@ -67,6 +67,7 @@ dev = [
     "rich",
     "ruff",
     "pre-commit",
+    "jupyter",
 ]
 docs = [
     "sphinx-autodoc-typehints",
@@ -103,22 +104,27 @@ dacapo = "dacapo.cli:cli"
 line-length = 88
 target-version = "py310"
 src = ["dacapo"]
+
+[tool.ruff.lint]
 # https://beta.ruff.rs/docs/rules/
+# We may want to enable some of these options later
 select = [
     "E",    # style errors
-    "W",    # style warnings
+#    "W",    # style warnings
     "F",    # flakes
-    "D",    # pydocstyle
-    "I",    # isort
-    "UP",   # pyupgrade
-    "C4",   # flake8-comprehensions
-    "B",    # flake8-bugbear
-    "A001", # flake8-builtins
-    "RUF",  # ruff-specific rules
+#    "D",    # pydocstyle
+#    "I",    # isort
+#    "UP",   # pyupgrade
+#    "C4",   # flake8-comprehensions
+#    "B",    # flake8-bugbear
+#    "A001", # flake8-builtins
+#    "RUF",  # ruff-specific rules
 ]
+extend-ignore = ["E501"]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "tests/*.py" = ["D", "S"]
+"__init__.py" = ["F401"]
 
 # https://docs.pytest.org/en/6.2.x/customize.html
 [tool.pytest.ini_options]
@@ -129,20 +135,85 @@ filterwarnings = [
     "ignore::DeprecationWarning",
     ]
 
-
 # https://mypy.readthedocs.io/en/stable/config_file.html
 [tool.mypy]
 files = "dacapo/**/"
-strict = true
+strict = false
 disallow_any_generics = false
 disallow_subclassing_any = false
 show_error_codes = true
 pretty = true
 
 # # module specific overrides
-# [[tool.mypy.overrides]]
-# module = ["numpy.*",]
-# ignore_errors = true
+[[tool.mypy.overrides]]
+module = ["funlib.*",]
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = ["gunpowder.*"]
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "scipy.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "augment.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module="tifffile.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "daisy.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "lazy_property.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "skimage.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "fibsem_tools.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "neuroglancer.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "tqdm.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "zarr.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "pymongo.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "bson.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "affogato.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "SimpleITK.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "bokeh.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "lsd.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "yaml.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "pytest_lazyfixture.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "neuclease.dvid.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "mwatershed.*"
+ignore_missing_imports = true
+[[tool.mypy.overrides]]
+module = "numpy_indexed.*"
+ignore_missing_imports = true
 
 
 # https://coverage.readthedocs.io/en/6.4/config.html