style(precommit): apply precommit changes and tomlock

.flake8

+[flake8]
+ignore = E203, E266, E501, W503, F403, F401
+max-line-length = 79
+select = B,C,E,F,W,T4,B9
+exclude =
+    # No need to traverse our git directory
+    .git,
+    # There's no value in checking cache directories
+    __pycache__,
+    # Ignore virtual environment contents
+    .venv
+    # The conf file is mostly autogenerated, ignore it
+    docs/source/conf.py,
+    # The old directory contains Flake8 2.0
+    old,
+    # This contains our built documentation
+    build,
+    # This contains builds of flake8 that we don't want to check
+    dist,
+    # Any data produced inside the folder during development
+    data/,
+    # Temporarily ignore tests
+    tests/
+max-complexity = 18

.gitlab-ci.yml

@@ -4,9 +4,8 @@ cache:
     key: "project-${CI_JOB_NAME}"
     paths:
       - .venv
-    key:
-      files:
-        - poetry.lock
+    files:
+      - poetry.lock
 
 variables:
   TRIGGER_PYPI_NAME: ""

.gitlab/issue_templates/bug.md

@@ -22,4 +22,3 @@ it's very hard to read otherwise.)
 ## Possible fixes
 
 (If you can, link to the line of code that might be responsible for the problem)
-

README.md

@@ -12,14 +12,14 @@ See [INSTALL.md](./INSTALL.md) for installation instructions.
 ## Quickstart Documentation
 ### Setting up a server
 For testing and development, the easiest way to set up an OMERO server is by
-using Docker images. 
+using Docker images.
 [The software carpentry](https://software-carpentry.org/) and the [Open
  Microscopy Environment](https://www.openmicroscopy.org), have provided
 [instructions](https://ome.github.io/training-docker/) to do this.
 
 The `docker-compose.yml` file can be used to create an OMERO server with an
 accompanying PostgreSQL database, and an OMERO web server.
-It is described in detail 
+It is described in detail
 [here](https://ome.github.io/training-docker/12-dockercompose/).
 
 Our version of the `docker-compose.yml` has been adapted from the above to
@@ -59,7 +59,7 @@ with Image(list(image_ids.values())[0], **server_info) as image:
     imgs = dimg[tps, image.metadata["channels"].index("Brightfield"), 2, ...].compute()
     # tps timepoints, Brightfield channel, z=2, all x,y
 ```
- 
+
 ### Tiling the raw data
 
 A `Tiler` object performs trap registration. It may be built in different ways but the simplest one is using an image and a the default parameters set.
@@ -72,7 +72,7 @@ with Image(list(image_ids.values())[0], **server_info) as image:
 ```
 
 The initialisation should take a few seconds, as it needs to align the images
-in time. 
+in time.
 
 It fetches the metadata from the Image object, and uses the TilerParameters values (all Processes in aliby depend on an associated Parameters class, which is in essence a dictionary turned into a class.)
 
@@ -97,7 +97,7 @@ seg_expt.channels # Get a list of channels
 channel = 'Brightfield'
 ch_id = seg_expt.get_channel_index(channel)
 
-n_traps = seg_expt.n_traps # Get the number of traps 
+n_traps = seg_expt.n_traps # Get the number of traps
 ```
 
 #### Get the traps for a given time point
@@ -105,7 +105,7 @@ Alternatively, if you want to get all the traps at a given timepoint:
 
 ```python
 timepoint = 0
-seg_expt.get_traps_timepoints(timepoint, tile_size=96, channels=None, 
+seg_expt.get_traps_timepoints(timepoint, tile_size=96, channels=None,
                                 z=[0,1,2,3,4])
 ```
 

aliby/io/dataset.py

 #!/usr/bin/env python3
 import shutil
-from typing import Union
 from pathlib import Path, PosixPath
+from typing import Union
 
 import omero
 
-from aliby.io.omero import Argo
 from aliby.io.image import ImageLocal
+from aliby.io.omero import Argo
 
 
 class DatasetLocal:

aliby/pipeline.py

@@ -2,10 +2,10 @@
 Pipeline and chaining elements.
 """
 import logging
-import typing as t
 import os
 import re
 import traceback
+import typing as t
 from copy import copy
 from itertools import groupby
 from pathlib import Path, PosixPath

docs/source/INSTALL.md

-# Installation 
+# Installation
 
 Tested on: Mac OSX Mojave and Ubuntu 20.04
 
 ## Requirements
-We strongly recommend installing within a python environment as there are many dependencies that you may not want polluting your regular python environment. 
+We strongly recommend installing within a python environment as there are many dependencies that you may not want polluting your regular python environment.
 Make sure you are using python 3.
 
 An environment can be created with using the conda package manager:
@@ -11,25 +11,25 @@ An environment can be created with using the conda package manager:
     $ conda create --name <env>
     $ conda activate <env>
 
-Which you can deactivate with: 
+Which you can deactivate with:
 
     $ conda deactivate
 
-Or using virtualenv: 
+Or using virtualenv:
 
     $ python -m virtualenv /path/to/venv/
     $ source /path/to/venv/bin/activate
 
-This will download all of your packages under `/path/to/venv` and then activate it. 
-Deactivate using 
+This will download all of your packages under `/path/to/venv` and then activate it.
+Deactivate using
 
     $ deactivate
 
 You will also need to make sure you have a recent version of pip.
-In your local environment, run: 
+In your local environment, run:
 
     $ pip install --upgrade pip
-    
+
 Or using [pyenv](https://github.com/pyenv/pyenv) with pyenv-virtualenv:
 
     $ pyenv install 3.7.9
@@ -48,7 +48,7 @@ Once you have created your local environment, run:
 
 ### Git version
 
-We use [ poetry ](https://python-poetry.org/docs/#installation) for dependency management. 
+We use [ poetry ](https://python-poetry.org/docs/#installation) for dependency management.
 
 
 In case you want to have local versions (usually for development) the main three aliby dependencies you must install them in a specific order:

docs/source/index.rst

@@ -12,4 +12,3 @@
 
 .. include:: ../../README.md
    :parser: myst_parser.sphinx_
-

extraction/core/functions/loaders.py

-from inspect import getmembers, isfunction, getfullargspec
+from inspect import getfullargspec, getmembers, isfunction
 
 import numpy as np
 

extraction/examples/tiler_error.py

+import matplotlib.pyplot as plt
 from core.experiment import Experiment
 from core.segment import Tiler
-import matplotlib.pyplot as plt
 
 expt = Experiment.from_source(
     19310,  # Experiment ID on OMERO

pyproject.toml

 [tool.poetry]
 name = "aliby"
-version = "0.1.35"
+version = "0.1.36"
 description = "Process and analyse live-cell imaging data"
 authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"]
 packages = [
@@ -32,16 +32,18 @@ xmltodict = "^0.13.0" # read ome-tiff metadata
 zeroc-ice = {version="3.6.5"} # networking interface, slow to build
 # zeroc-ice = {version="3.6.5", optional=true} # To be set as optional in the future
 
-
 [tool.poetry.dev-dependencies]
-black = "^22.3.0"
+black = "^22.6.0"
 Sphinx = "^4.3.2"
 pytest = "^6.2.5"
 mypy = "^0.930"
 numpydoc = "^1.3.1"
-pyflakes = "^2.4.0"
 isort = "^5.10.1"
 jupyter = "^1.0.0"
+flake8 = "^4.0.1"
+pyright = "^1.1.258"
+pre-commit = "^2.20.0"
+data-science-types = "^0.2.23"
 
 [build-system]
 requires = ["setuptools", "poetry-core>=1.0.0"]
@@ -52,12 +54,21 @@ line-length = 79
 target-version = ['py37']
 include = '\.pyi?$'
 extend-exclude = '''
-# A regex preceded with ^/ will apply only to files and directories
-# in the root of the project.
-^/foo.py  # exclude a file named foo.py in the root of the project (in addition to the defaults)
+/(
+    \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | _build
+  | buck-out
+  | build
+  | dist
+)/
 '''
+
 [tool.isort]
+profile = "black"
 multi_line_output = 3
 line_length = 79
 include_trailing_comma = true
-

setup.py

-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 print("find_packages outputs ", find_packages("aliby"))
 setup(

tests/aliby/test_post_processing.py

-import pytest
 import unittest
 
 import matplotlib.pyplot as plt
 import numpy as np
+import pytest
 import skimage.morphology as morph
 from scipy import ndimage
 from skimage import draw