Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Prepare for migration #261

Merged
merged 5 commits into from
Dec 13, 2023
Merged

Prepare for migration #261

Show file tree
Hide file tree
Changes from 4 commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
7adc741
Throw deprecation warning on import
willGraham01 Nov 15, 2023
18946e6
Update README with migration warning
willGraham01 Nov 15, 2023
e3325b7
Force dependencies <1.0.0 of brainglobe packages
willGraham01 Nov 15, 2023
cc3e642
Tell tox to ignore our own deprecation warning
willGraham01 Nov 15, 2023
d3a2d0b
Update cellfinder/__init__.py
willGraham01 Nov 15, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 9 additions & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,12 @@
# Cellfinder has moved!

As part of [our BrainGlobe version 1 update](https://brainglobe.info/blog/version1/version_1_announcement.html), the `cellfinder` workflow that can be run from the command line [has moved into `brainglobe-workflows`](https://github.com/brainglobe/brainglobe-workflows).
Please head over to that package to install an up-to-date version of `cellfinder`.

You can keep up to date with the version 1 rollout by [visiting our blog page](https://brainglobe.info/blog/index.html), or joining us [over on Zulip](https://brainglobe.zulipchat.com).

---

[![Python Version](https://img.shields.io/pypi/pyversions/cellfinder.svg)](https://pypi.org/project/cellfinder)
[![PyPI](https://img.shields.io/pypi/v/cellfinder.svg)](https://pypi.org/project/cellfinder)
[![Downloads](https://pepy.tech/badge/cellfinder)](https://pepy.tech/project/cellfinder)
Expand Down
7 changes: 7 additions & 0 deletions cellfinder/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,10 @@
import warnings

Check warning on line 1 in cellfinder/__init__.py

View check run for this annotation

Codecov / codecov/patch

cellfinder/__init__.py#L1 

Added line #L1 was not covered by tests

warnings.warn(

Check warning on line 3 in cellfinder/__init__.py

View check run for this annotation

Codecov / codecov/patch

cellfinder/__init__.py#L3 

Added line #L3 was not covered by tests
"cellfinder (CLI) has migrated. Please use brainglobe-workflows instead: https://github.com/brainglobe/brainglobe-workflows",
willGraham01 marked this conversation as resolved.
Show resolved Hide resolved
DeprecationWarning,
)

from importlib.metadata import metadata

__version__ = metadata("cellfinder")["version"]
Expand Down
10 changes: 7 additions & 3 deletions pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,11 +23,11 @@ classifiers = [
]
dependencies = [
"brainreg>=1.0.0",
"cellfinder-core>=0.2.4",
"cellfinder-core>=0.2.4,<1.0.0",
"configobj",
"fancylog>=0.0.7",
"imio",
"brainglobe-utils>=0.2.5",
"brainglobe-utils>=0.2.5,<1.0.0",
"multiprocessing-logging>=0.3.4",
"natsort",
"numpy",
Expand All @@ -52,7 +52,11 @@ dev = [
"pre-commit",
"setuptools_scm",
]
napari = ["napari[pyside2]", "brainglobe-napari-io", "cellfinder-napari"]
napari = [
"napari[pyside2]",
"brainglobe-napari-io<1.0.0",
"cellfinder-napari<1.0.0",
]

[project.urls]
source = "https://github.com/brainglobe/cellfinder"
Expand Down
2 changes: 1 addition & 1 deletion tox.ini
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ INPUT_COREDEV =
true: coredev

[testenv]
commands = pytest {toxinidir} -v --cov=./ --cov-report=xml
commands = pytest {toxinidir} -v --cov=./ --cov-report=xml -W ignore::DeprecationWarning
deps =
pytest-cov
pytest
Expand Down