Update metadata

Dockerfile

@@ -1,4 +1,4 @@
 FROM tensorflow/tensorflow:latest-gpu
 LABEL maintainer="[email protected]"
-RUN pip install cellfinder
+RUN pip install brainglobe-workflows
 CMD ["bash"]

MANIFEST.in

@@ -6,8 +6,8 @@ exclude *.yml
 exclude Dockerfile
 exclude *.ini
 
-recursive-include cellfinder *.py
-include cellfinder/config/*
+recursive-include brainglobe-workflows *.py
+include brainglobe-workflows/config/*
 
 global-include *.pxd
 

README.md

@@ -13,7 +13,8 @@
 [![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info/documentation/cellfinder/index.html)
 [![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
 
-# Cellfinder
+# Brainglobe Workflows
+
 Whole-brain cell detection, registration and analysis.
 
 **N.B. If you want to just use the cell detection part of cellfinder, please

brainglobe-workflows/__init__.py

@@ -0,0 +1,7 @@
+from importlib.metadata import metadata
+
+__version__ = metadata("brainglobe_workflows")["version"]
+__author__ = metadata("brainglobe_workflows")["author-email"]
+__license__ = metadata("brainglobe_workflows")["license"]
+
+del metadata

cellfinder/analyse/analyse.py → brainglobe-workflows/analyse/analyse.py

@@ -17,8 +17,7 @@
 from bg_atlasapi import BrainGlobeAtlas
 from brainglobe_utils.general.system import ensure_directory_exists
 from brainglobe_utils.pandas.misc import sanitise_df
-
-from cellfinder.export.export import export_points
+from brainglobe_workflows.export.export import export_points
 
 
 class Point:

cellfinder/export/export.py → brainglobe-workflows/export/export.py

@@ -1,5 +1,7 @@
-from cellfinder.export.abc4d import export_points as abc4d_export
-from cellfinder.export.brainrender import export_points as brainrender_export
+from brainglobe_workflows.export.abc4d import export_points as abc4d_export
+from brainglobe_workflows.export.brainrender import (
+    export_points as brainrender_export,
+)
 
 
 def export_points(

cellfinder/extract/extract_cubes.py → brainglobe-workflows/extract/extract_cubes.py

@@ -17,14 +17,13 @@
 from brainglobe_utils.cells.cells import group_cells_by_z
 from brainglobe_utils.general.numerical import is_even
 from brainglobe_utils.general.system import get_num_processes
+from brainglobe_workflows.tools import image_processing as img_tools
+from brainglobe_workflows.tools import system
 from numpy.linalg.linalg import LinAlgError
 from skimage import transform
 from tifffile import tifffile
 from tqdm import tqdm
 
-from cellfinder.tools import image_processing as img_tools
-from cellfinder.tools import system
-
 
 class StackSizeError(Exception):
     pass

cellfinder/figures/figures.py → brainglobe-workflows/figures/figures.py

@@ -1,6 +1,6 @@
 import logging
 
-from cellfinder.figures import heatmap
+from brainglobe_workflows.figures import heatmap
 
 
 def run(args, atlas, downsampled_shape):

cellfinder/main.py → brainglobe-workflows/main.py

@@ -42,10 +42,9 @@ def cells_exist(points_file):
 
 def main():
     suppress_tf_logging(tf_suppress_log_messages)
+    from brainglobe_workflows.tools import prep
     from brainreg.main import main as register
 
-    from cellfinder.tools import prep
-
     start_time = datetime.now()
     args, arg_groups, what_to_run, atlas = prep.prep_cellfinder_general()
 
@@ -100,18 +99,17 @@ def main():
 
 
 def run_all(args, what_to_run, atlas):
+    from brainglobe_workflows.analyse import analyse
+    from brainglobe_workflows.figures import figures
+    from brainglobe_workflows.tools.prep import (
+        prep_candidate_detection,
+        prep_channel_specific_general,
+    )
     from cellfinder_core.classify import classify
     from cellfinder_core.detect import detect
     from cellfinder_core.tools import prep
     from cellfinder_core.tools.IO import read_with_dask
 
-    from cellfinder.analyse import analyse
-    from cellfinder.figures import figures
-    from cellfinder.tools.prep import (
-        prep_candidate_detection,
-        prep_channel_specific_general,
-    )
-
     points = None
     signal_array = None
     args, what_to_run = prep_channel_specific_general(args, what_to_run)

cellfinder/tools/parser.py → brainglobe-workflows/tools/parser.py

@@ -16,6 +16,7 @@
     check_positive_float,
     check_positive_int,
 )
+from brainglobe_workflows import __version__
 from brainreg.cli import atlas_parse, geometry_parser, niftyreg_parse
 from brainreg.cli import backend_parse as brainreg_backend_parse
 from cellfinder_core.download.cli import (
@@ -24,8 +25,6 @@
 )
 from cellfinder_core.tools.source_files import source_custom_config_cellfinder
 
-from cellfinder import __version__
-
 # TODO: Gradually move all paths as strings to Path objects
 
 models = {

cellfinder/tools/prep.py → brainglobe-workflows/tools/prep.py

@@ -11,17 +11,16 @@
 from argparse import Namespace
 from pathlib import PurePath
 
+import brainglobe_workflows as program_for_log
+import brainglobe_workflows.tools.parser as parser
 from bg_atlasapi import BrainGlobeAtlas
 from brainglobe_utils.general.exceptions import CommandLineInputError
 from brainglobe_utils.general.system import ensure_directory_exists
+from brainglobe_workflows.tools import system, tools
+from brainglobe_workflows.tools.parser import cellfinder_parser
 from brainreg.paths import Paths as BrainRegPaths
 from fancylog import fancylog
 
-import cellfinder as program_for_log
-import cellfinder.tools.parser as parser
-from cellfinder.tools import system, tools
-from cellfinder.tools.parser import cellfinder_parser
-
 
 def get_arg_groups(args, parser):
     arg_groups = {}

environment.yml

@@ -1,7 +1,7 @@
-name: cellfinder
+name: brainglobe-workflows
 dependencies:
   - python=3.10
   - cudatoolkit
   - cudnn
   - pip:
-      - cellfinder
+      - brainglobe-workflows

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "cellfinder"
+name = "brainglobe-workflows"
 description = "Automated 3D cell detection and registration of whole-brain images"
 readme = "README.md"
 license = { file = "LICENSE" }
@@ -40,7 +40,7 @@ dependencies = [
 dynamic = ["version"]
 
 [project.scripts]
-cellfinder = "cellfinder.main:main"
+cellfinder = "brainglobe_workflows.main:main"
 
 [project.optional-dependencies]
 dev = [
@@ -55,8 +55,8 @@ dev = [
 napari = ["napari[pyside2]", "brainglobe-napari-io", "cellfinder-napari"]
 
 [project.urls]
-source = "https://github.com/brainglobe/cellfinder"
-bug_tracker = "https://github.com/brainglobe/cellfinder/issues"
+source = "https://github.com/brainglobe/brainglobe-workflows"
+bug_tracker = "https://github.com/brainglobe/brainglobe-workflows/issues"
 homepage = "https://brainglobe.info"
 documentation = "https://brainglobe.info/documentation/cellfinder"
 [build-system]
@@ -82,7 +82,7 @@ include-package-data = true
 zip-safe = false
 
 [tool.setuptools.packages.find]
-include = ["cellfinder"]
+include = ["brainglobe-workflows"]
 exclude = ["tests", "resources"]
 
 [tool.setuptools_scm]

pytest.ini

@@ -1,5 +1,5 @@
 [pytest]
-addopts = --cov=cellfinder
+addopts = --cov=brainglobe-workflows
 markers =
     slow: marks tests as slow (deselect with '-m "not slow"')
     serial

tests/tests/test_integration/test_detection.py

@@ -4,8 +4,7 @@
 
 import brainglobe_utils.IO.cells as cell_io
 import pytest
-
-from cellfinder.main import main as cellfinder_run
+from brainglobe_workflows.main import main as cellfinder_run
 
 data_dir = os.path.join(
     os.getcwd(), "tests", "data", "integration", "detection"

tests/tests/test_integration/test_extract.py

@@ -1,5 +1,6 @@
 import os
 
+import brainglobe_workflows.extract.extract_cubes as extract_cubes
 import imio
 import numpy as np
 import pytest
@@ -11,8 +12,6 @@
 from brainglobe_utils.IO.cells import get_cells
 from tifffile import tifffile
 
-import cellfinder.extract.extract_cubes as extract_cubes
-
 data_dir = os.path.join("tests", "data")
 
 signal_data_dir = os.path.join(data_dir, "signal")

tests/tests/test_integration/test_registration.py

@@ -5,10 +5,9 @@
 import numpy as np
 import pandas as pd
 import pytest
+from brainglobe_workflows.main import main as cellfinder_run
 from imio.load import load_any
 
-from cellfinder.main import main as cellfinder_run
-
 data_dir = os.path.join(
     os.getcwd(),
     "tests",

tests/tests/test_unit/test_tools/test_image_processing.py

@@ -1,8 +1,7 @@
 import random
 
 import numpy as np
-
-from cellfinder.tools import image_processing as img_tools
+from brainglobe_workflows.tools import image_processing as img_tools
 
 
 def test_crop_center_2d():

tests/tests/test_unit/test_tools/test_prep.py

@@ -2,8 +2,7 @@
 
 import pytest
 from brainglobe_utils.general.exceptions import CommandLineInputError
-
-from cellfinder.tools import prep
+from brainglobe_workflows.tools import prep
 
 # import shutil
 

tests/tests/test_unit/test_tools/test_system.py

@@ -2,12 +2,11 @@
 from math import isclose
 from pathlib import Path
 
+import brainglobe_workflows.tools.system as system
 import pytest
 from brainglobe_utils.general.exceptions import CommandLineInputError
 from brainglobe_utils.general.system import ensure_directory_exists
 
-import cellfinder.tools.system as system
-
 data_dir = Path("tests", "data")
 background_im_dir = os.path.join(data_dir, "background")
 

tests/tests/test_unit/test_tools/test_tools_general.py

@@ -1,10 +1,9 @@
 import random
 
+import brainglobe_workflows.tools.tools as tools
 import numpy as np
 import pytest
 
-import cellfinder.tools.tools as tools
-
 a = [1, "a", 10, 30]
 b = [30, 10, "c", "d"]