cellfinder 0.7.1__tar.gz → 0.8.1__tar.gz

{cellfinder-0.7.1/cellfinder.egg-info → cellfinder-0.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 0.7.1
+Version: 0.8.1
 Summary: Automated 3D cell detection and registration of whole-brain images
 Author: Christian Niedworok, Charly Rousseau
 Author-email: Adam Tyson <code@adamltyson.com>
@@ -48,11 +48,44 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: brainreg>=1.0.0
+Requires-Dist: cellfinder-core<1.0.0,>=0.2.4
+Requires-Dist: configobj
+Requires-Dist: fancylog>=0.0.7
+Requires-Dist: imio
+Requires-Dist: brainglobe-utils<1.0.0,>=0.2.5
+Requires-Dist: multiprocessing-logging>=0.3.4
+Requires-Dist: natsort
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: packaging
+Requires-Dist: scikit-image
+Requires-Dist: tifffile
+Requires-Dist: tqdm
 Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: gitpython; extra == "dev"
+Requires-Dist: coverage>=5.0.3; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: setuptools_scm; extra == "dev"
 Provides-Extra: napari
-License-File: LICENSE
+Requires-Dist: napari[pyside2]; extra == "napari"
+Requires-Dist: brainglobe-napari-io<1.0.0; extra == "napari"
+Requires-Dist: cellfinder-napari<1.0.0; extra == "napari"
+
+# 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)

{cellfinder-0.7.1 → cellfinder-0.8.1}/README.md

@@ -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)

cellfinder-0.8.1/cellfinder/__init__.py

@@ -0,0 +1,14 @@
+import warnings
+
+warnings.warn(
+    "cellfinder (the command line tool) has migrated. Please use brainglobe-workflows instead: https://github.com/brainglobe/brainglobe-workflows",
+    DeprecationWarning,
+)
+
+from importlib.metadata import metadata
+
+__version__ = metadata("cellfinder")["version"]
+__author__ = metadata("cellfinder")["author-email"]
+__license__ = metadata("cellfinder")["license"]
+
+del metadata

{cellfinder-0.7.1 → cellfinder-0.8.1}/cellfinder/analyse/analyse.py

@@ -16,7 +16,7 @@ import pandas as pd
 import tifffile
 from bg_atlasapi import BrainGlobeAtlas
 from brainglobe_utils.general.system import ensure_directory_exists
-from brainglobe_utils.pandas.misc import sanitise_df
+from brainglobe_utils.pandas.misc import safe_pandas_concat, sanitise_df
 
 from cellfinder.export.export import export_points
 
@@ -155,13 +155,16 @@ def get_region_totals(
                 ]
             )
             if n_points:
-                point_numbers = point_numbers.append(
-                    {
-                        "structure_name": structure,
-                        "hemisphere": hemisphere,
-                        "cell_count": n_points,
-                    },
-                    ignore_index=True,
+                point_numbers = safe_pandas_concat(
+                    point_numbers,
+                    pd.DataFrame(
+                        data=[[structure, hemisphere, n_points]],
+                        columns=[
+                            "structure_name",
+                            "hemisphere",
+                            "cell_count",
+                        ],
+                    ),
                 )
     sorted_point_numbers = point_numbers.sort_values(
         by=["cell_count"], ascending=False

{cellfinder-0.7.1 → cellfinder-0.8.1}/cellfinder/main.py

@@ -42,7 +42,7 @@ def cells_exist(points_file):
 
 def main():
     suppress_tf_logging(tf_suppress_log_messages)
-    from brainreg.main import main as register
+    from brainreg.core.main import main as register
 
     from cellfinder.tools import prep
 

{cellfinder-0.7.1 → cellfinder-0.8.1}/cellfinder/tools/parser.py

@@ -16,8 +16,8 @@ from brainglobe_utils.general.numerical import (
     check_positive_float,
     check_positive_int,
 )
-from brainreg.cli import atlas_parse, geometry_parser, niftyreg_parse
-from brainreg.cli import backend_parse as brainreg_backend_parse
+from brainreg.core.cli import atlas_parse, geometry_parser, niftyreg_parse
+from brainreg.core.cli import backend_parse as brainreg_backend_parse
 from cellfinder_core.download.cli import (
     download_directory_parser,
     model_parser,

{cellfinder-0.7.1 → cellfinder-0.8.1}/cellfinder/tools/prep.py

@@ -14,7 +14,7 @@ from pathlib import PurePath
 from bg_atlasapi import BrainGlobeAtlas
 from brainglobe_utils.general.exceptions import CommandLineInputError
 from brainglobe_utils.general.system import ensure_directory_exists
-from brainreg.paths import Paths as BrainRegPaths
+from brainreg.core.paths import Paths as BrainRegPaths
 from fancylog import fancylog
 
 import cellfinder as program_for_log

{cellfinder-0.7.1 → cellfinder-0.8.1}/cellfinder/tools/tools.py

@@ -80,9 +80,9 @@ def get_number_of_bins_nd(array_size, binning):
     :param binning: How many pixels in each edge of nD equal sized bins
     :return:
     """
-    if type(array_size) is tuple:
+    if isinstance(array_size, tuple):
         bins = [int(size / binning) for size in array_size]
-    elif type(array_size) is dict:
+    elif isinstance(array_size, dict):
         bins = [int(size / binning) for size in array_size.values()]
     else:
         raise NotImplementedError(

{cellfinder-0.7.1 → cellfinder-0.8.1/cellfinder.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 0.7.1
+Version: 0.8.1
 Summary: Automated 3D cell detection and registration of whole-brain images
 Author: Christian Niedworok, Charly Rousseau
 Author-email: Adam Tyson <code@adamltyson.com>
@@ -48,11 +48,44 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: brainreg>=1.0.0
+Requires-Dist: cellfinder-core<1.0.0,>=0.2.4
+Requires-Dist: configobj
+Requires-Dist: fancylog>=0.0.7
+Requires-Dist: imio
+Requires-Dist: brainglobe-utils<1.0.0,>=0.2.5
+Requires-Dist: multiprocessing-logging>=0.3.4
+Requires-Dist: natsort
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: packaging
+Requires-Dist: scikit-image
+Requires-Dist: tifffile
+Requires-Dist: tqdm
 Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: gitpython; extra == "dev"
+Requires-Dist: coverage>=5.0.3; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: setuptools_scm; extra == "dev"
 Provides-Extra: napari
-License-File: LICENSE
+Requires-Dist: napari[pyside2]; extra == "napari"
+Requires-Dist: brainglobe-napari-io<1.0.0; extra == "napari"
+Requires-Dist: cellfinder-napari<1.0.0; extra == "napari"
+
+# 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)

{cellfinder-0.7.1 → cellfinder-0.8.1}/cellfinder.egg-info/requires.txt

@@ -1,9 +1,9 @@
-brainreg
-cellfinder-core>=0.2.4
+brainreg>=1.0.0
+cellfinder-core<1.0.0,>=0.2.4
 configobj
 fancylog>=0.0.7
 imio
-brainglobe-utils>=0.2.5
+brainglobe-utils<1.0.0,>=0.2.5
 multiprocessing-logging>=0.3.4
 natsort
 numpy
@@ -24,5 +24,5 @@ setuptools_scm
 
 [napari]
 napari[pyside2]
-brainglobe-napari-io
-cellfinder-napari
+brainglobe-napari-io<1.0.0
+cellfinder-napari<1.0.0

{cellfinder-0.7.1 → cellfinder-0.8.1}/pyproject.toml

@@ -3,7 +3,7 @@ name = "cellfinder"
 description = "Automated 3D cell detection and registration of whole-brain images"
 readme = "README.md"
 license = { file = "LICENSE" }
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 authors = [
     { name = "Adam Tyson", email = "code@adamltyson.com" },
     { name = "Christian Niedworok" },
@@ -22,12 +22,12 @@ classifiers = [
     "Intended Audience :: Science/Research",
 ]
 dependencies = [
-    "brainreg",
-    "cellfinder-core>=0.2.4",
+    "brainreg>=1.0.0",
+    "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",
@@ -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"

cellfinder-0.7.1/cellfinder/__init__.py

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