cellfinder 0.7.0__tar.gz → 0.8.0__tar.gz

{cellfinder-0.7.0 → cellfinder-0.8.0}/.gitignore

@@ -2,7 +2,7 @@
 *.conf.custom
 
 # Byte-compiled / optimized / DLL files
-__pycache__/
+**/__pycache__/**
 *.py[cod]
 *$py.class
 
@@ -122,3 +122,5 @@ venv.bak/
 pip-wheel-metadata/
 
 *.DS_Store
+
+*.vscode/

cellfinder-0.8.0/MANIFEST.in

@@ -0,0 +1,18 @@
+include README.md
+include LICENSE
+
+exclude *.yaml
+exclude *.yml
+exclude Dockerfile
+exclude *.ini
+
+recursive-include cellfinder *.py
+include cellfinder/config/*
+
+global-include *.pxd
+
+prune tests
+prune resources
+
+prune .github
+prune .tox

{cellfinder-0.7.0 → cellfinder-0.8.0}/PKG-INFO

@@ -1,13 +1,43 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 0.7.0
+Version: 0.8.0
 Summary: Automated 3D cell detection and registration of whole-brain images
-Home-page: https://brainglobe.info/cellfinder
-Author: Adam Tyson, Christian Niedworok, Charly Rousseau
-Author-email: code@adamltyson.com
-Project-URL: Source Code, https://github.com/brainglobe/cellfinder
-Project-URL: Bug Tracker, https://github.com/brainglobe/cellfinder/issues
-Project-URL: Documentation, https://docs.brainglobe.info/cellfinder
+Author: Christian Niedworok, Charly Rousseau
+Author-email: Adam Tyson <code@adamltyson.com>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2020, University College London
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        * Redistributions of source code must retain the above copyright notice, this
+          list of conditions and the following disclaimer.
+        
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
+          and/or other materials provided with the distribution.
+        
+        * Neither the name of the copyright holder nor the names of its
+          contributors may be used to endorse or promote products derived from
+          this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: source, https://github.com/brainglobe/cellfinder
+Project-URL: bug_tracker, https://github.com/brainglobe/cellfinder/issues
+Project-URL: homepage, https://brainglobe.info
+Project-URL: documentation, https://brainglobe.info/documentation/cellfinder
 Classifier: Development Status :: 3 - Alpha
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Operating System :: Microsoft :: Windows :: Windows 10
@@ -18,11 +48,35 @@ 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
-Provides-Extra: napari
-Provides-Extra: dev
 License-File: LICENSE
+Requires-Dist: brainreg>=1.0.0
+Requires-Dist: cellfinder-core>=0.2.4
+Requires-Dist: configobj
+Requires-Dist: fancylog>=0.0.7
+Requires-Dist: imio
+Requires-Dist: brainglobe-utils>=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
+Requires-Dist: napari[pyside2]; extra == "napari"
+Requires-Dist: brainglobe-napari-io; extra == "napari"
+Requires-Dist: cellfinder-napari; extra == "napari"
 
 [![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-0.8.0/cellfinder/__init__.py

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

{cellfinder-0.7.0 → cellfinder-0.8.0}/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-0.7.0 → cellfinder-0.8.0}/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-0.7.0 → cellfinder-0.8.0}/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-0.7.0 → cellfinder-0.8.0}/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-0.7.0 → cellfinder-0.8.0}/cellfinder.egg-info/PKG-INFO

@@ -1,13 +1,43 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 0.7.0
+Version: 0.8.0
 Summary: Automated 3D cell detection and registration of whole-brain images
-Home-page: https://brainglobe.info/cellfinder
-Author: Adam Tyson, Christian Niedworok, Charly Rousseau
-Author-email: code@adamltyson.com
-Project-URL: Source Code, https://github.com/brainglobe/cellfinder
-Project-URL: Bug Tracker, https://github.com/brainglobe/cellfinder/issues
-Project-URL: Documentation, https://docs.brainglobe.info/cellfinder
+Author: Christian Niedworok, Charly Rousseau
+Author-email: Adam Tyson <code@adamltyson.com>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2020, University College London
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        * Redistributions of source code must retain the above copyright notice, this
+          list of conditions and the following disclaimer.
+        
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
+          and/or other materials provided with the distribution.
+        
+        * Neither the name of the copyright holder nor the names of its
+          contributors may be used to endorse or promote products derived from
+          this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: source, https://github.com/brainglobe/cellfinder
+Project-URL: bug_tracker, https://github.com/brainglobe/cellfinder/issues
+Project-URL: homepage, https://brainglobe.info
+Project-URL: documentation, https://brainglobe.info/documentation/cellfinder
 Classifier: Development Status :: 3 - Alpha
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Operating System :: Microsoft :: Windows :: Windows 10
@@ -18,11 +48,35 @@ 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
-Provides-Extra: napari
-Provides-Extra: dev
 License-File: LICENSE
+Requires-Dist: brainreg>=1.0.0
+Requires-Dist: cellfinder-core>=0.2.4
+Requires-Dist: configobj
+Requires-Dist: fancylog>=0.0.7
+Requires-Dist: imio
+Requires-Dist: brainglobe-utils>=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
+Requires-Dist: napari[pyside2]; extra == "napari"
+Requires-Dist: brainglobe-napari-io; extra == "napari"
+Requires-Dist: cellfinder-napari; extra == "napari"
 
 [![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-0.7.0 → cellfinder-0.8.0}/cellfinder.egg-info/SOURCES.txt

@@ -1,15 +1,8 @@
 .gitignore
-.pre-commit-config.yaml
-Dockerfile
 LICENSE
 MANIFEST.in
 README.md
-environment.yml
 pyproject.toml
-pytest.ini
-setup.cfg
-setup.py
-tox.ini
 cellfinder/__init__.py
 cellfinder/main.py
 cellfinder.egg-info/PKG-INFO
@@ -35,7 +28,4 @@ cellfinder/tools/image_processing.py
 cellfinder/tools/parser.py
 cellfinder/tools/prep.py
 cellfinder/tools/system.py
-cellfinder/tools/tools.py
-cellfinder/train/__init__.py
-cellfinder/train/curation.py
-cellfinder/train/curation_old.py
+cellfinder/tools/tools.py

cellfinder-0.8.0/cellfinder.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+cellfinder = cellfinder.main:main

{cellfinder-0.7.0 → cellfinder-0.8.0}/cellfinder.egg-info/requires.txt

@@ -1,4 +1,4 @@
-brainreg
+brainreg>=1.0.0
 cellfinder-core>=0.2.4
 configobj
 fancylog>=0.0.7
@@ -19,9 +19,8 @@ pytest-cov
 pytest
 gitpython
 coverage>=5.0.3
-bump2version
 pre-commit
-flake8
+setuptools_scm
 
 [napari]
 napari[pyside2]

cellfinder-0.8.0/pyproject.toml

@@ -0,0 +1,88 @@
+[project]
+name = "cellfinder"
+description = "Automated 3D cell detection and registration of whole-brain images"
+readme = "README.md"
+license = { file = "LICENSE" }
+requires-python = ">=3.9"
+authors = [
+    { name = "Adam Tyson", email = "code@adamltyson.com" },
+    { name = "Christian Niedworok" },
+    { name = "Charly Rousseau" },
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Microsoft :: Windows :: Windows 10",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering :: Image Recognition",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+]
+dependencies = [
+    "brainreg>=1.0.0",
+    "cellfinder-core>=0.2.4",
+    "configobj",
+    "fancylog>=0.0.7",
+    "imio",
+    "brainglobe-utils>=0.2.5",
+    "multiprocessing-logging>=0.3.4",
+    "natsort",
+    "numpy",
+    "pandas",
+    "packaging",
+    "scikit-image",
+    "tifffile",
+    "tqdm",
+]
+dynamic = ["version"]
+
+[project.scripts]
+cellfinder = "cellfinder.main:main"
+
+[project.optional-dependencies]
+dev = [
+    "black",
+    "pytest-cov",
+    "pytest",
+    "gitpython",
+    "coverage>=5.0.3",
+    "pre-commit",
+    "setuptools_scm",
+]
+napari = ["napari[pyside2]", "brainglobe-napari-io", "cellfinder-napari"]
+
+[project.urls]
+source = "https://github.com/brainglobe/cellfinder"
+bug_tracker = "https://github.com/brainglobe/cellfinder/issues"
+homepage = "https://brainglobe.info"
+documentation = "https://brainglobe.info/documentation/cellfinder"
+[build-system]
+requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[tool.black]
+target-version = ['py38', 'py39', 'py310']
+skip-string-normalization = false
+line-length = 79
+
+[tool.check-manifest]
+ignore = ["*.yaml"]
+
+[tool.ruff]
+line-length = 79
+exclude = ["__init__.py", "build", ".eggs"]
+select = ["I", "E", "F"]
+fix = true
+
+[tool.setuptools]
+include-package-data = true
+zip-safe = false
+
+[tool.setuptools.packages.find]
+include = ["cellfinder"]
+exclude = ["tests", "resources"]
+
+[tool.setuptools_scm]

cellfinder-0.8.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

cellfinder-0.7.0/.pre-commit-config.yaml

@@ -1,28 +0,0 @@
-repos:
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
-      hooks:
-          - id: check-docstring-first
-          - id: check-executables-have-shebangs
-          - id: check-merge-conflict
-          - id: check-toml
-          - id: end-of-file-fixer
-          - id: mixed-line-ending
-            args: [--fix=lf]
-          - id: requirements-txt-fixer
-          - id: trailing-whitespace
-    - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.0.281
-      hooks:
-        - id: ruff
-    - repo: https://github.com/psf/black
-      rev: 23.7.0
-      hooks:
-          - id: black
-    - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.4.1
-      hooks:
-          - id: mypy
-            additional_dependencies:
-                - types-setuptools
-                - types-requests

cellfinder-0.7.0/Dockerfile

@@ -1,4 +0,0 @@
-FROM tensorflow/tensorflow:latest-gpu
-LABEL maintainer="code@adamltyson.com"
-RUN pip install cellfinder
-CMD ["bash"]

cellfinder-0.7.0/MANIFEST.in

@@ -1,5 +0,0 @@
-include cellfinder/config/*
-global-include *.pxd
-prune tests
-prune resources
-prune .github

cellfinder-0.7.0/cellfinder/__init__.py

@@ -1,3 +0,0 @@
-__version__ = "0.7.0"
-__author__ = "Adam Tyson, Christian Niedworok, Charly Rousseau"
-__license__ = "BSD-3-Clause"