Merge pull request #289 from alexdaniel654/rel/v1.3.6

rel/v1.3.6

.github/workflows/python_ci.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.8, 3.9]
+        python-version: [3.8, 3.9, "3.10"]
 
     steps:
     - uses: actions/checkout@v2
@@ -32,7 +32,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov codecov wheel
+        pip install flake8 pytest pytest-cov codecov wheel attrdict3 
         pip install -r requirements.txt
         pip install -r requirements_gui.txt
     - name: Lint with flake8

CHANGELOG.md

@@ -1,5 +1,16 @@
 # Changelog
 
+## [1.3.6] - 2023-02-16
+
+### Added
+* Downloads counter to readme #287
+* Compatibility with Python 3.10
+
+### Changed
+* Lots of dependencies
+* Dependencies are now set to be compatible versions (~=) rather than pinned to an exact version (==)
+
+
 ## [1.3.5] - 2022-08-02
 
 ### Added

CITATION.cff

@@ -8,7 +8,7 @@ authors:
   given-names: "Susan T"
   orcid: "https://orcid.org/0000-0003-0903-7507"
 title: "Renal Segmentor"
-version: 1.3.5
+version: 1.3.6
 doi: 10.5281/zenodo.5796277
-date-released: 2022-08-02
+date-released: 2023-02-16
 url: "https://github.com/alexdaniel654/Renal_Segmentor"

README.md

@@ -1,6 +1,7 @@
 # Renal Segmentor
 [![Python CI](https://github.com/alexdaniel654/Renal_Segmentor/actions/workflows/python_ci.yml/badge.svg?branch=master)](https://github.com/alexdaniel654/Renal_Segmentor/actions/workflows/python_ci.yml)
 [![codecov](https://codecov.io/gh/alexdaniel654/Renal_Segmentor/branch/master/graph/badge.svg?token=6oSiDfrFpJ)](https://codecov.io/gh/alexdaniel654/Renal_Segmentor)
+[![Downloads](https://static.pepy.tech/badge/renalsegmentor)](https://pepy.tech/project/renalsegmentor)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![DOI](https://zenodo.org/badge/236753300.svg)](https://zenodo.org/badge/latestdoi/236753300)
 

renal_segmentor.py

@@ -114,8 +114,8 @@ def resource_path(relative_path):
                 'name': 'Renal Segmentor',
                 'description': 'Automatically segment the kidneys from MRI '
                                'data.',
-                'version': '1.3.5',
-                'copyright': '2022',
+                'version': '1.3.6',
+                'copyright': '2023',
                 'website': 'https://github.com/alexdaniel654/Renal_Segmentor',
                 'developer': 'https://www.researchgate.net/profile/'
                              'Alexander-Daniel-2',

requirements.txt

@@ -1,7 +1,7 @@
-nibabel==4.0.1
-numpy==1.23.1
-pandas==1.4.3
-pytest==7.1.2
-scikit-image==0.19.3
-tensorflow==2.9.1
-wget==3.2
+nibabel~=5.0.1
+numpy~=1.24.2
+pandas~=1.5.3
+pytest~=7.2.1
+scikit-image~=0.19.3
+tensorflow~=2.11.0
+wget~=3.2

requirements_gui.txt

@@ -1,2 +1,2 @@
-Gooey==1.0.8.1
-pyinstaller==5.3
+Gooey~=1.0.8.1
+pyinstaller~=5.3

segment/segment.py

@@ -186,7 +186,7 @@ def get_mask(self, weights_path=None, post_process=True,
         self.mask = self._rescale(self._mask_img.get_fdata(), 0, 1)
 
         if binary:
-            self.mask = np.round(self.mask).astype(np.int)
+            self.mask = np.round(self.mask).astype(np.uint16)
 
         self._mask_img = nib.Nifti1Image(self.mask, self._mask_img.affine)
         self.tkv = (np.sum(self.mask > 0.5) *

setup.py

@@ -11,7 +11,7 @@
 
 setup(
     name="renalsegmentor",
-    version="1.3.5",
+    version="1.3.6",
     description="Segment kidneys from MRI data",
     long_description=long_description,
     long_description_content_type="text/markdown",