Mic 3034

.pylintrc

@@ -387,4 +387,5 @@ max-locals=50
 
 # Exceptions that will emit a warning when being caught. Defaults to
 # "Exception"
-overgeneral-exceptions=Exception
+overgeneral-exceptions=builtins.BaseException,
+			bultins.Exception

environment.yml

@@ -3,27 +3,28 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- pip=22.3.1
-- python=3.11.0
+- pip=24.0.0
+- python=3.12.0
 - pip:
-  - astroid==2.12.13
-  - attrs==22.1.0
-  - coverage==6.5.0
+  - astroid>=3.2.3
+  - attrs>=23.2.0
+  - coverage>=7.6.0
   - jupyter==1.0.0
-  - matplotlib==3.6.2
-  - mock==4.0.3
-  - numpy==1.23.5
-  - pandas==1.2.3
-  - pillow==9.3.0
-  - pylint==2.15.6
-  - pytest==7.2.0
-  - python-dotenv==0.21.0
-  - requests==2.28.1
-  - scikit-image==0.19.3
-  - scikit-learn==1.1.3
-  - setuptools==65.5.1
-  - sphinx-argparse==0.2.2
-  - sphinx==5.3.0
-  - tifffile==2022.10.10
-  - tox==3.27.1
-  - tqdm==4.64.1
+  - matplotlib>=3.9.0
+  - mock>=5.1.0
+  - numpy<2.0.0
+  - pandas>=2.2.0
+  - pillow>=10.4.0
+  - pylint>=3.2.0
+  - py>=1.11.0
+  - pytest>=8.3.0
+  - python-dotenv>=1.0.0
+  - requests>=2.32.0
+  - scikit-image>=0.24.0
+  - scikit-learn>=1.5.0
+  - setuptools>=70.3.0
+  - sphinx-argparse>=0.4.0
+  - sphinx>=7.4.0
+  - tifffile<2024.6.18
+  - tox>=4.16.0
+  - tqdm>=4.66.0

mibidata/tests/test_segmentation.py

@@ -187,9 +187,9 @@ def test_extract_cell_dataframe(self):
         second_total = [1, 3]
         # Check coords and areas only
         expected_from_labels = pd.DataFrame(
-            np.array([areas, x_centroids, y_centroids]).T,
+            np.array([areas, x_centroids, y_centroids]).T.astype(np.int64),
             columns=['area', 'x_centroid', 'y_centroid'],
-            index=pd.Index(labels, name='label'))
+            index=pd.Index(labels, name='label', dtype=np.int64))
         pdt.assert_frame_equal(
             segmentation.extract_cell_dataframe(cell_labels),
             expected_from_labels)
@@ -272,13 +272,13 @@ def test_filter_by_size(self):
             [1, 1, 3, 3],
             [4, 4, 3, 3],
             [0, 4, 3, 3]
-        ])
+        ], dtype=np.int64)
         expected = np.array([
             [0, 1, 1, 0],
             [1, 1, 0, 0],
             [2, 2, 0, 0],
             [0, 2, 0, 0]
-        ])
+        ], dtype=np.int64)
         df = segmentation.extract_cell_dataframe(expected)
         filtered_image, filtered_df = segmentation.filter_by_size(
             cell_labels, 3, 5)

mibitracker/request_helpers.py

@@ -1,7 +1,6 @@
 """Helper class for making and retrying requests to the MIBItracker.
 
 Copyright (C) 2021 Ionpath, Inc.  All rights reserved."""
-
 import datetime
 import io
 import json
@@ -94,7 +93,7 @@ def __init__(self,
         # The token will be used in lieu of email and password if provided
         if token is not None:
             self.session.headers.update({
-                'Authorization': 'JWT {}'.format(token)
+                'Authorization': f'JWT {token}'
             })
             self.session.options(self.url)
         elif email is not None and password is not None:
@@ -104,7 +103,7 @@ def __init__(self,
                 'Provide either both an email and password or a token'
             )
 
-        retry = Retry(status=retries, method_whitelist=retry_methods,
+        retry = Retry(status=retries, allowed_methods=retry_methods,
                       status_forcelist=retry_codes, backoff_factor=0.3)
         # Set this session to use these retry settings for all http[s] requests
         self.session.mount('http://', HTTPAdapter(max_retries=retry))
@@ -113,24 +112,24 @@ def __init__(self,
     def _auth(self, url, email, password):
         """Adds an authorization token to the session's default header."""
         response = self.session.post(
-            '{}/api-token-auth/'.format(url),
+            f'{url}/api-token-auth/',
             headers={'content-type': 'application/json'},
             data=json.dumps({'email': email, 'password': password}))
         token = response.json()['token']
-        self.session.headers.update({'Authorization': 'JWT {}'.format(token)})
+        self.session.headers.update({'Authorization': f'JWT {token}'})
 
     def refresh(self):
         """Refreshes the authorization token stored in the session header.
 
         Raises HTTP 400 if attempting to refresh an expired token."""
         token = self.session.post(  # use the session to avoid recursion
-            '{}/api-token-refresh/'.format(self.url),
+            f'{self.url}/api-token-refresh/',
             data=json.dumps(
                 {'token': self.session.headers['Authorization'][4:]}
             ),
             headers={'content-type': 'application/json'},
         ).json()['token']
-        self.session.headers.update({'Authorization': 'JWT {}'.format(token)})
+        self.session.headers.update({'Authorization': f'JWT {token}'})
 
     def _check_refresh(self):
         current_time = datetime.datetime.now()
@@ -143,7 +142,7 @@ def _check_refresh(self):
     @staticmethod
     def _prepare_route(route):
         if not route.startswith('/'):
-            return '/{}'.format(route)
+            return f'/{route}'
         return route
 
     def get(self, route, *args, **kwargs):
@@ -159,8 +158,8 @@ def get(self, route, *args, **kwargs):
             The response from ``requests.Session.get``.
         """
         self._check_refresh()
-        return self.session.get('{}{}'.format(
-            self.url, self._prepare_route(route)), *args, **kwargs)
+        return self.session.get(f'{self.url}{self._prepare_route(route)}',
+                                *args, **kwargs)
 
     def post(self, route, *args, **kwargs):
         """Makes a POST request to the url using the session.
@@ -174,8 +173,8 @@ def post(self, route, *args, **kwargs):
             The response from ``requests.Session.post``.
         """
         self._check_refresh()
-        return self.session.post('{}{}'.format(
-            self.url, self._prepare_route(route)), *args, **kwargs)
+        return self.session.post(f'{self.url}{self._prepare_route(route)}',
+                                 *args, **kwargs)
 
     def put(self, route, *args, **kwargs):
         """Makes a PUT request to the url using the session.
@@ -189,8 +188,8 @@ def put(self, route, *args, **kwargs):
             The response from ``requests.Session.put``.
         """
         self._check_refresh()
-        return self.session.put('{}{}'.format(
-            self.url, self._prepare_route(route)), *args, **kwargs)
+        return self.session.put(f'{self.url}{self._prepare_route(route)}',
+                                 *args, **kwargs)
 
     def delete(self, route, *args, **kwargs):
         """Makes a DELETE request to the url using the session.
@@ -204,8 +203,8 @@ def delete(self, route, *args, **kwargs):
             The response from ``requests.Session.delete``.
         """
         self._check_refresh()
-        return self.session.delete('{}{}'.format(
-            self.url, self._prepare_route(route)), *args, **kwargs)
+        return self.session.delete(f'{self.url}{self._prepare_route(route)}',
+                                   *args, **kwargs)
 
     def download_file(self, path):
         """Downloads a file from MIBItracker storage.
@@ -264,13 +263,14 @@ def copy_run(self, old_label, new_label, **kwargs):
         """
         # We don't expect there to be many runs with the same label, so it is
         # safe to turn paging off.
-        response = self.get('/runs/?label={}&paging=no'.format(old_label))
+        response = self.get(f'/runs/?label={old_label}&paging=no')
         data = response.json()
         try:
             assert len(data) == 1
-        except AssertionError:
-            raise MibiTrackerError('Expected 1 run with label {}, but {} were '
-                                   'found'.format(old_label, len(data)))
+        except AssertionError as err:
+            raise MibiTrackerError(f'Expected 1 run with label {old_label},'
+                                   f' but {len(data)} were found')\
+                                    from err
         data = data[0]
 
         # Get the XMLs from the original runs. They may not have the date and
@@ -288,7 +288,7 @@ def copy_run(self, old_label, new_label, **kwargs):
             'project': data['project'] and data['project']['id'],  # optional
             'description': data['description'],
             'operator': data['operator'],  # Not yet used, but field exists
-            'user_run_date': '{}T00:00:00'.format(data['run_date']),
+            'user_run_date': f"{data['run_date']}T00:00:00",
         }
         # The old run date supercedes the possibly-missing date in the xml
         # A timestamp is temporarily added for the JSON encoded but will be
@@ -320,15 +320,15 @@ def copy_run_image_metadata(self, old_run_label, new_run_label, **kwargs):
             response JSON returned when updating the new images.
         """
         old_images = self.get(
-            '/images/?run__label={}&paging=no'.format(old_run_label))
+            f'/images/?run__label={old_run_label}&paging=no')
 
         image_map = {}
         for item in old_images.json():
 
             # Get image from copied run
             response = self.get(
-                '/images/?run__label={}&folder={}&paging=no'.format(
-                    new_run_label, item['folder']))
+                f"/images/?run__label={new_run_label}&folder={item['folder']}"
+                '&paging=no')
             assert len(response.json()) == 1
             new_image = response.json()[0]
             # Update the section and tissue of the copied image using
@@ -371,6 +371,7 @@ def copy_run_image_metadata(self, old_run_label, new_run_label, **kwargs):
                     content_type = 'image/png'
 
                 buf = self.download_file(sed_path)
+                # pylint: disable=possibly-used-before-assignment
                 files = {'attachment': (sed, buf, content_type)}
                 data = updated_image
             else:
@@ -381,7 +382,7 @@ def copy_run_image_metadata(self, old_run_label, new_run_label, **kwargs):
                 headers.update({'content-type': 'application/json'})
 
             response = self.put(
-                '/images/{}/'.format(new_image['id']),
+                f"/images/{new_image['id']}/",
                 files=files,
                 data=data,
                 headers=headers
@@ -429,11 +430,12 @@ def upload_mibitiff(self, tiff_file, run_id=None):
         try:
             with open(tiff_file, 'rb') as fh:
                 self._upload_mibitiff(response['url'], fh)
-        except TypeError:
+        except TypeError as err:
             try:
                 tiff_file.seek(0)
             except:
-                raise TypeError('tiff_file must be a string or file object')
+                raise TypeError('tiff_file must be a string'
+                                'or file object') from err
             self._upload_mibitiff(response['url'], tiff_file)
         return self.post(
             '/upload_mibitiff/',
@@ -447,7 +449,7 @@ def _upload_channel(self, image_id, image_file, filename):
         files = {
             'attachment': (filename,
                            image_file,
-                           'image/{}'.format(ext[1:].lower()))
+                           f'image/{ext[1:].lower()}')
         }
 
         response = self.post(
@@ -480,17 +482,19 @@ def upload_channel(self, image_id, image_file, filename=None):
                 if not filename:
                     filename = os.path.basename(image_file)
                 return self._upload_channel(image_id, fh, filename)
-        except TypeError:
+        except TypeError as err:
             try:
                 image_file.seek(0)
             except:
-                raise TypeError('image_file must be a string or file object')
+                raise TypeError('image_file must be a '
+                                'string or file object') from err
             if not filename:
                 try:
                     filename = os.path.basename(image_file.name)
-                except AttributeError:
+                except AttributeError as aErr:
                     raise ValueError('filename must be provided with a file '
-                                     'object that does not have a name')
+                                     'object that does not have a name'
+                                     ) from aErr
             return self._upload_channel(image_id, image_file, filename)
 
     def run_images(self, run_label):
@@ -518,7 +522,7 @@ def image_conjugates(self, image_id):
             section assigned, or if its section does not have a panel assigned.
         """
         return self.get(
-            '/images/{}/conjugates/'.format(image_id),
+            f'/images/{image_id}/conjugates/',
             params={'paging': 'no'}).json()
 
     def image_id(self, run_label, fov_id):
@@ -580,7 +584,7 @@ def get_mibi_image(self, image_id):
         Return:
             A MibiImage instance of the requested image.
         """
-        image_info = self.get('images/{}/'.format(image_id)).json()
+        image_info = self.get(f'images/{image_id}/').json()
         tiff_path = '/'.join((image_info['run']['path'], image_info['folder'],
                               'summed_image.tiff'))
         tiff_data = self.download_file(tiff_path)
@@ -605,10 +609,11 @@ def get_channel_data(self, image_id, channel_name):
             response.raise_for_status()
         except HTTPError as e:
             if e.response.status_code == 404:
-                raise MibiTrackerError(
-                    f'Channel \'{channel_name}\' not found in the image.')
+                raise MibiTrackerError(f'Channel \'{channel_name}\' '
+                                       'not found in the image.') from e
             raise e
 
+        # pylint: disable=missing-timeout
         png = requests.get(response.json()['url'])
         buf = io.BytesIO()
         buf.write(png.content)
@@ -647,7 +652,7 @@ class StatusCheckedSession(requests.Session):
     """Raises for HTTP errors and adds any response JSON to the message."""
 
     def __init__(self, timeout=SESSION_TIMEOUT):
-        super(StatusCheckedSession, self).__init__()
+        super().__init__()
         self.timeout = timeout
 
     @staticmethod
@@ -659,7 +664,8 @@ def _check_status(response):
                 response_json = response.json()
             except json.decoder.JSONDecodeError:
                 response_json = None
-            raise HTTPError(str(e), response_json, response=response)
+            raise HTTPError(str(e), response_json,
+                            response=response) from e
         return response
 
     def _set_timeout(self, kwargs):

setup.py

@@ -11,17 +11,17 @@
       url='https://github.com/ionpath/mibilib',
       description='Python utilities for IONpath MIBItracker and MIBItiff data',
       license='GNU General Public License v3.0',
-      python_requires='~=3.11.0',
+      python_requires='>=3.8',
       install_requires=[
-          'matplotlib==3.6.2',
-          'numpy==1.23.5',
-          'pandas==1.2.3',
-          'pillow==9.3.0',
-          'requests>=2.28.1',
-          'scikit-image==0.19.3',
-          'scikit-learn==1.1.3',
-          'tifffile==2022.10.10',
-          'tqdm==4.64.1',
+          'matplotlib>=3.6',
+          'numpy<2.0',
+          'pandas>=1.0',
+          'pillow>=9.0',
+          'requests>=2.28',
+          'scikit-image>=0.19',
+          'scikit-learn>=1.1',
+          'tifffile<2024.6.18',
+          'tqdm>=4.64',
       ],
       packages=['mibitracker', 'mibidata']
      )