Bug fix/exceptions

.github/workflows/run-pr-tests.yml → .github/workflows/run-tests.yml

@@ -1,12 +1,32 @@
-name: run-PR-tests
+name: run-tests
 
 on:
   pull_request:
   push:
-    branches: main
 
 jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: install dependencies
+        run: pip install .[dev]
+        shell: bash
+
+      - name: run Ruff linter
+        run: ruff check --output-format=github .
+        shell: bash
+
   run-tests:
+    needs: lint
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -24,10 +44,6 @@ jobs:
       - name: install dependencies
         run: pip install .[dev]
         shell: bash
-
-      - name: run Ruff linter
-        run: ruff check .
-        shell: bash
 
       - name: run tests
         run: pytest

.gitignore

@@ -111,6 +111,9 @@ ipython_config.py
 .pdm-python
 .pdm-build/
 
+# uv
+uv.lock
+
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
 

.pre-commit-config.yaml

@@ -1,6 +1,9 @@
 repos:
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.2
+  - repo: local
     hooks:
       - id: ruff
-
+        name: ruff
+        entry: uv run --extra dev ruff check --force-exclude
+        language: system
+        types_or: [python, pyi]
+        require_serial: true

pyproject.toml

@@ -30,13 +30,6 @@ dependencies = [
     "sum-buddy",
 ]
 
-[project.optional-dependencies]
-dev = [
-    "pytest",
-    "ruff",
-    "pre-commit"
-]
-
 keywords = [
     "imageomics",
     "metadata",
@@ -52,6 +45,13 @@ keywords = [
     "sum-buddy",
 ]
 
+[project.optional-dependencies]
+dev = [
+  "pytest",
+  "ruff==0.16.0",
+  "pre-commit"
+]
+
 [project.urls]
 Homepage = "https://github.com/Imageomics/cautious-robot"
 Repository = "https://github.com/Imageomics/cautious-robot.git"

src/cautiousrobot/__init__.py

@@ -2,11 +2,4 @@
 from cautiousrobot.download import download_images
 from cautiousrobot.utils import downsample_and_save_image
 
-# Create instance of the class
-buddy_check_instance = BuddyCheck()
-
-# Expose instance methods by executing them
-buddy_check_instance.validate_download #noqa: B018
-buddy_check_instance.check_alignment #noqa: B018
-
-__all__ = ["check_alignment", "download_images", "downsample_and_save_image", "validate_download"]
+__all__ = ["BuddyCheck", "download_images", "downsample_and_save_image"]

src/cautiousrobot/__main__.py

@@ -7,14 +7,14 @@
 
 import argparse
 import hashlib
-import sys
 
 import pandas as pd
 from sumbuddy import get_checksums
 
 from cautiousrobot.__about__ import __version__
 from cautiousrobot.buddy_check import BuddyCheck
 from cautiousrobot.download import download_images
+from cautiousrobot.exceptions import BuddyCheckError, ChecksumError
 from cautiousrobot.roll_call import RollCall
 from cautiousrobot.utils import process_csv
 
@@ -77,9 +77,8 @@ def process_checksums(img_dir, metadata_path, args, source_df):
         print(f"There are {checksum_df.shape[0]} files in {img_dir}. Based on {args.input_file}, there should be {expected_num_imgs} images.")
 
         return checksum_df, expected_num_imgs
-    except Exception as e:  # noqa: BLE001
-        print(f"checksum calculation of downloaded images was unsuccessful due to {e}.")
-        print(f"you can get checksums for the images downloaded to {img_dir} by running sum-buddy directly.")
+    except (ChecksumError, OSError, ValueError, pd.errors.ParserError) as e: 
+        print(e)
         return None, None
 
 
@@ -102,10 +101,8 @@ def verify_downloads(args, source_df, checksum_df, filename_col, metadata_path,
             print(f"See {metadata_path}_missing.csv for missing image info and check logs.")
         else:
             print(f"Buddy check successful. All {expected_num_imgs} expected images accounted for.")
-    except Exception as e:  # noqa: BLE001
-        print(f"Verification of download failed due to {type(e).__name__}: {e}.")
-        print("'BuddyCheck.validate_download' can be run directly on DataFrames of the source and checksum CSVs after correcting for this error.")
-
+    except (BuddyCheckError, OSError, ValueError, KeyError) as e:
+        print(e)
 
 def main():
     args = parse_args()
@@ -118,10 +115,8 @@ def main():
 
     # Set up expected columns and process CSV
     expected_cols, subfolders = roll_call.setup_expected_columns(args)
-    try:
-        data_df = process_csv(csv_path, expected_cols)
-    except Exception as missing_cols: # noqa: BLE001
-        sys.exit(f"{missing_cols} Please adjust inputs and try again.")
+    data_df = process_csv(csv_path, expected_cols) #Exception handling process_csv
+
 
     # Validate data and handle missing filenames
     filename_col = expected_cols["filename_col"]

src/cautiousrobot/download.py

@@ -68,7 +68,7 @@ def get_content_type_from_url(url):
         content_type = response.headers.get('content-type', '')
         # Split off parameters like '; charset=utf-8'
         return content_type.split(';')[0].strip() if content_type else None
-    except Exception:   # noqa: BLE001
+    except requests.RequestException:
         return None
 
 
@@ -273,15 +273,15 @@ def download_single_image(url, image_name, image_dir_path, log_data, log_errors,
     while redo and attempts_remaining > 0:
         try:
             response = requests.get(url, stream=True)
-        except Exception as e:  # noqa: BLE001
+        except requests.RequestException as error: 
             redo = True
             attempts_remaining -= 1
             if attempts_remaining <= 0:
                 log_errors = log_response(log_errors,
                                         index=i,
                                         image=image_name,
                                         file_path=url,
-                                        response_code=str(e))
+                                        response_code=str(error))
                 update_log(log=log_errors, index=i, filepath=error_log_filepath)
             continue
 

src/cautiousrobot/exceptions.py

@@ -2,3 +2,23 @@ class EmptyDataFrameError(Exception):
     def __init__(self, df_name):
         message = f"Input DataFrame {df_name} is empty."
         super().__init__(message)
+
+class MissingColumnsError(Exception):
+    def __init__(self, csv_path, column_names, expected_columns):
+        message = f"The CSV at {csv_path} is missing column(s): {column_names}, defined as {expected_columns}."
+        super().__init__(message)
+
+class ChecksumError(Exception):
+    def __init__(self, error, img_dir):
+        self.error = error
+        self.img_dir = img_dir
+        message = f"Checksum calculation of downloaded images was unsuccessful due to {self.error}.\n You can get checksums for the images downloaded to {self.img_dir} by running sum-buddy directly."
+        super().__init__(message)
+
+class BuddyCheckError(Exception):
+    def __init__(self, error, reason):
+        self.error = error
+        self.reason = reason
+        message = f"Verification of download failed due to {self.error}: {self.reason}.\n'BuddyCheck.validate_download' can be run directly on DataFrames of the source and checksum CSVs after correcting for this error."
+        super().__init__(message)
+

src/cautiousrobot/utils.py

@@ -4,7 +4,9 @@
 import os
 
 import pandas as pd
-from PIL import Image
+from PIL import Image, UnidentifiedImageError
+
+from cautiousrobot.exceptions import MissingColumnsError
 
 
 def log_response(log_data, index, image, file_path, response_code):
@@ -44,7 +46,7 @@ def process_csv(csv_path, expected_cols):
         if expected_cols[col] not in list(df.columns):
             missing_cols.append(col)
     if len(missing_cols) > 0:
-        raise Exception(f"The CSV at {csv_path} is missing column(s): {missing_cols}, defined as {[expected_cols[col] for col in missing_cols]}.") # noqa: TRY002
+        raise MissingColumnsError(csv_path, missing_cols, [expected_cols[col] for col in missing_cols])
 
     return df
 
@@ -71,13 +73,12 @@ def downsample_and_save_image(image_dir_path, image_name, downsample_dir_path, d
     try:
         img = Image.open(f"{image_dir_path}/{image_name}")
         img.resize((downsample_size, downsample_size)).save(f"{downsample_dir_path}/{image_name}")
-    except Exception as e:  # noqa: BLE001
-        print(e)
+    except (OSError, UnidentifiedImageError) as error:
         log_errors = log_response(
             log_errors,
             index=image_index,
             image="downsized_" + image_name,
             file_path=file_path,
-            response_code=str(e)
+            response_code=str(error)
         )
         update_log(log=log_errors, index=image_index, filepath=error_log_filepath)

tests/test_buddycheck.py

@@ -14,22 +14,23 @@ def setUp(self):
         self.buddy_check_filename = BuddyCheck(buddy_id='filename')
         self.buddy_check_id_col = BuddyCheck(buddy_id = "filename", buddy_col = "sha256")
 
-        self.img_source_file = tempfile.NamedTemporaryFile(delete=False, mode='w') # noqa: SIM115
-        self.checksum_source_file = tempfile.NamedTemporaryFile(delete=False, mode='w') # noqa: SIM115
+        #self.img_source_file = tempfile.NamedTemporaryFile(delete=False, mode='w') 
+        #self.checksum_source_file = tempfile.NamedTemporaryFile(delete=False, mode='w') 
 
-        self.img_source_file.write("""filename,checksum
+
+        with tempfile.NamedTemporaryFile(delete=False, mode='w', suffix=".csv") as f:
+            f.write("""filename,checksum
 image1.jpg,abc123
 image2.jpg,def456
-image3.jpg,ghi789
-""")
-        self.img_source_file.close()
+image3.jpg,ghi789""")
+            self.img_source_file = f
 
-        self.checksum_source_file.write("""filename,md5
+        with tempfile.NamedTemporaryFile(delete=False, mode='w', suffix=".csv") as f:
+            f.write("""filename,md5
 image1.jpg,abc123
 image2.jpg,def456
-image3.jpg,ghi789
-""")
-        self.checksum_source_file.close()
+image3.jpg,ghi789""")
+            self.checksum_source_file = f
 
 
     def tearDown(self):

tests/test_download.py

@@ -2,6 +2,7 @@
 from unittest.mock import patch
 
 import pandas as pd
+import requests
 
 from cautiousrobot.download import download_images
 
@@ -16,7 +17,7 @@
 class TestDownload(unittest.TestCase):
     @patch('requests.get')
     def test_response_exception(self, get_mock):
-        get_mock.side_effect = Exception
+        get_mock.side_effect = requests.exceptions.ConnectionError("Connection failed")
         download_images(DUMMY_DATA, img_dir = IMG_DIR, log_filepath = LOG_FILEPATH,
                         error_log_filepath = ERROR_LOG_FILEPATH)