Replace print statements with logging (#4)

* Replace print statements with logging

- defaults to only console logging
- defaults to WARNING level
   - configurable with: `export APP_LOG_LEVEL=[INFO|DEBUG]`

* Merge awoods-logging into logging (#3)

* linter for box reader after logging

* comment out diff cover

remove socket

* skip processing of files where n value is not 1

* tests with 65% cvg

* add in github actions install of diff cover globally

* update paths for diff cover

* test diff cover install and check path

* uncomment diff cover test

* uncomment diff cover test 2

* new coverage test

* full test coverage

* flake8 passes all files

* check flake8 version

* mod flake8 command for 120 line length

* add additional test coverage, stops early if not 85

---------

Co-authored-by: kim pham <[email protected]>

.github/workflows/test.yml

@@ -32,8 +32,9 @@ jobs:
       - name: Run flake8
         run: | 
           pip install flake8
+          flake8 --version
           # stop the build if there are flake8 errors
-          flake8 . --count --show-source --statistics
+          flake8 . --count --show-source --statistics --max-line-length 120
 
       - name: Run unit tests
         run: |
@@ -45,25 +46,26 @@ jobs:
           pip install coverage
           python -m coverage run -p -m pytest src/jp2_remediator/tests/unit
           python -m coverage combine
-          python -m coverage report -m --skip-covered
+          python -m coverage report -m --skip-covered --fail-under=85
           python -m coverage xml
       
       # Fetch base branch for comparison (e.g., main)
       - name: Fetch base branch
         run: git fetch origin main
 
-      # Compare coverage with the base branch
+      - name: Install diff-cover
+        run: |
+          pip install --user diff-cover
+          find $HOME -name "diff-cover" || echo "diff-cover not found"
+
+      - name: Add diff-cover to PATH
+        run: echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      # Compare coverage with the base branch, if decreases fails, if under 85 percent fails
       - name: Compare coverage
         run: |
-         pip install diff-cover
          git checkout main
          python -m coverage run -p -m pytest src/jp2_remediator/tests/unit
          python -m coverage xml -o coverage-base.xml
          git checkout -
-         python diff-cover --compare-branch=main coverage.xml
-         
-      # Fail if coverage decreases
-      - name: Fail if coverage decreases
-        run: |
-          python diff-cover --compare-branch=main coverage.xml --fail-under=100
-
+         diff-cover --compare-branch=main coverage.xml --fail-under=85

.gitignore

@@ -1,10 +1,14 @@
 *~
 *.swp
+
+logs/
+
 input/*
 output/*
 .coverage
 coverage.*
 
+
 dist/*
 */*.egg-info/*
 __pycache__

README.md

@@ -16,29 +16,29 @@ pip install jp2_remediator==0.0.2
 ## Usage
 
 ## Process one file
-`python3 box_reader.py --file tests/test-images/7514499.jp2`
+`python3 main.py --file tests/test-images/7514499.jp2`
 
-`python3 box_reader.py --file tests/test-images/481014278.jp2`
+`python3 main.py --file tests/test-images/481014278.jp2`
 
 ## Process directory
-`python3 box_reader.py --directory tests/test-images/`
+`python3 main.py --directory tests/test-images/`
 
 ## Process Amazon S3 bucket
-`python3 box_reader.py --bucket your-bucket-name --prefix optional-prefix`
+`python3 main.py --bucket your-bucket-name --prefix optional-prefix`
 
 ## Process all .jp2 files in the bucket:
-`python3 box_reader.py --bucket remediation-folder`
+`python3 main.py --bucket remediation-folder`
 
 ## Process only files with a specific prefix (folder):
-`python3 box_reader.py --bucket remediation-folder --prefix testbatch_20240923`
+`python3 main.py --bucket remediation-folder --prefix testbatch_20240923`
 
-`python3 box_reader.py --help`
+`python3 main.py --help`
 
 ## Run Tests
 `python3 test_aws_connection.py`
 
 ### Run from src folder
-`python3 -m unittest jp2_remediator.tests.test_box_reader`
+`python3 -m unittest jp2_remediator.tests.unit.test_box_reader`
 
 ## Docker environment
 

pyproject.toml

@@ -34,4 +34,4 @@ omit = [
 
 [tool.project-paths]
 dir_unit_out = "src/jp2_remediator/tests/out/"
-dir_unit_resources = "src/jp2_remediator/tests/resources/"
+dir_unit_resources = "src/jp2_remediator/tests/resources/"

requirements.txt

@@ -1,10 +1,15 @@
 boto3==1.35.39
 botocore==1.35.39
+flake8==7.1.1
 jmespath==1.0.1
 jpylyzer==2.2.1
+mccabe==0.7.0
 project-paths==1.1.1
+pycodestyle==2.12.1
+pyflakes==3.2.0
 python-dateutil==2.9.0.post0
 s3transfer==0.10.3
+setuptools==73.0.1
 six==1.16.0
 toml==0.10.2
 urllib3==2.2.3

src/jp2_remediator/__init__.py

@@ -0,0 +1,41 @@
+import logging
+from logging.handlers import TimedRotatingFileHandler
+import os
+from datetime import datetime
+
+LOG_FILE_BACKUP_COUNT = int(os.getenv('LOG_FILE_BACKUP_COUNT', '30'))
+LOG_ROTATION = "midnight"
+
+timestamp = datetime.today().strftime('%Y-%m-%d')
+
+
+def configure_logger(name):  # pragma: no cover
+    log_level = os.getenv("APP_LOG_LEVEL", "WARNING")
+    log_dir = os.getenv("LOG_DIR", "logs/")
+    # create log directory if it doesn't exist
+    if not os.path.exists(log_dir):
+        os.makedirs(log_dir)
+
+    log_file_path = os.path.join(log_dir, "jp2_remediator.log")
+    formatter = logging.Formatter(
+        '%(levelname)s - %(asctime)s - %(name)s - %(message)s')
+
+    console_handler = logging.StreamHandler()
+    console_handler.setFormatter(formatter)
+
+    logger = logging.getLogger(name)
+    logger.addHandler(console_handler)
+    # Defaults to console logging
+    if os.getenv("CONSOLE_LOGGING_ONLY", "true") == "false":
+        # make log_file_path if it doesn't exist
+        # os.makedirs(log_file_path, exist_ok=True)
+        file_handler = TimedRotatingFileHandler(
+            filename=log_file_path,
+            when=LOG_ROTATION,
+            backupCount=LOG_FILE_BACKUP_COUNT
+        )
+        file_handler.setFormatter(formatter)
+        logger.addHandler(file_handler)
+
+    logger.setLevel(log_level)
+    return logger