[Snyk] Security upgrade python from 3.11.13-alpine3.22 to 3.14.4-alpine3.22

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.11.13-alpine3.22
+FROM python:3.11.15-alpine3.23
 
 # Create a non-root user
 RUN addgroup -g 1001 -S appgroup && \
@@ -9,10 +9,10 @@
 
 # Copy requirements and install dependencies as root (needed for pip install)
 COPY requirements.txt .
 RUN pip install --no-cache-dir -r requirements.txt
 
 # Copy application files
-COPY scripts/ ./scripts/
+COPY src/xnat_maintenance_monitoring_scripts/ ./scripts/
 COPY entrypoint.py ./
 
 # Change ownership of the app directory to the non-root user

README.md

@@ -48,12 +48,12 @@ You can also run the scripts directly with Python if you have the dependencies i
 
 Run in the terminal with:
 ```bash
-python scripts/users_per_project.py --xnat_url https://xnat.health-ri.nl
+python src/xnat_maintenance_monitoring_scripts/users_per_project.py --xnat_url https://xnat.health-ri.nl
 ```
 to query the whole XNAT.
 Run the following to query only 'sandbox'
 ```bash
-python scripts/users_per_project.py --xnat_url https://xnat.health-ri.nl --project sandbox
+python src/xnat_maintenance_monitoring_scripts/users_per_project.py --xnat_url https://xnat.health-ri.nl --project sandbox
 ```
 
 You need to have 'Owner' or 'Site admin' priviliges to run this script on a project.
@@ -75,7 +75,7 @@ This script returns a CSV file "./{today}_XNAT_users_per_project.csv", with the
 
 Run in the terminal with:
 ```bash
-python scripts/disk_usages.py --xnat_url https://xnat.health-ri.nl --report_path ./input_disk_usage_report.txt --study_overview ./studyoverview.csv
+python src/xnat_maintenance_monitoring_scripts/disk_usages.py --xnat_url https://xnat.health-ri.nl --report_path ./input_disk_usage_report.txt --study_overview ./studyoverview.csv
 ```
 to query the whole XNAT.
 

pyproject.toml

@@ -36,7 +36,7 @@ Repository = "https://github.com/Health-RI/XNAT-Maintenance-Monitoring-scripts.g
 Issues = "https://github.com/Health-RI/XNAT-Maintenance-Monitoring-scripts/issues"
 
 [tool.hatch.build.targets.wheel]
-packages = ["scripts"]
+packages = ["src/xnat_maintenance_monitoring_scripts"]
 
 [tool.hatch.version]
 source = "vcs"
@@ -53,16 +53,15 @@ python = ["3.9", "3.10", "3.11", "3.12"]
 [tool.hatch.envs.test.scripts]
 test = "pytest {args:tests}"
 test-cov = "coverage run -m pytest {args:tests}"
-cov-report = ["- coverage combine", "coverage report", "coverage xml"]
+cov-report = ["- coverage combine", "- coverage report", "- coverage xml"]
 cov = ["test-cov", "cov-report"]
 
 [tool.coverage.run]
-source_pkgs = ["scripts", "tests"]
+source_pkgs = ["xnat_maintenance_monitoring_scripts"]
 branch = true
 parallel = true
 
 [tool.coverage.paths]
-sempyro = ["scripts"]
 tests = ["tests"]
 
 [tool.coverage.report]

tests/test_stub.py

@@ -1,2 +1,5 @@
+import xnat_maintenance_monitoring_scripts.disk_usages
+import xnat_maintenance_monitoring_scripts.users_per_project
+
 def test_pass():
     assert True