chore: Update dependencies, apply fixes (code, and tox), and update docs

.github/dependabot.yml

@@ -0,0 +1,37 @@
+version: 2
+
+updates:
+  - package-ecosystem: pip
+    directories:
+      #- "/analysis_module"
+      #- "/analysis_ui_module"
+      - "/anonymizer_module"
+      - "/collector_module"
+      - "/corrector_module"
+      #- "/opendata_collector_module"
+      - "/opendata_module"
+      - "/reports_module"
+    schedule:
+        interval: "weekly"
+        day: "thursday"
+    groups:
+      python-minor-patch:
+        applies-to: version-updates
+        update-types:
+          - "minor"
+          - "patch"
+      python-major:
+        applies-to: version-updates
+        update-types:
+          - "major"
+
+  - package-ecosystem: "github-actions"
+    directory: "/.github/workflows"
+    schedule:
+      interval: "weekly"
+      day: "thursday"
+    groups:
+      actions-update:
+        applies-to: version-updates
+        patterns:
+          - "*"

.github/workflows/run-tests.yml

@@ -1,7 +1,8 @@
-name: X-Road Metrics tests
+name: X-Road Metrics Tests
 on: [pull_request]
 jobs:
   Test-Anonymizer:
+    name: Anonymizer Tests
     runs-on: ubuntu-22.04
     defaults:
       run:
@@ -13,13 +14,15 @@ jobs:
         with:
           python-version: '3.8'
           cache: 'pip'
+          cache-dependency-path: ./anonymizer_module/setup.py
       - name: Install dependencies
         run: pip install -r test_requirements.txt
       - name: Install tox
         run: pip install tox
       - name: Run tox tests
         run: tox
   Test-Collector:
+    name: Collector Tests
     runs-on: ubuntu-22.04
     defaults:
       run:
@@ -31,13 +34,15 @@ jobs:
         with:
           python-version: '3.8'
           cache: 'pip'
+          cache-dependency-path: ./collector_module/setup.py
       - name: Install dependencies
         run: pip install -r test_requirements.txt
       - name: Install tox
         run: pip install tox
       - name: Run tox tests
         run: tox
   Test-Corrector:
+    name: Corrector Tests
     runs-on: ubuntu-22.04
     defaults:
       run:
@@ -49,13 +54,15 @@ jobs:
         with:
           python-version: '3.8'
           cache: 'pip'
+          cache-dependency-path: ./corrector_module/setup.py
       - name: Install dependencies
         run: pip install -r test_requirements.txt
       - name: Install tox
         run: pip install tox
       - name: Run tox tests
         run: tox
   Test-Opendata:
+    name: OpenData Tests
     runs-on: ubuntu-22.04
     defaults:
       run:
@@ -67,31 +74,35 @@ jobs:
         with:
           python-version: '3.8'
           cache: 'pip'
+          cache-dependency-path: ./opendata_module/setup.py
       - name: Install dependencies
         run: pip install -r test_requirements.txt
       - name: Install tox
         run: pip install tox
       - name: Run tox tests
         run: tox
-  Test-Opendata-Collector:
-    runs-on: ubuntu-22.04
-    defaults:
-      run:
-        working-directory: ./opendata_collector_module
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.8'
-          cache: 'pip'
-      - name: Install dependencies
-        run: pip install -r test_requirements.txt
-      - name: Install tox
-        run: pip install tox
-      - name: Run tox tests
-        run: tox
+  # Test-Opendata-Collector:
+  #   name: OpenData Collector Tests
+  #   runs-on: ubuntu-22.04
+  #   defaults:
+  #     run:
+  #       working-directory: ./opendata_collector_module
+  #   steps:
+  #     - uses: actions/checkout@v3
+  #     - name: Set up Python 3.8
+  #       uses: actions/setup-python@v4
+  #       with:
+  #         python-version: '3.8'
+  #         cache: 'pip'
+  #         cache-dependency-path: ./opendata_collector_module/setup.py
+  #     - name: Install dependencies
+  #       run: pip install -r test_requirements.txt
+  #     - name: Install tox
+  #       run: pip install tox
+  #     - name: Run tox tests
+  #       run: tox
   Test-Reports:
+    name: Reports Tests
     runs-on: ubuntu-22.04
     defaults:
       run:
@@ -103,6 +114,7 @@ jobs:
         with:
           python-version: '3.8'
           cache: 'pip'
+          cache-dependency-path: ./reports_module/setup.py
       - name: Install dependencies
         run: pip install -r test_requirements.txt
       - name: Install tox

.gitignore

@@ -48,7 +48,7 @@ nosetests.xml
 coverage.xml
 *,cover
 .hypothesis/
-test_results.xml
+test_results.*
 
 # Translations
 *.mo

analysis_module/Makefile

@@ -0,0 +1,10 @@
+clean:
+	@echo "Cleaning project..."
+	@find . -type d -name "__pycache__" -exec rm -rf {} +
+	@rm -rf .coverage
+	@rm -rf .tox/
+	@rm -rf build/
+	@rm -rf dist/
+	@rm -rf *.egg-info/
+	@rm -rf opmon_collector/tests/responses/Test/
+	@echo "Project cleaned."

analysis_module/setup.py

@@ -25,12 +25,12 @@
 from setuptools import setup, find_packages
 
 requirements = [
-    'dill==0.3.1.1',
-    'pymongo==3.10.1',
-    'pyyaml==5.4.1',
+    'dill==0.3.8',
+    'pymongo==4.6.3',
+    'pyyaml==6.0.1',
     'numpy==1.24.4',
     'pandas==2.0.3',
-    'scipy==1.10.1'
+    'scipy==1.10.1',
 ]
 
 classifiers = [

analysis_module/test_requirements.txt

@@ -2,4 +2,5 @@ coverage
 pytest
 pytest-mock
 pytest-pycodestyle
+pytest-html
 mongomock

analysis_module/tox.ini

@@ -5,7 +5,7 @@ envlist = py38
 deps = -rtest_requirements.txt
 install_command=pip install --only-binary=numpy {opts} numpy {packages}
 commands =
-    - coverage run --source opmon_analyzer -m pytest opmon_analyzer/
+    coverage run --source opmon_analyzer -m pytest opmon_analyzer/
     coverage report --include=opmon_analyzer/*
     coverage html -d ../htmlcov/analysis_module --include=opmon_analyzer/*
 

analysis_ui_module/Makefile

@@ -0,0 +1,10 @@
+clean:
+	@echo "Cleaning project..."
+	@find . -type d -name "__pycache__" -exec rm -rf {} +
+	@rm -rf .coverage
+	@rm -rf .tox/
+	@rm -rf build/
+	@rm -rf dist/
+	@rm -rf *.egg-info/
+	@rm -rf opmon_collector/tests/responses/Test/
+	@echo "Project cleaned."

analysis_ui_module/setup.py

@@ -25,10 +25,10 @@
 from setuptools import setup, find_packages
 
 requirements = [
-    'dill==0.3.1.1',
+    'dill==0.3.8',
     'django==2.2.28',
-    'pymongo==3.10.1',
-    'pyyaml==5.4.1',
+    'pymongo==4.6.3',
+    'pyyaml==6.0.1',
     'numpy==1.24.4'
 ]
 

analysis_ui_module/test_requirements.txt

@@ -2,4 +2,5 @@ coverage
 pytest
 pytest-mock
 pytest-pycodestyle
+pytest-html
 mongomock

analysis_ui_module/tox.ini

@@ -5,7 +5,7 @@ envlist = py38
 deps = -rtest_requirements.txt
 install_command=pip install --only-binary=numpy {opts} numpy {packages}
 commands =
-    - coverage run --source opmon_analyzer_ui -m pytest opmon_analyzer_ui/
+    coverage run --source opmon_analyzer_ui -m pytest opmon_analyzer_ui/
     coverage report --include=opmon_analyzer_ui/*
     coverage html -d ../htmlcov/analysis_ui_module --include=opmon_analyzer_ui/*
 

anonymizer_module/Makefile

@@ -0,0 +1,10 @@
+clean:
+	@echo "Cleaning project..."
+	@find . -type d -name "__pycache__" -exec rm -rf {} +
+	@rm -rf .coverage
+	@rm -rf .tox/
+	@rm -rf build/
+	@rm -rf dist/
+	@rm -rf *.egg-info/
+	@rm -rf opmon_collector/tests/responses/Test/
+	@echo "Project cleaned."

anonymizer_module/setup.py

@@ -26,10 +26,10 @@
 
 requirements = [
     'setuptools==67.4.0',
-    'pymongo==3.10.1',
-    'pyyaml==5.4.1',
-    'psycopg2==2.8.6',
-    'python-dateutil==2.8.1',
+    'pymongo==4.6.3',
+    'pyyaml==6.0.1',
+    'psycopg2==2.9.9',
+    'python-dateutil==2.9.0.post0',
 ]
 
 classifiers = [

anonymizer_module/test_requirements.txt

@@ -2,6 +2,7 @@ coverage
 pytest
 pytest-mock
 pytest-pycodestyle
+pytest-html
 mongomock
 psycopg2-binary
 mypy

anonymizer_module/tox.ini

@@ -5,10 +5,9 @@ envlist = py38-{pytest,mypy}
 deps = -rtest_requirements.txt
 install_command=pip install --only-binary=numpy {opts} numpy {packages}
 commands =
-    - coverage run --source opmon_anonymizer -m pytest opmon_anonymizer/
+    coverage run --source opmon_anonymizer,metrics_statistics -m pytest opmon_anonymizer/ metrics_statistics/
     coverage report --include=opmon_anonymizer/*
     coverage html -d ../htmlcov/anonymizer_module --include=opmon_anonymizer/*
-    - coverage run --source metrics_statistics -m pytest metrics_statistics/
 [testenv:py38-mypy]
 description = Run mypy
 deps =

collector_module/Makefile

@@ -0,0 +1,10 @@
+clean:
+	@echo "Cleaning project..."
+	@find . -type d -name "__pycache__" -exec rm -rf {} +
+	@rm -rf .coverage
+	@rm -rf .tox/
+	@rm -rf build/
+	@rm -rf dist/
+	@rm -rf *.egg-info/
+	@rm -rf opmon_collector/tests/responses/Test/
+	@echo "Project cleaned."

collector_module/setup.py

@@ -26,11 +26,11 @@
 
 requirements = [
     'setuptools==67.4.0',
-    'pymongo==3.10.1',
-    'requests==2.31.0',
-    'tqdm==4.30.0',
-    'pyyaml==5.4.1',
-    'urllib3==1.26.14',
+    'pymongo==4.6.3',
+    'requests==2.32.3',
+    'tqdm==4.66.4',
+    'pyyaml==6.0.1',
+    'urllib3==1.26.18',
 ]
 
 classifiers = [

collector_module/test_requirements.txt

@@ -2,5 +2,6 @@ coverage
 pytest
 pytest-mock
 pytest-pycodestyle
+pytest-html
 responses
 mongomock

collector_module/tox.ini

@@ -5,7 +5,7 @@ envlist = py38
 deps = -rtest_requirements.txt
 install_command=pip install --only-binary=numpy {opts} numpy {packages}
 commands =
-    - coverage run --source opmon_collector,opmon_mongodb_maintenance -m pytest opmon_collector/ opmon_mongodb_maintenance/
+    coverage run --source opmon_collector,opmon_mongodb_maintenance -m pytest opmon_collector/ opmon_mongodb_maintenance/
     coverage report --include=opmon_collector/*,opmon_mongodb_maintenance/*
     coverage html -d ../htmlcov/collector_module --include=opmon_collector/*,opmon_mongodb_maintenance/*
 

corrector_module/Makefile

@@ -0,0 +1,10 @@
+clean:
+	@echo "Cleaning project..."
+	@find . -type d -name "__pycache__" -exec rm -rf {} +
+	@rm -rf .coverage
+	@rm -rf .tox/
+	@rm -rf build/
+	@rm -rf dist/
+	@rm -rf *.egg-info/
+	@rm -rf opmon_collector/tests/responses/Test/
+	@echo "Project cleaned."