chore: minor renaming stuff

Author: JaeAeich

.dockerignore

@@ -1,19 +1,18 @@
-# cache and dot files
+# Cache and dot files
+.coverage/
 .eggs/
-.venv/
+.github/
+.gitignore
 .mypy_cache/
 .pytest_cache/
-.coverage/
 .ruff/
 .ruff_cache/
-.eggs/
-.github/
-.gitignore
-# Docs and atifacts
+.venv/
+# Docs and artifacts
 ./deployment
 ./docs
-/images
-# build
+./images
+# Build
 ./build
 ./dist
 # Scripts and tools

.github/workflows/helm_test.yaml renamed to .github/workflows/build_and_publish_charts.yaml

@@ -1,12 +1,18 @@
-name: Helm Chart Testing
+name: Build and Publish Helm Charts
 
 on:
-  pull_request: 
-    branches: [main]
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
 
 jobs:
-  helm-test:
+  create-cluster:
+    name: Create k3s Cluster
     runs-on: ubuntu-latest
+    needs: checkout
     steps:
       - name: Checkout
         uses: actions/[email protected]
@@ -20,31 +26,71 @@ jobs:
 
       - name: Create namespace
         run: kubectl create ns tesk
-        
+
+  helm-deps:
+    name: Helm Dependencies
+    runs-on: ubuntu-latest
+    needs: checkout
+    steps:
+      - name: Checkout
+        uses: actions/[email protected]
+        with:
+          fetch-depth: 0
+
       - name: Helm Deps
         run: |
           for dir in $(ls -d deployment/charts/*); do
             helm dependency update $dir;
           done
-    
+
+  helm-lint:
+    name: Helm Lint
+    runs-on: ubuntu-latest
+    needs: [helm-deps]
+    steps:
+      - name: Checkout
+        uses: actions/[email protected]
+        with:
+          fetch-depth: 0
+
       - name: Helm Lint
         run: |
           for dir in $(ls -d deployment/charts/*); do
             helm lint $dir
           done
-        
+
+  helm-install:
+    name: Helm Install
+    runs-on: ubuntu-latest
+    needs: [create-cluster, helm-deps, helm-lint]
+    steps:
+      - name: Checkout
+        uses: actions/[email protected]
+        with:
+          fetch-depth: 0
+
       - name: Apply Helm file
         run: helm install -n tesk tesk . -f values.yaml
         working-directory: deployment/charts/tesk
 
       - name: Sleep for 30 seconds
         run: sleep 30
-           
+
       - name: Get Helm and k8s
         run: helm list -n tesk && kubectl get all -n tesk
 
       - name: curl URL
         run: curl localhost -vL
+
+  chart-releaser:
+    name: Run chart-releaser
+    runs-on: ubuntu-latest
+    needs: helm-install
+    steps:
+      - name: Checkout
+        uses: actions/[email protected]
+        with:
+          fetch-depth: 0
 
       - name: Configure Git
         run: |
@@ -57,4 +103,3 @@ jobs:
           skip_existing: true
         env:
           CR_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
-    

.github/workflows/docker_build_publish_filer.yaml renamed to .github/workflows/build_and_publish_filer.yaml

@@ -1,4 +1,4 @@
-name: tesk-core-filer
+name: Build and Publish Filer
 
 on:
   push:
@@ -14,6 +14,7 @@ on:
 
 jobs:
   build-from-source:
+    name: Build and publish Docker image
     runs-on: ubuntu-latest
     steps:
       - name: Checkout elixir-cloud-aai/tesk-core

.github/workflows/docker_build_publish_taskmaster.yaml renamed to .github/workflows/build_and_publish_taskmaster.yaml

@@ -1,4 +1,4 @@
-name: tesk-core-taskmaster
+name: Build and Publish Taskmaster
 
 on:
   push:

.github/workflows/code_quality.yaml

@@ -10,6 +10,7 @@ on:
 
 jobs:
   lint:
+    name: Lint
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
@@ -25,15 +26,14 @@ jobs:
           python-version: '3.11'
           cache: 'poetry'
 
-      # Install lint deps only
-      - name: Install dependencies
-        # if: steps.cq.outputs.cache-hit != 'true'
+      - name: Install lint dependencies
         run: poetry install --only=lint --no-interaction --no-root
 
       - name: Check code quality
         run: poetry run ruff check .
 
   format:
+    name: Format
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
@@ -49,15 +49,14 @@ jobs:
           python-version: '3.11'
           cache: 'poetry'
 
-      # Install lint deps only
-      - name: Install dependencies
-        # if: steps.cq.outputs.cache-hit != 'true'
+      - name: Install lint dependencies
         run: poetry install --only=lint --no-interaction --no-root
 
       - name: Check code style
         run: poetry run ruff format --check
 
   type-check:
+    name: Type Check
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
@@ -73,15 +72,14 @@ jobs:
           python-version: '3.11'
           cache: 'poetry'
 
-      # Install only type check dependency
-      - name: Install dependencies
-        # if: steps.cqtc.outputs.cache-hit != 'true'
+      - name: Install types and mypy dependencies
         run: poetry install --only=types --no-interaction --no-root
 
       - name: Check types
         run: poetry run mypy tesk/
 
   spell-check:
+    name: Spell Check
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
@@ -97,9 +95,7 @@ jobs:
           python-version: '3.11'
           cache: 'poetry'
 
-      # Install lint deps only
-      - name: Install dependencies
-        # if: steps.cq.outputs.cache-hit != 'true'
+      - name: Install lint dependencies
         run: poetry install --only=lint --no-interaction --no-root
 
       - name: Check spellings

.github/workflows/code_test.yaml renamed to .github/workflows/code_test_unit.yaml

@@ -1,4 +1,4 @@
-name: Code Test
+name: Code Test Unit
 
 on:
   push:
@@ -10,29 +10,23 @@ on:
 
 jobs:
   unit-test:
+    name: Unit Test
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.11', '3.12', '3.13']
-
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
 
       - name: Install poetry
         run: pipx install poetry
 
-      # Set up python versions with matrix to test on multiple versions
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python
         uses: actions/setup-python@v5
-        id: ct-${{ matrix.python-version}}
+        id: ct
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: '3.11'
           cache: 'poetry'
 
-      # Install all test dependencies
-      - name: Install dependencies
-        # if: steps.ct-${{ matrix.python-version }}.outputs.cache-hit != 'true'
+      - name: Install test dependencies
         run: poetry install --only=test --no-interaction --no-root
 
       - name: Run ATS

tests/test_unit/service/resources/copyDirTest/dst1/3.txt renamed to .github/workflows/validation_helm.yaml

@@ -15,8 +15,6 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
-          # Configure which types are allowed (newline-delimited).
-          # Default: https://github.com/commitizen/conventional-commit-types
           types: |
             fix
             feat
@@ -29,12 +27,7 @@ jobs:
             ci
             chore
             revert
-          # Configure additional validation for the subject based on a regex.
-          # This example ensures the subject doesn't start with an uppercase character & has more than 50 chars.
           subjectPattern: ^(?![A-Z])(?=.{1,50}$).+$
-          # If `subjectPattern` is configured, you can use this property to override
-          # the default error message that is shown when the pattern doesn't match.
-          # The variables `subject` and `title` can be used within the message.
           subjectPatternError: |
             The subject "{subject}" found in the pull request title "{title}"
             didn't match the configured pattern. Please ensure that the subject
@@ -49,6 +42,4 @@ jobs:
       - name: List files with merge conflict markers
         run: git --no-pager grep "<<<<<<<" ":(exclude).github/" || true
       - name: Fail or succeed job if any files with merge conflict markers have been checked in
-        # Find lines containing "<<<<<<<", then count the number of lines.
-        # 0 matching lines results in exit code 0, i.e. success.
         run: exit $(git grep "<<<<<<<" ":(exclude).github/" | wc --lines)

.github/workflows/pr_evaulations.yaml renamed to .github/workflows/validation_pr.yaml

@@ -10,6 +10,7 @@ on:
 
 jobs:
   code-vulnerabilities:
+    name: Code
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
@@ -25,15 +26,14 @@ jobs:
           python-version: '3.11'
           cache: 'poetry'
 
-      # Install only vulnerability check dependency
-      - name: Install dependencies
-        # if: steps.vt.outputs.cache-hit != 'true'
+      - name: Install vulnerabilities check dependencies
         run: poetry install --only=security --no-interaction --no-root
 
-      - name: Check code vulnerabilities
+      - name: Check code vulnerabilities with bandit
         run: poetry run bandit -c pyproject.toml -r tesk/
 
   dependency-vulnerabilities:
+    name: Dependencies
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
@@ -49,10 +49,8 @@ jobs:
           python-version: '3.11'
           cache: 'poetry'
 
-      # Install only vulnerabilities check dependency
-      - name: Install dependencies
-        # if: steps.vt.outputs.cache-hit != 'true'
+      - name: Install vulnerabilities check dependencies
         run: poetry install --only=security --no-interaction --no-root
 
-      - name: Check dependency vulnerabilities
+      - name: Check dependency vulnerabilities with safety
         run: poetry run safety check --full-report

.github/workflows/vulnerability_test.yaml renamed to .github/workflows/vulnerabilities.yaml

@@ -1,6 +1,3 @@
-# TODO: Add commands to be compatible for windows
-# TODO: Add commands for tesk_api
-
 # Define variables
 PYTHON_CMD := $(shell command -v python3 2> /dev/null)
 BUILDAH_CMD := $(shell command -v buildah 2> /dev/null)

Makefile

@@ -1,21 +1,19 @@
 [tool.poetry]
 name = "tesk"
 version = "0.1.0"
-description = "An implementation of a task execution engine based on the TES standard running on Kubernetes."
-authors = ["TBA <[email protected]>"]
-maintainers = ["TBA <[email protected]>", "TBA <[email protected]>"]
+description = "An implementation of a task execution engine based on the GA4GH Task Execution Service (TES) API standard running on Kubernetes."
+authors = ["Elixir Cloud AAI <[email protected]>"]
+maintainers = ["Elixir Cloud AAI <[email protected]>"]
 license = "Apache-2.0"
 readme = "README.md"
 repository = "https://github.com/elixir-cloud-aai/TESK"
 keywords = ["TES", "Kubernetes", "Task Execution", "ebi", "TESK", "workflow", "automation"]
 classifiers = [
-    "Development Status :: 4 - Alpha",
+    "Development Status :: 4 - Beta",
     "Intended Audience :: System Administrators",
     "License :: OSI Approved :: Apache Software License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.11"
 ]
 
 [tool.poetry.scripts]

pyproject.toml

@@ -25,7 +25,7 @@
 )
 from tesk.service.filer_s3 import S3Transput
 from tesk.service.path import containerPath
-from tests.test_unit.service.assertThrows import AssertThrowsMixin
+from tests.test_unit.test_service.assertThrows import AssertThrowsMixin
 
 
 def getTree(rootDir):
@@ -139,7 +139,7 @@ def test_copyDir(self):
 		def rmDir(d):
 			os.system(f'rm -r {d}')
 
-		baseDir = 'tests/test_unit/service/resources/copyDirTest/'
+		baseDir = 'tests/test_unit/test_service/resources/copyDirTest/'
 		src = os.path.join(baseDir, 'src')
 		dst1 = os.path.join(baseDir, 'dst1')
 		dst2 = os.path.join(baseDir, 'dst2')

tests/test_unit/service/FilerClassTest.py renamed to tests/test_unit/test_service/FilerClassTest.py

@@ -7,7 +7,7 @@
 from tesk.service.filer import HTTPTransput, Type
 
 PATH_DOWN = 'test_download_file.txt'
-PATH_UP = 'tests/test_unit/service/test_filer_http_pytest.py'
+PATH_UP = 'tests/test_unit/test_service/test_filer_http_pytest.py'
 SUCCESS = 200
 FAIL = 300
 URL = 'http://www.foo.bar'