feat: clean up & refactor majorly

.dockerignore

@@ -1,5 +1,22 @@
-.coverage
+# cache and dot files
+.eggs/
+.venv/
+.mypy_cache/
 .pytest_cache/
-.tox/
+.coverage/
+.ruff/
+.ruff_cache/
 .eggs/
-tesk-core/containers/
+.github/
+.gitignore
+# Docs and atifacts
+./deployment
+./docs
+/images
+# build
+./build
+./dist
+# Scripts and tools
+./scripts
+Makefile
+PULL_REQUEST_TEMPLATE.md

.github/ISSUE_TEMPLATE/general-purpose.md

@@ -0,0 +1,33 @@
+Your issue may already be reported!
+Please search on the [issue tracker](https://github.com/elixir-cloud-aai/TESK/issues) before creating one.
+
+## Expected Behavior
+<!--- If you're describing a bug, tell us what should happen -->
+<!--- If you're suggesting a change/improvement, tell us how it should work -->
+
+## Current Behavior
+<!--- If describing a bug, tell us what happens instead of the expected behavior -->
+<!--- If suggesting a change/improvement, explain the difference from current behavior -->
+
+## Possible Solution
+<!--- Not obligatory, but suggest a fix/reason for the bug, -->
+<!--- or ideas how to implement the addition or change -->
+
+## Steps to Reproduce (for bugs)
+<!--- Provide a link to a live example, or an unambiguous set of steps to -->
+<!--- reproduce this bug. Include code to reproduce, if relevant -->
+1.
+2.
+3.
+4.
+
+## Context
+<!--- How has this issue affected you? What are you trying to accomplish? -->
+<!--- Providing context helps us come up with a solution that is most useful in the real world -->
+
+## Your Environment
+<!--- Include as many relevant details about the environment you experienced the bug in -->
+* Version used:
+* Browser Name and version:
+* Operating System and version (desktop or mobile):
+* Link to your project:

.github/workflows/code_lint_format.yaml

@@ -0,0 +1,58 @@
+name: Code Quality
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install poetry
+        run: pipx install poetry
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        id: cql
+        with:
+          python-version: '3.11'
+          cache: 'poetry'
+
+      # Install lint deps only
+      - name: Install dependencies
+        if: steps.cql.outputs.cache-hit != 'true'
+        run: poetry install --only=lint --no-interaction --no-root
+
+      - name: Check code quality
+        run: poetry run ruff check .
+
+  format:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install poetry
+        run: pipx install poetry
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        id: cqf
+        with:
+          python-version: '3.11'
+          cache: 'poetry'
+
+      # Install lint deps only
+      - name: Install dependencies
+        if: steps.cqf.outputs.cache-hit != 'true'
+        run: poetry install --only=lint --no-interaction --no-root
+
+      - name: Check code style
+        run: poetry run ruff format --check

.github/workflows/code_test.yaml

@@ -0,0 +1,45 @@
+name: Code Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  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 ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        id: ctut-${{ matrix.python-version}}
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'poetry'
+
+      # Install all test dependencies
+      - name: Install dependencies
+        if: steps.ctut-${{ matrix.python-version }}.outputs.cache-hit != 'true'
+        run: poetry install --only=test --no-interaction --no-root
+
+      - name: Run tests
+        run: poetry run pytest tests/test_unit
+
+    # # Upload coverage reports to Codecov once the tests start running 😭
+    # - name: Upload coverage reports to Codecov
+    #   uses: codecov/codecov-action@v3
+    #   env:
+    #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/docker-build-publish-filer.yml → .github/workflows/docker_build_publish_filer.yaml

@@ -43,7 +43,7 @@ jobs:
         with:
           context: .
           push: true
-          file: ./containers/filer.Dockerfile
+          file: ./deployment/containers/filer.Dockerfile
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
 

.github/workflows/docker-build-publish-taskmaster.yml → .github/workflows/docker_build_publish_taskmaster.yaml

@@ -43,7 +43,7 @@ jobs:
         with:
           context: .
           push: true
-          file: ./containers/taskmaster.Dockerfile
+          file: ./deployment/containers/taskmaster.Dockerfile
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
 

.github/workflows/build.yaml → .github/workflows/helm_test.yaml

@@ -2,10 +2,10 @@ name: Helm Chart Testing
 
 on:
   pull_request: 
-    branches: [master]
+    branches: [main]
 
 jobs:
-  helm:
+  helm-test:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -23,19 +23,19 @@ jobs:
 
       - name: Helm Deps
         run: |
-          for dir in $(ls -d charts/*); do
+          for dir in $(ls -d deployment/charts/*); do
             helm dependency update $dir;
           done
 
       - name: Helm Lint
         run: |
-          for dir in $(ls -d charts/*); do
+          for dir in $(ls -d deployment/charts/*); do
             helm lint $dir
           done
 
       - name: Apply Helm file
         run: helm install -n tesk tesk . -f values.yaml
-        working-directory: charts/tesk
+        working-directory: deployment/charts/tesk
 
       - name: Sleep for 30 seconds
         run: sleep 30

.github/workflows/pr_evaulations.yaml

@@ -0,0 +1,54 @@
+name: PR Evaluation
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review, edited]
+    branches: ['main']
+
+jobs:
+  semantic_pr: 
+    name: Semantic PR title
+    runs-on: ubuntu-latest
+    if: ${{ github.event.action != 'edited' || github.event.changes.title != null }}
+    steps:
+      - uses: amannn/action-semantic-pull-request@v5
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          # Configure which types are allowed (newline-delimited).
+          # Default: https://github.com/commitizen/conventional-commit-types
+          types: |
+            fix
+            feat
+            docs
+            style
+            refactor
+            perf
+            test
+            build
+            ci
+            chore
+            revert
+          # Configure additional validation for the subject based on a regex.
+          # This example ensures the subject doesn't start with an uppercase character & has more than 50 chars.
+          subjectPattern: ^(?![A-Z])(?=.{1,50}$).+$
+          # 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
+            doesn't start with an uppercase character & not have more than 50 characters.
+
+  detect-unresolved-conflicts:
+    name: Detect unresolved merge conflicts
+    runs-on: ubuntu-latest
+    needs: semantic_pr
+    steps:
+      - uses: actions/checkout@v3
+      - 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/type_check.yaml

@@ -0,0 +1,37 @@
+# # This workflow should work but will fail
+# # as the code has no types, will add types to the
+# # code and then uncomment it 👍
+# name: Type Check
+
+# on:
+#   push:
+#     branches:
+#       - main
+#   pull_request:
+#     branches:
+#       - main
+
+# jobs:
+#   check-type:
+#     runs-on: ubuntu-latest
+#     steps:
+#       - name: Check out repository
+#         uses: actions/checkout@v4
+
+#       - name: Install poetry
+#         run: pipx install poetry
+
+#       - name: Set up python
+#         id: tcct
+#         uses: actions/setup-python@v5
+#         with:
+#           python-version: '3.11'
+#           cache: 'poetry'
+
+#       # Install only type check dependency
+#       - name: Install dependencies
+#         if: steps.tcct.outputs.cache-hit != 'true'
+#         run: poetry install --only=type --no-root
+
+#       - name: Check types
+#         run: poetry run mypy tesk/