feat: add hooks to have consistent styles for non py files and other …

…neccessary hooks.

.dockerignore

@@ -18,4 +18,4 @@
 # Scripts and tools
 ./scripts
 Makefile
-PULL_REQUEST_TEMPLATE.md
+PULL_REQUEST_TEMPLATE.md

.github/ISSUE_TEMPLATE/general-purpose.md

@@ -1,33 +1,47 @@
-Your issue may already be reported!
-Please search on the [issue tracker](https://github.com/elixir-cloud-aai/TESK/issues) before creating one.
+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.
+1.
+1.
 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:
+
+- Version used:
+- Browser Name and version:
+- Operating System and version (desktop or mobile):
+- Link to your project:

.github/workflows/build_and_publish_charts.yaml

@@ -18,12 +18,12 @@ jobs:
         uses: actions/[email protected]
         with:
           fetch-depth: 0
-            
+
       - name: Create k3s Cluster
         uses: debianmaster/[email protected]
         with:
           version: 'latest'
-            
+
       - name: Create namespace
         run: kubectl create ns tesk
 
@@ -67,12 +67,12 @@ jobs:
         uses: actions/[email protected]
         with:
           fetch-depth: 0
-            
+
       - name: Configure Git
         run: |
           git config user.name "$GITHUB_ACTOR"
           git config user.email "[email protected]"
-    
+
       - name: Run chart-releaser
         uses: helm/[email protected]
         with:

.github/workflows/build_and_publish_filer.yaml

@@ -38,7 +38,7 @@ jobs:
         with:
           images: |
             elixircloud/${{ github.workflow }}
-      
+
       - name: Build and push Docker images
         uses: docker/build-push-action@v3
         with:
@@ -47,4 +47,3 @@ jobs:
           file: ./deployment/containers/filer.Dockerfile
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-

.github/workflows/build_and_publish_taskmaster.yaml

@@ -37,7 +37,7 @@ jobs:
         with:
           images: |
             elixircloud/${{ github.workflow }}
-      
+
       - name: Build and push Docker images
         uses: docker/build-push-action@v3
         with:
@@ -46,4 +46,3 @@ jobs:
           file: ./deployment/containers/taskmaster.Dockerfile
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-

.github/workflows/code_quality.yaml

@@ -99,4 +99,4 @@ jobs:
         run: poetry install --only=lint --no-interaction --no-root
 
       - name: Check spellings
-        run: poetry run typos . 
+        run: poetry run typos .

.github/workflows/validation_pr.yaml

@@ -6,7 +6,7 @@ on:
     branches: ['main']
 
 jobs:
-  semantic_pr: 
+  semantic_pr:
     name: Semantic PR title
     runs-on: ubuntu-latest
     if: ${{ github.event.action != 'edited' || github.event.changes.title != null }}

.gitignore

@@ -173,4 +173,4 @@ poetry.toml
 # LSP config files
 pyrightconfig.json
 
-# End of https://www.toptal.com/developers/gitignore/api/python
+# End of https://www.toptal.com/developers/gitignore/api/python

.pre-commit-config.yaml

@@ -1,21 +1,61 @@
+---
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+# Common commands:
+# pre-commit install
+# pre-commit autoupdate
+# pre-commit run --all-files --hook-stage commit
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v4.6.0
     hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-      - id: check-yaml
       - id: check-added-large-files
       - id: check-builtin-literals
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: ''  # Use the sha / tag you want to point at
-    hooks:
-    -   id: mypy
+      - id: check-added-large-files
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-vcs-permalinks
+      - id: debug-statements
+      - id: destroyed-symlinks
+      - id: detect-private-key
+        exclude: |
+          (?x)^(
+            deployment/charts/tesk/templates/.*\.yaml|deployment/charts/tesk/tls_secret_name\.yml-TEMPLATE
+          )$
+      - id: double-quote-string-fixer
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: fix-encoding-pragma
+        args: [--remove]
+      - id: mixed-line-ending
+        args: [--fix=auto]
+      - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.4.5
     hooks:
       - id: ruff
       - id: ruff-format
-        args: [ --check ]
+        args: [--check]
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.17
+    hooks:
+      - id: mdformat
+        additional_dependencies:
+          - mdformat-config
+          - mdformat-black
+          - mdformat-frontmatter
+        args: [--wrap=80]
+        # exclude: _.+\.md|CHANGELOG\.md  # Add when changelog is implemented
+  # - repo: https://github.com/adrienverge/yamllint.git # nice to have, but it's will change alot of files.
+  #   rev: v1.35.1
+  #   hooks:
+  #     - id: yamllint
+  #       ignore: deployment/charts
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
+    hooks:
+      - id: toml-sort-fix
+        args: [--in-place, --all, --trailing-comma-inline-array]
+        exclude: poetry\.lock

.safety-policy.yml

@@ -46,4 +46,3 @@ security-updates:
   dependency-vulnerabilities:
     auto-security-updates-limit:
       - patch
-

Makefile

@@ -153,7 +153,7 @@ run-service:
 		exit 1; \
 	fi
 
-.PHONY: clean-service-image 
+.PHONY: clean-service-image
 clean-service-image:
 		@if [ -x "$(BUILDAH_CMD)" ]; then \
 				if $(BUILDAH_CMD) inspect $(ELIXIR_CLOUD_REGISTRY)/tesk-core-$(IMAGE):$(TAG) > /dev/null 2>&1; then \

PULL_REQUEST_TEMPLATE.md

@@ -1,26 +1,37 @@
 ## Description
 
-Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.
+Please include a summary of the change and which issue is fixed. Please also
+include relevant motivation and context. List any dependencies that are required
+for this change.
 
 Fixes # (issue)
 
 ## Type of change
 
 Please delete options that are not relevant.
 
-- [ ] Bug fix (non-breaking change which fixes an issue)
-- [ ] New feature (non-breaking change which adds functionality)
-- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
-- [ ] Documentation update
+- \[ \] Bug fix (non-breaking change which fixes an issue)
+- \[ \] New feature (non-breaking change which adds functionality)
+- \[ \] Breaking change (fix or feature that would cause existing functionality
+  to not work as expected)
+- \[ \] Documentation update
 
 ## Checklist:
 
-- [ ] My code follows the [style guidelines](https://github.com/elixir-cloud-aai/elixir-cloud-aai/blob/dev/resources/contributing_guidelines.md#language-specific-guidelines) of this project
-- [ ] I have performed a self-review of my own code
-- [ ] I have commented my code, particularly in hard-to-understand areas
-- [ ] My changes generate no new warnings
-- [ ] I have added tests that prove my fix is effective or that my feature works
-- [ ] New and existing unit tests pass locally with my changes
-- [ ] I have not reduced the existing code coverage
-- [ ] I have added docstrings following the [Python style guidelines](https://github.com/elixir-cloud-aai/elixir-cloud-aai/blob/dev/resources/python.md) of this project to all new modules, classes, methods and functions are documented with docstrings following; I have updated any previously existing docstrings, if applicable
-- [ ] I have updated any sections of the app's documentation that are affected by the proposed changes, if applicable
+- \[ \] My code follows the
+  [style guidelines](https://github.com/elixir-cloud-aai/elixir-cloud-aai/blob/dev/resources/contributing_guidelines.md#language-specific-guidelines)
+  of this project
+- \[ \] I have performed a self-review of my own code
+- \[ \] I have commented my code, particularly in hard-to-understand areas
+- \[ \] My changes generate no new warnings
+- \[ \] I have added tests that prove my fix is effective or that my feature
+  works
+- \[ \] New and existing unit tests pass locally with my changes
+- \[ \] I have not reduced the existing code coverage
+- \[ \] I have added docstrings following the
+  [Python style guidelines](https://github.com/elixir-cloud-aai/elixir-cloud-aai/blob/dev/resources/python.md)
+  of this project to all new modules, classes, methods and functions are
+  documented with docstrings following; I have updated any previously existing
+  docstrings, if applicable
+- \[ \] I have updated any sections of the app's documentation that are affected
+  by the proposed changes, if applicable

README.md

@@ -9,33 +9,59 @@
 
 <img src="images/TESKlogowfont.png" height="200">
 
-An implementation of a task execution engine based on the [TES standard](https://github.com/ga4gh/task-execution-schemas) running on `Kubernetes`. For more details on `TES`, see the (very) brief [introduction to TES](docs/tesintro.md).
+An implementation of a task execution engine based on the
+[TES standard](https://github.com/ga4gh/task-execution-schemas) running on
+`Kubernetes`. For more details on `TES`, see the (very) brief
+[introduction to TES](docs/tesintro.md).
 
 For organisational reasons, this project is split into 3 repositories:
 
 - This one, which contains documentation and deployment files
-- [tesk-api](https://github.com/elixir-cloud-aai/tesk-api): Contains the service that implements the TES API and translates tasks into kubernetes batch calls
-- [tesk-core](https://github.com/elixir-cloud-aai/tesk-core): Contains the code that is launched as images into the kubernetes cluster by tesk-api.
+- [tesk-api](https://github.com/elixir-cloud-aai/tesk-api): Contains the service
+  that implements the TES API and translates tasks into kubernetes batch calls
+- [tesk-core](https://github.com/elixir-cloud-aai/tesk-core): Contains the code
+  that is launched as images into the kubernetes cluster by tesk-api.
 
-If the API is running on your cluster it will pull the images from our `docker.io` repository automatically.
+If the API is running on your cluster it will pull the images from our
+`docker.io` repository automatically.
 
-`TESK` is designed with the goal to support any `Kubernetes` cluster, for its deployment please refer to the [deployment](deployment/documentation/deployment.md) page.
+`TESK` is designed with the goal to support any `Kubernetes` cluster, for its
+deployment please refer to the
+[deployment](deployment/documentation/deployment.md) page.
 
-The technical documentation is available in the [documentation](deployment/documentation) folder.
+The technical documentation is available in the
+[documentation](deployment/documentation) folder.
 
 ## Architecture
 
 <!-- TODO: Change the image remove tomcat, change naming etc -->
 
-**Description**: The first pod in the task lifecycle is the API pod, a pod which runs a web server (`Tomcat`) and exposes the `TES` specified endpoints. It consumes `TES` requests, validates them and translates them to `Kubernetes` jobs. The API pod then creates a `task controller` pod, or `taskmaster`.
+**Description**: The first pod in the task lifecycle is the API pod, a pod which
+runs a web server (`Tomcat`) and exposes the `TES` specified endpoints. It
+consumes `TES` requests, validates them and translates them to `Kubernetes`
+jobs. The API pod then creates a `task controller` pod, or `taskmaster`.
 
-The `taskmaster` consumes the executor jobs, inputs and outputs. It first creates `filer` pod, which creates a persistent volume claim (PVC) to mount as scratch space. All mounts are initialized and all files are downloaded into the locations specified in the TES request; the populated PVC can then be used by each executor pod one after the other. After the `filer` has finished, the taskmaster goes through the executors and executes them as pods one by one. **Note**: Each TES task has a separate taskmaster, PVC and executor pods belonging to it; the only 'singleton' pod across tasks is the API pod.
+The `taskmaster` consumes the executor jobs, inputs and outputs. It first
+creates `filer` pod, which creates a persistent volume claim (PVC) to mount as
+scratch space. All mounts are initialized and all files are downloaded into the
+locations specified in the TES request; the populated PVC can then be used by
+each executor pod one after the other. After the `filer` has finished, the
+taskmaster goes through the executors and executes them as pods one by one.
+**Note**: Each TES task has a separate taskmaster, PVC and executor pods
+belonging to it; the only 'singleton' pod across tasks is the API pod.
 
-After the last executor, the `filer` is called once more to process the outputs and push them to remote locations from the PVC. The PVC is the scrubbed, deleted and the taskmaster ends, completing the task.
+After the last executor, the `filer` is called once more to process the outputs
+and push them to remote locations from the PVC. The PVC is the scrubbed, deleted
+and the taskmaster ends, completing the task.
 
 ## Requirements
 
 - A working [Kubernetes](https://kubernetes.io/) cluster version 1.9 and later.
-- If you want TESK to handle tasks with I/O (and you probably want), you additionally need:
-- A default storage class, which TESK will use to create temporary PVCs. It is enough that the storage class supports the RWO mode.
-- And, if you want TESK to integrate with workflow managers, you additionally need either an FTP account or a PVC that can be accessed from within or from outside of the cluster by the workflow manager (more in the [deployment](deployment/documentation/deployment.md) page).
+- If you want TESK to handle tasks with I/O (and you probably want), you
+  additionally need:
+- A default storage class, which TESK will use to create temporary PVCs. It is
+  enough that the storage class supports the RWO mode.
+- And, if you want TESK to integrate with workflow managers, you additionally
+  need either an FTP account or a PVC that can be accessed from within or from
+  outside of the cluster by the workflow manager (more in the
+  [deployment](deployment/documentation/deployment.md) page).

deployment/charts/tesk/.helmignore

@@ -20,4 +20,3 @@
 .idea/
 *.tmproj
 .vscode/
-