Refactoring

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,25 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+
+1. Command executed
+2. Environment used
+3. Some data to reproduce the problem
+4. User
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/custom.md

@@ -0,0 +1,8 @@
+---
+name: Custom issue template
+about: Describe this issue template's purpose here.
+title: ''
+labels: ''
+assignees: ''
+
+---

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,16 @@
+# Description
+
+Please include a summary of the changes and the related issue.
+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)
+- [ ] This change requires a documentation update

.github/workflows/dev.yml

@@ -0,0 +1,66 @@
+name: dev build CI
+
+# Controls when the action will run.
+on:
+  # Triggers the workflow on push or pull request events
+  push:
+    branches:
+    - '*'
+  pull_request:
+    branches:
+    - '*'
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# contains 3 jobs: test, publish_dev_build and notification
+jobs:
+  test:
+    # The type of runner that the job will run on
+    strategy:
+      matrix:
+        python-versions: ['3.9', '3.10', '3.11']
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-versions }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox tox-gh-actions poetry
+
+    - name: test with tox
+      run: tox
+
+  publish_dev_build:
+    # if test failed, we should not publish
+    needs: test
+    # you may need to change os below
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 # fetch all commits/branches for mike
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install poetry tox tox-gh-actions
+
+    - name: build documentation
+      run: |
+        poetry install -E doc
+        poetry run mkdocs build
+        git config --global user.name Docs deploy
+        git config --global user.email docs@dummy.bot.com
+        poetry run mike deploy -p "`poetry version --short`.dev"
+        poetry run mike set-default -p "`poetry version --short`.dev"

.gitignore

@@ -6,9 +6,6 @@ __pycache__/
 # C extensions
 *.so
 
-# cythonized files
-stpipeline/common/*.c
-
 # Distribution / packaging
 .Python
 env/
@@ -46,52 +43,32 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
-*,cover
+*.cover
 .hypothesis/
+.pytest_cache/
+pytest-report.xml
 
 # Translations
 *.mo
 *.pot
 
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
+# mkdocs documentation
+/site
 
-# celery beat schedule file
-celerybeat-schedule
+# mypy
+.mypy_cache/
 
-# SageMath parsed files
-*.sage.py
+# IDE settings
+.vscode/
 
-# dotenv
-.env
+# mkdocs build dir
+site/
 
-# virtualenv
-.venv
-venv/
-ENV/
+# vscode extension - local history
+.history/
 
-# Spyder project settings
-.spyderproject
+# Cache
+__pycache__
 
-# Rope project settings
-.ropeproject
+# OSX
+.DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+repos:
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+  rev: v1.5.4
+  hooks:
+  - id: forbid-crlf
+  - id: remove-crlf
+  - id: forbid-tabs
+    exclude_types: [csv, tsv]
+    exclude: makefile
+  - id: remove-tabs
+    exclude_types: [csv, tsv]
+    exclude: makefile
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.1.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-merge-conflict
+  - id: pretty-format-json
+    args: [--autofix]
+  - id: check-yaml
+    args: [--unsafe]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.1.14
+  hooks:
+  - id: ruff
+    args: [--fix]
+  - id: ruff-format
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.12.0
+  hooks:
+  - id: pretty-format-yaml
+    args: [--autofix, --indent, '2']
+- repo: local
+  hooks:
+  - id: mypy
+    name: mypy
+    entry: mypy
+    exclude: ^tests
+    language: python
+    types: [python]
+    require_serial: true
+    verbose: true

AUTHORS.md

@@ -0,0 +1,5 @@
+## Author:
+- Jose Fernandez Navarro <jc.fernandez.navarro@gmail.com>
+
+## Contributors:
+- Erik Borgström <erik.borgstrom@scilifelab.se>