Adopt pyproject.toml and poetry packaging system

.editorconfig

@@ -0,0 +1,24 @@
+# Check http://editorconfig.org for more information
+# This is the main config file for this project:
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true
+
+[*.{py, pyi}]
+indent_style = space
+indent_size = 4
+
+[Makefile]
+indent_style = tab
+
+[*.md]
+trim_trailing_whitespace = false
+
+[*.{diff,patch}]
+trim_trailing_whitespace = false

.github/workflows/main.yml

@@ -1,97 +1,51 @@
-# This is a basic workflow to help you get started with Actions
-
 name: CI
 
-# Controls when the action will run. Triggers the workflow on push request
-# events for the master branch, and pull request events for all branches.
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ '**' ]
+on: [push, pull_request]
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
   build:
-    # The type of runner that the job will run on
-    runs-on: ${{ matrix.os }} #ubuntu-latest
-
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os:  [ubuntu-latest, macos-latest, windows-latest] # Run macos tests if really required, since they charge 10 times more for macos
         python-version: ["3.8", "3.9", "3.10"]
+        os: [ubuntu-latest, macos-latest, windows-latest] # Run macos tests if really required, since they charge 10 times more for macos
+        include:
+          - os: ubuntu-latest
+            path: ~/.cache/pip
+          - os: macos-latest
+            path: ~/Library/Caches/pip
+          - os: windows-latest
+            path: ~\AppData\Local\pip\Cache
 
-    # 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@v2
-
-      # Ref: https://docs.github.com/en/free-pro-team@latest/actions/guides/building-and-testing-python
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v2.2.2
         with:
           python-version: ${{ matrix.python-version }}
 
-      # You can test your matrix by printing the current Python version
-      - name: Display Python version
-        run: python -c "import sys; print(sys.version)"
+      - name: Install poetry
+        run: make poetry-download
 
-      # Cache the pip requirmenets for other tests. If requirements cached use them to speed up the build.
-      # Ref: https://github.com/actions/cache/blob/main/examples.md#python---pip
-      - name: Cache pip Linux
-        uses: actions/cache@v2
-        if: startsWith(runner.os, 'Linux')
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-      - name: Cache pip MacOS
-        uses: actions/cache@v2
-        if: startsWith(runner.os, 'macOS')
+      - name: Set up cache
+        uses: actions/cache@v3
         with:
-          path: ~/Library/Caches/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Cache pip Windows
-        uses: actions/cache@v2
-        if: startsWith(runner.os, 'Windows')
-        with:
-          path: ~\AppData\Local\pip\Cache
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          path: ${{ matrix.path }}
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('poetry.lock') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Install dependencies
         run: |
-          echo update pip
-          python -m pip install --upgrade pip
-          echo update requirments
-          pip install -r requirements.txt
-          echo update test requirements
-          pip install -r tests/requirements.txt
-
-      # Runs a single command using the runners shell
-      - name: Welcome message
-        run: echo Hello, world! Welcome MiV-OS Build, lets start testing!
+          poetry config virtualenvs.in-project true
+          poetry install
 
-      # Formatting test with black and flake8
-      - name: Black and Flake8 formatting tests
-        if: startsWith(runner.os, 'macOS')
+      - name: Run style checks
         run: |
-          if [[ "${{ matrix.python-version }}" == "3.8" ]]; then
-            black --version
-            black --check miv tests
-            flake8 --version
-            flake8 miv tests
-          fi
+          make check-codestyle
 
-      # General PyTest for all matrix strategy
-      - name: PyTest and MyPy
+      - name: Run tests
         run: |
-          make ci
+          make test
 
       # Set environment variables for coverage test. Coverage test is done using python 3.8
       # Test MiV-OS using pytest

.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,25 @@
+name: publish
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/[email protected]
+        with:
+          python-version: "3.x"
+      - name: Install Poetry
+        uses: snok/[email protected]
+      - name: Build
+        run: |
+          poetry build
+      - name: Publish distribution 📦 to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

.pre-commit-config.yaml

@@ -1,18 +1,43 @@
+default_language_version:
+  python: python3.8
+
+default_stages: [commit, push]
+
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v2.3.0
-  hooks:
-  - id: trailing-whitespace
-  - id: check-json
-  - id: end-of-file-fixer
-  - id: requirements-txt-fixer
-- repo: https://github.com/psf/black
-  rev: 21.12b0
-  hooks:
-  - id: black
-    additional_dependencies: ['click==8.0.4']
-    # args: [--line-length=120]
-- repo: https://github.com/pycqa/flake8
-  rev: 4.0.0
-  hooks:
-  - id: flake8
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-json
+      - id: check-yaml
+      - id: end-of-file-fixer
+        exclude: LICENSE
+
+  - repo: local
+    hooks:
+      - id: pyupgrade
+        name: pyupgrade
+        entry: poetry run pyupgrade --py37-plus
+        types: [python]
+        language: system
+
+  - repo: local
+    hooks:
+      - id: isort
+        name: isort
+        entry: poetry run isort --settings-path pyproject.toml
+        types: [python]
+        language: system
+
+  - repo: local
+    hooks:
+      - id: black
+        name: black
+        entry: poetry run black --config pyproject.toml
+        types: [python]
+        language: system
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 4.0.0
+    hooks:
+      - id: flake8

Makefile

@@ -1,11 +1,83 @@
+#* Variables
+PYTHON := python
+PYTHONPATH := `pwd`
+
+#* Poetry
+.PHONY: poetry-download
+poetry-download:
+	curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | $(PYTHON) -
+
+.PHONY: poetry-remove
+poetry-remove:
+	curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | $(PYTHON) - --uninstall
+
+#* Installation
+.PHONY: install
+install:
+	poetry lock -n && poetry export --without-hashes > requirements.txt
+	poetry install -n
+	-poetry run mypy --install-types --non-interactive ./
+
+.PHONY: pre-commit-install
+pre-commit-install:
+	poetry run pre-commit install
+
+#* Formatters
+.PHONY: codestyle
+codestyle:
+	poetry run pyupgrade --exit-zero-even-if-changed --py38-plus **/*.py
+	poetry run isort --settings-path pyproject.toml ./
+	poetry run black --config pyproject.toml ./
+
+.PHONY: formatting
+formatting: codestyle
+
+#* Linting
+.PHONY: test
 test:
-	@python -m pytest
+	PYTHONPATH=$(PYTHONPATH) poetry run pytest -c pyproject.toml --cov-report=html --cov=miv tests/
+
+.PHONY: check-codestyle
+check-codestyle:
+	poetry run isort --diff --check-only --settings-path pyproject.toml ./
+	poetry run black --diff --check --config pyproject.toml ./
+	poetry run darglint --verbosity 2 miv tests
 
+.PHONY: mypy
 mypy:
-	@mypy --ignore-missing-imports miv
+	poetry run mypy --config-file pyproject.toml ./
+
+.PHONY: lint
+lint: test check-codestyle mypy check-safety
+
+.PHONY: update-dev-deps
+update-dev-deps:
+	poetry add -D "isort[colors]@latest" mypy@latest pre-commit@latest pydocstyle@latest pylint@latest pytest@latest pyupgrade@latest coverage@latest pytest-html@latest pytest-cov@latest black@latest
+
+#* Cleaning
+.PHONY: pycache-remove
+pycache-remove:
+	find . | grep -E "(__pycache__|\.pyc|\.pyo$$)" | xargs rm -rf
+
+.PHONY: dsstore-remove
+dsstore-remove:
+	find . | grep -E ".DS_Store" | xargs rm -rf
+
+.PHONY: mypycache-remove
+mypycache-remove:
+	find . | grep -E ".mypy_cache" | xargs rm -rf
+
+.PHONY: ipynbcheckpoints-remove
+ipynbcheckpoints-remove:
+	find . | grep -E ".ipynb_checkpoints" | xargs rm -rf
+
+.PHONY: pytestcache-remove
+pytestcache-remove:
+	find . | grep -E ".pytest_cache" | xargs rm -rf
 
-coverage:
-	@pytest --cov=miv tests/
+.PHONY: build-remove
+build-remove:
+	rm -rf build/
 
-all:test mypy coverage
-ci: test mypy
+.PHONY: cleanup
+cleanup: pycache-remove dsstore-remove mypycache-remove ipynbcheckpoints-remove pytestcache-remove

docs/conf.py

@@ -18,8 +18,7 @@
 
 sys.path.insert(0, os.path.abspath("../"))
 
-from miv.version import VERSION
-
+from miv import get_version
 
 # -- Project information -----------------------------------------------------
 
@@ -28,7 +27,7 @@
 author = "Gazzola Lab"
 
 # The full version, including alpha/beta/rc tags
-release = VERSION
+release = get_version()
 
 # -- General configuration ---------------------------------------------------
 

examples/post_processing/spike_detection.py

@@ -1,20 +1,19 @@
 import os
+
+import matplotlib.pyplot as plt
+import neo
 import numpy as np
 import quantities as pq
+from viziphant.rasterplot import rasterplot_rates
 
 from miv.io import load_data
 from miv.signal.filter import butter_bandpass_filter
 from miv.signal.spike import (
+    align_to_minimum,
     compute_spike_threshold,
     detect_threshold_crossings,
-    align_to_minimum,
 )
 
-import neo
-from viziphant.rasterplot import rasterplot_rates
-
-import matplotlib.pyplot as plt
-
 
 def main():
     """Example spike detection script"""

miv/__init__.py

@@ -0,0 +1,15 @@
+# type: ignore[attr-defined]
+"""Python software for analysis and computing framework used in MiV project."""
+
+import sys
+from importlib import metadata as importlib_metadata
+
+
+def get_version() -> str:
+    try:
+        return importlib_metadata.version(__name__)
+    except importlib_metadata.PackageNotFoundError:  # pragma: no cover
+        return "unknown"
+
+
+version: str = get_version()

miv/io/__init__.py

@@ -1,2 +1,2 @@
-from miv.io.data import *
 from miv.io.binary import *
+from miv.io.data import *