Python implementation refactor, numba kernel optimizations, some GPU implementations

.flake8

@@ -0,0 +1,6 @@
+[flake8]
+max-complexity = 10
+max-line-length = 88
+extend-ignore = E203
+exclude =
+    __pycache__

.github/workflows/build.yml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.7, 3.8]
+        python-version: ["3.9", "3.10"]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -37,9 +37,9 @@ jobs:
         run: conda --version
       - name: Install depedencies and package
         shell: bash
-        run: pip install -U -e .'[tests]'; conda install match-series
+        run: pip install -U -e .'[dev]'; conda install match-series
       - name: Run tests
-        run: pytest --cov=pymatchseries --pyargs pymatchseries
+        run: pytest --cov=pymatchseries -vv
       - name: Generate line coverage
         if: ${{ matrix.os == 'ubuntu-latest' }}
         run: coverage report --show-missing

.gitignore

@@ -1,3 +1,4 @@
+Exclude
 tags
 examples/data/**
 examples/sample_data_HAADF

Makefile

@@ -0,0 +1,87 @@
+.PHONY: clean clean-build clean-pyc clean-test coverage dist docs help install lint lint/flake8 lint/black
+.DEFAULT_GOAL := help
+
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+
+from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+check: lint test
+
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test: ## remove test and coverage artifacts
+	rm -fr .tox/
+	rm -f .coverage
+	rm -fr htmlcov/
+	rm -fr .pytest_cache
+
+lint:
+	black .
+	isort .
+	mypy ./pymatchseries
+	flake8 ./pymatchseries
+
+test: ## run tests quickly with the default Python
+	pytest -vv
+
+coverage: ## check code coverage quickly with the default Python
+	coverage run --source pymatchseries -m pytest
+	coverage report -m
+	coverage html
+	$(BROWSER) htmlcov/index.html
+
+docs: ## generate Sphinx HTML documentation, including API docs
+	rm -f docs/pymatchseries.rst
+	rm -f docs/modules.rst
+	sphinx-apidoc -o docs/ pymatchseries
+	$(MAKE) -C docs clean
+	$(MAKE) -C docs html
+	$(BROWSER) docs/_build/html/index.html
+
+servedocs: docs ## compile the docs watching for changes
+	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
+
+release: dist ## package and upload a release
+	twine upload dist/*
+
+dist: clean ## builds source and wheel package
+	python setup.py sdist
+	python setup.py bdist_wheel
+	ls -l dist
+
+install: clean ## install the package to the active Python's site-packages
+	python setup.py install

dev-requirements.in

@@ -0,0 +1,11 @@
+sphinx>=3.0.2
+sphinx-rtd-theme>=0.4.3
+pytest>=5.4
+pytest-cov>=2.8.1
+coverage>=5.0
+black>=19.3b0
+pre-commit>=1.16
+flake8>=3.9.2
+mypy>=0.990
+mypy-extensions>=0.4.2
+isort>=5.10.1

environment.yml

@@ -0,0 +1,9 @@
+name: pyMatchSeries
+channels:
+  - conda-forge
+dependencies:
+  - hyperspy
+  - cupy
+  - match-series
+  - numba
+  - pydantic