big reorganization

- remove unused stuff
- port existing noxfile.py with general tasks
- pin dependencies with pip-deepfreeze
- switch to pyproject.toml and hatch as build tool
- use hatch for version bumping
- most tests removed in order to get a clean slate:
  - the work mapper ones were self contained so I kept them

.coveragerc

@@ -0,0 +1,19 @@
+[run]
+branch = True
+parallel = True
+omit =
+    tests/*
+
+source = src/
+
+[report]
+exclude_lines =
+    @overload
+    pragma: no cover
+    raise NotImplementedError
+    if TYPE_CHECKING:
+    pass
+    if __name__ == "__main__":
+
+# SNIPPET: use this to fail CI for missing test coverage
+# fail_under = 100

CONTRIBUTING.md

@@ -0,0 +1,49 @@
+# Contributing 
+
+Developing on wepy
+
+After you have cloned the repo you should have a copy of Python 3.10 installed
+and accessible to path as `python3.10`.
+
+Then you should be able to start coding and running tests:
+
+```sh
+make test-unit
+```
+
+To build the package:
+
+```sh
+make build
+```
+
+To see all the commands run `make` or:
+
+```sh
+make help
+```
+
+All the virtual environment creation and installation is taken care behind the
+scenes.
+
+If you want a standalone environment you can activate in your shell run:
+
+```sh
+make env
+```
+
+Which creates the `.venv` folder. For convenience it can be activated with:
+
+```sh
+. ./env.sh
+```
+
+
+## TODOs
+
+Note that there are stubs for performing checks like linting, formatting etc.
+that aren't used in this project, but could be added at a later time.
+
+In order to get tests passing many bad tests were deleted.
+
+Building of documentation is also not implemented at the moment.

Makefile

@@ -0,0 +1,127 @@
+## Notes on this file. The `help` target parses the file and can generate
+## headings and docstrings for targets, in the order they are in the file. To
+## create a heading make a comment like `##@ Heading Content`. To document
+## targets make a comment on the same line as the target name with two `##
+## docstring explanation...`. To leave a target undocumented simply provide no
+## docstring.
+
+PYTHON=python3.11
+TMPDIR=.tmp
+
+##@ Getting Started
+
+env: ## Rebuild the main development environment
+	nox -s dev_external
+	echo "Run this to activate dev env: . env.sh"
+.PHONY: env
+
+##@ Housekeeping
+
+clean-all: clean clean-docs clean-env clean-compose clean-hooks ## run all clean commands
+.PHONY: clean-all
+
+clean: ## Clean temporary files, directories etc.
+	rm -rf $(TMPDIR)
+	rm -rf dist .pytest_cache .mypy_cache .coverage .venv .nox .hatch htmlcov
+	find . -type f -name "*.pyc" -print -delete
+	hatch clean
+.PHONY: clean
+
+clean-env: ## Clean the dev environments
+	rm -rf .venv
+.PHONY: clean-env
+
+##@ QA (TODO)
+
+# format: ## Run source code formatters manually.
+# 	nox -s format
+# .PHONY: docstrings
+
+# validate:  ## Run all linters, type checks, static analysis, etc.
+# 	nox -s validate
+# .PHONY: validate
+
+# format-check: ## Run code formatting checks
+# 	nox -s format_check
+# .PHONY: format-check
+
+# # check: ## Run only miscellaneous maintenance checks
+# # .PHONY: check
+
+# lint: ## Run only the linters (non-autoformatters).
+# 	nox -s lint
+# .PHONY: lint
+
+# docstring-check: ## Run docstring coverage only.
+# 	nox -s docstring_lint
+# .PHONY: docstring
+
+# typecheck: ## Run only the type checker (requires mypy)
+# 	nox -s typecheck
+# .PHONY: typecheck
+
+##@ Dev
+
+test-unit: ## Run unit tests with coverage report
+	nox -s tests_unit
+.PHONY: test
+
+coverage: ## Report on missing coverage. (Run 'test-unit' to generate new stats)
+	nox -s coverage
+.PHONY: coverage
+
+serve-coverage: ## Run a temporary web server to display detailed coverage report
+	python3 -m http.server --directory htmlcov 4322
+.PHONY: serve-coverage
+
+
+##@ Documentation (TODO)
+
+# docs: ## TODO: Build the documentation
+# 	nox -s docs
+# .PHONY: docs
+
+# clean-docs: ## TODO: Clean temporary files for documentation
+# 	rm -rf docs/_api docs/_build
+# .PHONY: clean-docs
+
+# serve-docs: ## TODO: Run a temporary web server to display current documentation build
+# 	python3 -m http.server --directory docs/_build 4323
+# .PHONY: serve-docs
+
+
+##@ Release Management
+
+pin: pyproject.toml ## Pin the project dependency versions
+	nox -s pin
+.PHONY: pin
+
+bumpversion: ## Bump the minor version for the project
+	nox -s bumpversion
+.PHONY: bumpversion
+
+build: ## Run the python build/packaging, generate sdist & wheel
+	nox -s build
+.PHONY: build
+
+publish: ## Publish the package to indices
+	nox -s publish
+.PHONY: publish
+
+##@ Help
+
+# An automatic help command: https://www.padok.fr/en/blog/beautiful-makefile-awk
+.DEFAULT_GOAL := help
+
+help: ## (DEFAULT) This command, show the help message
+	@echo "See CONTRIBUTING.md for dependencies, then run this:"
+	@echo ""
+	@echo "If you want a shell in a virtual environment with everything:"
+	@echo "  > make env"
+	@echo "  > . ./env.sh"
+	@echo ""
+	@echo "Do testing:"
+	@echo "  > make test-unit"
+	@echo ""
+	@awk 'BEGIN {FS = ":.*##"; printf "\nUsage:\n  make \033[36m<target>\033[0m\n"} /^[a-zA-Z_0-9-]+:.*?##/ { printf "  \033[36m%-15s\033[0m %s\n", $$1, $$2 } /^##@/ { printf "\n\033[1m%s\033[0m\n", substr($$0, 5) } ' $(MAKEFILE_LIST)
+.PHONY: help

dev/README.md

@@ -0,0 +1,6 @@
+This contains external specifications of the different profiles of dependencies
+needed for different tasks.
+
+They are split up this way to allow for the absolute minimum dependencies needed
+in environments like CI where we want performance to be optimal and reducing the
+number of dependencies can help that a lot.

dev/docs.requirements.txt

@@ -0,0 +1,7 @@
+sphinx
+sphinxcontrib-napoleon
+sphinxcontrib-newsfeed
+sphinxcontrib-bibtex
+sphinxcontrib-newsfeed
+nbsphinx
+notebook

dev/interactive.requirements.txt

@@ -0,0 +1,2 @@
+ipython
+pdbpp

dev/qa.requirements.txt

@@ -0,0 +1,5 @@
+black
+isort
+flake8
+flake8-bugbear
+interrogate

dev/testing.requirements.txt

@@ -0,0 +1,3 @@
+pytest
+coverage
+pytest-cov

dev/typechecking.requirements.txt

@@ -0,0 +1 @@
+mypy

env.sh

@@ -0,0 +1 @@
+. ./.venv/bin/activate