refactor: separate results handling from core simulation logic

Makefile

@@ -1,177 +1,77 @@
-# From http://peterdowns.com/posts/first-time-with-pypi.html
-# To register a package on PyPiTest:
-# python setup.py register -r pypitest
+# OPGEE Makefile
 #
-# Then to upload the actual package:
-# python setup.py sdist upload -r pypitest
-#
-# Do the same with pypi instead of pypitest to go live
-.ONESHELL:
-SHELL=/bin/bash
-CONDA_ENV = opgee
-CONDA_ACTIVATE = source $$(conda info --base)/etc/profile.d/conda.sh; conda activate; conda activate
-
-LOCK=opgee.conda.lock
-ifeq ($(OS),Windows_NT)
-    CONDA_INIT_CMD = call "$(shell where conda | grep Scripts\\conda.exe | sed 's/conda.exe/activate.bat/')"
-    CONDA_PATH_CHECK = where conda
-    CONDA_INIT_IN_SUBSHELL = call activate.bat
-else
-    UNAME_S := $(shell uname -s)
-    ifeq ($(UNAME_S),Linux)
-        CONDA_ROOT = ~/anaconda3
-        CONDA_INIT_CMD = source $(CONDA_ROOT)/bin/activate
-        CONDA_PATH_CHECK = which conda
-    else
-        UNAME_P := $(shell uname -p)
-        ifeq ($(UNAME_P),arm)
-            CONDA_ROOT = /opt/homebrew/anaconda3
-            CONDA_INIT_CMD = source $(CONDA_ROOT)/bin/activate
-            CONDA_PATH_CHECK = which conda
-        else
-            CONDA_ROOT = ~/anaconda3
-            CONDA_INIT_CMD = source $(CONDA_ROOT)/bin/activate
-            CONDA_PATH_CHECK = which conda
-        endif
-    endif
-    CONDA_INIT_IN_SUBSHELL = source $(CONDA_ROOT)/bin/activate
-endif
-
-check-conda:
-	@$(CONDA_PATH_CHECK) >/dev/null 2>&1 || \
-	(echo "Conda not found. Initializing conda..." && \
-	$(CONDA_INIT_CMD))
-
-act:
-	$(CONDA_ACTIVATE)
-a: act
-	# py=$$(which python3)
-	# @echo "before $$py"
-	# $(CONDA_ACTIVATE) base
-	py2=$$(which python)
-	echo "after $$py2"
-
-t: 
-	py=$$(which python3)
-	echo "after $$py"
-
-list:
-	@$(CONDA_ACTIVATE) ./foo; conda list
-
-dc:
-	$(conda deactivate)
-
-check-active-env: check-conda
-	@bash -c '$(CONDA_INIT_IN_SUBSHELL) && \
-	active_env=$$(conda info --envs | grep "*" | cut -d" " -f1) && \
-	echo "Current environment: $$active_env" && \
-	if [ "$$active_env" = "$(CONDA_ENV)" ]; then \
-		echo "Deactivating $(CONDA_ENV) environment..." && \
-		conda deactivate; \
-	else \
-		echo "Environment $(CONDA_ENV) is not active"; \
-	fi'
-
-remove-opgee: check-conda check-active-env
-	@echo "Removing $(CONDA_ENV) environment..."
-	@conda env remove -n $(CONDA_ENV)
-all: clean html sdist wheel
-
-version = `./version.sh`
-
-test-upload: # sdist
-	twine upload dist/opgee-$(version).tar.gz -r testpypi
-
-upload: pypi-upload
-
-pypi-upload: sdist
-	twine upload dist/opgee-$(version).tar.gz
-
-clean-html:
-	make -C docs clean
+# Uses uv for Python package management
+# See: https://docs.astral.sh/uv/
 
-html:
-	make -C docs html
+.PHONY: test test-v test-cov lint format check clean build upload docs help
 
-pdf:
-	make -C docs latexpdf
+# ============================================
+# Development
+# ============================================
 
-clean-setup:
-	python setup.py clean
+test:  ## Run tests
+	uv run pytest
 
-sdist:
-	python setup.py sdist
+test-v:  ## Run tests (verbose)
+	uv run pytest -v
 
-wheel:
-	python setup.py bdist_wheel
+test-cov:  ## Run tests with coverage
+	uv run pytest --cov=opgee
 
-clean: clean-html clean-setup clean-requirements
+lint:  ## Run linter
+	uv run ruff check .
 
-dev:
-	pip install -e .
+format:  ## Format code
+	uv run ruff format .
 
-EMPTY :=
-SPACE := $(EMPTY) $(EMPTY)
-RQMTS := $(shell cat requirements.in)
-MODS  := $(subst $(SPACE),|,$(RQMTS))
-EXPR  := $(shell printf "^(%s)=\n" '$(MODS)')
+check: lint test  ## Run all checks (lint + test)
+	@echo "All checks passed"
 
-RTD_REQS = rtd.requirements.txt
-TRAVIS_REQS = requirements.txt
+dev:  ## Install in development mode
+	uv sync
 
-clean-reqs:
-	rm $(RTD_REQS) $(TRAVIS_REQS)
+# ============================================
+# Build & Release
+# ============================================
 
-rtd-reqs $(RTD_REQS): requirements.in
-	python -V|sed -e 's/Python /python==/' > $(RTD_REQS)
-	pip freeze | egrep '$(EXPR)' >> $(RTD_REQS)
+build:  ## Build sdist and wheel
+	uv build
 
-# "pip freeze" erroneously reports pytest==0.0.0
-travis-reqs $(TRAVIS_REQS): requirements.in
-	./update-reqs.py
+clean-build:  ## Clean build artifacts
+	rm -rf dist/ build/ *.egg-info/
 
-#
-# Virtual environment / package dependency support
-#
-YML_FILE=py3-opgee.yml
+upload-test: build  ## Upload to TestPyPI
+	uv run twine upload dist/* -r testpypi
 
+upload: build  ## Upload to PyPI
+	uv run twine upload dist/*
 
-#INPUT_YML=py3-opgee-macos.yml
-#
-#test-yml: $(TEST_YML)
-#
-## drops all commment lines
-#$(TEST_YML) : $(INPUT_YML)
-#	egrep -v '^#' $(INPUT_YML) > $(TEST_YML)
-
-# remove-opgee:
-# 	conda env remove -n opgee
-
-create-opgee: $(YML_FILE)
-	conda env create -f $(YML_FILE)
-
-install-opgee:
-	bash -l -c 'conda activate opgee && pip install -e .'
-
-rebuild-opgee: remove-opgee create-opgee travis-reqs install-opgee
-
-# Generate a detailed package list to cache for validation of
-# environment on CI platform (currently github actions)
-env-pkg-list:
-	conda list --export > opgee.pkg_list.txt
-
-NUITKA_EXE    = opgee.exe
-NUITKA_OUTDIR = /tmp/opgee-nuitka
-NUITKA_LOG    = /tmp/opgee-nuitka.txt
-
-$(NUITKA_EXE):
-	python -m nuitka opgee/main.py -o $@ \
-		--output-dir=$(NUITKA_OUTDIR) \
-		--include-package-data=opgee \
-		--onefile \
-		--plugin-enable=numpy \
-		--plugin-enable=pylint-warnings \
-		--warn-unusual-code \
-		--warn-implicit-exceptions \
-		--verbose --verbose-output=$(NUITKA_LOG)
-#		--standalone
+# ============================================
+# Documentation
+# ============================================
+
+docs:  ## Build HTML documentation
+	uv run make -C docs html
+
+docs-pdf:  ## Build PDF documentation
+	uv run make -C docs latexpdf
+
+clean-docs:  ## Clean documentation build
+	make -C docs clean
+
+# ============================================
+# Cleanup
+# ============================================
+
+clean: clean-build clean-docs  ## Clean all build artifacts
+	find . -type d -name __pycache__ -exec rm -rf {} + 2>/dev/null || true
+	find . -type f -name "*.pyc" -delete 2>/dev/null || true
+
+# ============================================
+# Help
+# ============================================
+
+help:  ## Show this help
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-15s\033[0m %s\n", $$1, $$2}'
+
+.DEFAULT_GOAL := help