build: update Makefile README.md pyproject.toml requirements-dev.txt requirements.txt requirements/dev.in setup.cfg from main

Author: paulschreiber

Makefile

@@ -1,23 +1,27 @@
-pip-tools: ${VIRTUAL_ENV}/scripts/pip-sync
-
-format:
-	isort --atomic soil_id
-	black soil_id
+ifeq ($(DC_ENV),ci)
+	UV_FLAGS = "--system"
+endif
 
 install:
-	pip install -r requirements.txt
+	uv pip install -r requirements.txt $(UV_FLAGS)
 
 install-dev:
-	pip install -r requirements-dev.txt
+	uv pip install -r requirements-dev.txt $(UV_FLAGS)
+
+setup-git-hooks:
+	@pre-commit install
 
 lint:
-	flake8 soil_id && isort -c soil_id && black --check soil_id
+	ruff check soil_id
+
+format:
+	ruff format soil_id
 
-lock: pip-tools
-	CUSTOM_COMPILE_COMMAND="make lock" pip-compile --upgrade --generate-hashes --strip-extras --resolver=backtracking --output-file requirements.txt requirements/base.in
+lock:
+	CUSTOM_COMPILE_COMMAND="make lock" uv pip compile --upgrade --generate-hashes requirements/base.in -o requirements.txt
 
-lock-dev: pip-tools
-	CUSTOM_COMPILE_COMMAND="make lock-dev" pip-compile --upgrade --generate-hashes --strip-extras --resolver=backtracking --output-file requirements-dev.txt requirements/dev.in
+lock-dev:
+	CUSTOM_COMPILE_COMMAND="make lock-dev" uv pip compile --upgrade --generate-hashes requirements/dev.in -o requirements-dev.txt
 
 build:
 	echo "Building TK..."
@@ -50,18 +54,12 @@ graphs:
 	gprof2dot -f pstats  prof/test_soil_location.prof | dot -Tsvg -o prof/test_soil_location.svg
 	flameprof prof/test_soil_location.prof > prof/test_soil_location_flame.svg
 
-generate_bulk_test_results_us:
+generate_bulk_test_results:
 	python -m soil_id.tests.us.generate_bulk_test_results
 
-process_bulk_test_results_us:
+process_bulk_test_results:
 	python -m soil_id.tests.us.process_bulk_test_results $(RESULTS_FILE)
 
-generate_bulk_test_results_global:
-	python -m soil_id.tests.global.generate_bulk_test_results
-
-process_bulk_test_results_global:
-	python -m soil_id.tests.global.process_bulk_test_results $(RESULTS_FILE)
-
 # Donwload Munsell CSV, SHX, SHP, SBX, SBN, PRJ, DBF
 download-soil-data:
 	mkdir -p Data
@@ -73,6 +71,3 @@ download-soil-data:
 	gdown 185Qjb9pJJn4AzOissiTz283tINrDqgI0; \
 	gdown 1P3xl1YRlfcMjfO_4PM39tkrrlL3hoLzv; \
 	gdown 1K0GkqxhZiVUND6yfFmaI7tYanLktekyp \
-
-${VIRTUAL_ENV}/scripts/pip-sync:
-	pip install pip-tools

README.md

@@ -1,5 +1,25 @@
 # Soil ID Algorithm
 
+## Requirements
+
+-   Python: 3.12 or better
+
+# Contributing
+
+Configure git to automatically lint your code and validate validate your commit messages:
+
+```sh
+$ make setup-git-hooks
+```
+
+Set up a virtual environment and install dependencies:
+
+```sh
+$ uv venv
+$ source .venv/bin/activate
+$ make install && make install-dev
+```
+
 ## explanation of algorithm
 
 ### terminology
@@ -63,8 +83,8 @@ There is a large suite of integration tests which takes many hours to run. It co
 
 ## Acknowledgements
 
-* Beaudette, D., Roudier, P., Brown, A. (2023). [aqp: Algorithms for Quantitative Pedology](https://CRAN.R-project.org/package=aqp). R package version 2.0.
- 
-* Beaudette, D.E., Roudier, P., O'Geen, A.T. [Algorithms for quantitative pedology: A toolkit for soil scientists, Computers & Geosciences](http://dx.doi.org/10.1016/j.cageo.2012.10.020), Volume 52, March 2013, Pages 258-268, ISSN 0098-3004.
- 
-* soilDB: Beaudette, D., Skovlin, J., Roecker, S., Brown, A. (2024). [soilDB: Soil Database Interface](https://CRAN.R-project.org/package=soilDB). R package version 2.8.3.
+-   Beaudette, D., Roudier, P., Brown, A. (2023). [aqp: Algorithms for Quantitative Pedology](https://CRAN.R-project.org/package=aqp). R package version 2.0.
+
+-   Beaudette, D.E., Roudier, P., O'Geen, A.T. [Algorithms for quantitative pedology: A toolkit for soil scientists, Computers & Geosciences](http://dx.doi.org/10.1016/j.cageo.2012.10.020), Volume 52, March 2013, Pages 258-268, ISSN 0098-3004.
+
+-   soilDB: Beaudette, D., Skovlin, J., Roecker, S., Brown, A. (2024). [soilDB: Soil Database Interface](https://CRAN.R-project.org/package=soilDB). R package version 2.8.3.

pyproject.toml

@@ -9,12 +9,15 @@ authors = [
 ]
 dynamic = ["version", "description", "classifiers", "dependencies"]
 
-[tool.black]
+[tool.ruff]
+exclude = ["migrations"]
 line-length = 100
 
-[tool.isort]
-profile = "black"
-known_first_party = "soil_id"
+[tool.ruff.lint.isort]
+known-first-party = ["soil_id"]
+
+[tool.ruff.lint]
+extend-ignore = ["E203"]
 
 [tool.pytest.ini_options]
 log_cli = true