Replace black, flake8 and isort for Ruff (#572)

Remove unused packages in `requirements-style.txt`, `environment.yml`
and add Ruff to them. Update the `Makefile` targets. Remove `.flake8`.
Add Ruff configuration to `pyproject.toml`. Apply fixes to comply with
Ruff rules. Replace `l` and `m` loop vars for `i` and `j` in forward
modelling nested for loops. Minor fixes to a few error messages. Revert
"Ignore RST299 warning in tesseroid example (#571)" (commit
5471998). Remove mutable class
attributes in equivalent sources: remove mutable class attributes for
dispatching the predict and jacobian kernels depending on the choice for
parallelization; obtain the desired kernel as needed in the `predict`
and `jacobian` methods instead.

Author: santisoler

.flake8

@@ -7,7 +7,6 @@ prune paper
 prune tutorials
 exclude .*.yml
 exclude .*rc
-exclude .flake8
 exclude license_notice.py
 exclude Makefile
 exclude .gitignore

MANIFEST.in

@@ -13,13 +13,13 @@ help:
 	@echo ""
 	@echo "  install   install in editable mode"
 	@echo "  test      run the test suite (including doctests) and report coverage"
-	@echo "  format    run isort and black to automatically format the code"
-	@echo "  check     run code style and quality checks (black, isort and flake8)"
+	@echo "  format    run ruff to automatically format the code"
+	@echo "  check     run code style and quality checks (ruff and burocrata)"
 	@echo "  build     build source and wheel distributions"
 	@echo "  clean     clean up build and generated files"
 	@echo ""
 
-.PHONY: build, install, test, test_coverage, test_numba, format, check, black, black-check, isort, isort-check, license, license-check, flake8, clean
+.PHONY: build, install, test, test_coverage, test_numba, format, check, check-format, check-style, check-actions, clean
 
 build:
 	python -m build .
@@ -43,19 +43,18 @@ test_numba:
 	rm -rvf $(TESTDIR)
 
 format:
-	isort $(STYLE_CHECK_FILES)
-	black $(STYLE_CHECK_FILES)
+	ruff check --select I --fix $(STYLE_CHECK_FILES) # fix isort errors
+	ruff format $(STYLE_CHECK_FILES)
 	burocrata --extension=py $(STYLE_CHECK_FILES)
 
-check: check-format check-style
+check: check-format check-style check-actions
 
 check-format:
-	isort --check $(STYLE_CHECK_FILES)
-	black --check $(STYLE_CHECK_FILES)
-	burocrata --check --extension=py $(STYLE_CHECK_FILES)
+	ruff format --check $(STYLE_CHECK_STYLE)
+	burocrata --check --extension=py $(STYLE_CHECK_STYLE)
 
 check-style:
-	flake8 $(STYLE_CHECK_FILES)
+	ruff check $(STYLE_CHECK_FILES)
 
 check-actions:
 	zizmor $(GITHUB_ACTIONS)

Makefile

@@ -39,6 +39,7 @@
 shift beneath the median location obtained during the block-averaging process).
 The depth of the sources can be set through the ``depth`` parameter.
 """
+
 import ensaio
 import pandas as pd
 import pygmt

doc/gallery_src/equivalent_sources/block_averaged_sources.py

@@ -29,6 +29,7 @@
 least-squares fitting process. The main disadvantage is the increased
 computational load (both in terms of time and memory).
 """
+
 import ensaio
 import pandas as pd
 import pygmt

doc/gallery_src/equivalent_sources/cartesian.py

@@ -28,6 +28,7 @@
 to use them on a small example.
 
 """
+
 import boule as bl
 import ensaio
 import pandas as pd

doc/gallery_src/equivalent_sources/gradient_boosted.py

@@ -18,6 +18,7 @@
 equivalent sources (:class:`harmonica.EquivalentSources`) while taking into
 account the curvature of the Earth.
 """
+
 import boule as bl
 import ensaio
 import numpy as np

doc/gallery_src/equivalent_sources/spherical.py

@@ -18,6 +18,7 @@
 grid given in Cartesian coordinates using the
 :func:`harmonica.point_gravity` function.
 """
+
 import pygmt
 import verde as vd
 

doc/gallery_src/forward/point_gravity.py

@@ -21,6 +21,7 @@
 be used together with the :func:`harmonica.prism_gravity` to compute the
 gravitational effect of the layer.
 """
+
 import numpy as np
 import pygmt
 import verde as vd

doc/gallery_src/forward/prism_layer.py

@@ -18,6 +18,7 @@
 compute the gravity effect of the model on a regular grid of observation
 points.
 """
+
 import ensaio
 import pygmt
 import pyproj