[WIP] Inplement linting with Ruff

.pre-commit-config.yaml

@@ -30,58 +30,39 @@ repos:
           hooks:
                 - id: absolufy-imports
 
-        # Format the code aggressively using black
-        - repo: https://github.com/psf/black
-          rev: 24.10.0
+        # Ruff linter and code formatter
+        - repo: https://github.com/astral-sh/ruff-pre-commit
+          # Ruff version.
+          rev: v0.8.6
           hooks:
-                  - id: black
-                    args: [--line-length=120]
+            # Run the linter.
+            - id: ruff
+            # Run the formatter.
+            - id: ruff-format
 
-        # Lint the code using flake8
-        - repo: https://github.com/pycqa/flake8
-          rev: 7.1.1
+        # Enable lint fixes with ruff
+        - repo: https://github.com/astral-sh/ruff-pre-commit
+          # Ruff version.
+          rev: v0.8.6
           hooks:
-                - id: flake8
-                  # More than one argument in the second list, so need to pass arguments as below (and -- to finish)
-                  args: [
-                          '--max-line-length', '120',  # we can write dicts however we want
-                          '--extend-ignore', 'E203,C408,B028', # flake8 disagrees with black, so this should be ignored.
-                          '--'
-                  ]
-                  additional_dependencies:
-                          - flake8-comprehensions
-                          - flake8-bugbear
-                  files: ^(xdem|tests)
-
-        # Lint the code using mypy
-        - repo: https://github.com/pre-commit/mirrors-mypy
-          rev: v1.13.0
-          hooks:
-                - id: mypy
-                  args: [
-                        --config-file=mypy.ini,
-                        --strict,
-                        --implicit-optional,
-                        --ignore-missing-imports,  # Don't warn about stubs since pre-commit runs in a limited env
-                        --allow-untyped-calls,  # Dynamic function/method calls are okay. Untyped function definitions are not okay.
-                        --show-error-codes,
-                        --no-warn-unused-ignores,  # Ignore 'type: ignore' comments that are not used.
-                        --disable-error-code=attr-defined,  # "Module has no attribute 'XXX'" occurs because of the pre-commit env.
-                        --disable-error-code=name-defined,  # "Name 'XXX' is not defined" occurs because of the pre-commit env.
-                        --disable-error-code=var-annotated,
-                        --disable-error-code=no-any-return
-
-                  ]
-                  additional_dependencies: [tokenize-rt==3.2.0, numpy==1.26]
-                  files: ^(xdem|tests|doc/code)
-
+            # Run the linter.
+            - id: ruff
+              args: [ --fix ]
+            # Run the formatter.
+            - id: ruff-format
 
-        # Sort imports using isort
-        - repo: https://github.com/PyCQA/isort
-          rev: 5.13.2
+        # To run ruff over Jupyter Notebooks
+        - repo: https://github.com/astral-sh/ruff-pre-commit
+          # Ruff version.
+          rev: v0.8.6
           hooks:
-                  - id: isort
-                    args: ["--profile", "black"]
+            # Run the linter.
+            - id: ruff
+              types_or: [ python, pyi, jupyter ]
+              args: [ --fix ]
+            # Run the formatter.
+            - id: ruff-format
+              types_or: [ python, pyi, jupyter ]
 
         # Automatically upgrade syntax to a minimum version
         - repo: https://github.com/asottile/pyupgrade

.ruff.toml

@@ -0,0 +1,83 @@
+# Exclude a variety of commonly ignored directories.
+exclude = ["ALL"]
+
+extend-exclude = [
+    ".github",
+    "binder",
+    "doc",
+    "xdem.egg-info",
+    ".coveragerc",
+    ".gitignore",
+    ".pre-commit-config.yaml",
+    ".readthedocs.yaml",
+    ".relint.yml",
+]
+
+# Support Python 3.10+.
+target-version = "py310"
+
+# Same as Black.
+# The formatter wraps lines at a length of 120 when enforcing long-lines violations (like E501).
+line-length = 120
+# Number of spaces per tabulation, used by the formatter and when enforcing long-line violations.
+indent-width = 4
+
+[lint.pycodestyle]
+# E501 reports lines that exceed the length of 120.
+max-line-length = 120
+
+[lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default (10).
+select = ["ALL"]
+
+# Skip To do format annotations rules (FIX002, TD002, TD003)
+# Skip pydocstyle rules (D101, D205, D400, D401, D415)
+# Skip flake8-simplify rules (SIM102, SIM108, SIM115)
+# Skip pygrep-hooks rules (PGH003, PGH004)
+# Skip pylint refactor rules (PLR0912, PLR0913, PLR0915, PLR2004)
+# Skip the use of assert (S101)
+# Skip flake8-type-checking rules (TC001, TC002, TC003)
+# Skip tryceratops rules (TRY003, TRY201)
+# Skip pyupgrade rule : non-pep604-isinstance (UP038)
+# ...
+ignore = ["ANN401", "ARG002", "B028", "B904", "BLE001", "C901", "D101", "D205", "D400", "D401", "D415", "EM101",
+          "EM102", "ERA001", "F541", "FBT001", "FBT002", "FBT003", "FIX002", "INP001", "PD011", "PGH003", "PGH004",
+          "PLR0912", "PLR0913", "PLR0915", "PLR2004", "PLW0127", "PT011", "PTH118", "PYI041", "PYI051", "RET504",
+          "S101", "SIM102", "SIM108", "SIM115", "T201", "TC001", "TC002", "TC003", "TD002", "TD003", "TRY003",
+          "TRY201", "UP038"]
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+# Enable auto-formatting of code examples in docstrings. Markdown,
+# reStructuredText code/literal blocks and doctests are all supported.
+#
+# This is currently disabled by default, but it is planned for this
+# to be opt-out in the future.
+docstring-code-format = false
+
+# Set the line length limit used when formatting code snippets in
+# docstrings.
+#
+# This only has an effect when the `docstring-code-format` setting is
+# enabled.
+docstring-code-line-length = "dynamic"

Makefile

@@ -82,6 +82,26 @@ test: ## run tests
 		${VENV}/bin/pytest; \
 	fi
 
+## Code quality, linting section
+
+.PHONY: lint
+lint: ruff	## Apply the ruff linter.
+
+.PHONY: lint-check
+lint-check:  ## Check whether the codebase satisfies the linter rules.
+	@echo
+	@echo "Checking linter rules..."
+	@echo "========================"
+	@echo
+	@ruff check $(PATH)
+
+.PHONY: ruff
+ruff: ## Apply ruff.
+	@echo "Applying ruff..."
+	@echo "================"
+	@echo
+	@ruff --fix $(PATH)
+
 ## Clean section
 
 .PHONY: clean

examples/__init__.py

@@ -0,0 +1,18 @@
+# Copyright (c) 2024 Centre National d'Etudes Spatiales (CNES).
+#
+# This file is part of the xDEM project:
+# https://github.com/glaciohack/xdem
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+#
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""xDEM examples module init file."""

examples/advanced/__init__.py

@@ -0,0 +1,18 @@
+# Copyright (c) 2024 Centre National d'Etudes Spatiales (CNES).
+#
+# This file is part of the xDEM project:
+# https://github.com/glaciohack/xdem
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+#
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" """ # noqa

examples/advanced/plot_blockwise_coreg.py

@@ -1,11 +1,12 @@
-"""
-Blockwise coregistration
+"""Blockwise coregistration
 ========================
 
 Often, biases are spatially variable, and a "global" shift may not be enough to coregister a DEM properly.
-In the :ref:`sphx_glr_basic_examples_plot_nuth_kaab.py` example, we saw that the method improved the alignment significantly, but there were still possibly nonlinear artefacts in the result.
+In the :ref:`sphx_glr_basic_examples_plot_nuth_kaab.py` example, we saw that the method improved the alignment
+significantly, but there were still possibly nonlinear artefacts in the result.
 Clearly, nonlinear coregistration approaches are needed.
-One solution is :class:`xdem.coreg.BlockwiseCoreg`, a helper to run any ``Coreg`` class over an arbitrarily small grid, and then "puppet warp" the DEM to fit the reference best.
+One solution is :class:`xdem.coreg.BlockwiseCoreg`, a helper to run any ``Coreg`` class over an arbitrarily small grid,
+and then "puppet warp" the DEM to fit the reference best.
 
 The ``BlockwiseCoreg`` class runs in five steps:
 
@@ -43,7 +44,8 @@
 ]
 
 # %%
-# The DEM to be aligned (a 1990 photogrammetry-derived DEM) has some vertical and horizontal biases that we want to avoid, as well as possible nonlinear distortions.
+# The DEM to be aligned (a 1990 photogrammetry-derived DEM) has some vertical and horizontal biases that we want to
+# avoid, as well as possible nonlinear distortions.
 # The product is a mosaic of multiple DEMs, so "seams" may exist in the data.
 # These can be visualized by plotting a change map:
 
@@ -75,11 +77,12 @@
 
 # %%
 # The estimated shifts can be visualized by applying the coregistration to a completely flat surface.
-# This shows the estimated shifts that would be applied in elevation; additional horizontal shifts will also be applied if the method supports it.
+# This shows the estimated shifts that would be applied in elevation; additional horizontal shifts will also be applied
+# if the method supports it.
 # The :func:`xdem.coreg.BlockwiseCoreg.stats` method can be used to annotate each block with its associated Z shift.
 
 z_correction = blockwise.apply(
-    np.zeros_like(dem_to_be_aligned.data), transform=dem_to_be_aligned.transform, crs=dem_to_be_aligned.crs
+    np.zeros_like(dem_to_be_aligned.data), transform=dem_to_be_aligned.transform, crs=dem_to_be_aligned.crs,
 )[0]
 plt.title("Vertical correction")
 plt.imshow(z_correction, cmap="RdYlBu", vmin=-10, vmax=10, extent=plt_extent)

examples/advanced/plot_demcollection.py

@@ -1,16 +1,17 @@
-"""
-Working with a collection of DEMs
+"""Working with a collection of DEMs
 =================================
 
 .. caution:: This functionality might be removed in future package versions.
 
 Oftentimes, more than two timestamps (DEMs) are analyzed simultaneously.
 One single dDEM only captures one interval, so multiple dDEMs have to be created.
-In addition, if multiple masking polygons exist (e.g. glacier outlines from multiple years), these should be accounted for properly.
-The :class:`xdem.DEMCollection` is a tool to properly work with multiple timestamps at the same time, and makes calculations of elevation/volume change over multiple years easy.
+In addition, if multiple masking polygons exist (e.g. glacier outlines from multiple years),
+these should be accounted for properly.
+The :class:`xdem.DEMCollection` is a tool to properly work with multiple timestamps at the same time, and makes
+calculations of elevation/volume change over multiple years easy.
 """
 
-from datetime import datetime
+from datetime import datetime, timezone
 
 import geoutils as gu
 import matplotlib.pyplot as plt
@@ -32,8 +33,12 @@
 # These parts can be delineated with masks or polygons.
 # Here, we have glacier outlines from 1990 and 2009.
 outlines = {
-    datetime(1990, 8, 1): gu.Vector(xdem.examples.get_path("longyearbyen_glacier_outlines")),
-    datetime(2009, 8, 1): gu.Vector(xdem.examples.get_path("longyearbyen_glacier_outlines_2010")),
+    datetime(1990, 8, 1, tzinfo=timezone.utc): gu.Vector(
+        xdem.examples.get_path("longyearbyen_glacier_outlines"),
+    ),
+    datetime(2009, 8, 1, tzinfo=timezone.utc): gu.Vector(
+        xdem.examples.get_path("longyearbyen_glacier_outlines_2010"),
+    ),
 }
 
 # %%
@@ -42,7 +47,9 @@
 # Fake a 2060 DEM by assuming twice the change from 1990-2009 between 2009 and 2060
 dem_2060 = dem_2009 + (dem_2009 - dem_1990).data * 3
 
-timestamps = [datetime(1990, 8, 1), datetime(2009, 8, 1), datetime(2060, 8, 1)]
+timestamps = [datetime(1990, 8, 1, tzinfo=timezone.utc),
+              datetime(2009, 8, 1, tzinfo=timezone.utc),
+              datetime(2060, 8, 1, tzinfo=timezone.utc)]
 
 # %%
 # Now, all data are ready to be collected in an :class:`xdem.DEMCollection` object.
@@ -52,7 +59,7 @@
 #
 
 demcollection = xdem.DEMCollection(
-    dems=[dem_1990, dem_2009, dem_2060], timestamps=timestamps, outlines=outlines, reference_dem=1
+    dems=[dem_1990, dem_2009, dem_2060], timestamps=timestamps, outlines=outlines, reference_dem=1,
 )
 
 # %%
@@ -69,9 +76,11 @@
 # These are saved internally, but are also returned as a list.
 #
 # An elevation or volume change series can automatically be generated from the ``DEMCollection``.
-# In this case, we should specify *which* glacier we want the change for, as a regional value may not always be required.
+# In this case, we should specify *which* glacier we want the change for,
+# as a regional value may not always be required.
 # We can look at the glacier called "Scott Turnerbreen", specified in the "NAME" column of the outline data.
-# `See here for the outline filtering syntax <https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html>`_.
+# `See here for the outline filtering syntax
+# <https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html>`_.
 
 demcollection.get_cumulative_series(kind="dh", outlines_filter="NAME == 'Scott Turnerbreen'")
 

examples/advanced/plot_deramp.py

@@ -1,5 +1,4 @@
-"""
-Bias-correction with deramping
+"""Bias-correction with deramping
 ==============================
 
 Deramping can help correct rotational or doming errors in elevation data.