Add and Run precommit hooks

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 119

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+repos:
+  - repo: https://github.com/ambv/black
+    rev: 23.12.0
+    hooks:
+      - id: black
+        language_version: python3.11
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+    -   id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort (python)
+        args: ["--profile", "black"]

Makefile

@@ -6,41 +6,58 @@
 .ONESHELL:
 SHELL = /bin/bash
 
-deploy: check
-	twine upload dist/*
 
-check: dist/ign-pdal-tool*.tar.gz
-	twine check dist/*
+##############################
+# Install
+##############################
 
-dist/ign-pdal-tool*.tar.gz:
-	python -m build
+mamba-env-create:
+	mamba env create -n pdaltools -f environment.yml
 
-build: clean
-	python -m build
+mamba-env-update:
+	mamba env update -n pdaltools -f environment.yml
 
 install:
 	pip install -e .
 
+
+##############################
+# Dev/Contrib tools
+##############################
+
 testing:
 	python -m pytest ./test -s --log-cli-level DEBUG -m "not geoportail"
 
 testing_full:
 	python -m pytest ./test -s --log-cli-level DEBUG
 
+install-precommit:
+	pre-commit install
+
+
+##############################
+# Build/deploy pip lib
+##############################
+
+deploy: check
+	twine upload dist/*
+
+check: dist/ign-pdal-tool*.tar.gz
+	twine check dist/*
+
+dist/ign-pdal-tool*.tar.gz:
+	python -m build
+
+build: clean
+	python -m build
+
 clean:
 	rm -rf tmp
 	rm -rf ign_pdal_tools.egg-info
 	rm -rf dist
 
-mamba-env-create:
-	mamba env create -n pdaltools -f environment.yml
-
-mamba-env-update:
-	mamba env update -n pdaltools -f environment.yml
-
-
 ##############################
-# Docker
+# Build/deploy Docker image
 ##############################
 
 PROJECT_NAME=ignimagelidar/ign-pdal-tools

README.md

@@ -62,18 +62,20 @@ Every time the code is changed, think of updating the version file: [pdaltools/_
 
 Please log your changes in [CHANGELOG.md](CHANGELOG.md)
 
+Before committing your changes, run the precommit hooks. They can be installed to run automatically with `make install-precommit`
+
 ## Tests
 
-Create the conda environment: `./script/createCondaEnv.sh`
+Create the conda environment: `make mamba-env-create`
 
-Run unit tests: `./script/test.sh`
+Run unit tests: `make testing`
 
 ## Pip package
 
 To generate a pip package and deploy it on pypi, use the [Makefile](Makefile) at the root of the repo:
 
 * `make build`: build the library
-* `make install`: instal the library in an editable way (`pip -e`)
+* `make install`: install the library in an editable way (`pip -e`)
 * `make deploy` : deploy it on pypi
 
 ## Docker image

pdaltools/count_occurences/count_occurences_for_attribute.py

@@ -40,7 +40,7 @@ def compute_count_one_file(filepath: str, attribute: str = "Classification") ->
         # Try to prettify the value by converting it to an integer (eg. for Classification that
         # returns values such as 1.0000 instead of 1 or 1.)
         counts = Counter({str(int(float(value))): int(count) for value, count in split_counts})
-    except ValueError as e:
+    except ValueError:
         # in case value is not a number, float(value) returns a ValueError
         # fallback: use the raw value
         counts = Counter({value: int(count) for value, count in split_counts})

pdaltools/las_info.py

@@ -65,7 +65,7 @@ def las_info_pipeline(filename: str, spatial_ref: str = "EPSG:2154"):
     # Extract metadata
     metadata = pipeline.metadata
 
-    if type(metadata) == str:
+    if isinstance(metadata, str):
         metadata = json.loads(metadata)
 
     return metadata["metadata"]["filters.info"]
@@ -94,10 +94,10 @@ def las_get_xy_bounds(filename: str, buffer_width: int = 0, spatial_ref: str = "
         metadata = las_info_metadata(filename)
         bounds_dict = metadata["bounds"]
 
-    except RuntimeError as e:
+    except RuntimeError:
         metadata = las_info_pipeline(filename, spatial_ref)
         bounds_dict = metadata["bbox"]
-    if type(metadata) == str:
+    if isinstance(metadata, str):
         metadata = json.loads(metadata)
     # Export bound (maxy, maxy, minx and miny), then creating a buffer with 100 m
     _x.append(float((bounds_dict["minx"]) - buffer_width))  # coordinate minX

test/count_occurences/test_count_occurences_for_attribute.py

@@ -4,10 +4,7 @@
 import shutil
 from collections import Counter
 
-import pytest
-
-from pdaltools.count_occurences.count_occurences_for_attribute import \
-    compute_count
+from pdaltools.count_occurences.count_occurences_for_attribute import compute_count
 
 test_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))  # File is in subdirectory
 tmp_path = os.path.join(test_path, "tmp")
@@ -51,7 +48,7 @@ def test_count_by_attribute_values_with_json():
 
 
 def test_count_by_attribute_values_one_file():
-    count = compute_count([single_input_file], attribute, output_file)
+    compute_count([single_input_file], attribute, output_file)
     with open(counts_single_json, "r") as f:
         expected = Counter(json.load(f))
     with open(output_file, "r") as f:

test/count_occurences/test_merge_occurences_counts.py

@@ -3,8 +3,6 @@
 import shutil
 from collections import Counter
 
-import pytest
-
 from pdaltools.count_occurences.merge_occurences_counts import merge_counts
 
 test_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))  # File is in subdirectory

test/test_las_add_buffer.py

@@ -4,7 +4,6 @@
 
 import laspy
 import numpy as np
-import pytest
 
 from pdaltools.las_add_buffer import create_las_with_buffer
 
@@ -35,7 +34,7 @@ def setup_module(module):
     os.mkdir(tmp_path)
 
 
-## Utils functions
+# Utils functions
 def get_nb_points(path):
     """Get number of points in a las file"""
     with laspy.open(path) as f:
@@ -53,7 +52,7 @@ def get_2d_bounding_box(path):
     return mins[:2], maxs[:2]
 
 
-## Tests
+# Tests
 def test_create_las_with_buffer():
     buffer_width = 10
     create_las_with_buffer(

test/test_las_clip.py

@@ -4,7 +4,6 @@
 
 import laspy
 import numpy as np
-import pytest
 
 from pdaltools.las_clip import las_crop
 
@@ -34,7 +33,7 @@ def setup_module(module):
     os.mkdir(tmp_path)
 
 
-## Utils functions
+# Utils functions
 def get_nb_points(path):
     """Get number of points in a las file"""
     with laspy.open(path) as f:
@@ -52,7 +51,7 @@ def get_2d_bounding_box(path):
     return mins[:2], maxs[:2]
 
 
-## Tests
+# Tests
 def test_las_crop():
     bounds = ([expected_out_mins[0], expected_out_maxs[0]], [expected_out_mins[1], expected_out_maxs[1]])
     las_crop(input_file, output_file, bounds)

test/test_las_merge.py

@@ -1,10 +1,8 @@
 import logging
 import os
-import shutil
 
 import laspy
 import numpy as np
-import pytest
 
 from pdaltools.las_merge import las_merge
 
@@ -34,7 +32,7 @@
 #     os.mkdir(tmp_path)
 
 
-## Utils functions
+# Utils functions
 def get_nb_points(path):
     """Get number of points in a las file"""
     with laspy.open(path) as f:
@@ -52,7 +50,7 @@ def get_2d_bounding_box(path):
     return mins[:2], maxs[:2]
 
 
-## Tests
+# Tests
 def test_las_merge():
     las_merge(input_dir, input_file, output_file, tile_width=tile_width, tile_coord_scale=tile_coord_scale)
 

test/test_replace_attribute_in_las.py

@@ -8,11 +8,14 @@
 
 import pytest
 
-from pdaltools.count_occurences.count_occurences_for_attribute import \
-    compute_count_one_file
+from pdaltools.count_occurences.count_occurences_for_attribute import (
+    compute_count_one_file,
+)
 from pdaltools.replace_attribute_in_las import (
-    parse_replacement_map_from_path_or_json_string, replace_values,
-    replace_values_clean)
+    parse_replacement_map_from_path_or_json_string,
+    replace_values,
+    replace_values_clean,
+)
 from pdaltools.standardize_format import get_writer_parameters
 
 test_path = os.path.dirname(os.path.abspath(__file__))

test/test_standardize_format.py

@@ -7,8 +7,7 @@
 import pdal
 import pytest
 
-from pdaltools.standardize_format import (exec_las2las, rewrite_with_pdal,
-                                          standardize)
+from pdaltools.standardize_format import exec_las2las, rewrite_with_pdal, standardize
 
 # Note: tile 77050_627760 is cropped to simulate missing data in neighbors during merge
 test_path = os.path.dirname(os.path.abspath(__file__))
@@ -46,7 +45,7 @@ def _test_standardize_format_one_params_set(params):
         metadata = json_info["summary"]["metadata"][1]
     else:
         metadata = json_info["summary"]["metadata"]
-    assert metadata["compressed"] == True
+    assert metadata["compressed"] is True
     assert metadata["minor_version"] == 4
     assert metadata["global_encoding"] == 17
     assert metadata["dataformat_id"] == params["dataformat_id"]
@@ -90,7 +89,9 @@ def test_exec_las2las_error():
 
 def test_standardize_does_NOT_produce_any_warning_with_Lasinfo():
     # bad file on the store (44 Mo)
-    # input_file = "/var/data/store-lidarhd/developpement/standaLAS/demo_standardization/Semis_2022_0584_6880_LA93_IGN69.laz"
+    # input_file = (
+    #     "/var/data/store-lidarhd/developpement/standaLAS/demo_standardization/Semis_2022_0584_6880_LA93_IGN69.laz"
+    # )
 
     input_file = os.path.join(test_path, "data/classified_laz/test_data_77050_627755_LA93_IGN69.laz")
     output_file = os.path.join(tmp_path, "test_standardize_produce_no_warning_with_lasinfo.las")