Merge pull request #8 from cogeotiff/fixCLIandAddValue

fix CLI and value

.pre-commit-config.yaml

@@ -1,32 +1,34 @@
 repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.12.1
+    hooks:
+      - id: validate-pyproject
+
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 22.12.0
     hooks:
       - id: black
         language_version: python
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.4.2
+    rev: 5.12.0
     hooks:
       - id: isort
         language_version: python
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 3.8.3
-    hooks:
-      - id: flake8
-        language_version: python
-
-  - repo: https://github.com/PyCQA/pydocstyle
-    rev: 6.1.1
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.238
     hooks:
-      - id: pydocstyle
-        language_version: python
-        additional_dependencies:
-          - toml
+      - id: ruff
+        args: ["--fix"]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.812
+    rev: v0.991
     hooks:
       - id: mypy
         language_version: python
+        # No reason to run if only tests have changed. They intentionally break typing.
+        exclude: tests/.*
+        additional_dependencies:
+        - types-attrs
+        - types-cachetools

CHANGES.md

@@ -1,5 +1,11 @@
 # Release Notes
 
+## 0.2.1 (2023-04-13)
+
+* Fix issue with CLI path
+* add Alpha band value forwarding
+* add `--value` option to set a custom value in the data
+
 ## 0.2.0 (2022-10-25)
 
 * remove python 3.7 support

pyproject.toml

@@ -42,7 +42,7 @@ Source = "https://github.com/cogeotiff/rio-faux"
 Documentation = "https://cogeotiff.github.io/rio-faux/"
 
 [project.entry-points."rasterio.rio_plugins"]
-cogeo = "rio_faux.cli:faux"
+faux = "rio_faux.cli:faux"
 
 [build-system]
 requires = ["flit>=3.2,<4"]
@@ -62,16 +62,36 @@ exclude = [
     "mkdocs.yml",
 ]
 
+[tool.coverage.run]
+branch = true
+parallel = true
+
+[tool.coverage.report]
+exclude_lines = [
+  "no cov",
+  "if __name__ == .__main__.:",
+  "if TYPE_CHECKING:",
+]
+
 [tool.isort]
 profile = "black"
 known_first_party = ["rio_fake"]
 known_third_party = ["rasterio", "click"]
 default_section = "THIRDPARTY"
 
 [tool.mypy]
-no_strict_optional = "True"
-ignore_missing_imports = "True"
+no_strict_optional = true
 
-[tool.pydocstyle]
-select = "D1"
-match = "(?!test).*.py"
+[tool.ruff]
+select = [
+    "D1",  # pydocstyle errors
+    "E",  # pycodestyle errors
+    "W",  # pycodestyle warnings
+    "C",  # flake8-comprehensions
+    "B",  # flake8-bugbear
+]
+ignore = [
+    "E501",  # line too long, handled by black
+    "B008",  # do not perform function calls in argument defaults
+    "B905",  # ignore zip() without an explicit strict= parameter, only support with python >3.10
+]

rio_faux/cli.py

@@ -4,6 +4,7 @@
 import warnings
 
 import click
+import numpy
 import rasterio
 from rasterio.enums import ColorInterp, MaskFlags
 from rasterio.enums import Resampling as ResamplingEnums
@@ -27,6 +28,12 @@ def has_mask_band(src_dst):
 @click.command()
 @options.file_in_arg
 @options.file_out_arg
+@click.option(
+    "--value",
+    default=None,
+    type=float,
+    help="Set a custom value in the data.",
+)
 @click.option(
     "--forward-band-tags",
     default=False,
@@ -51,6 +58,7 @@ def has_mask_band(src_dst):
 def faux(
     input,
     output,
+    value,
     forward_band_tags,
     forward_dataset_tags,
     creation_options,
@@ -68,17 +76,20 @@ def faux(
             overview_blocksize = src_dst.profile.get("blockxsize", overview_blocksize)
 
     config.update(
-        dict(
-            GDAL_NUM_THREADS="ALL_CPUS",
-            GDAL_TIFF_INTERNAL_MASK=os.environ.get("GDAL_TIFF_INTERNAL_MASK", True),
-            GDAL_TIFF_OVR_BLOCKSIZE=str(overview_blocksize),
-        )
+        {
+            "GDAL_NUM_THREADS": "ALL_CPUS",
+            "GDAL_TIFF_INTERNAL_MASK": os.environ.get("GDAL_TIFF_INTERNAL_MASK", True),
+            "GDAL_TIFF_OVR_BLOCKSIZE": str(overview_blocksize),
+        }
     )
+
     with rasterio.Env(**config):
         with rasterio.open(input) as src_dst:
             meta = src_dst.meta
             with MemoryFile() as m:
                 with m.open(**meta) as tmp_dst:
+                    tmp_dst.colorinterp = src_dst.colorinterp
+
                     if tmp_dst.colorinterp[0] is ColorInterp.palette:
                         try:
                             tmp_dst.write_colormap(1, src_dst.colormap(1))
@@ -91,6 +102,22 @@ def faux(
                     if has_mask_band(src_dst):
                         tmp_dst.write_mask(src_dst.dataset_mask())
 
+                    if value:
+                        tmp_dst.write(
+                            numpy.full(
+                                (tmp_dst.count, tmp_dst.height, tmp_dst.width),
+                                value,
+                                dtype=tmp_dst.dtypes[0],
+                            ),
+                        )
+
+                    if ColorInterp.alpha in tmp_dst.colorinterp:
+                        alpha_bidx = src_dst.colorinterp.index(ColorInterp.alpha) + 1
+                        tmp_dst.write(
+                            src_dst.read(indexes=alpha_bidx),
+                            indexes=alpha_bidx,
+                        )
+
                     tags = src_dst.tags()
 
                     overview_resampling = tags.get(
@@ -118,7 +145,7 @@ def faux(
 
                     output_profile = src_dst.profile
                     output_profile.update(
-                        dict(BIGTIFF=os.environ.get("BIGTIFF", "IF_SAFER"))
+                        {"BIGTIFF": os.environ.get("BIGTIFF", "IF_SAFER")}
                     )
                     if creation_options:
                         output_profile.update(creation_options)

tests/test_cli.py

@@ -3,6 +3,7 @@
 import math
 import os
 
+import numpy
 import pytest
 import rasterio
 from click.testing import CliRunner
@@ -85,3 +86,62 @@ def test_tags():
             assert src_dst.tags() == faux_dst.tags()
             assert src_dst.descriptions == faux_dst.descriptions
             assert src_dst.tags(0) == faux_dst.tags(0)
+
+
+def test_alpha():
+    """Check if alpha forwarded."""
+    runner = CliRunner()
+    src_path = os.path.join(os.path.dirname(__file__), "fixtures", "image_rgba.tif")
+    with runner.isolated_filesystem():
+        result = runner.invoke(faux, [src_path, "output.tif"])
+        assert not result.exception
+        assert result.exit_code == 0
+        with rasterio.open(src_path) as src_dst, rasterio.open(
+            "output.tif"
+        ) as faux_dst:
+            assert src_dst.colorinterp == faux_dst.colorinterp
+            numpy.testing.assert_array_equal(
+                src_dst.read(indexes=4), faux_dst.read(indexes=4)
+            )
+
+
+def test_mask():
+    """Check if alpha forwarded."""
+    runner = CliRunner()
+    src_path = os.path.join(os.path.dirname(__file__), "fixtures", "image_rgb_mask.tif")
+    with runner.isolated_filesystem():
+        result = runner.invoke(faux, [src_path, "output.tif"])
+        assert not result.exception
+        assert result.exit_code == 0
+        with rasterio.open(src_path) as src_dst, rasterio.open(
+            "output.tif"
+        ) as faux_dst:
+            assert src_dst.mask_flag_enums == faux_dst.mask_flag_enums
+            numpy.testing.assert_array_equal(
+                src_dst.dataset_mask(), faux_dst.dataset_mask()
+            )
+
+
+def test_value():
+    """Check value."""
+    runner = CliRunner()
+    src_path = os.path.join(os.path.dirname(__file__), "fixtures", "image_rgba.tif")
+    with runner.isolated_filesystem():
+        result = runner.invoke(faux, [src_path, "output.tif", "--value", 100])
+        assert not result.exception
+        assert result.exit_code == 0
+        with rasterio.open(src_path) as src_dst, rasterio.open(
+            "output.tif"
+        ) as faux_dst:
+
+            assert numpy.unique(faux_dst.read(indexes=1)) == 100
+
+        # Check that we are casting values to the output data type
+        result = runner.invoke(faux, [src_path, "output.tif", "--value", 100.3])
+        assert not result.exception
+        assert result.exit_code == 0
+        with rasterio.open(src_path) as src_dst, rasterio.open(
+            "output.tif"
+        ) as faux_dst:
+
+            assert numpy.unique(faux_dst.read(indexes=1)) == 100