🔖 Release 0.6.1 (#43)

* 🐛 Fix Writing MPP To NGFF v0.4 Zarr (#37)

* 🐛 Change CoordinateTransform Order To YXC (#41)

* 🐛 Fix Reading TIFF Resolution Tag

* 🐛 Minor Bug Fixes (#40)

* 🐛 Ensure cv2 Arg Is an int Tuple

* ✨ Add TIFF Writer For CLI Based On Ext

* 🐛 Add Missing **kwargs

* 🚸 Change TIFFWriter OME Default To False

* ✏️ Typo Fix transcribed -> transcoded

* ♻️ Move CLI Tests To Seperate Module

* 🐛 Fix Typo in Class For Transcoding From DICOM

* ✅ Add CLI Tests

* 🔧 Add release Branch To Workflows

* 🔖 Bump version: 0.5.1 → 0.6.1

* 🔧 Set Tag To False In bump2version Config

* ♻️ Rename Module To Avoid Shadowing

* 📝 Update History

* 📝 Reverse History Ordering

.github/workflows/python-app.yml

@@ -5,10 +5,10 @@ name: Python application
 
 on:
   push:
-    branches: [ dev, main ]
+    branches: [ dev, main, release ]
     tags: v*
   pull_request:
-    branches: [ dev, main ]
+    branches: [ dev, main, release ]
 
 permissions:
   contents: read

HISTORY.md

@@ -1,9 +1,60 @@
 # History
 
-## 0.1.0 (2022-02-22)
+## 0.6.1 (2022-10-21)
 
-- First release on PyPI.
+- Select Writer class based on file extension from CLI.
+- Bug fixes:
+  - Fix writing MPP to NGFF v0.4.
+  - Change coordinate transformation ordering.
+  - Fix reading TIFF resolution tag. Previously only the numerator of
+    the resolution fraction was being read.
+  - Other minor bug fixes.
+
+## 0.6.0 (2022-10-03)
+
+- Add ability to write resolution metadata to JP2. Thanks to
+  @quintusdias for helping get this implemented in glymur.
+- Remove QOI codec code as this is not included in imagecodes. Thanks to
+  Christoph Gohlke for adding this.
+- Add a "How do I?" documentation page.
+
+## 0.5.1 (2022-06-27)
+
+- Bug fixes:
+  - Fix parsing of OpenSlide MPP to float.
+
+## 0.5.0 (2022-06-25)
+
+- Add ability to transcode/repackage to a TIFF file (from DICOM or SVS).
+- Refactor `ZarrReaderWriter` to seperate `ZarrWriter` and `ZarrReader`.
+- Bug fixes:
+  - Fix thumbnaiul generation for zarr.
+  - Fix NGFF metadata `CoordinateTransformation` field default factor.
+
+## 0.4.0 (2022-06-20)
+
+- Add ability to write JPEG compressed SVS files.
+- Add support for thumbnail generation and a CLI command.
+- Swap from strings to enums for codecs and color spaces.
+
+## 0.3.0 (2022-05-13)
+
+- Remove unused CLI debug option.
+- Add generation of OME-NGFF metadata (JSON .zattrs file).
+- Add timeout when copying tiles to prevent indefinite hanging.
+- Improve joining/termination of child processes at shutdown.
+- Use the TIFF resolution tag if present.
+- Add `get_tile` method to all `Reader` classes.
+- Update supported Python versions to 3.8, 3.9, 3.10.
+- Bug fixes:
+  - Fix and issue with concatenation of pyramid downsamples.
+  - Add a custom Queue class for multiprocessing on macOS.
+  - Fix handling of `pyramid_downsamples` argument when `None`.
 
 ## 0.2.0 (2022-03-22)
 
 - Add Support To Read DICOM WSI and transform to zarr.
+
+## 0.1.0 (2022-02-22)
+
+- First release on PyPI.

setup.cfg

@@ -1,9 +1,9 @@
 [bumpversion]
-current_version = 0.6.0
+current_version = 0.6.1
 message = :bookmark: Bump version: {current_version} → {new_version}
 tag_message = :bookmark: Bump version: {current_version} → {new_version}
 commit = True
-tag = True
+tag = False
 
 [bumpversion:file:setup.py]
 search = version="{current_version}"

setup.py

@@ -106,6 +106,6 @@
     tests_require=test_requirements,
     extras_require=extra_requirements,
     url="https://github.com/john-p/wsic",
-    version="0.6.0",
+    version="0.6.1",
     zip_safe=False,
 )

tests/test_cli.py

@@ -0,0 +1,182 @@
+import sys
+import warnings
+from pathlib import Path
+
+import pytest
+from click.testing import CliRunner
+
+from wsic import cli
+
+
+def test_convert_timeout(samples_path, tmp_path):
+    """Check that CLI convert raises IOError when reading times out."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "XYC.jp2")
+        out_path = str(Path(td) / "XYC.tiff")
+        warnings.simplefilter("ignore")
+        with pytest.raises(IOError, match="timed out"):
+            runner.invoke(
+                cli.convert,
+                ["-i", in_path, "-o", out_path, "--timeout", "0"],
+                catch_exceptions=False,
+            )
+
+
+def test_thumbnail(samples_path, tmp_path):
+    """Check that CLI thumbnail works."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = samples_path / "XYC.jp2"
+        out_path = Path(td) / "XYC.jpeg"
+        runner.invoke(
+            cli.thumbnail,
+            ["-i", str(in_path), "-o", str(out_path), "-s", "512", "512"],
+            catch_exceptions=False,
+        )
+        assert out_path.exists()
+        assert out_path.is_file()
+        assert out_path.stat().st_size > 0
+
+
+def test_thumbnail_downsample(samples_path, tmp_path):
+    """Check that CLI thumbnail works with downsample option."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = samples_path / "XYC.jp2"
+        out_path = Path(td) / "XYC.jpeg"
+        result = runner.invoke(
+            cli.thumbnail,
+            ["-i", str(in_path), "-o", str(out_path), "-d", "16"],
+            catch_exceptions=False,
+        )
+        assert result.exit_code == 0
+        assert out_path.exists()
+        assert out_path.is_file()
+        assert out_path.stat().st_size > 0
+
+
+def test_thumbnail_no_cv2(samples_path, tmp_path, monkeypatch):
+    """Check that CLI thumbnail works without OpenCV (cv2)."""
+    monkeypatch.setitem(sys.modules, "cv2", None)
+    with pytest.raises(ImportError):
+        import cv2  # noqa # skipcq
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = samples_path / "XYC.jp2"
+        out_path = Path(td) / "XYC.jpeg"
+        runner.invoke(
+            cli.thumbnail,
+            ["-i", str(in_path), "-o", str(out_path), "-s", "512", "512"],
+            catch_exceptions=False,
+        )
+        assert out_path.exists()
+        assert out_path.is_file()
+        assert out_path.stat().st_size > 0
+
+
+def test_help():
+    """Test the help output."""
+    runner = CliRunner()
+    help_result = runner.invoke(cli.main, ["--help"])
+    assert help_result.exit_code == 0
+    assert "Console script for wsic." in help_result.output
+
+
+def test_transcode_svs_to_zarr(samples_path, tmp_path):
+    """Test the CLI for transcoding SVS to zarr."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "CMU-1-Small-Region.svs")
+        out_path = str(Path(td) / "CMU-1-Small-Region.zarr")
+        result = runner.invoke(
+            cli.transcode,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 0
+
+
+def test_transcode_svs_to_tiff(samples_path, tmp_path):
+    """Test the CLI for transcoding SVS to (tiled) TIFF."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "CMU-1-Small-Region.svs")
+        out_path = str(Path(td) / "CMU-1-Small-Region.tiff")
+        result = runner.invoke(
+            cli.transcode,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 0
+
+
+def test_transcode_dicom_to_tiff(samples_path, tmp_path):
+    """Test the CLI for transcoding DICOM to (tiled) TIFF."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "CMU-1-Small-Region")
+        out_path = str(Path(td) / "CMU-1-Small-Region.tiff")
+        result = runner.invoke(
+            cli.transcode,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 0
+
+
+def test_convert_jp2_to_tiff(samples_path, tmp_path):
+    """Test the CLI for converting JP2 to tiled TIFF."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "XYC.jp2")
+        out_path = str(Path(td) / "XYC.tiff")
+        result = runner.invoke(
+            cli.convert,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 0
+
+
+def test_convert_jp2_to_zarr(samples_path, tmp_path):
+    """Test the CLI for converting JP2 to zarr."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "XYC.jp2")
+        out_path = str(Path(td) / "XYC.zarr")
+        result = runner.invoke(
+            cli.convert,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 0
+
+
+def test_transcode_bad_input_file_ext(samples_path, tmp_path):
+    """Test the CLI for transcoding with a bad input file extension."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        # in_path must exists but not be a valid input
+        in_path = str(samples_path / "XYC.jp2")
+        out_path = str(Path(td) / "XYC.tiff")
+        result = runner.invoke(
+            cli.transcode,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 2
+
+
+def test_transcode_bad_output_file_ext(samples_path, tmp_path):
+    """Check that CLI raises click.BadParameter when output file extension is bad."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = samples_path / "XYC-half-mpp.tiff"
+        out_path = Path(td) / "XYC.foo"
+        result = runner.invoke(
+            cli.transcode,
+            ["-i", str(in_path), "-o", str(out_path)],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 2