roifile 2024.1.10__tar.gz → 2024.5.24__tar.gz

{roifile-2024.1.10 → roifile-2024.5.24}/CHANGES.rst

@@ -1,6 +1,14 @@
 Revisions
 ---------
 
+2024.5.24
+
+- Fix GitHub not correctly rendering docstring examples.
+
+2024.3.20
+
+- Fix writing generator of ROIs (#9).
+
 2024.1.10
 
 - Support text rotation.

{roifile-2024.1.10/roifile.egg-info → roifile-2024.5.24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roifile
-Version: 2024.1.10
+Version: 2024.5.24
 Summary: Read and write ImageJ ROI format
 Home-page: https://www.cgohlke.com
 Author: Christoph Gohlke
@@ -38,7 +38,7 @@ interest, geometric shapes, paths, text, and whatnot for image overlays.
 
 :Author: `Christoph Gohlke <https://www.cgohlke.com>`_
 :License: BSD 3-Clause
-:Version: 2024.1.10
+:Version: 2024.5.24
 :DOI: `10.5281/zenodo.6941603 <https://doi.org/10.5281/zenodo.6941603>`_
 
 Quickstart
@@ -47,7 +47,7 @@ Quickstart
 Install the roifile package and all dependencies from the
 `Python Package Index <https://pypi.org/project/roifile/>`_::
 
-    python -m pip install -U roifile[all]
+    python -m pip install -U "roifile[all]"
 
 View overlays stored in a ROI, ZIP, or TIFF file::
 
@@ -64,14 +64,22 @@ Requirements
 This revision was tested with the following requirements and dependencies
 (other versions may work):
 
-- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.4, 3.12.1
-- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.3
-- `Tifffile <https://pypi.org/project/tifffile/>`_ 2023.12.9 (optional)
-- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.2 (optional)
+- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.9, 3.12.3
+- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.4
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.5.22 (optional)
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.4 (optional)
 
 Revisions
 ---------
 
+2024.5.24
+
+- Fix GitHub not correctly rendering docstring examples.
+
+2024.3.20
+
+- Fix writing generator of ROIs (#9).
+
 2024.1.10
 
 - Support text rotation.
@@ -101,21 +109,6 @@ Revisions
 
 2022.7.29
 
-- Update metadata.
-
-2022.3.18
-
-- Fix creating ROIs from float coordinates exceeding int16 range (#7).
-- Fix bottom-right bounds in ImagejRoi.frompoints.
-
-2022.2.2
-
-- Add type hints.
-- Change ImagejRoi to dataclass.
-- Drop support for Python 3.7 and numpy < 1.19 (NEP29).
-
-2021.6.6
-
 - …
 
 Refer to the CHANGES file for older revisions.

{roifile-2024.1.10 → roifile-2024.5.24}/README.rst

@@ -1,3 +1,6 @@
+..
+  This file is generated by setup.py
+
 Read and write ImageJ ROI format
 ================================
 
@@ -9,7 +12,7 @@ interest, geometric shapes, paths, text, and whatnot for image overlays.
 
 :Author: `Christoph Gohlke <https://www.cgohlke.com>`_
 :License: BSD 3-Clause
-:Version: 2024.1.10
+:Version: 2024.5.24
 :DOI: `10.5281/zenodo.6941603 <https://doi.org/10.5281/zenodo.6941603>`_
 
 Quickstart
@@ -18,7 +21,7 @@ Quickstart
 Install the roifile package and all dependencies from the
 `Python Package Index <https://pypi.org/project/roifile/>`_::
 
-    python -m pip install -U roifile[all]
+    python -m pip install -U "roifile[all]"
 
 View overlays stored in a ROI, ZIP, or TIFF file::
 
@@ -35,14 +38,22 @@ Requirements
 This revision was tested with the following requirements and dependencies
 (other versions may work):
 
-- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.4, 3.12.1
-- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.3
-- `Tifffile <https://pypi.org/project/tifffile/>`_ 2023.12.9 (optional)
-- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.2 (optional)
+- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.9, 3.12.3
+- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.4
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.5.22 (optional)
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.4 (optional)
 
 Revisions
 ---------
 
+2024.5.24
+
+- Fix GitHub not correctly rendering docstring examples.
+
+2024.3.20
+
+- Fix writing generator of ROIs (#9).
+
 2024.1.10
 
 - Support text rotation.
@@ -72,21 +83,6 @@ Revisions
 
 2022.7.29
 
-- Update metadata.
-
-2022.3.18
-
-- Fix creating ROIs from float coordinates exceeding int16 range (#7).
-- Fix bottom-right bounds in ImagejRoi.frompoints.
-
-2022.2.2
-
-- Add type hints.
-- Change ImagejRoi to dataclass.
-- Drop support for Python 3.7 and numpy < 1.19 (NEP29).
-
-2021.6.6
-
 - …
 
 Refer to the CHANGES file for older revisions.
@@ -112,37 +108,45 @@ Examples
 
 Create a new ImagejRoi instance from an array of x, y coordinates:
 
->>> roi = ImagejRoi.frompoints([[1.1, 2.2], [3.3, 4.4], [5.5, 6.6]])
->>> roi.roitype = ROI_TYPE.POINT
->>> roi.options |= ROI_OPTIONS.SHOW_LABELS
+.. code-block:: python
+
+    >>> roi = ImagejRoi.frompoints([[1.1, 2.2], [3.3, 4.4], [5.5, 6.6]])
+    >>> roi.roitype = ROI_TYPE.POINT
+    >>> roi.options |= ROI_OPTIONS.SHOW_LABELS
 
 Export the instance to an ImageJ ROI formatted byte string or file:
 
->>> out = roi.tobytes()
->>> out[:4]
-b'Iout'
->>> roi.tofile('_test.roi')
+.. code-block:: python
+
+    >>> out = roi.tobytes()
+    >>> out[:4]
+    b'Iout'
+    >>> roi.tofile('_test.roi')
 
 Read the ImageJ ROI from the file and verify the content:
 
->>> roi2 = ImagejRoi.fromfile('_test.roi')
->>> roi2 == roi
-True
->>> roi.roitype == ROI_TYPE.POINT
-True
->>> roi.subpixelresolution
-True
->>> roi.coordinates()
-array([[1.1, 2.2],
-       [3.3, 4.4],
-       [5.5, 6.6]], dtype=float32)
->>> roi.left, roi.top, roi.right, roi.bottom
-(1, 2, 7, 8)
+.. code-block:: python
+
+    >>> roi2 = ImagejRoi.fromfile('_test.roi')
+    >>> roi2 == roi
+    True
+    >>> roi.roitype == ROI_TYPE.POINT
+    True
+    >>> roi.subpixelresolution
+    True
+    >>> roi.coordinates()
+    array([[1.1, 2.2],
+           [3.3, 4.4],
+           [5.5, 6.6]], dtype=float32)
+    >>> roi.left, roi.top, roi.right, roi.bottom
+    (1, 2, 7, 8)
 
 Plot the ROI using matplotlib:
 
->>> roi.plot()
+.. code-block:: python
+
+    >>> roi.plot()
 
 View the overlays stored in a ROI, ZIP, or TIFF file from a command line::
 
-    python -m roifile _test.roi
+    python -m roifile _test.roi

{roifile-2024.1.10 → roifile-2024.5.24}/roifile/roifile.py

@@ -39,7 +39,7 @@ interest, geometric shapes, paths, text, and whatnot for image overlays.
 
 :Author: `Christoph Gohlke <https://www.cgohlke.com>`_
 :License: BSD 3-Clause
-:Version: 2024.1.10
+:Version: 2024.5.24
 :DOI: `10.5281/zenodo.6941603 <https://doi.org/10.5281/zenodo.6941603>`_
 
 Quickstart
@@ -48,7 +48,7 @@ Quickstart
 Install the roifile package and all dependencies from the
 `Python Package Index <https://pypi.org/project/roifile/>`_::
 
-    python -m pip install -U roifile[all]
+    python -m pip install -U "roifile[all]"
 
 View overlays stored in a ROI, ZIP, or TIFF file::
 
@@ -65,14 +65,22 @@ Requirements
 This revision was tested with the following requirements and dependencies
 (other versions may work):
 
-- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.4, 3.12.1
-- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.3
-- `Tifffile <https://pypi.org/project/tifffile/>`_ 2023.12.9 (optional)
-- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.2 (optional)
+- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.9, 3.12.3
+- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.4
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.5.22 (optional)
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.4 (optional)
 
 Revisions
 ---------
 
+2024.5.24
+
+- Fix GitHub not correctly rendering docstring examples.
+
+2024.3.20
+
+- Fix writing generator of ROIs (#9).
+
 2024.1.10
 
 - Support text rotation.
@@ -102,21 +110,6 @@ Revisions
 
 2022.7.29
 
-- Update metadata.
-
-2022.3.18
-
-- Fix creating ROIs from float coordinates exceeding int16 range (#7).
-- Fix bottom-right bounds in ImagejRoi.frompoints.
-
-2022.2.2
-
-- Add type hints.
-- Change ImagejRoi to dataclass.
-- Drop support for Python 3.7 and numpy < 1.19 (NEP29).
-
-2021.6.6
-
 - …
 
 Refer to the CHANGES file for older revisions.
@@ -181,7 +174,7 @@ View the overlays stored in a ROI, ZIP, or TIFF file from a command line::
 
 from __future__ import annotations
 
-__version__ = '2024.1.10'
+__version__ = '2024.5.24'
 
 __all__ = [
     'roiread',
@@ -253,14 +246,20 @@ def roiwrite(
     if mode is None:
         mode = 'a' if os.path.exists(filename) else 'w'
 
-    if name is None:
-        name = [r.name if r.name else r.autoname for r in roi]
-    name = [n if n[-4:].lower() == '.roi' else n + '.roi' for n in name]
+    if name is not None:
+        if isinstance(name, str):
+            raise ValueError("'name' is not an iterable of str")
+        name = iter(name)
 
     import zipfile
 
     with zipfile.ZipFile(filename, mode) as zf:
-        for n, r in zip(name, roi):
+        for r in roi:
+            if name is None:
+                n = r.name if r.name else r.autoname
+            else:
+                n = next(name)
+            n = n if n[-4:].lower() == '.roi' else n + '.roi'
             with zf.open(n, 'w') as fh:
                 fh.write(r.tobytes())
     return None
@@ -1272,7 +1271,12 @@ def test(verbose: bool = False) -> None:
         os.remove('_test.zip')
     except OSError:
         pass
-    roiwrite('_test.zip', rois)
+
+    def roi_iter():
+        # issue #9
+        yield from rois
+
+    roiwrite('_test.zip', roi_iter())
     assert roiread('_test.zip') == rois
 
     # verify box_combined

{roifile-2024.1.10 → roifile-2024.5.24/roifile.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roifile
-Version: 2024.1.10
+Version: 2024.5.24
 Summary: Read and write ImageJ ROI format
 Home-page: https://www.cgohlke.com
 Author: Christoph Gohlke
@@ -38,7 +38,7 @@ interest, geometric shapes, paths, text, and whatnot for image overlays.
 
 :Author: `Christoph Gohlke <https://www.cgohlke.com>`_
 :License: BSD 3-Clause
-:Version: 2024.1.10
+:Version: 2024.5.24
 :DOI: `10.5281/zenodo.6941603 <https://doi.org/10.5281/zenodo.6941603>`_
 
 Quickstart
@@ -47,7 +47,7 @@ Quickstart
 Install the roifile package and all dependencies from the
 `Python Package Index <https://pypi.org/project/roifile/>`_::
 
-    python -m pip install -U roifile[all]
+    python -m pip install -U "roifile[all]"
 
 View overlays stored in a ROI, ZIP, or TIFF file::
 
@@ -64,14 +64,22 @@ Requirements
 This revision was tested with the following requirements and dependencies
 (other versions may work):
 
-- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.4, 3.12.1
-- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.3
-- `Tifffile <https://pypi.org/project/tifffile/>`_ 2023.12.9 (optional)
-- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.2 (optional)
+- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.9, 3.12.3
+- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.4
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.5.22 (optional)
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.4 (optional)
 
 Revisions
 ---------
 
+2024.5.24
+
+- Fix GitHub not correctly rendering docstring examples.
+
+2024.3.20
+
+- Fix writing generator of ROIs (#9).
+
 2024.1.10
 
 - Support text rotation.
@@ -101,21 +109,6 @@ Revisions
 
 2022.7.29
 
-- Update metadata.
-
-2022.3.18
-
-- Fix creating ROIs from float coordinates exceeding int16 range (#7).
-- Fix bottom-right bounds in ImagejRoi.frompoints.
-
-2022.2.2
-
-- Add type hints.
-- Change ImagejRoi to dataclass.
-- Drop support for Python 3.7 and numpy < 1.19 (NEP29).
-
-2021.6.6
-
 - …
 
 Refer to the CHANGES file for older revisions.

{roifile-2024.1.10 → roifile-2024.5.24}/roifile_demo.py

@@ -9,11 +9,10 @@ segmentation from/to ImageJ TIFF files.
 
 import numpy
 from matplotlib import pyplot
+from roifile import ImagejRoi
 from skimage.measure import find_contours, label, regionprops
 from tifffile import TiffFile, imwrite
 
-from roifile import ImagejRoi
-
 
 def plot_image_overlays(image, overlays, **kwargs):
     """Plot image and overlays (bytes) using matplotlib."""

{roifile-2024.1.10 → roifile-2024.5.24}/setup.py

@@ -8,14 +8,32 @@ import sys
 from setuptools import setup
 
 
-def search(pattern, code, flags=0):
-    # return first match for pattern in code
-    match = re.search(pattern, code, flags)
+def search(pattern, string, flags=0):
+    """Return first match of pattern in string."""
+    match = re.search(pattern, string, flags)
     if match is None:
         raise ValueError(f'{pattern!r} not found')
     return match.groups()[0]
 
 
+def fix_docstring_examples(docstring):
+    """Return docstring with examples fixed for GitHub."""
+    start = True
+    indent = False
+    lines = ['..', '  This file is generated by setup.py', '']
+    for line in docstring.splitlines():
+        if not line.strip():
+            start = True
+            indent = False
+        if line.startswith('>>> '):
+            indent = True
+            if start:
+                lines.extend(['.. code-block:: python', ''])
+                start = False
+        lines.append(('    ' if indent else '') + line)
+    return '\n'.join(lines)
+
+
 with open('roifile/roifile.py', encoding='utf-8') as fh:
     code = fh.read().replace('\r\n', '\n').replace('\r', '\n')
 
@@ -36,7 +54,7 @@ if 'sdist' in sys.argv:
     # update README, LICENSE, and CHANGES files
 
     with open('README.rst', 'w', encoding='utf-8') as fh:
-        fh.write(readme)
+        fh.write(fix_docstring_examples(readme))
 
     license = search(
         r'(# Copyright.*?(?:\r\n|\r|\n))(?:\r\n|\r|\n)+""',