Merge pull request #145 from BBQuercus/qol_create

Prepare for release 0.1.4

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.3
+current_version = 0.1.4
 commit = False
 tag = True
 

.github/workflows/main.yaml

@@ -10,37 +10,37 @@ jobs:
   unittest:
     strategy:
       matrix:
-        python-version: ["3.6", "3.7", "3.8"]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
         os: [windows-latest, ubuntu-latest]
 
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: install tox
-      run: python -m pip install --upgrade tox virtualenv setuptools pip codecov
-    - name: run tox
-      run: tox -e py
-    - name: upload coverage reports to Codecov
-      run: codecov
-      env:
-        super_secret: ${{ secrets.CODECOV_TOKEN }}
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: install tox
+        run: python -m pip install --upgrade tox virtualenv setuptools pip codecov
+      - name: run tox
+        run: tox -e py
+      - name: upload coverage reports to Codecov
+        run: codecov
+        env:
+          super_secret: ${{ secrets.CODECOV_TOKEN }}
 
   # Important checks but not reliant on different versions
   check:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
-      with:
-        python-version: "3.8"
-    - name: install tox
-      run: python -m pip install --upgrade tox virtualenv setuptools pip
-    - name: run tox deploy
-      run: tox -e deploy
-    - name: run tox safety
-      run: tox -e safety
-    - name: run tox style
-      run: tox -e style
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: install tox
+        run: python -m pip install --upgrade tox virtualenv setuptools pip
+      - name: run tox deploy
+        run: tox -e deploy
+      - name: run tox safety
+        run: tox -e safety
+      - name: run tox style
+        run: tox -e style

conda/meta.yaml

@@ -1,6 +1,6 @@
 package:
     name: "deepblink"
-    version: 0.1.3
+    version: 0.1.4
 source:
     path: ..
 
@@ -17,7 +17,7 @@ requirements:
       - pip
       - setuptools
     run:
-      - python>=3.6,<3.9
+      - python>=3.7,<3.11
       - matplotlib>=3.0.0
       - requests>=2.0.0
       - numpy>=1.17.0

deepblink/__init__.py

@@ -16,7 +16,7 @@
 - util: Basic utility functions not fitting into a category.
 """
 
-__version__ = "0.1.3"
+__version__ = "0.1.4"
 
 from . import augment
 from . import cli

deepblink/cli/_argparse.py

@@ -161,7 +161,7 @@ def _parse_args_create(
             "If given, will convert all labels to pixel coordinates. "
             "Can be a single value or a tuple of two values for x and y, respectively. "
             "If only one value is given, it will be used for both x and y. "
-            "[default: 1]"
+            "[default: None]"
         ),
     )
     group2.add_argument(

deepblink/cli/_parseutil.py

@@ -172,7 +172,7 @@ def _add_utils(parser: argparse.ArgumentParser):
         "-V",
         "--version",
         action="version",
-        version="%(prog)s 0.1.3",
+        version="%(prog)s 0.1.4",
         help="Show %(prog)s's version number.",
     )
     group.add_argument(

deepblink/util.py

@@ -6,6 +6,7 @@
 import random
 
 from PIL import Image
+from PIL import UnidentifiedImageError
 from PIL.TiffTags import TAGS
 import numpy as np
 import pandas as pd
@@ -139,8 +140,16 @@ def predict_pixel_size(fname: Union[str, "os.PathLike[str]"]) -> Tuple[float, fl
         raise ValueError(f"{fname} is not a tif file.")
     if not os.path.isfile(fname):
         raise ValueError(f"{fname} does not exist.")
+    if not os.path.getsize(fname):
+        raise ValueError(f"{fname} does not contain any data.")
 
-    image = Image.open(fname)
+    try:
+        image = Image.open(fname)
+    except UnidentifiedImageError as err:
+        raise ValueError(
+            f"{fname} could not be read by PIL. "
+            f"Check the format or pass a pixel-size directly."
+        ) from err
     if len(image.size) != 2:
         raise ValueError(f"Image {fname} has more than 2 dimensions.")
 

docs/conf.py

@@ -37,7 +37,7 @@
 year = "2020"
 author = "Bastian Eichenberger"
 copyright = f"{year}, {author}"
-version = release = "0.1.3"
+version = release = "0.1.4"
 
 pygments_style = "trac"
 templates_path = ["."]

setup.py

@@ -11,7 +11,7 @@
 setup(
     # Description
     name="deepblink",
-    version="0.1.3",
+    version="0.1.4",
     license="MIT",
     description="Threshold independent detection and localization of diffraction-limited spots.",
     long_description_content_type="text/plain",

tox.ini

@@ -1,6 +1,6 @@
 [tox]
 envlist = 
-    py{36,37,38},
+    py{37,38,39,310,311},
     deploy,
     safety,
     style