From 63bcd9acc872e5d5cddd042778c54b84681b3a6e Mon Sep 17 00:00:00 2001
From: Bastian Eichenberger <bastian@eichenbergers.ch>
Date: Tue, 1 Nov 2022 14:28:53 +0100
Subject: [PATCH 1/4] :pencil: Improved error handling for non-standard tif
 files

---
 deepblink/cli/_argparse.py |  2 +-
 deepblink/util.py          | 11 ++++++++++-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/deepblink/cli/_argparse.py b/deepblink/cli/_argparse.py
index 75c2251..0d8edd4 100644
--- a/deepblink/cli/_argparse.py
+++ b/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(
diff --git a/deepblink/util.py b/deepblink/util.py
index 5f58b8b..84a3f34 100755
--- a/deepblink/util.py
+++ b/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.")
 

From acbc0855a851808d44c65422a4630151c6ca0d66 Mon Sep 17 00:00:00 2001
From: Bastian Eichenberger <bastian@eichenbergers.ch>
Date: Tue, 1 Nov 2022 14:40:10 +0100
Subject: [PATCH 2/4] :green_heart: Change versions for python suport

---
 .github/workflows/main.yaml | 50 ++++++++++++++++++-------------------
 tox.ini                     |  2 +-
 2 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index aa3880a..5a4ec54 100644
--- a/.github/workflows/main.yaml
+++ b/.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", "3.11"]
         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
diff --git a/tox.ini b/tox.ini
index 0ad1d85..ae5f435 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,6 +1,6 @@
 [tox]
 envlist = 
-    py{36,37,38},
+    py{37,38,39,310,311},
     deploy,
     safety,
     style

From ab4d5e9c66e6ca60a477bf7eed2141802f9a6442 Mon Sep 17 00:00:00 2001
From: Bastian Eichenberger <bastian@eichenbergers.ch>
Date: Tue, 1 Nov 2022 14:44:50 +0100
Subject: [PATCH 3/4] :gem: Bumpversion to 0.1.4

---
 .bumpversion.cfg            | 2 +-
 conda/meta.yaml             | 4 ++--
 deepblink/__init__.py       | 2 +-
 deepblink/cli/_parseutil.py | 2 +-
 docs/conf.py                | 2 +-
 setup.py                    | 2 +-
 6 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 6ffaa47..1306b54 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.3
+current_version = 0.1.4
 commit = False
 tag = True
 
diff --git a/conda/meta.yaml b/conda/meta.yaml
index 2ef36d2..8034322 100644
--- a/conda/meta.yaml
+++ b/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
diff --git a/deepblink/__init__.py b/deepblink/__init__.py
index 98e1df4..1936ef7 100644
--- a/deepblink/__init__.py
+++ b/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
diff --git a/deepblink/cli/_parseutil.py b/deepblink/cli/_parseutil.py
index e94eb37..6d7269f 100644
--- a/deepblink/cli/_parseutil.py
+++ b/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(
diff --git a/docs/conf.py b/docs/conf.py
index faacc27..4121d93 100644
--- a/docs/conf.py
+++ b/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 = ["."]
diff --git a/setup.py b/setup.py
index 63a56cd..3142f8c 100755
--- a/setup.py
+++ b/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",

From 42798aea5253d0a754b6cccee509594ac1dcde2e Mon Sep 17 00:00:00 2001
From: Bastian Eichenberger <bastian@eichenbergers.ch>
Date: Tue, 1 Nov 2022 14:51:12 +0100
Subject: [PATCH 4/4] :arrow_down: Remove 3.11 to accomodate tensorflow

---
 .github/workflows/main.yaml | 2 +-
 conda/meta.yaml             | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 5a4ec54..46f5d65 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -10,7 +10,7 @@ jobs:
   unittest:
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
         os: [windows-latest, ubuntu-latest]
 
     runs-on: ${{ matrix.os }}
diff --git a/conda/meta.yaml b/conda/meta.yaml
index 8034322..f61a739 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -17,7 +17,7 @@ requirements:
       - pip
       - setuptools
     run:
-      - python>=3.7,<=3.11
+      - python>=3.7,<3.11
       - matplotlib>=3.0.0
       - requests>=2.0.0
       - numpy>=1.17.0