From dbf6dc18038fc2b18c49ef8bad5da35a505d5b19 Mon Sep 17 00:00:00 2001
From: Helmut Hoffer von Ankershoffen <helmut@aignostics.com>
Date: Tue, 26 Nov 2024 22:23:45 +0100
Subject: [PATCH] fix: dev environment and account for broken jpype 1.5.1

---
 README.md              | 10 ++++------
 environment.devenv.yml | 20 +++++++++++---------
 setup.cfg              |  2 +-
 3 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/README.md b/README.md
index 7582559..a8e26fa 100644
--- a/README.md
+++ b/README.md
@@ -32,16 +32,17 @@ You can find `paquo`'s documentation at
 ## Installation
 
 paquo's stable releases can be installed via `pip`:
+
 ```bash
 pip install paquo
 ```
 
 or via `conda`:
+
 ```bash
 conda install -c conda-forge paquo
 ```
 
-
 ## Getting QuPath
 
 After installing, paquo requires a QuPath installation to run. To get QuPath follow the
@@ -68,31 +69,28 @@ paquo to use that version. Currently, paquo supports every version of QuPath fro
 /some/path/on/your/machine/QuPath-0.5.0
 ```
 
-
 ## Development Installation
 
 1. Install conda and git
 2. Clone paquo `git clone https://github.com/bayer-science-for-a-better-life/paquo.git`
-3. Run `conda env create -f environment.devenv.yaml`
+3. Run `conda env create -f environment.devenv.yml`
 4. Activate the environment `conda activate paquo`
 
 Note that in this environment `paquo` is already installed in development mode,
 so go ahead and hack.
 
-
 ## Contributing Guidelines
 
 - Please follow [pep-8 conventions](https://www.python.org/dev/peps/pep-0008/) but:
   - We allow 120 character long lines (try anyway to keep them short)
 - Please use [numpy docstrings](https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard).
 - When contributing code, please try to use Pull Requests.
-- tests go hand in hand with modules on ```tests``` packages at the same level. We use ```pytest```.
+- tests go hand in hand with modules on `tests` packages at the same level. We use `pytest`.
 
 You can set up your IDE to help you to adhere to these guidelines.
 <br>
 _([Santi](https://github.com/sdvillal) is happy to help you to set up pycharm in 5 minutes)_
 
-
 ## Acknowledgements
 
 Build with love by Andreas Poehlmann and Santi Villalba from the _Machine
diff --git a/environment.devenv.yml b/environment.devenv.yml
index 41b1186..0567600 100644
--- a/environment.devenv.yml
+++ b/environment.devenv.yml
@@ -1,26 +1,28 @@
 #
 # Conda devenv environment for paquo
 #
-# Create the environment, do not install pado in development mode:
+# Create the environment:
 #   conda devenv
-# equivalent to:
-#   PAQUO_DEVEL="" conda devenv
-# Create the environment, install pado in development mode:
-#   PAQUO_DEVEL=TRUE conda devenv
 #
 
-{% set PAQUO_DEVEL = os.environ.get('PAQUO_DEVEL', False) %}
-{% set WITH_OME = os.environ.get('WITH_OME', False) %}
-
 name: paquo
 
 channels:
   - conda-forge
+  - defaults
+
+variables:
+  PAQUO_DEVEL: $PAQUO_DEVEL
+  WITH_OME: $WITH_OME
+
+environment:
+  PAQUO_DEVEL: ${PAQUO_DEVEL:-false}
+  WITH_OME: ${WITH_OME:-false}
 
 dependencies:
   - python>=3.7
   - pip
-  - jpype1>=1.0.1
+  - jpype1>=1.0.1,!=1.5.1
   - dynaconf>=3,!=3.1.0,!=3.1.7
   - ome-types   # [ WITH_OME ]
   - shapely
diff --git a/setup.cfg b/setup.cfg
index 85e7026..a3c1ed1 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -37,7 +37,7 @@ packages = find:
 python_requires = >=3.8
 install_requires =
     dynaconf>=3,!=3.1.0
-    JPype1>=1.0.1
+    JPype1>=1.0.1,!=1.5.1
     shapely
     packaging