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fix: dev environment and account for broken jpype 1.5.1 #123

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fix: dev environment and account for broken jpype 1.5.1 #123

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10 changes: 4 additions & 6 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
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20 changes: 11 additions & 9 deletions environment.devenv.yml
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Original file line number Diff line number Diff line change
@@ -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
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Please remove the defaults channel here. It potentially requires licenses. Better to leave that up to the user they have anaconda installation with activated licenses and want to have defaults as the base channel.


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
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2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -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

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