higlass / higlass/higlass-python

Opening display from a script

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描述

I've got higlass working from within a Jupyter notebook, but the same code gives an error when I run it from a script. Is there something different that needs to be done for non-jupyter notebook usage?

Here is the error:
```
Process Process-1:
Traceback (most recent call last):
File "/Users/wnoble/opt/anaconda3/envs/ppx/lib/python3.9/site-packages/multiprocess/process.py", line 315, in _bootstrap
self.run()
File "/Users/wnoble/opt/anaconda3/envs/ppx/lib/python3.9/site-packages/multiprocess/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/Users/wnoble/opt/anaconda3/envs/ppx/lib/python3.9/site-packages/flask/app.py", line 1188, in run
run_simple(t.cast(str, host), port, self, **options)
File "/Users/wnoble/opt/anaconda3/envs/ppx/lib/python3.9/site-packages/werkzeug/serving.py", line 1069, in run_simple
fd = int(os.environ["WERKZEUG_SERVER_FD"])
File "/Users/wnoble/opt/anaconda3/envs/ppx/lib/python3.9/os.py", line 679, in __getitem__
raise KeyError(key) from None
KeyError: 'WERKZEUG_SERVER_FD'

```

And here is the code:

```
my_array = sparse_matrix.toarray().astype(float)

ts = Tileset(
tileset_info=lambda: npmatrix.tileset_info(my_array),
tiles=lambda tids: npmatrix.tiles_wrapper(my_array, tids)
)

display, server, viewconf = higlass.display([
View([
Track(track_type='top-axis', position='top'),
Track(track_type='left-axis', position='left'),
Track(track_type='heatmap',
position='center',
tileset=ts,
height=500),

])
], fuse=False)
display
```

I am running this on MacOS 12.5.1.

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调研方向

首先,使用 higlass.display(..., fuse=False) 在非 Jupyter 脚本中复现该故障,然后将其启动路径与正常工作的 notebook 用法进行比较。调查涉及 WERKZEUG_SERVER_FD 的 Flask 服务器错误;当脚本打开显示内容且不引发报告的 KeyError 时,即表示完成。

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评估

技术栈
flask, jupyter-notebook, python
领域
api, backend
Issue 类型
缺陷
难度
3/5
预计耗时
1-2 天
活跃度
停滞
描述清晰度
基本清楚
新手友好度
35/100

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