lilab-bcb/cirrocumulus

Breaking changes with latest release of Werkzeug (2.1.0)

romanhaa opened this issue · 1 comments

romanhaa commented

Describe the bug
Werkzeug released a version 2.1.0 on 2020-03-28 and I believe it introduced breaking changes for Cirrocumulus. Following the instructions in the README (running pip install cirrocumulus; cirro launch ... with the human lymph node example dataset) returns:

Traceback (most recent call last):
  File "/Users/roman/.virtualenvs/cirrocumulus1/bin/cirro", line 8, in <module>
    sys.exit(main())
  File "/Users/roman/.virtualenvs/cirrocumulus1/lib/python3.9/site-packages/cirrocumulus/__main__.py", line 20, in main
    cmd.main(command_args)
  File "/Users/roman/.virtualenvs/cirrocumulus1/lib/python3.9/site-packages/cirrocumulus/launch.py", line 123, in main
    app.run(host=args.host, port=args.port, debug=False)
  File "/Users/roman/.virtualenvs/cirrocumulus1/lib/python3.9/site-packages/flask/app.py", line 920, in run
    run_simple(t.cast(str, host), port, self, **options)
  File "/Users/roman/.virtualenvs/cirrocumulus1/lib/python3.9/site-packages/werkzeug/serving.py", line 1047, in run_simple
    fd = int(os.environ["WERKZEUG_SERVER_FD"])
  File "/Users/roman/.pyenv/versions/3.9.6/lib/python3.9/os.py", line 679, in __getitem__
    raise KeyError(key) from None
KeyError: 'WERKZEUG_SERVER_FD'

This can be fixed by downgrading Werkzeug to < 2.1.0 (see below).

To Reproduce

pip install cirrocumulus
cirro launch V1_Human_Lymph_Node/V1_Human_Lymph_Node.h5ad

Expected behavior
Cirrocumulus should launch and host the application.

Desktop (please complete the following information):

  • OS: macOS

Additional context

$ python --version
Python 3.9.6

$ pip list
Package            Version
------------------ ---------
anndata            0.8.0
asciitree          0.3.3
Brotli             1.0.9
CacheControl       0.12.10
certifi            2021.10.8
charset-normalizer 2.0.12
cirrocumulus       1.1.26
click              8.1.0
fasteners          0.17.3
Flask              2.1.0
Flask-Compress     1.11
fsspec             2022.2.0
gunicorn           20.1.0
h5py               3.6.0
idna               3.3
importlib-metadata 4.11.3
itsdangerous       2.1.2
Jinja2             3.1.1
llvmlite           0.38.0
loompy             3.0.7
MarkupSafe         2.1.1
msgpack            1.0.3
natsort            8.1.0
numba              0.55.1
numcodecs          0.9.1
numpy              1.21.5
numpy-groupies     0.9.14
packaging          21.3
pandas             1.4.1
pip                21.3.1
pyarrow            7.0.0
pymongo            4.0.2
pyparsing          3.0.7
python-dateutil    2.8.2
pytz               2022.1
requests           2.27.1
scipy              1.8.0
setuptools         60.9.3
six                1.16.0
urllib3            1.26.9
Werkzeug           2.1.0
wheel              0.37.1
zarr               2.11.1
zipp               3.7.0

Solution

Downgrade Werkzeug to < 2.1.0:

pip install "werkzeug<2.1.0"
$ pip list
Package            Version
------------------ ---------
anndata            0.8.0
asciitree          0.3.3
Brotli             1.0.9
CacheControl       0.12.10
certifi            2021.10.8
charset-normalizer 2.0.12
cirrocumulus       1.1.26
click              8.1.0
fasteners          0.17.3
Flask              2.1.0
Flask-Compress     1.11
fsspec             2022.2.0
gunicorn           20.1.0
h5py               3.6.0
idna               3.3
importlib-metadata 4.11.3
itsdangerous       2.1.2
Jinja2             3.1.1
llvmlite           0.38.0
loompy             3.0.7
MarkupSafe         2.1.1
msgpack            1.0.3
natsort            8.1.0
numba              0.55.1
numcodecs          0.9.1
numpy              1.21.5
numpy-groupies     0.9.14
packaging          21.3
pandas             1.4.1
pip                22.0.4
pyarrow            7.0.0
pymongo            4.0.2
pyparsing          3.0.7
python-dateutil    2.8.2
pytz               2022.1
requests           2.27.1
scipy              1.8.0
setuptools         60.9.3
six                1.16.0
urllib3            1.26.9
Werkzeug           2.0.3
wheel              0.37.1
zarr               2.11.1
zipp               3.7.0

Now it works as expected.

joshua-gould commented

Thanks so much for the report. It's fixed in version 1.1.27.

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