smart_open Version 1.8.1 Incompatibilities

[BennettRand]

The smart_open.smart_open function has been deprecated in version 1.8.1 of the smart_open library in favor of smart_open.open.

This throws a warning in the console whenever a sample sheet is opened.
piskvorky/smart_open#268

Version 1.8.1 also added SSH/SCP/SFTP support which throws a warning if paramiko is not installed.
piskvorky/smart_open#267

This could be solved by adding a paramiko requirement and changing smart_open calls or setting the version of smart_open to 1.8.0 in the setup file.

[clintval]

Well that's annoying. But thanks for pointing out!

[clintval]

I confirm the warning, which is ugly.

python3.6/site-packages/smart_open/ssh.py:34: UserWarning: paramiko missing, opening SSH/SCP/SFTP paths will be disabled.  `pip install paramiko` to suppress
    warnings.warn('paramiko missing, opening SSH/SCP/SFTP paths will be disabled.  `pip install paramiko` to suppress')

Since smart_open now requires more large dependencies such as boto3, requests, and paramiko I'm inclined to make smart_open support in this library optional on install:

https://setuptools.readthedocs.io/en/latest/setuptools.html#declaring-extras-optional-features-with-their-own-dependencies

This will keep the sample-sheet library slimmer by default, and for default use cases (reading the files from disk).

[clintval]

Hi @BennettRand, I just released version 0.9.0 of this library and have dropped smart_open from the install requirements.

The library still supports opening any kind of objects using the smart_open library, but you have to install seperately.

Like:

❯ pip install sample_sheet>=0.9.0 smart_open

Or:

❯ pip install 'sample_sheet[smart_open]'

[averagehat]

Is smart_open the default? I installed via pip (without [smart_open]) into a fresh miniconda install, and hit this while following the QuickStart docs; reinstalling with sample_sheet[smart_open] fixed it.

>>> import sys; print(sys.version)
3.7.3 (default, Mar 27 2019, 22:11:17) 
[GCC 7.3.0]
>>> import sample_sheet
Traceback (most recent call last):
  File "/home/mpanciera/nova/novaseq-sync/miniconda/lib/python3.7/site-packages/sample_sheet/__init__.py", line 29, in <module>
    from smart_open import open  # Migration for smart_open 1.8.1 # type: ignore
ModuleNotFoundError: No module named 'smart_open'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/mpanciera/nova/novaseq-sync/miniconda/lib/python3.7/site-packages/sample_sheet/__init__.py", line 31, in <module>
    from smart_open import smart_open as open  # type: ignore
ModuleNotFoundError: No module named 'smart_open'
>>> 
[mpanciera@node22 novaseq-sync]$ pip freeze | grep sample
sample-sheet==0.9.2

[clintval]

Welp. I can fix. Thanks @averagehat

[clintval]

@averagehat thanks for reporting. I had introduced a bug in 0.9.2. I have tested under matrix of sample-sheet and smart_open versions and am happy to report I've fixed the mess.

I just released 1.9.3, so please consider reinstalling, or upgrading.