Jupyter notebook import scanpy.api

[TamaraO]

I have followed these instructions to install scanpy into my miniconda environment:

Whether I try to import scanpy straight from terminal, it keeps giving me an error:

Python 3.5.5 |Anaconda, Inc.| (default, Mar 12 2018, 23:12:44)
[GCC 7.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scanpy.api as sc
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/unix/tamarao/miniconda3/envs/tamara_env/lib/python3.5/site-packages/scanpy/__init__.py", line 24, in <module>
    import anndata
  File "/home/unix/tamarao/miniconda3/envs/tamara_env/lib/python3.5/site-packages/anndata/__init__.py", line 1, in <module>
    from .base import AnnData, _MAIN_NARRATIVE
  File "/home/unix/tamarao/miniconda3/envs/tamara_env/lib/python3.5/site-packages/anndata/base.py", line 287
    return f'Backing file manager of file {self._filename}.'
                                                           ^
SyntaxError: invalid syntax
>>>

I also get the error when I try to use it with jupyter notebook:

import scanpy.api as sc

Traceback (most recent call last):

  File "/home/unix/tamarao/miniconda3/envs/tamara_env/lib/python3.5/site-packages/IPython/core/interactiveshell.py", line 2910, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)

  File "<ipython-input-1-4a13c503728c>", line 1, in <module>
    import scanpy.api as sc

  File "/home/unix/tamarao/miniconda3/envs/tamara_env/lib/python3.5/site-packages/scanpy/__init__.py", line 24, in <module>
    import anndata

  File "/home/unix/tamarao/miniconda3/envs/tamara_env/lib/python3.5/site-packages/anndata/__init__.py", line 1, in <module>
    from .base import AnnData, _MAIN_NARRATIVE

  File "/home/unix/tamarao/miniconda3/envs/tamara_env/lib/python3.5/site-packages/anndata/base.py", line 287
    return f'Backing file manager of file {self._filename}.'
                                                           ^
SyntaxError: invalid syntax

What is the issue? How can I get over this?

Thank you!

[flying-sheep]

Hi! Thanks for using scanpy!

The error is in anndata so filing a bug there would be more fitting. I did it for you: scverse/anndata#23

---

Lastly, please do ```pytb for your python tracebacks blocks so we get syntax highlighting:

I also get the error when I try to use it with jupyter notebook:

```pytb
import scanpy.api as sc

Traceback (most recent call last):

  File "/home/unix/tamarao/miniconda3/envs/tamara_env/lib/python3.5/site-> packages/IPython/core/interactiveshell.py", line 2910, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)

  […]

SyntaxError: invalid syntax
```

This would look like this:

I also get the error when I try to use it with jupyter notebook:

import scanpy.api as sc

Traceback (most recent call last):

  File "/home/unix/tamarao/miniconda3/envs/tamara_env/lib/python3.5/site-packages/IPython/core/interactiveshell.py", line 2910, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)

  […]

SyntaxError: invalid syntax

[flying-sheep]

fixed in scverse/anndata@555c15c

the fix should be in the next anndata release (0.6.2 or 0.7)

[TamaraO]

Thank you for the prompt response! I did not install anndata separately, I just followed instructions from https://scanpy.readthedocs.io/en/latest/installation.html to install scanpy using pip install scanpy in miniconda environment. Do I need to reinstall another version of anndata? Or of scanpy? Sorry, still not sure how to fix this. Thank you!

[flying-sheep]

yeah, this was fixed inside of anndata, so you need to update anndata, not scanpy.

pip install anndata~=0.6.4 should get you a version where this is fixed! 😄

[TamaraO]

Perfect! That fixed it! Thanks a lot!