Syntax Error in det.py file

[vidalarroyo]

Hello!

There seems to be a syntax error issue in the 'det.py' file under cellex/metrics/. I am trying to install and run cellex, but whenever I try to install cellex it always gives me an 'invalid syntax' error at the following line:

 Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/Users/vidalarroyo/CELLECT/CELLEX/setup.py", line 5, in <module>
        from cellex import __author__, __email__
      File "cellex/__init__.py", line 17, in <module>
        from . import metrics
      File "cellex/metrics/__init__.py", line 1, in <module>
        from .det import det
      File "cellex/metrics/det.py", line 9
        def _det(mean: pd.DataFrame, var: pd.DataFrame, n_cells: pd.DataFrame, verbose: bool=False):
                     ^
    SyntaxError: invalid syntax

[tstannius]

Hi!

Could you add the command that resulted in this error, to see if I can reproduce it? Thanks in advance.

[vidalarroyo]

Yes! The command was 'pip install -e'. I was going through the walkthrough on https://github.com/perslab/CELLEX , using Option B on the setup

[tstannius]

How odd. I am having trouble reproducing the error. Does my approach differ from yours?

Alternatively – how does it work for you installing directly from PyPi? I.e.

pip install cellex

The development version matches the release version ATM, so there's not much to gain by installing from the development branch.

[vidalarroyo]

Hmm, I gave both a try (both the way you did it in the gif and installing cellex via pip) and neither worked :/ i'm thinking it may be the version of python my terminal is set up with.... what version is used?

[tstannius]

Bummer, but we'll just have to try something else then :-) and thank you for your patience in that regard.

CELLEX has been developed for use in a Python 3 environment.

I generally use conda environments (miniconda3) to manage the installation. Here's what I do step by step in my terminal:

# create environment
conda create --no-default-packages --name myenv python

# activate env
source activate myenv

# check python version, should be >3.8
python --version

# install cellex – various dependencies will be installed first
pip install cellex

# test installation in interactive python
python

>>> import cellex
>>>

If this does not help, could you provide my some more details about your system and each step you do to produce the error?

[vidalarroyo]

Yes! And thank you so much for your help with all of this. I will be re-trying this tomorrow on a cluster environment, and this will help me tons. I will keep you posted!

[tstannius]

Hi again Vidal,

Have you made any progress on this issue? 🙂

[vidalarroyo]

Hey Tobias,

Firstly, thanks for checking in! In short, yes and no - I actually realized that I need to run CELLECT/CELLEX on a cluster, so I am working with my university to get all the necessary software (IE Python 3.8+, Snakemake v. 5.4.5) installed before I continue some of this.

Once I do, I will be sure to reach out once I am able to continue the tutorial :) thanks for checking in!

Best,

Vidal Arroyo MSc by Research in Statistics University College, Oxford https://www.linkedin.com/in/vidalarroyo

On Apr 14, 2020, at 11:21 AM, Tobias Overlund Stannius notifications@github.com wrote:

Hi again Vidal,

Have you made any progress on this issue? 🙂

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/perslab/CELLEX/issues/18#issuecomment-613354867, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALH34Z7KH2GOIIA33LNDTELRMQ2KFANCNFSM4MD5SOQA.

[vidalarroyo]

Hello Tobias,

Just following up, what are the bare minimum requirements in terms of software (IE python, snakemake, etc.) and versions to run CELLECT/CELLEX? We are working with our clustering management team to download any necessary software, so I want to make sure have all that up front :)

[tstannius]

Hi again Vidal!

CELLECT/CELLEX were developed on a server, so I'm not entirely sure how it will behave if run on a cluster – nevertheless ... We have sought to make both CELLECT and CELLEX self-contained. Ideally the environment manager (conda) and package manager (pip) should take care of everything, i.e. installing dependencies. The workflow is essentially: 1) create a virtual environment, 2) install the needed dependencies in the environment, 3) run the analysis. Therefore I would recommend that you start off with the most recent version of conda, pip and python3.

For CELLEX

• Get conda
• Create a new python3 environment and activate it
• Run pip install cellex, which will also install the required dependencies.
• Play around with CELLEX

For CELLECT

• (Get conda)
• Follow this tutorial.
• Step 1: The principle is almost the same as for CELLEX. To run the GWAS munge workflow, you create an environment (including all dependencies) as specified in this settings file.
• Step 2: Run CELLEX
• Step 3: Once again, create a new environment with snakemake (pip install snakemake for the most recent version).

If this doesn't work out, I'll try and get an expert opinion from the CELLECT devs or our server admin :-)

[vidalarroyo]

Tobias - thank you so much for all of this info! I am also sorry that this has taken a lot of effort and time on your end without much output on our end yet. I am realizing that a lot of these issues are actually driven by my current cluster access situation, so I am going to work within my group to solve those. I will reach out again if I think there is a larger issue - but for the time being I'm set :) thank you and take care!

[tstannius]

Hi! Thanks for following up and don't worry – I'm happy to help :-) Don't hesitate to file a new issue if needed. Take care!