🐛 Bug: ersilia --help producing traceback error instead of the expected output

[EstherIdabor]

Describe the bug.

installing the Ersilia python package and running pip install -e happened fine without producing any error, however running the ersilia --help to see the CLI options produce the error below:

Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 584, in _build_master ws.require(requires)

File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 901, in require needed = self.resolve(parse_requirements(requirements))

File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 792, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (urllib3 1.25.8 (/usr/lib/python3/dist-packages), Requirement.parse('urllib3>=1.26.0'), {'docker'})

Describe the steps to reproduce the behavior

ersilia --help

Expected behavior.

output the CLI options without any traceback errors

Screenshots.

No response

Operating environment

windows 10, WSL Ubuntu 20.04.4 LTS

Additional context

No response

[EstherIdabor]

Hi @GemmaTuron, Please I am stuck here, and would glad to use some help

[GemmaTuron]

Hi @EstherIdabor This is just the test I was asking in #313 . It seems an installation issue, can you paste here the commands you followed to install Ersilia?

[GemmaTuron]

I'd suggest:

1. Make sure you are on WSL or a UNIX system with conda and git-lfs installed
2. Updating pip (@Zainab-ik can have more insight on this)
3. Deleting the conda environment and creating it anew
4. Cloning Ersilia's repository again
5. Run the pip install -e .

[EstherIdabor]

Hi @GemmaTuron I've been on it all day trying to figure out what could be wrong, the installation up to that point went on fine, and I followed every single instructions on the ersillia book, and every was alright. However researching on the problem made me realize the pip install -e I ran lead to the install of some packages with different versions than what is required for instance it installs urllib1.25.8 and is required to parse is 1.26.0. leading to a VersionConflict error,

[EstherIdabor]

I'm on a Unix system with conda and git-lfs installed, I created a new conda and tried to clone the repo again but got an error, fatal: destination path 'ersilia' already exists and is not an empty directory

I'd suggest:

1. Make sure you are on WSL or a UNIX system with conda and git-lfs installed
2. Updating pip (@Zainab-ik can have more insight on this)
3. Deleting the conda environment and creating it anew
4. Cloning Ersilia's repository again
5. Run the pip install -e .

I'm on a Unix system with conda and git-lfs installed, I created a new conda and tried to clone the repo again but got an error, fatal: destination path 'ersilia' already exists and is not an empty directory

[EstherIdabor]

Hi @GemmaTuron I am now able to get past ersillia--help and ersillia catalogue, firstly I have Ubuntu 18.04 which I wasn't using before now, I was using Ubuntu 20.04.4 LTS, I switched over to 18.04 and started the whole process of installing ersillia from the beginning, ensuring I miss no step and now it's not showing me any error.

Thank you

[Zainab-ik]

@EstherIdabor , regarding the pip and getting the CLI to work on terminal. Has everything been resolved. And which version of ubuntu are using exactly, the 18.04 or 20.04.

[Zainab-ik]

I'd suggest:

1. Make sure you are on WSL or a UNIX system with conda and git-lfs installed
2. Updating pip (@Zainab-ik can have more insight on this)
3. Deleting the conda environment and creating it anew
4. Cloning Ersilia's repository again
5. Run the pip install -e .

@GemmaTuron I'd take her through

[EstherIdabor]

@EstherIdabor , regarding the pip and getting the CLI to work on terminal. Has everything been resolved. And which version of ubuntu are using exactly, the 18.04 or 20.04.

Yes it has, I am now using 18.04, thank you

[EstherIdabor]

To anyone who will encounter this error, I suggest you reinstall Ubuntu and start all over from the beginning without missing a step, and everything should work just fine.

[Zainab-ik]

that's great @EstherIdabor

[GemmaTuron]

Fantastic, thanks @EstherIdabor and @Zainab-ik I'll close this issue then!