filesystem error: cannot make absolute path with 0.26

[erwanp]

Hello;

Our package doesn't build anymore using Mamba, although it has always been in the past. It might be related to the new 0.26 version.

Details https://app.travis-ci.com/github/radis/radis/jobs/584458524#L310

info     libmamba ****************** Backtrace Start ******************
debug    libmamba Loading configuration
trace    libmamba Compute configurable 'create_base'
trace    libmamba Compute configurable 'no_env'
trace    libmamba Compute configurable 'no_rc'
trace    libmamba Compute configurable 'rc_files'
trace    libmamba Compute configurable 'root_prefix'
trace    libmamba Get RC files configuration from locations up to HomeDir
trace    libmamba Configuration not found at '/home/travis/.mambarc'
trace    libmamba Configuration not found at '/home/travis/.condarc'
trace    libmamba Configuration not found at '/home/travis/.conda/condarc.d'
trace    libmamba Configuration not found at '/home/travis/.conda/condarc'
trace    libmamba Configuration not found at '/home/travis/.conda/.condarc'
trace    libmamba Configuration not found at '/home/travis/micromamba/.mambarc'
trace    libmamba Configuration not found at '/home/travis/micromamba/condarc.d'
trace    libmamba Configuration not found at '/home/travis/micromamba/condarc'
trace    libmamba Configuration not found at '/home/travis/micromamba/.condarc'
trace    libmamba Configuration not found at '/var/lib/conda/.mambarc'
trace    libmamba Configuration not found at '/var/lib/conda/condarc.d/'
trace    libmamba Configuration not found at '/var/lib/conda/condarc'
trace    libmamba Configuration not found at '/var/lib/conda/.condarc'
trace    libmamba Configuration not found at '/etc/conda/.mambarc'
trace    libmamba Configuration not found at '/etc/conda/condarc.d/'
trace    libmamba Configuration not found at '/etc/conda/condarc'
trace    libmamba Configuration not found at '/etc/conda/.condarc'
trace    libmamba Update configurable 'no_env'
trace    libmamba Compute configurable 'file_specs'
critical libmamba filesystem error: cannot make absolute path: Invalid argument []

I do not understand what's wrong from the error message. What informations do you need to debug ?

[jonashaag]

Hm that's curious. Can you please add a

micromamba config list

to your CI?

Btw, if you're open to switching to GitHub Actions you might want to try https://github.com/mamba-org/provision-with-micromamba, it will remove that 2 minute Conda env setup time. Also FYI on Travis you have 2 cores so you might want to use pytest-xdist to speed up your CI.

[erwanp]

Thanks for the answer. That's the only result :

> micromamba config list
show_banner: false

Thanks for the tips, too, we'll definitly implement them !

[jonashaag]

Can try removing everything else from the CI scripts except for the env creation? Just to see if that’s a problem with your specific setup or with Micromamba on Travis in any setup.

[jonashaag]

also can you run with trace log level

[wolfv]

We did change the filesystem implementation so it's possible there is a new bug now :/ I'll take a look!

[alonisser]

Also just hit this bug. was going to post this., never used mamba before but hitting this now in gitlab with both the micromamba docker and installing micromamba within the run

This is my trace

I'm getting critical libmamba filesystem error: cannot make absolute path: Invalid argument []
(With either this docker, or straight micromamba installation) 
When trying to run in gitlab CI runner 
```bash
create -f conda.yaml -y

Adding -p and a specific sub path didn't help, nor changing MAMBA_ROOT_PREFIX to be in the project folder

the full stack trace

info     libmamba ****************** Backtrace Start ******************
debug    libmamba Loading configuration
trace    libmamba Compute configurable 'create_base'
trace    libmamba Compute configurable 'no_env'
trace    libmamba Compute configurable 'no_rc'
trace    libmamba Compute configurable 'rc_files'
trace    libmamba Compute configurable 'root_prefix'
trace    libmamba Get RC files configuration from locations up to HomeDir
trace    libmamba Configuration not found at '/root/.mambarc'
trace    libmamba Configuration not found at '/root/.condarc'
trace    libmamba Configuration not found at '/root/.conda/condarc.d'
trace    libmamba Configuration not found at '/root/.conda/condarc'
trace    libmamba Configuration not found at '/root/.conda/.condarc'
trace    libmamba Configuration not found at '/builds/ourcompany/data-science/surveys-clustering/survey-answers-clustering/mamba/.mambarc'
trace    libmamba Configuration not found at '/builds/ourcompany/data-science/surveys-clustering/survey-answers-clustering/mamba/condarc.d'
trace    libmamba Configuration not found at '/builds/ourcompany/data-science/surveys-clustering/survey-answers-clustering/mamba/condarc'
trace    libmamba Configuration not found at '/builds/ourcompany/data-science/surveys-clustering/survey-answers-clustering/mamba/.condarc'
trace    libmamba Configuration not found at '/var/lib/conda/.mambarc'
trace    libmamba Configuration not found at '/var/lib/conda/condarc.d/'
trace    libmamba Configuration not found at '/var/lib/conda/condarc'
trace    libmamba Configuration not found at '/var/lib/conda/.condarc'
trace    libmamba Configuration not found at '/etc/conda/.mambarc'
trace    libmamba Configuration not found at '/etc/conda/condarc.d/'
trace    libmamba Configuration not found at '/etc/conda/condarc'
trace    libmamba Configuration not found at '/etc/conda/.condarc'
trace    libmamba Update configurable 'no_env'
trace    libmamba Compute configurable 'file_specs'
critical libmamba filesystem error: cannot make absolute path: Invalid argument []
info     libmamba ****************** Backtrace End ********************

And my conda.yaml

name: survey-answers-clustering-mlflow-env
channels:
  - conda-forge

dependencies:
      - python=3.8
      - hdbscan=0.8.28
      - joblib=1.1.0 #because of problematic hdbscan dependency
      - bertopic=0.9.4
      - python-flair
      - spacy>=2.0.0,<3.0.0
      - numpy=1.21.0
      - pandas=1.3.5
      - spacy-model-en_core_web_sm=2.2.0
      - inflection=0.5.1
      - protobuf>=3.12.0,3.20
      - poetry
      - pip
      - pip:
        - mlflow==1.28.0
        - cloudpickle==1.6.0

Note this isn't happening with mamba installed directly via conda in the run, (with the continuumio/anaconda3 base image) but does happen with micromamba

[alonisser]

Verified this doesn't happen with micromamba 0.25

[erwanp]

Thanks for checking. How can I download
Micromamba 0.25? What is the wget link?

[wolfv]

@erwanp you can use https://micro.mamba.pm/api/micromamba/$PLATFORM-$ARCH/$VERSION

E.g. https://micro.mamba.pm/api/micromamba/linux-64/0.25.1

[wolfv]

OK, I could reproduce the bug quite easily with a minimal env file:

name: survey-answers-clustering-mlflow-env
channels:
  - conda-forge

dependencies:
  - python=3.8
  - pip
  - pip:
    - rich

I'll check our calls to fs::absolute in the pip part now ... I think that's where the issue originates.

[wolfv]

I think I've isolated the issue – it happens when calling fs::absolute(yaml_file.parent_path()).string() }); which will call fs::absolute with an empty string when the yaml_file is passed like -f env.yml.

However, -f ./env.yml works fine.

I think we should transform the yaml_file to an absolute path before.

[Klaim]

Confirmed, doing so works for me so I pushed a potential fix.

[jonashaag]

@alonisser @erwanp Can you try one of the binaries on the bottom of this page? https://github.com/mamba-org/mamba/actions/runs/3173625108

I'm also attaching them there, you should be able to use:

curl -L https://github.com/mamba-org/mamba/files/9697211/micromamba-linux64.gz | gunzip > /tmp/micromamba

micromamba-osx64.gz

micromamba-linux64.gz

[alonisser]

Thanks for the fas fix @wolfv! when would this be integrated to the docker? I'm not working with the binary directly

[wolfv]

@alonisser we'll try to release a fix today (after hopefully fixing #1979 as well)

[wholtz]

when would this be integrated to the docker? I'm not working with the binary directly

I'll try to get the docker images out shortly after the new micromamba version lands on conda-forge. Generally it has been less than 24 hours after they appear on conda-forge, but I'll watch closely today and move them along quickly.

[alonisser]

Interesting. No automation for this? Would you be interested in an automation for that? (not sure if I can pull this off but I would look if possible) בתאריך יום ב׳, 3 באוק׳ 2022, 18:21, מאת Will Holtz ‏< ***@***.***>:

…

when would this be integrated to the docker? I'm not working with the binary directly I'll try to get the docker images out shortly after the new micromamba version lands on conda-forge. Generally it has been less than 24 hours after they appear on conda-forge, but I'll watch closely today and move them along quickly. — Reply to this email directly, view it on GitHub <#1975 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAK6K4GW46HQMUOQ75B2P6DWBL2YJANCNFSM6AAAAAAQ23WUD4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[thomas-fred]

Will this fix also handle a relative requirements.txt?

For me, the following environment.yml snippet:

dependencies:
  - pip
  - pip:  # delegate to pip for some packages
    - -r requirements.txt
  - ...

Will fail with:

Installing pip packages: -r ./requirements.txt
ERROR: Could not open requirements file: [Errno 2] No such file or directory: '/tmp/./requirements.txt'

But using an absolute path for the requirements.txt succeeds.

Thanks for micromamba -- it's great!

[wolfv]

@thomas-fred I am not sure those two things are related. I think for relative requirements.txt some additional "inspection" would be necessary... it would be nice if you could file a new issue or open a PR :)

[wolfv]

@alonisser I think there is quite a bit of automation in the micromamba-docker project, but I am sure that more help is always welcome!

[alonisser]

Thanks, just saw it runs every 6 hours after the release.. I'll wait

[wholtz]

Interesting. No automation for this? Would you be interested in an automation for that? (not sure if I can pull this off but I would look if possible)

@alonisser - I am interested in PRs to improve the automation. I have done a fair amount already. If you want to work on this, I suggest you start by reading mamba-org/micromamba-docker issue #120. There are some restrictions to how an automatic workflow performing an on:pull-request can trigger another workflow and these restrictions have shaped the current set of automation.

[wholtz]

@thomas-fred I am not sure those two things are related. I think for relative requirements.txt some additional "inspection" would be necessary... it would be nice if you could file a new issue or open a PR :)

I think issue #1726 already covers this.

[wholtz]

0.27.0 images are now on Dockerhub.

[alonisser]

Confirmed that 0.27.0 works as expected

[wolfv]

awesome, thanks!