repo2docker hangs when the lcoal directory from where the comand is run matches the repo

[ncclementi]

Bug description

I run jupyter-repo2docker https://github.com/coiled/dask-tutorial while locally being in the repo, and the build kept hanging in step 40/53

This is where it hangs

Step 40/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time ${MAMBA_EXE} env update -p ${NB_PYTHON_PREFIX} --file "binder/environment.yml" && time ${MAMBA_EXE} clean --all -f -y && ${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX} '
 ---> [Warning] The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
 ---> Running in 5c35ca366acf
Transaction

  Prefix: /srv/conda/envs/notebook

  Updating specs:

   - dask==2023.5.0
   - distributed==2023.5.0
   - numpy==1.23.5
   - pandas==2.0.1
   - coiled==0.6.6
   - pyarrow==10.0.1
   - dask-labextension==6.1.0
   - s3fs==2023.5.0
   - python-graphviz==0.20.1
   - matplotlib==3.6.2
   - python==3.10
   - ipykernel==6.21.2
   - jupyterlab==3.5.0
   - beautifulsoup4==4.11.1



### some more lines of packages here. removed for line limit
  Change:
���────────────────────────────────────────────────────────────────────────────────────────────────

  - libssh2                        1.10.0  haa6b8db_3            conda-forge                   
  + libssh2                        1.10.0  hf14f497_3            conda-forge/linux-64     239kB
  - pycurl                         7.45.1  py310h2aed498_2       conda-forge                   
  + pycurl                         7.45.1  py310h60f9ec7_3       conda-forge/linux-64      76kB

  Upgrade:
─────────────────────────────────────────────────────────────────────────────────────────────────

  - c-ares                         1.18.1  h7f98852_0            conda-forge                   
  + c-ares                         1.19.1  hd590300_0            conda-forge/linux-64     113kB
  - cryptography                   38.0.2  py310h597c629_0       conda-forge                   
  + cryptography                   40.0.2  py310h34c0648_0       conda-forge/linux-64       2MB
  - debugpy                         1.6.3  py310hd8f1fbe_0       conda-forge                   
  + debugpy                         1.6.7  py310heca2aa9_0       conda-forge/linux-64       2MB
  - importlib-metadata             4.11.4  py310hff52083_0       conda-forge                   
  + importlib-metadata              6.6.0  pyha770c72_0          conda-forge/noarch        26kB
  - ipykernel                      6.16.0  pyh210e3f2_0          conda-forge                   
  + ipykernel                      6.21.2  pyh210e3f2_0          conda-forge/noarch       111kB
  - jupyter_core                   4.11.1  py310hff52083_0       conda-forge                   
  + jupyter_core                    5.3.0  py310hff52083_0       conda-forge/linux-64      91kB
  - jupyterlab                      3.4.8  pyhd8ed1ab_0          conda-forge                   
  + jupyterlab                      3.5.0  pyhd8ed1ab_0          conda-forge/noarch         6MB
  - krb5                           1.19.3  h3790be6_0            conda-forge                   
  + krb5                           1.20.1  h81ceb04_0            conda-forge/linux-64       1MB
  - libcurl                        7.85.0  h7bff187_0            conda-forge                   
  + libcurl                         8.1.1  h409715c_0            conda-forge/linux-64     372kB
  - libnghttp2                     1.47.0  hdcd2b5c_1            conda-forge                   
  + libnghttp2                     1.52.0  h61bc06f_0            conda-forge/linux-64     622kB
  - libsqlite                      3.39.4  h753d276_0            conda-forge                   
  + libsqlite                      3.42.0  h2797004_0            conda-forge/linux-64     829kB
  - libzlib                        1.2.12  h166bdaf_4            conda-forge                   
  + libzlib                        1.2.13  h166bdaf_4            conda-forge/linux-64      66kB
  - nodejs                        16.17.1  h96d913c_0            conda-forge                   
  + nodejs                        18.15.0  h8d033a5_0            conda-forge/linux-64      15MB
  - openssl                        1.1.1q  h166bdaf_0            conda-forge                   
  + openssl                         3.1.0  hd590300_3            conda-forge/linux-64       3MB
  - pyopenssl                      22.1.0  pyhd8ed1ab_0          conda-forge                   
  + pyopenssl                      23.1.1  pyhd8ed1ab_0          conda-forge/noarch       128kB
  - zlib                           1.2.12  h166bdaf_4            conda-forge                   
  + zlib                           1.2.13  h166bdaf_4            conda-forge/linux-64      94kB

  Downgrade:
─────────���───────────────────────────────────────────────────────────────────────────────────────

  - python                         3.10.6  h582c2e5_0_cpython    conda-forge                   
  + python                         3.10.0  h543edf9_3_cpython    conda-forge/linux-64      31MB

  Summary:

  Install: 206 packages
  Change: 2 packages
  Upgrade: 16 packages
  Downgrade: 1 packages

  Total download: 478MB

─────────────────────────────────────────────────────────────────────────────────────────────────

Expected behaviour

To finish the build.

Actual behaviour

While on the repo directory locally, it hang for over an hour until I interrupted it, but I noticed that if I was on any other directory (not the repo one) the build finished.

How to reproduce

I'm assuming docker is installed

1. Clone this repo https://github.com/coiled/dask-tutorial
2. Create an environment mamba create -n test-bug python=3.9
3. mamba activate test-bug
4. pip install jupyter-repo2docker
5. from the repo directory run jupyter-repo2docker https://github.com/coiled/dask-tutorial
6. See how it hangs around step 40/53

Your personal set up

• OS: Mac OS - Ventura 13.3.1
• Installed Docker desktop
• Docker version:

Client:
 Cloud integration: v1.0.31
 Version:           23.0.5
 API version:       1.42
 Go version:        go1.19.8
 Git commit:        bc4487a
 Built:             Wed Apr 26 16:12:52 2023
 OS/Arch:           darwin/arm64
 Context:           default

Server: Docker Desktop 4.19.0 (106363)
 Engine:
  Version:          23.0.5
  API version:      1.42 (minimum version 1.12)
  Go version:       go1.19.8
  Git commit:       94d3ad6
  Built:            Wed Apr 26 16:17:14 2023
  OS/Arch:          linux/arm64
  Experimental:     false
 containerd:
  Version:          1.6.20
  GitCommit:        2806fc1057397dbaeefbea0e4e17bddfbd388f38
 runc:
  Version:          1.1.5
  GitCommit:        v1.1.5-0-gf19387a
 docker-init:
  Version:          0.19.0
  GitCommit:        de40ad0

• repo2docker version repo2docker --version
2022.10.0

[welcome]

Thank you for opening your first issue in this project! Engagement like this is essential for open source projects! 🤗

If you haven't done so already, check out Jupyter's Code of Conduct. Also, please try to follow the issue template as it helps other other community members to contribute more effectively.

You can meet the other Jovyans by joining our Discourse forum. There is also an intro thread there where you can stop by and say Hi! 👋

Welcome to the Jupyter community! 🎉