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environment.yml with only python >=x,<y fails #1301

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bollwyvl opened this issue Jul 23, 2023 · 3 comments
Closed

environment.yml with only python >=x,<y fails #1301

bollwyvl opened this issue Jul 23, 2023 · 3 comments

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@bollwyvl
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Bug description

A very simple environment fails to build on BinderHub when python is expressed as a range:

channels:
  - conda-forge
  - nodefaults
dependencies:
  - python >=3.9,<3.10

Expected behaviour

A working vanilla environment with python.

Actual behaviour

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockervsy0c9rp'...
HEAD is now at b311f5b
Python version unspecified, using current default Python version 3.10. This will change in the future.Building conda environment for python=3.10
Using CondaBuildPack builder
Step 1/50 : FROM docker.io/library/buildpack-deps:bionic
 ---> 0f137f206fa8
Step 2/50 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 9a60f92d78f4
Step 3/50 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 950fb7d941f4
Step 4/50 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> aad2c1ce6dff
Step 5/50 : ENV LC_ALL=en_US.UTF-8     LANG=en_US.UTF-8     LANGUAGE=en_US.UTF-8
 ---> Using cache
 ---> cb934374e1b5
Step 6/50 : ENV SHELL=/bin/bash
 ---> Using cache
 ---> 60a0cfa7ff62
Step 7/50 : ARG NB_USER
 ---> Using cache
 ---> 27c992051258
Step 8/50 : ARG NB_UID
 ---> Using cache
 ---> 626362bf33c6
Step 9/50 : ENV USER=${NB_USER}     HOME=/home/${NB_USER}
 ---> Using cache
 ---> 24abacc0f0c6
Step 10/50 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 5ba34ac3f7e1
Step 11/50 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        gettext-base        less        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 1a113221114c
Step 12/50 : EXPOSE 8888
 ---> Using cache
 ---> 43ece9cde4f1
Step 13/50 : ENV APP_BASE=/srv
 ---> Using cache
 ---> 5657b39a0484
Step 14/50 : ENV CONDA_DIR=${APP_BASE}/conda
 ---> Using cache
 ---> f8f78313702d
Step 15/50 : ENV NB_PYTHON_PREFIX=${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 1c67ea477fb9
Step 16/50 : ENV NPM_DIR=${APP_BASE}/npm
 ---> Using cache
 ---> 4e5d9aece07c
Step 17/50 : ENV NPM_CONFIG_GLOBALCONFIG=${NPM_DIR}/npmrc
 ---> Using cache
 ---> b86f9c4bccc3
Step 18/50 : ENV NB_ENVIRONMENT_FILE=/tmp/env/environment.lock
 ---> Using cache
 ---> 80ae064b87a3
Step 19/50 : ENV MAMBA_ROOT_PREFIX=${CONDA_DIR}
 ---> Using cache
 ---> 4cafd175b65f
Step 20/50 : ENV MAMBA_EXE=${CONDA_DIR}/bin/mamba
 ---> Using cache
 ---> a2fd0ffb89ec
Step 21/50 : ENV CONDA_PLATFORM=linux-64
 ---> Using cache
 ---> e0bfd399f34a
Step 22/50 : ENV KERNEL_PYTHON_PREFIX=${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 3cc71cfd4d10
Step 23/50 : ENV PATH=${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 7ca083140a37
Step 24/50 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e10-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-44e764 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> 0cbd98e041a6
Step 25/50 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e10-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e10-2dlinux-2d64-2elock-388e0b /tmp/env/environment.lock
 ---> Using cache
 ---> 3242406b91b0
Step 26/50 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e10-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dbase-2denv-2ebash-e5509f /tmp/install-base-env.bash
 ---> Using cache
 ---> fbe47a0ddf87
Step 27/50 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-base-env.bash' && rm -rf /tmp/install-base-env.bash /tmp/env
 ---> Using cache
 ---> bee2cdf4ee28
Step 28/50 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 95f7e95b6a04
Step 29/50 : USER root
 ---> Using cache
 ---> 2120b46739b8
Step 30/50 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> be02981960cc
Step 31/50 : ENV REPO_DIR=${REPO_DIR}
 ---> Using cache
 ---> 7c41df45494f
Step 32/50 : RUN if [ ! -d "${REPO_DIR}" ]; then         /usr/bin/install -o ${NB_USER} -g ${NB_USER} -d "${REPO_DIR}";     fi
 ---> Using cache
 ---> 7208f01def75
Step 33/50 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> e3f692b0f6ac
Step 34/50 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> f50acf41adcd
Step 35/50 : ENV PATH=${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 7e582363e01c
Step 36/50 : ENV CONDA_DEFAULT_ENV=${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 2ffbb645f077
Step 37/50 : COPY --chown=1000:1000 src/environment.yml ${REPO_DIR}/environment.yml
 ---> 6f6509589908
Step 38/50 : USER ${NB_USER}
 ---> Running in 0a38d4272e9d
Removing intermediate container 0a38d4272e9d
 ---> f8056503a786
Step 39/50 : RUN TIMEFORMAT='time: %3R' bash -c 'time ${MAMBA_EXE} env update -p ${NB_PYTHON_PREFIX} --file "environment.yml" && time ${MAMBA_EXE} clean --all -f -y && ${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX} '
 ---> Running in b0383944f1b8

Looking for: ["python[version='>=3.9,<3.10']"]


Transaction


Prefix: /srv/conda/envs/notebook


Updating specs:
  • python[version='>=3.9,<3.10']

Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────────────────────────
Change:
───────────────────────────────────────────────────────────────────────────────────────────

  • pycparser 2.21 pyhd8ed1ab_0 conda-forge
  • pycparser 2.21 pyhd8ed1ab_0 conda-forge 103kB
  • tornado 6.3.2 py310h2372a71_0 conda-forge
  • tornado 6.3.2 py39hd1e30aa_0 conda-forge 629kB
  • ruamel.yaml.clib 0.2.7 py310h1fa729e_1 conda-forge
  • ruamel.yaml.clib 0.2.7 py39h72bdee0_1 conda-forge 143kB
  • pyzmq 25.1.0 py310h5bbb5d0_0 conda-forge
  • pyzmq 25.1.0 py39hb257651_0 conda-forge 450kB
  • pyyaml 6.0 py310h5764c6d_5 conda-forge
  • pyyaml 6.0 py39hb9d737c_5 conda-forge 184kB
  • pyrsistent 0.19.3 py310h1fa729e_0 conda-forge
  • pyrsistent 0.19.3 py39h72bdee0_0 conda-forge 99kB
  • psutil 5.9.5 py310h1fa729e_0 conda-forge
  • psutil 5.9.5 py39h72bdee0_0 conda-forge 359kB
  • markupsafe 2.1.3 py310h2372a71_0 conda-forge
  • markupsafe 2.1.3 py39hd1e30aa_0 conda-forge 24kB
  • y-py 0.5.9 py310h4426083_0 conda-forge
  • y-py 0.5.9 py39h50f1755_0 conda-forge 1MB
  • greenlet 2.0.2 py310hc6cd4ac_1 conda-forge
  • greenlet 2.0.2 py39h3d6467e_1 conda-forge 190kB
  • debugpy 1.6.7 py310heca2aa9_0 conda-forge
  • debugpy 1.6.7 py39h227be39_0 conda-forge 2MB
  • cffi 1.15.1 py310h255011f_3 conda-forge
  • cffi 1.15.1 py39he91dace_3 conda-forge 235kB
  • argon2-cffi-bindings 21.2.0 py310h5764c6d_3 conda-forge
  • argon2-cffi-bindings 21.2.0 py39hb9d737c_3 conda-forge 35kB

Reinstall:
───────────────────────────────────────────────────────────────────────────────────────────

o wheel 0.40.0 pyhd8ed1ab_0 conda-forge
o setuptools 67.7.2 pyhd8ed1ab_0 conda-forge
o pip 23.1.2 pyhd8ed1ab_0 conda-forge
o zipp 3.15.0 pyhd8ed1ab_0 conda-forge
o widgetsnbextension 4.0.7 pyhd8ed1ab_0 conda-forge
o websocket-client 1.5.2 pyhd8ed1ab_0 conda-forge
o webencodings 0.5.1 py_1 conda-forge
o typing_extensions 4.6.3 pyha770c72_0 conda-forge
o traitlets 5.9.0 pyhd8ed1ab_0 conda-forge
o tomli 2.0.1 pyhd8ed1ab_0 conda-forge
o soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
o sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
o six 1.16.0 pyh6c4a22f_0 conda-forge
o send2trash 1.8.2 pyh41d4057_0 conda-forge
o rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
o pytz 2023.3 pyhd8ed1ab_0 conda-forge
o python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
o python-fastjsonschema 2.17.1 pyhd8ed1ab_0 conda-forge
o pysocks 1.7.1 pyha2e5f31_6 conda-forge
o pyjwt 2.7.0 pyhd8ed1ab_0 conda-forge
o pygments 2.15.1 pyhd8ed1ab_0 conda-forge
o pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
o ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
o prometheus_client 0.17.0 pyhd8ed1ab_0 conda-forge
o pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
o pickleshare 0.7.5 py_1003 conda-forge
o parso 0.8.3 pyhd8ed1ab_0 conda-forge
o pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
o pamela 1.0.0 py_0 conda-forge
o packaging 23.1 pyhd8ed1ab_0 conda-forge
o nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
o mistune 2.0.5 pyhd8ed1ab_0 conda-forge
o jupyterlab_widgets 3.0.7 pyhd8ed1ab_1 conda-forge
o json5 0.9.5 pyh9f0ad1d_0 conda-forge
o ipython_genutils 0.2.0 py_1 conda-forge
o idna 3.4 pyhd8ed1ab_0 conda-forge
o flit-core 3.9.0 pyhd8ed1ab_0 conda-forge
o executing 1.2.0 pyhd8ed1ab_0 conda-forge
o exceptiongroup 1.1.1 pyhd8ed1ab_0 conda-forge
o entrypoints 0.4 pyhd8ed1ab_0 conda-forge
o defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
o decorator 5.1.1 pyhd8ed1ab_0 conda-forge
o charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge
o certifi 2023.5.7 pyhd8ed1ab_0 conda-forge
o blinker 1.6.2 pyhd8ed1ab_0 conda-forge
o backports 1.0 pyhd8ed1ab_3 conda-forge
o backcall 0.2.0 pyh9f0ad1d_0 conda-forge
o attrs 23.1.0 pyh71513ae_1 conda-forge
o async_generator 1.10 py_0 conda-forge
o aiofiles 22.1.0 pyhd8ed1ab_0 conda-forge
o importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge
o importlib-metadata 6.6.0 pyha770c72_0 conda-forge
o tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
o typing-extensions 4.6.3 hd8ed1ab_0 conda-forge
o matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
o comm 0.1.3 pyhd8ed1ab_0 conda-forge
o beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
o rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
o python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
o asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
o babel 2.12.1 pyhd8ed1ab_1 conda-forge
o urllib3 2.0.3 pyhd8ed1ab_0 conda-forge
o jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
o pexpect 4.8.0 pyh1a96a4e_2 conda-forge
o jedi 0.18.2 pyhd8ed1ab_0 conda-forge
o bleach 6.0.0 pyhd8ed1ab_0 conda-forge
o anyio 3.7.0 pyhd8ed1ab_1 conda-forge
o backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
o platformdirs 3.5.1 pyhd8ed1ab_0 conda-forge
o aiosqlite 0.19.0 pyhd8ed1ab_0 conda-forge
o stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
o requests 2.31.0 pyhd8ed1ab_0 conda-forge
o wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge
o ipython 8.14.0 pyh41d4057_0 conda-forge
o prompt-toolkit 3.0.38 pyha770c72_0 conda-forge
o terminado 0.17.1 pyh41d4057_0 conda-forge
o jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge
o mako 1.2.4 pyhd8ed1ab_0 conda-forge
o jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
o ypy-websocket 0.8.2 pyhd8ed1ab_0 conda-forge
o jupyter_ydoc 0.2.4 pyhd8ed1ab_0 conda-forge
o jupyter_client 8.2.0 pyhd8ed1ab_0 conda-forge
o pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge
o oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge
o argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
o nbformat 5.9.0 pyhd8ed1ab_0 conda-forge
o jupyter_telemetry 0.1.0 pyhd8ed1ab_1 conda-forge
o jupyter_events 0.6.3 pyhd8ed1ab_0 conda-forge
o alembic 1.11.1 pyhd8ed1ab_0 conda-forge
o ipykernel 6.23.1 pyh210e3f2_0 conda-forge
o certipy 0.1.3 py_0 conda-forge
o nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
o ipywidgets 8.0.6 pyhd8ed1ab_0 conda-forge
o jupyterhub-base 3.1.1 pyh2a2186d_0 conda-forge
o nbconvert-core 7.4.0 pyhd8ed1ab_0 conda-forge
o nbconvert-pandoc 7.4.0 pyhd8ed1ab_0 conda-forge
o jupyter_server 1.23.6 pyhd8ed1ab_0 conda-forge
o nbconvert 7.4.0 pyhd8ed1ab_0 conda-forge
o notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
o jupyterlab_server 2.22.1 pyhd8ed1ab_0 conda-forge
o jupyter_server_fileid 0.9.0 pyhd8ed1ab_0 conda-forge
o jupyter-resource-usage 0.7.1 pyhd8ed1ab_0 conda-forge
o nbclassic 1.0.0 pyhb4ecaf3_1 conda-forge
o jupyter_server_ydoc 0.8.0 pyhd8ed1ab_0 conda-forge
o notebook 6.5.4 pyha770c72_0 conda-forge
o jupyterlab 3.6.4 pyhd8ed1ab_0 conda-forge
o jupyter-offlinenotebook 0.2.2 pyh1d7be83_0 conda-forge
o jupyterhub-singleuser 3.1.1 pyh2a2186d_0 conda-forge

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

  • jupyter_core 5.3.0 py310hff52083_0 conda-forge
  • jupyter_core 5.3.1 py39hf3d152e_0 conda-forge 92kB
  • ruamel.yaml 0.17.31 py310h2372a71_0 conda-forge
  • ruamel.yaml 0.17.32 py39hd1e30aa_0 conda-forge 200kB
  • sqlalchemy 2.0.15 py310h2372a71_0 conda-forge
  • sqlalchemy 2.0.19 py39hd1e30aa_0 conda-forge 3MB
  • cryptography 41.0.1 py310h75e40e8_0 conda-forge
  • cryptography 41.0.2 py39hd4f0224_0 conda-forge 2MB

Downgrade:
───────────────────────────────────────────────────────────────────────────────────────────

  • python 3.10.11 he550d4f_0_cpython conda-forge
  • python 3.9.16 h2782a2a_0_cpython conda-forge 24MB
  • python_abi 3.10 3_cp310 conda-forge
  • python_abi 3.9 3_cp39 conda-forge 6kB

Summary:

Change: 13 packages
Reinstall: 108 packages
Upgrade: 4 packages
Downgrade: 2 packages

Total download: 35MB

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

�[91m

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/srv/conda/lib/python3.11/site-packages/conda/exception_handler.py", line 16, in __call__
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/srv/conda/lib/python3.11/site-packages/conda_env/cli/main.py", line 49, in do_call
    exit_code = getattr(module, func_name)(args, parser)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/srv/conda/lib/python3.11/site-packages/conda/notices/core.py", line 123, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/srv/conda/lib/python3.11/site-packages/conda_env/cli/main_update.py", line 139, in execute
    result[installer_type] = installer.install(prefix, specs, args, env)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/srv/conda/lib/python3.11/site-packages/mamba/mamba_env.py", line 153, in mamba_install
    transaction.fetch_extract_packages()
RuntimeError: Could not set URL (code: 14 - url = /wheel-0.40.0-pyhd8ed1ab_0.conda)

$ /srv/conda/bin/mamba update -p /srv/conda/envs/notebook --file environment.yml

environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=/srv/conda/envs/notebook
CONDA_DIR=/srv/conda
CONDA_PLATFORM=linux-64
CONDA_ROOT=/srv/conda
CURL_CA_BUNDLE=
LD_PRELOAD=
PATH=/home/jovyan/.local/bin:/home/jovyan/.local/bin:/srv/conda/envs/notebo
ok/bin:/srv/conda/bin:/srv/npm/bin:/usr/local/sbin:/usr/local/bin:/usr
/sbin:/usr/bin:/sbin:/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=

 active environment : None
   user config file : /home/jovyan/.condarc

populated config files : /srv/conda/.condarc
conda version : 23.5.2
conda-build version : not installed
python version : 3.11.4.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.27=0
__linux=5.15.0=0
__unix=0=0
base environment : /srv/conda (writable)
conda av data dir : /srv/conda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /srv/conda/pkgs
/home/jovyan/.conda/pkgs
envs directories : /srv/conda/envs
/home/jovyan/.conda/envs
platform : linux-64
user-agent : conda/23.5.2 requests/2.31.0 CPython/3.11.4 Linux/5.15.0-69-generic ubuntu/18.04.6 glibc/2.27
UID:GID : 1000:1000
netrc file : None
offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

�[0m�[91mtime: 37.255
�[0mRemoving intermediate container b0383944f1b8
The command '/bin/sh -c TIMEFORMAT='time: %3R' bash -c 'time ${MAMBA_EXE} env update -p ${NB_PYTHON_PREFIX} --file "environment.yml" && time ${MAMBA_EXE} clean --all -f -y && ${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX} '' returned a non-zero code: 1

How to reproduce

  • view this gist
  • click the binder badge

Your personal set up

  • OS: linux
  • Docker version: docker version binderhub
  • repo2docker version repo2docker --version binderhub

c/f robots-from-jupyter/robotkernel#145
@nrbgt nrbgt mentioned this issue Aug 3, 2023
Merged
14 tasks
This was referenced Aug 14, 2023
Merged
Merged
@Mikejmnez Mikejmnez mentioned this issue Sep 8, 2023
Closed
@bollwyvl
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the minimal reproducer above no longer appears to fail on binderhub, so I guess this is fixed?

@manics
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manics commented Oct 23, 2023

Maybe the Mamba upgrade fixed it?
#1313

@bollwyvl
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🤷 ?

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@bollwyvl @manics