# \`mamba env update\` instead of \`mamba env create\`?

**URL:** <https://discourse.jupyter.org/t/mamba-env-update-instead-of-mamba-env-create/16007>\
**Category:** discuss\
**Created:** [September 28, 2022, 5:07pm UTC](https://discourse.jupyter.org/t/mamba-env-update-instead-of-mamba-env-create/16007 "2022-09-28T17:07:38Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![sluna](https://yyz1.discourse-cdn.com/flex031/user_avatar/discourse.jupyter.org/sluna/32/2892_2.png) [@sluna](https://discourse.jupyter.org/u/sluna)\
**Post date:** [September 28, 2022, 5:07pm UTC](https://discourse.jupyter.org/t/mamba-env-update-instead-of-mamba-env-create/16007/1 "2022-09-28T17:07:38Z")

</div>

Hello,

I have used [mybinder.org](http://mybinder.org) for a repository for a couple of years now:

```auto
https://mybinder.org/v2/gh/AMIGA-IAA/hcg-16/udocker-1.3.3

```

It’s been working until recently but now I get

```auto
Encountered problems while solving:
  - package aplpy-2.0-py_0 requires reproject >=0.4, but none of the providers can be installed

```

In the logs I see:

```auto
Step 40/53 : 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} '

```

Why is mamba doing `env update` instead of `env create`?

A local installation with mamba and the environment file works:

```auto
https://github.com/AMIGA-IAA/hcg-16/blob/8c110ee6f9e39e5d285c74678c806bf273b558b3/environment.yml

```

Many thanks,  
Sebastian

---

<div class="post-metadata">

**Author:** ![bollwyvl](https://yyz1.discourse-cdn.com/flex031/user_avatar/discourse.jupyter.org/bollwyvl/32/904_2.png) [@bollwyvl](https://discourse.jupyter.org/u/bollwyvl)\
**Post date:** [September 28, 2022, 5:45pm UTC](https://discourse.jupyter.org/t/mamba-env-update-instead-of-mamba-env-create/16007/2 "2022-09-28T17:45:17Z")

</div>

This is mostly for speed and image size. The `mamba env update` command is used as often folk only need to specify a few packages, and get them installed into the default env, running with most of the jupyter stack ready to go on python3.7. The default stance leaves less of a delta on disk, even if some packages are out-of-date.

Your specific `environment.yml` has a _lot_ of tight pins, and a _lot_ of channels, including the dreaded `conda-forge/labels/broken`. The `jupyter` metapackage is also rather troublesome, and you should drop that if you can, as `qt` doesn’t buy you much on binder without a lot of _other_ tricks.

You could sacrifice speed and cache-ability by forcing more behavior with a renamed `environment-foo.yml` and a `postBuild`, e.g.

For binder, you’d need to ensure you had the `jupyterhub-singleuser` package installed.

```bash
#!/usr/bin/env bash
mamba env create \
  --file .binder/environment-foo.yml \
  --prefix ${NB_PYTHON_PREFIX}
mamba clean -yaf # clean up downloaded files and indexes

```

I’d also highly recommend investigating [conda-lock](https://github.com/conda-incubator/conda-lock), and check a known-good, binder-compatible solve of your specific env in.

```auto
conda-lock --kind=explicit --platform linux-64 --file 

```

this will generate a lockfile that you can check in and use with any `conda` or `mamba` install, and get _exactly_ the packages you want, and install with the same `mamba create` technique above.

---

<div class="post-metadata">

**Author:** ![sluna](https://yyz1.discourse-cdn.com/flex031/user_avatar/discourse.jupyter.org/sluna/32/2892_2.png) [@sluna](https://discourse.jupyter.org/u/sluna)\
**Post date:** [September 29, 2022, 10:40am UTC](https://discourse.jupyter.org/t/mamba-env-update-instead-of-mamba-env-create/16007/3 "2022-09-29T10:40:23Z")

</div>

Thanks @bollwyvl

I added `conda-forge/labels/broken` after reading:

```auto
https://mybinder.readthedocs.io/en/latest/tutorials/reproducibility.html

```

The `jupyter` metapackage is there since we intend to use the same environment to execute the code both locally and on binder (and being consistent across). Reading `https://jupyter.org/install` I also tried `jupyterlab` but `qt` is also installed with it. Any other suggestion?

I just played a bit with `conda-lock` but it wasn’t a great experience, and I couldn’t get it to work properly. Not sure if I will use this at the moment.

I have also played a bit with the `postBuild`, adding:

```auto
mamba env create \
  --file hcg16.yml \
  --prefix ${NB_PYTHON_PREFIX}
mamba clean -yaf # clean up downloaded files and indexes

conda activate hcg-16

```

However, when I run the notebooks on binder, I don’t see the environment available?

```auto
!conda env list
# conda environments:
#
base /srv/conda
notebook * /srv/conda/envs/notebook

```

Do you know what would be the issue?  
Thanks,  
Sebastian

---

<div class="post-metadata">

**Author:** ![bollwyvl](https://yyz1.discourse-cdn.com/flex031/user_avatar/discourse.jupyter.org/bollwyvl/32/904_2.png) [@bollwyvl](https://discourse.jupyter.org/u/bollwyvl)\
**Post date:** [September 29, 2022, 1:39pm UTC](https://discourse.jupyter.org/t/mamba-env-update-instead-of-mamba-env-create/16007/4 "2022-09-29T13:39:49Z")

</div>

> `jupyterlab` but `qt`

There are any number of packages that will pull it: `jupyter` is just a likely candidate due to `qtconsole`. Another candidate is `matplotlib`, vs `matplotlib-base`.

Really, unless your desktop work actively uses `qt`-based UIs, it’s worth trying to avoid the 200mb and rather arcane pins it sometimes forces.

> `conda-lock`

Seems to work, with some of the above changes: [a conda-lock · GitHub](https://gist.github.com/bollwyvl/084ee1b86615ee8842b9988d100142eb)

note, it also needed some extra pins, as many newer conda-forge packages don’t take EOL python versions into account.

> I don’t see the environment

`--prefix` overrides `--name` (or the `name:` field in the environment). The rest of the machinery is looking to start `${NB_PYTHON_PREFIX}/bin/jupyter`.

If there is hard-coded stuff in the code referring to `hcg-16` (vs `$CONDA_PREFIX` or `sys.prefix`) then the user is likely in for even more adventures.