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jorgensd / adios4dolfinx

Extending DOLFINx with checkpointing functionality
http://jsdokken.com/adios4dolfinx/
MIT License
20 stars 7 forks source link

ipyparallel missing in installation instructions #95

Closed Chilipp closed 6 months ago

Chilipp commented 7 months ago

hey @jorgensd! I am just reviewing your software as part of https://github.com/openjournals/joss-reviews/issues/6451 and I am trying to install it. The conda installation works well, but in your documentation you heavily make use of the ipyparallel library, that is not mentioned in your installation instructions. this needs to be added

jorgensd commented 7 months ago

IPython parallel is listed under optional dependencies: https://github.com/jorgensd/adios4dolfinx/blob/main/pyproject.toml#L13-L17 I've made a clarification in the installation instructions: https://github.com/jorgensd/adios4dolfinx/pull/96 Let me know if that is a sufficient clarification.

Please note that it is v0.8.0 of this software that is under review. Unfortunately we do not have a conda release compatible with 0.8.0 yet (as DOLFINx hasn't had a 0.8.0 release, and the current version of the code relies on some interface changes in DOLFINx that I introduced).

Therefore, I would advice you to use docker for the time being, for instance with: docker run -ti -v $(pwd):/root/shared -w /root/shared --rm ghcr.io/fenics/dolfinx/dolfinx:nightly

Chilipp commented 6 months ago

@jorgensd unfortunately your fix in #96 did not solve the problem, as you did install v0.7.3 in the instructions. this version however does not list ipyparallel in the optional dependencies and as far as I understood, it's not the version we are supposed to review :wink: so please reopen this issue

jorgensd commented 6 months ago

@Chilipp I’m a bit uncertain as to what you would like me to specify? The version under review is 0.8 (which would be equivalent to the main branch, as i will make a new release (0.8.1) once the review is finalized).

Could you elaborate on what you think the current issue (with the main branch) of the software is?

Chilipp commented 6 months ago

ah, my apologies @jorgensd, I copied the installation instruction for the test setup from the conda section, and not from the docker section. In docker, you indeed referenced the main branch which is ok (see #97)