Container docs #1539
Container docs #1539
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For further background, see ICB-DCM#1448. We don't have to compute the full gradient in every model simulation. Some entries might not be required because of fixed parameter or some condition-specific objective parameter mapping. The former was supported (however, not tested), the latter was not supported. Now both are tested an supported. There was no good way to communicate the fixed parameters to AmiciCalculator where ExpData.plist gets set. Passing this information is currently only possible through the parameter mapping, based on which the required sensitivities are determined. Therefore, in addition to the general parameter mapping, there is now a parameter mapping that accounts for the fixed parameters. Not sure what could be a more elegant way to handle that.
stephanmg
requested review from
dweindl,
FFroehlich,
Doresic,
PaulJonasJost and
vwiela
as code owners
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@stephanmg : Please rebase / remove the unrelated changes |
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| We provide a pyPESTO docker image in OCI format through `docker.io/stephanmg/pypesto`. | ||
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| Develop versions are pushed as tag ``latest``. |
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Are they? I don't see any at https://hub.docker.com/r/stephanmg/pypesto.
Also, the workflow uses ICB_DCM/pypesto.
(-> #1538)
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Should be also published now, manually pushed latest image with commit from develop latest from today: commit sha 20fd9de
| If you manually build your container and need to convert to Apptainer, first export your docker image to `.tar` by: | ||
| `docker save -o pypesto.tar pypesto:latest` and pull the image before from docker.io by `docker pull docker.io/stephanmg/pypesto:latest`. |
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Why should one go through docker if one wants to use apptainer? apptainer pull docker://stephanmg/pypesto:latest?
"first export ... pull before..." is somewhat unclear.
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Fixed. Has never been triggered from the GHA workflow, merged to develop yesterday, so next commit should trigger a build and push of the image.
| Likewise for singularity: | ||
| ``singularity build pypesto.sif docker-archive://pypesto.tar`` | ||
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I'd leave that out. They are interchangeable.
| If you manually build your container and need to convert to Apptainer, first export your docker image to `.tar` by: | ||
| `docker save -o pypesto.tar pypesto:latest` and pull the image before from docker.io by `docker pull docker.io/stephanmg/pypesto:latest`. | ||
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| Then execute for generating a `.sif` file: | ||
| ``apptainer build pypesto.sif docker-archive://pypesto.tar`` | ||
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| Likewise for singularity: | ||
| ``singularity build pypesto.sif docker-archive://pypesto.tar`` | ||
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Move that down under the respective heading?
Co-authored-by: Daniel Weindl <[email protected]>
Co-authored-by: Daniel Weindl <[email protected]>
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