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Fix CI #10

Merged
merged 13 commits into from
Jun 25, 2023
Merged

Fix CI #10

merged 13 commits into from
Jun 25, 2023

Commits on Jun 23, 2023

  1. Change base docker image.

    @luciansmith
    luciansmith committed Jun 23, 2023
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  2. Try Python 3.11 base, too.

    @luciansmith
    luciansmith committed Jun 23, 2023
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  3. Install sympy by hand. 

    It should be a requirement of amici, but perhaps it was missed?
    @luciansmith
    luciansmith committed Jun 23, 2023
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  4. Try pinning pip to 23.0.1 

    As of 23.1, pip updated to no longer allow how all biosimulations projects are installed.
    @luciansmith
    luciansmith committed Jun 23, 2023
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  5. Amici should have already been installed? 

    Install it explicitly, but it shouldn't make a difference.
    @luciansmith
    luciansmith committed Jun 23, 2023
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  6. Explicitly install sympy.

    @luciansmith
    luciansmith committed Jun 23, 2023
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  7. Try not explicitly installing amici 

    Explicitly installing it seems to have problems with sympy, even if sympy is clearly already installed.  However, amici is a dependency of biosimulators_amici, so it should be installed already anyway?  Let's see what happens.
    @luciansmith
    luciansmith committed Jun 23, 2023
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  8. Fix comment.

    @luciansmith
    luciansmith committed Jun 23, 2023
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Commits on Jun 24, 2023

  1. Fix observable IDs 

    IDs in AMICI models have to be globally unique.

Fixes errors of type `E           amici.import_utils.SBMLException: AMICI tried to add a local symbol AL with value AL, but AL was already instantiated with AL. This means that there are multiple SBML elements with SId AL, which is invalid SBML. This can be fixed by renaming the elements with SId AL.`
    @dweindl
    dweindl committed Jun 24, 2023
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  2. Merge pull request #9 from biosimulators/fix_observable_ids 

    Fix observable IDs
    @luciansmith
    luciansmith committed Jun 24, 2023
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  3. Set actual value, not 'none'.

    @luciansmith
    luciansmith committed Jun 24, 2023
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  4. Relax tolerance 

    (Might have the argument names wrong)
    @luciansmith
    luciansmith committed Jun 24, 2023
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  5. Remove sphinxprettysearchresults 

    It broke, and isn't being updated.
    @luciansmith
    luciansmith committed Jun 24, 2023
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