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how to pass an observable file to petablint? #302

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FFroehlich opened this issue Feb 18, 2020 · 1 comment · Fixed by #357
Closed

how to pass an observable file to petablint? #302

FFroehlich opened this issue Feb 18, 2020 · 1 comment · Fixed by #357
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@dweindl
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bug Something isn't working good first issue Good for newcomers

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@FFroehlich
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There doesn't seem, to be an -o option, but petablint displays

Observable table not available. Skipping.

so it seems to expect something
@dweindl dweindl added bug Something isn't working good first issue Good for newcomers labels Feb 18, 2020
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dweindl commented Feb 18, 2020

The standard way to go would be specifying a YAML file. But you are right that there should be a CLI optional to specify an observable table. Somehow I thought I implemented that. Labeling as bug.

@dweindl dweindl added this to the v0.1.3 milestone Feb 28, 2020
@dweindl dweindl self-assigned this Feb 28, 2020
dweindl added a commit that referenced this issue Feb 28, 2020
@dweindl
petablint: allow specifying observables file via CLI (Closes #302)
1e05504
dweindl added a commit that referenced this issue Feb 28, 2020
@dweindl
petablint: allow specifying observables file via CLI (Closes #302)
dab3e4f
@dweindl dweindl mentioned this issue Feb 28, 2020
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dweindl added a commit that referenced this issue Feb 28, 2020
@dweindl
Merge pull request #357 from PEtab-dev/release_0.1.3
7b9d189 
Release 0.1.3

File format:

* Updated documentation
* Observables table in YAML file now mandatory in schema (was implicitly 
  mandatory before, as observable table was required already)

Library:
* petablint:
  * Fix: allow specifying observables file via CLI (Closes #302)
  * Fix: nominalValue is optional unless estimated!=1 anywhere (Fixes #303)
  * Fix: handle undefined observables more gracefully (Closes #300) (#351)
* Parameter mapping: 
  * Fix / refactor parameter mapping (breaking change) (#344)
    (now performing parameter value and scale mapping together)
  * check optional measurement cols in mapping (#350)
* allow calculating llhs (#349), chi2 values (#348) and residuals (#345)
* Visualization
  * Basic Scatterplots & lot of bar plot fixes (#270)
  * Fix incorrect length of bool `bool_preequ` when subsetting with ind_meas 
    (Closes #322)
* make libcombine optional (#338)
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Release 0.1.3 PEtab-dev/PEtab
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@FFroehlich @dweindl