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change timeseries "format" kw to "order" #1453

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orbeckst opened this Issue Jul 6, 2017 · 9 comments

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orbeckst commented Jul 6, 2017

In various issues and discussions we sort-of decided that the Reader.timeseries() method should not use format="afc" as a kwarg but order="afc" (which make it consistent with the MemoryReader, avoids clashes with the builtin format, ... and avoids clashes with the format kwarg of Universe (yes, that one clashes with the builtin, too)).

@orbeckst orbeckst added the API label Jul 6, 2017

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orbeckst Jul 21, 2017

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I think we should consider adding this to 0.17 so that we have some deprecation time.

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orbeckst commented Jul 21, 2017

I think we should consider adding this to 0.17 so that we have some deprecation time.

@orbeckst orbeckst added this to the 0.17.0 milestone Jul 21, 2017

@richardjgowers richardjgowers referenced this issue Jul 21, 2017

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release 0.17.0 #1536

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Note to myself: While playing around with the memory reader for the Examples for RMSF I found that not all orderings (keyword order=...) work for Universe.load_new(array_like, order="..."). At least I got a cryptic error with fac (something that there were too few dimensions) when I tried a array_like for a single frame. It worked with afc, which I put explicitly in the example (but it is also the default for e.g. DCReader.timeseries).

Need to investigate more and possibly add tests for all permutations when reading with the MemoryReader.

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orbeckst commented Aug 21, 2017

Note to myself: While playing around with the memory reader for the Examples for RMSF I found that not all orderings (keyword order=...) work for Universe.load_new(array_like, order="..."). At least I got a cryptic error with fac (something that there were too few dimensions) when I tried a array_like for a single frame. It worked with afc, which I put explicitly in the example (but it is also the default for e.g. DCReader.timeseries).

Need to investigate more and possibly add tests for all permutations when reading with the MemoryReader.

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Also note that the docs for the MemoryReader need to be update:

  • When a array_like is provided then it is automatically passed to the MemoryReader and the format="MEMORY" or format=MemoryReader is not needed anymore.
  • Same for Universe.load_new()

In general we need to clarify how file types are recognized.

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orbeckst commented Aug 21, 2017

Also note that the docs for the MemoryReader need to be update:

  • When a array_like is provided then it is automatically passed to the MemoryReader and the format="MEMORY" or format=MemoryReader is not needed anymore.
  • Same for Universe.load_new()

In general we need to clarify how file types are recognized.

@orbeckst orbeckst self-assigned this Oct 27, 2017

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I'll try to do this in my ample spare time ;-) – unless anyone else wants to: feel free to snatch this issue from me.

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orbeckst commented Oct 27, 2017

I'll try to do this in my ample spare time ;-) – unless anyone else wants to: feel free to snatch this issue from me.

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@orbeckst do you have any code for your experiments of order that you did in august.

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kain88-de commented Jan 2, 2018

@orbeckst do you have any code for your experiments of order that you did in august.

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No, sorry. But you can take the Example at https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/rms.html#MDAnalysis.analysis.rms.RMSF and just change order in the line

# make a reference structure (need to reshape into a 1-frame "trajectory")
reference = mda.Merge(protein).load_new(
            reference_coordinates[:, None, :], order="afc")

and it should fail.

(I am travelling and if you want to work on this please by all means do so and also assign yourself/un-assign me. Thanks!)

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orbeckst commented Jan 2, 2018

No, sorry. But you can take the Example at https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/rms.html#MDAnalysis.analysis.rms.RMSF and just change order in the line

# make a reference structure (need to reshape into a 1-frame "trajectory")
reference = mda.Merge(protein).load_new(
            reference_coordinates[:, None, :], order="afc")

and it should fail.

(I am travelling and if you want to work on this please by all means do so and also assign yourself/un-assign me. Thanks!)

@kain88-de kain88-de referenced this issue Jan 2, 2018

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REF: Format to order for timeseries #1751

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Your example case works now with my changes.

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kain88-de commented Jan 2, 2018

Your example case works now with my changes.

@kain88-de kain88-de assigned kain88-de and unassigned orbeckst Jan 2, 2018

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@kain88-de many thanks for finishing the PR, I very much appreciate you jumping in. Sorry I wasn't able to be more helpful.

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orbeckst commented Jan 5, 2018

@kain88-de many thanks for finishing the PR, I very much appreciate you jumping in. Sorry I wasn't able to be more helpful.

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kain88-de commented Jan 5, 2018

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