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Add timeseries for all readers #3890
Add timeseries for all readers #3890
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Let’s be consistent with Python range. |
@orbeckst to be clear this will mean making API break for memoryreader. Are we happy with that? |
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mostly reformatting to avoid the if/else tree
I'd be accepting of calling the MemoryReader weird indexing a bug rather than a feature, unless it's documented as inclusive. If it is documented to be a given way, then we'll need to do the whole deprecation warning + allow for both options specifically for the MemoryReader. |
Unfortunately, MemoryReader.timeseries is documented as start and stop as inclusive https://docs.mdanalysis.org/stable/documentation_pages/coordinates/memory.html?highlight=memoryreader#MDAnalysis.coordinates.memory.MemoryReader.timeseries , this is probably a remnant of the very earliest versions of timeseries that was linked closely to the old DCDReader (even though DCDReader.timeseries now contains exclusive stop). Let’s deprecate the behavior for MemoryReader and change in 3.0. Make everything else consistent and range-like. |
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Let’s deprecate the behavior for MemoryReader and change in 3.0. Make everything else consistent and range-like.
I will PR deprecating the indexing of the memory reader separately. |
Co-authored-by: Irfan Alibay <[email protected]>
Issue raised #3893 |
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couple of small things
Codecov ReportBase: 94.35% // Head: 94.36% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## develop MDAnalysis/mdanalysis#3890 +/- ##
===========================================
+ Coverage 94.35% 94.36% +0.01%
===========================================
Files 194 194
Lines 25060 25109 +49
Branches 3392 3398 +6
===========================================
+ Hits 23645 23694 +49
Misses 1366 1366
Partials 49 49
Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. ☔ View full report at Codecov. |
Co-authored-by: Irfan Alibay <[email protected]>
I have added an exception on empty atomgroup for |
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Just temp blocking as a follow up from #3898, the folks that have the stronger stance on the use of NoDataError
probably will have strong views.
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Just two changelog things - I'm going to approve so that this can be merged once those comments are addressed.
Co-authored-by: Irfan Alibay <[email protected]>
@orbeckst this should be good to roll if you have a second to review? 😺 |
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lgtm
Fixes #3881 #2271 #3898 #2948 MDAnalysis/mdaencore#30
Changes made in this Pull Request:
ReaderBase
@MDAnalysis/coredevs one issue to be discussed. The MemoryReader has inclusive start, stop, step which is not in line with python
range
while this has PR been set up to have non-inclusive start-stop-step. Which would we prefer? One of the two implementations will need to change for consistency.PR Checklist