Closed rkurchin closed 2 years ago
NB's for people:
The only concrete FD I'm keeping in CF for now is the EFD since that's quite generic and also depends very little on the nature of the structure representation. But I may split out modules for different sources of lookup tables e.g. pymatgen, matminer, etc...
@rkurchin test failures seem to be primarily because we are still using Conda
in deps/build.jl
, when Conda.jl was removed as a dependency in 352044ffd4ad2829c82bfc348851c56c38ded5c8.
Thanks, yeah I haven't finished fixing all the tests yet. Will keep that in mind, hoping to get to it later today!
Merging #132 (899fbac) into main (ef30f5f) will increase coverage by
4.38%
. The diff coverage is86.72%
.:exclamation: Current head 899fbac differs from pull request most recent head 08cca74. Consider uploading reports for the commit 08cca74 to get more accurate results
@@ Coverage Diff @@
## main #132 +/- ##
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+ Coverage 80.80% 85.18% +4.38%
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Files 20 11 -9
Lines 573 162 -411
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- Hits 463 138 -325
+ Misses 110 24 -86
Impacted Files | Coverage Δ | |
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src/ChemistryFeaturization.jl | 0.00% <0.00%> (-80.00%) |
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src/featurizedatoms.jl | 44.44% <66.66%> (+4.44%) |
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src/codecs/onehotonecold_utils.jl | 78.94% <78.94%> (ø) |
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src/codecs/onehotonecold.jl | 84.44% <83.33%> (+0.23%) |
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src/features/features.jl | 80.00% <87.50%> (-8.89%) |
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src/codecs/codecs.jl | 100.00% <100.00%> (ø) |
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src/codecs/directcodec.jl | 100.00% <100.00%> (ø) |
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src/codecs/simplecodec.jl | 100.00% <100.00%> (ø) |
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src/features/elementfeature.jl | 100.00% <100.00%> (+15.00%) |
:arrow_up: |
src/features/elementfeature_utils.jl | 100.00% <100.00%> (ø) |
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... and 2 more |
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I'd like to go ahead and get this merged so that I can register and then merge/register the associated AtomGraphs and AGN updates (and @DhairyaLGandhi can do so with WeaveModel as well). Once everything is registered I'll be able to fix the docs issues so that they can build again.
Anyway, would love any additional feedback you guys have here! I think we were generally in agreement about these changes. so I may just merge in a day or so if I don't hear any objections.
I'm generally on board with the utils/
directory idea, but it doesn't seem necessary to me when there would only be one file in it. I think if/when we add more such things we can introduce that level to the hierarchy.
This is currently a WIP where I'm implementing a bunch of the stuff we've discussed vis a vis splitting out functionalities, "interface-ifying" things, and further separating concerns wrt the codec syntax. Some broad remarks..
OIther specific changes:
encode
function as inencode(fd, atoms, codec)
but the final argument is optional because it will default todefault_codec(fd)
if not providedInterfaces and associated functions:
encode
,decode
,output_shape
get_value
,encodable_elements
,default_codec
elements
functionRemaining todos: