[query] Use EncodedLiteral instead of Literal from python to scala #13814
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
danking
previously requested changes
Oct 13, 2023
hail/python/hail/expr/types.py
Outdated
| @@ -1754,6 +1851,9 @@ def call_allele_pair(i): | |||
|
|
|||
| return genetics.Call(alleles, phased) | |||
|
|
|||
| def _convert_to_encoding(self, byte_writer, value): | |||
| pass # TODO | |||
There was a problem hiding this comment.
heh yeah this one is a bit complex
hail/python/test/hail/test_ir.py
Outdated
| ) | ||
| def test_literal_encoding(value): | ||
| lit = hl.literal(value) | ||
| round_trip = lit.dtype._from_encoding(lit.dtype._to_encoding(value)) |
There was a problem hiding this comment.
love me a round-trip test
daniel-goldstein
force-pushed
the
encode-literals-python-to-scala
branch
from
ac19f23
to
9cb4764
Compare
daniel-goldstein
dismissed
danking’s stale review
Should be mostly if not entirely passing now.
hail/python/hail/expr/types.py
Outdated
| byte_writer.write_int64(dim) | ||
|
|
||
| if self.element_type in _numeric_types: | ||
| byte_writer.write_bytes(value.data) |
There was a problem hiding this comment.
Getting the element ordering right here makes me a little nervous. Should maybe have some more rigorous tests.
danking
requested changes
Oct 16, 2023
| interval = hl.Interval(start=start, end=end, includes_start=True, includes_end=False) | ||
| _assert_encoding_roundtrip(start) | ||
| _assert_encoding_roundtrip(end) | ||
| _assert_encoding_roundtrip(interval) |
There was a problem hiding this comment.
Each of these three tests is slightly different, but they all ultimately call the same method. What's the argument against just parameterizing _assert_encoding_roundtrip itself?
There was a problem hiding this comment.
I tried that at first, and looks like I can do this with Call, but I can't instantiate a Locus before init (because it tries to load a reference genome) so I can't include a Locus in the parametrize.
hail/python/test/hail/test_ir.py
Outdated
| {"foo", "bar", "baz"}, | ||
| {"a": 1, "b": 2}, | ||
| np.array([[1, 2], [3, 4], [5, 6]]), | ||
| np.array([[1, 2], [3, 4], [5, 6]]).T, |
There was a problem hiding this comment.
Pursuant to your comment above can we add:
- Test for 0d np.array
- Test for 1d np.array
- Test for 2d np.array
- Test for 4d np.array
- Transposition of all of the above
danking
previously approved these changes
Oct 18, 2023
| byte_writer.write_bytes(value.data) | ||
| else: | ||
| for elem in np.nditer(value, order='F'): | ||
| self.element_type._convert_to_encoding(byte_writer, elem) |
There was a problem hiding this comment.
I feel good about this now. You're using ENDArrayColumnMajor and the column ordering is Fortran, so ti all checks out.
danking
reviewed
Oct 18, 2023
hail/python/hail/expr/types.py
Outdated
| while i < length: | ||
| missing_byte = 0 | ||
| for j in range(min(8, length - i)): | ||
| if value[i + j] is None: |
There was a problem hiding this comment.
Suggested change
| if value[i + j] is None: | |
| if value[i + j] in (None, pd.NA): |
danking
reviewed
Oct 18, 2023
hail/python/hail/expr/types.py
Outdated
| while i < length: | ||
| missing_byte = 0 | ||
| for j in range(min(8, length - i)): | ||
| if value[keys[i + j]] is None: |
There was a problem hiding this comment.
same here for missing values from pandas.
daniel-goldstein
force-pushed
the
encode-literals-python-to-scala
branch
2 times, most recently
from
6756fff
to
b5719f9
Compare
daniel-goldstein
dismissed
danking’s stale review
dismissing as theres been a non-trivial change
|
Hmm. Seems like the ArraySorter still isn't quite right? I also saw some issues with sockets timing out but I don't know what to make of those yet. |
danking
requested changes
Oct 20, 2023
|
|
||
| val sorter = new ArraySorter(EmitRegion(cb.emb, region), ab) | ||
| def lessThan(cb: EmitCodeBuilder, region: Value[Region], l: Value[_], r: Value[_]): Value[Boolean] = { | ||
| val lk = cb.memoize(sct.loadToSValue(cb, l).asBaseStruct.loadField(cb, 0)) |
There was a problem hiding this comment.
@patrick-schultz is a missing key value handled correctly by this code?
There was a problem hiding this comment.
See failure here: https://batch.hail.is/batches/8064082/jobs/83
There was a problem hiding this comment.
Given how we're generating these from Python, how could a key value ever be missing?
There was a problem hiding this comment.
I don't see anything obviously wrong. I can try checking out the branch and debugging.
There was a problem hiding this comment.
Thanks Patrick!
|
Hmm. What's special about The other issue seems like it might be simpler, we're just setting a bad type on a field: |
|
Ah we have the same ordering problem with sets as we have with dicts |
|
We sure do |
danking
approved these changes
Oct 25, 2023
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
CHANGELOG: Pipelines that are memory-bound by copious use of
hl.literal, such asvds.filter_intervals, require substantially less memory.Closes #13757