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Relax protobuf dependencies further in python package #390

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holtgrewe opened this issue Sep 7, 2024 · 4 comments · May be fixed by #393
Open

Relax protobuf dependencies further in python package #390

holtgrewe opened this issue Sep 7, 2024 · 4 comments · May be fixed by #393
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@iimpulse

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@holtgrewe
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You are limiting the protobuf versions to >=3.20.2,<4.0.0. Is this necessary? protobuf 4.x is available since 2022.

phenopacket-schema/python/pyproject.toml

Line 36 in d69fc9e

"protobuf>=3.20.2,<4.0.0",

This prevents anything else depending on phenopackets to use a more recent protobuf version.
@julesjacobsen
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@iimpulse can you look into this, please?

@gilmorera
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@iimpulse This is also an issue for me. Is there a specific reason the version is pinned?

@ielis
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ielis commented Jan 13, 2025

Hi @gilmorera @holtgrewe

Is there a specific reason the version is pinned?

Phenopacket Schema uses Protobuf 3.20.3:

phenopacket-schema/pom.xml

Line 53 in d69fc9e

<protobuf.version>3.20.3</protobuf.version>

therefore, out of caution, we allow protobuf<4.0.0, per Semantic versioning. In principle, protobuf>=4.0.0 may work OK, it's hard to be sure though..

I would like to fix this issue with a PR where that checks if the messages serialized by protobuf-java==3.20.3 are decoded properly with a newer Python protobuf.

This seems to work for Python bindings generated with Protobuf compiler 3.20.3 (in Phenopacket Schema) or with 4.29.3 (latest protobuf-java) and for protobuf==5.29.3 (latest Protobuf release for Python).

I'll be posting updates here..

@ielis ielis linked a pull request Jan 13, 2025 that will close this issue
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@gilmorera
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Thanks for your quick response. I'll check back later for your updates.

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Relax protobuf version in Python ielis/phenopacket-schema
5 participants
@holtgrewe @julesjacobsen @iimpulse @ielis @gilmorera