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Project description

semsimian

Semsimian is a package to provide fast semantic similarity calculations for ontologies. It is a Rust library with a Python interface.

This includes implementation of Jaccard and Resnik similarity of terms in an ontology, as well as a method to calculate the similarity of two sets of terms (so-called termset similarity). Other methods will be added in the future.

Semsimian is currently integrated into OAK and the Monarch app to provide fast semantic similarity calculations.

Installation

Set up your virtual environment of choice.
cd semsimian (home directory of this project)
pip install maturin
maturin develop
python

Python 3.9.16 (main, Jan 11 2023, 10:02:19) 
[Clang 14.0.6 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from semsimian import Semsimian
>>> s = Semsimian([('banana', 'is_a', 'fruit'), ('cherry', 'is_a', 'fruit')])
>>> s.jaccard_similarity('banana', 'cherry')

This should yield a value of 1.0.

Releases

As of version 0.1.14, the semsimian source is released on GitHub, with a corresponding set of Python wheels released to Pypi.

To trigger a new set of builds, first update the version number in Cargo.toml, then create a new release.

Wheels are prepared for the following environments and architectures:

OS	Architectures	Python Versions
Linux	x86_64, x86_64-unknown-linux-musl, aarch64-unknown-linux-gnu, aarch64-unknown-linux-musl	3.7, 3.8, 3.9, 3.10, 3.11
MacOS	x86_64, universal2	3.7, 3.8, 3.9, 3.10, 3.11
Windows	x86_64	3.7, 3.8, 3.9, 3.10, 3.11

Troubleshooting

Building for Mac ARM M1 architectures

If a import semsimian results in a ImportError warning about incompatible architecture, try the following:

Install conda. This guide may be helpful.
Set up a virtual environment with conda so that your Python build is aligned with your processor architecture (in this case, ARM). Try something like:

$ conda create -n myenv python=3.9
...setup happens...
$ conda activate myenv

and then proceed as above.

Code Coverage via Docker

Build a docker image:

docker build -t my-rust-app .

Run your tests inside a Docker container and generate coverage:

docker run -v "$(pwd)":/usr/src/app -t my-rust-app bash -c "CARGO_INCREMENTAL=0 RUSTFLAGS='-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Coverflow-checks=off -Zpanic_abort_tests -Cpanic=abort' cargo test && grcov . -s . --binary-path ./target/debug/ -t html --branch --ignore-not-existing -o ./target/debug/coverage/"

Get Coverage report from:

open ./target/debug/coverage/index.html

Project details

Release history Release notifications | RSS feed

0.2.19

Aug 26, 2024

0.2.18

Aug 2, 2024

0.2.17

Jul 23, 2024

0.2.17rc1 pre-release

Jul 15, 2024

0.2.16

May 7, 2024

0.2.15

Mar 14, 2024

0.2.14 yanked

Mar 13, 2024

Reason this release was yanked:

error: linking with `cc` failed: exit status: 1

0.2.14rc3 pre-release

Mar 13, 2024

0.2.14rc2 pre-release

Mar 13, 2024

0.2.14rc1 pre-release

Mar 12, 2024

0.2.13

Mar 6, 2024

0.2.12

Feb 6, 2024

0.2.11

Nov 29, 2023

0.2.10

Nov 16, 2023

0.2.9

Nov 16, 2023

0.2.8

Sep 27, 2023

0.2.6

Sep 15, 2023

0.2.5

Sep 2, 2023

This version

0.2.5rc2 pre-release

Sep 1, 2023

0.2.5rc1 pre-release

Sep 1, 2023

0.2.4

Aug 28, 2023

0.2.3 yanked

Aug 28, 2023

Reason this release was yanked:

Not all wheels uploaded: GH failed midway

0.2.2

Aug 25, 2023

0.2.1

Aug 21, 2023

0.2.0

Aug 15, 2023

0.2.0rc3 pre-release

Aug 12, 2023

0.2.0rc2 pre-release

Aug 9, 2023

0.2.0rc1 pre-release

Aug 9, 2023

0.1.20

Aug 4, 2023

0.1.19rc2 pre-release

Aug 3, 2023

0.1.19rc1 pre-release

Aug 3, 2023

0.1.18

Jul 25, 2023

0.1.18rc2 pre-release

Jul 24, 2023

0.1.18rc1 pre-release

Jul 24, 2023

0.1.17 yanked

Jul 21, 2023

Reason this release was yanked:

Output incorrect for allxall pairwise similarity

0.1.17rc6 pre-release

Jul 21, 2023

0.1.17rc5 pre-release

Jul 21, 2023

0.1.17rc4 pre-release

Jul 15, 2023

0.1.17rc3 pre-release

Jul 14, 2023

0.1.17rc2 pre-release

Jul 11, 2023

0.1.17rc1 pre-release

Jun 15, 2023

0.1.16

Jun 13, 2023

0.1.15

Jun 12, 2023

0.1.14

May 22, 2023

0.1.13

May 9, 2023

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Download URL: semsimian-0.2.5rc2-cp37-cp37m-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl
Upload date: Sep 1, 2023
Size: 3.0 MB
Tags: CPython 3.7m, macOS 10.9+ universal2 (ARM64, x86-64), macOS 10.9+ x86-64, macOS 11.0+ ARM64
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Details for the file semsimian-0.2.5rc2-cp37-cp37m-macosx_10_7_x86_64.whl.

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Download URL: semsimian-0.2.5rc2-cp37-cp37m-macosx_10_7_x86_64.whl
Upload date: Sep 1, 2023
Size: 1.6 MB
Tags: CPython 3.7m, macOS 10.7+ x86-64
Uploaded using Trusted Publishing? No
Uploaded via: maturin/1.2.3

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