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Version bump for 0.2.5 release #64

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Dec 28, 2023
Merged

Version bump for 0.2.5 release #64

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13 changes: 5 additions & 8 deletions CHANGELOG.md
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### 0.2.6 (Unreleased)


### 0.2.5 (28/12/2023)

#### Datasets

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* Fix `num_classes` for GO datamodules * Set `in_memory=True` as default for most (downstream) datasets for improved performance [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/)
* Fixes GO labelling [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/)


### Features

* Improves positional encoding performance by adding a `seq_pos` attribute on `Data/Protein` objects in the base dataset getter. [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/)

### Models

* Implement ESM embedding encoder ([#33](https://github.com/a-r-j/ProteinWorkshop/pull/33), [#41](https://github.com/a-r-j/ProteinWorkshop/pull/33))
* Adds CDConv implementation [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/)
* Adds tuned hparams for models [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/)

### Framework

* Refactors beartype/jaxtyping to use latest recommended syntax [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/)
* Adds explainability module for performing attribution on a trained model [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/)
* Change default finetuning features in config: `ca_base` -> `ca_seq` [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/)
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* Adds multi-hot label encoding transform [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/)
* Fixes auto PyG install for `torch>2.1.0` [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/)
* Adds `proteinworkshop.model_io` containing utils for loading trained models [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/)

### 0.2.5 (25/09/2024)

* Implement ESM embedding encoder ([#33](https://github.com/a-r-j/ProteinWorkshop/pull/33), [#41](https://github.com/a-r-j/ProteinWorkshop/pull/33))
* Add script for plotting UMAP embeddings of any dataset given a pre-trained encoder model

### 0.2.4 (10/09/2024)
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2 changes: 1 addition & 1 deletion docs/source/conf.py
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
project = "Protein Workshop"
author = "Arian R. Jamasb"
release = "0.2.4"
release = "0.2.5"
copyright = f"{datetime.datetime.now().year}, {author}"

# -- General configuration ---------------------------------------------------
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32 changes: 6 additions & 26 deletions poetry.lock
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2 changes: 1 addition & 1 deletion pyproject.toml
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[tool.poetry]
name = "proteinworkshop"
version = "0.2.4"
version = "0.2.5"
description = ""
authors = ["Arian Jamasb <arian@jamasb.io>"]
readme = "README.md"
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