diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 1fb98abf..3214d26c 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -50,10 +50,10 @@ jobs: # uses: actions/setup-python@v2 # with: #python-version: ${{ matrix.python-version }} - - name: Setup conda environment - run: conda env create -n graphein-dev python=${{ matrix.python-version }} - - name: Activate Conda Environment - run: source activate graphein-dev + #- name: Setup conda environment + # run: conda env create -n graphein-dev python=${{ matrix.python-version }} + #- name: Activate Conda Environment + # run: source activate graphein-dev - name: Install DSSP run: conda install -c salilab dssp - name: Install PyTorch diff --git a/CHANGELOG.md b/CHANGELOG.md index 180702af..2e513489 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,21 +1,26 @@ -### 1.5.2 - UNRELEASED +### 1.5.2 - 19/9/2022 #### Protein + * [Bugfix] - [#206](https://github.com/a-r-j/graphein/pull/206) Fixes `KeyError` when using `graphein.protein.edges.distance.node_coords` +* [Bugfix] - Includes missing data files in `MANIFEST.in` #205 #### GRN + * [Bugfix] - [#208](https://github.com/a-r-j/graphein/pull/208) - Resolves SSL issues with RegNetwork. #### ML + * [Feature] - [#208](https://github.com/a-r-j/graphein/pull/208) support for loading local pdb files by ``ProteinGraphDataset`` and ``InMemoryProteinGraphDataset``. + >by adding a params:`pdb_paths` and set the `self.raw_dir` to the root path(`self.pdb_path`) of pdb_paths list (the root path should be only one, pdb files should be under the same folder). > ->it will works from loading pdb files from the `self.pdb_path` instead of loading from self.raw. -> If desire to download from af2 or pdb, just set `pdb_paths` to `None` and it goes back to the former version. +> it allows loading pdb files from the `self.pdb_path` instead of loading from `self.raw`. +> If you wish to download from af2 or pdb, just set `pdb_paths` to `None` and it goes back to the former version. #### CI -* [Bugfix] - [#208](https://github.com/a-r-j/graphein/pull/208) explicitly installs `jupyter_contrib_nbextensions` in Docker. +* [Bugfix] - [#208](https://github.com/a-r-j/graphein/pull/208) explicitly installs `jupyter_contrib_nbextensions` in Docker. ### 1.5.1 diff --git a/MANIFEST.in b/MANIFEST.in index 45737818..0b5c85a3 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -3,3 +3,5 @@ include graphein/_version.py include versioneer.py include README.md include .requirements/* +include graphein/protein/features/nodes/amino_acid_properties.csv +include graphein/protein/features/nodes/meiler_embeddings.csv \ No newline at end of file diff --git a/docs/source/conf.py b/docs/source/conf.py index f3a0a9ff..d5d81be7 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -29,7 +29,7 @@ author = "Arian Jamasb" # The full version, including alpha/beta/rc tags -release = "1.5.1" +release = "1.5.2" # -- General configuration --------------------------------------------------- diff --git a/graphein/__init__.py b/graphein/__init__.py index 97a72298..342b1a92 100644 --- a/graphein/__init__.py +++ b/graphein/__init__.py @@ -12,7 +12,7 @@ from .testing import * __author__ = "Arian Jamasb " -__version__ = "1.5.1" +__version__ = "1.5.2" logger.configure( diff --git a/graphein/grn/parse_regnetwork.py b/graphein/grn/parse_regnetwork.py index 8677866b..43950239 100644 --- a/graphein/grn/parse_regnetwork.py +++ b/graphein/grn/parse_regnetwork.py @@ -8,13 +8,13 @@ # Code Repository: https://github.com/a-r-j/graphein import logging import os +import ssl import zipfile from pathlib import Path from typing import Callable, List, Optional import pandas as pd import wget -import ssl from graphein.utils.utils import filter_dataframe, ping diff --git a/setup.py b/setup.py index df550f23..bdbe4e3b 100644 --- a/setup.py +++ b/setup.py @@ -135,7 +135,7 @@ def run(self): setup( name="graphein", - version="1.5.1", + version="1.5.2", # versioneer.get_version(), # cmdclass=versioneer.get_cmdclass(), description="Protein & Interactomic Graph Construction for Machine Learning",