Release v1.1.5

CHANGELOG.md

@@ -5,7 +5,19 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
-[Unreleased]: https://github.com/bioinf-MCB/Metagenomic-DeepFRI/compare/v1.1.4...HEAD
+[Unreleased]: https://github.com/bioinf-MCB/Metagenomic-DeepFRI/compare/v1.1.5...HEAD
+
+## [1.1.5] - 2024-04-01
+[1.1.5]: https://github.com/bioinf-MCB/Metagenomic-DeepFRI/compare/v1.1.4...v1.1.5
+
+### Added
+- improved logging
+- support for ESM databases (closes #80)
+
+### Changed
+- retrieval of structures from PDB & FoldComp databases
+- optimized contact map alignment via Cython - improved search in large databases (ESM)
+
 
 ## [v1.1.4] - 2024-03-23
 [v1.1.4]: https://github.com/bioinf-MCB/Metagenomic-DeepFRI/compare/v1.1.3...v1.1.4

README.md

@@ -23,17 +23,18 @@ Metagenomic-DeepFRI addresses such need, building upon efficient libraries. It i
 
 ## 🔧 Installation
 
-1. Clone repo locally
+1. Download environment YAML.
 ```{code-block} bash
-git clone https://github.com/bioinf-mcb/Metagenomic-DeepFRI
-cd Metagenomic-DeepFRI
+wget https://raw.githubusercontent.com/bioinf-mcb/Metagenomic-DeepFRI/main/environment.yml
 ```
-2. Setup conda environment
+2. Setup conda environment and actiate it.
 ```{code-block} bash
 conda env create --name deepfri --file environment.yml
 conda activate deepfri
+# Optional cleanup
+rm environment.yml
 ```
-3. Show help message
+3. Run and view the help message.
 ```{code-block} bash
 mDeepFRI --help
 ```

mDeepFRI/__init__.py

@@ -1,6 +1,6 @@
 import os
 
-__version__ = "1.1.4"
+__version__ = "1.1.5"
 
 repo_url = "https://huggingface.co/valentynbez/mDeepFRI/resolve/main/"
 

mDeepFRI/predict.pyx

@@ -1,3 +1,5 @@
+import json
+
 import numpy as np
 
 cimport numpy as np