v.0.0.37

What's Changed

• 🛠️ Code-dev: Support for butina partitioning algorithm by @RaulFD-creator in #87
• 🪲 Bug-fix: Include the foldseek tmp in hestia_tmp by @RaulFD-creator in #88

Full Changelog: v.0.0.36...v.0.0.37

v.0.0.36

What's Changed

• 🧹 Tidy code: Shortening class names by @RaulFD-creator in #81
• 🏎️ Optim: Substitutting pandas for polars (#82) by @RaulFD-creator in #83
• 🪲 Bug fix: pbar.close only when verbose by @RaulFD-creator in #84
• 🪲 Bug fix: Query indexing for AU-GOOD calculation by @RaulFD-creator in #85
• 🧹 TIdy code: Better logging by @RaulFD-creator in #86

Full Changelog: v.0.0.35...v.0.0.36

v.0.0.35

What's Changed

Summary

1. 📝 Docs: Minor changes to documentation. Added examples for molecules
2. 🧹 Tidy code: Improved progress bars for similarity calculation
3. 🛠️ Code-dev: Change distance in SimilarityArguments for sim_function in the case of 'embeddings' calculation to harmonize with the rest of similarity functions
4. 🛠️ Code-dev: Introduction of Canberra distance
5. 🛠️ Code-dev: Introduction of Lipinski vector to molecular_similarity
6. 🛠️ Code-dev: Substituted gzip for pickle for saving the precalculated partitions and additional metadata
7. 🪲 Bug fix: Multiple bug fixes with if-else statements
8. 🪲 Bug fix: Bug fix with metadata for embeddings trying to savequery_embds as well.
9. 🪲 Bug fix: Small bug fixes with similarity calculations
10. 🪲 Bug fix: Avoid the situation where fp='ecfp' and sim_function='jaccard' and derive it to tanimoto by default.
11. 🪲 Bug fix: Apply distance to similarity transformation
12. 🏎️ Optim: Optimize bulk similarity functions using vectorized numpy operations, almost 25x speedup with target_df of 20,000, probably scales better than original implementation
13. 🏎️ Optim: Small optimization of the ccpart algorithm

Merge trail

• 🛠️ Code-dev: More convenient storing of meta-data by @RaulFD-creator in #67
• 🪲 Bug fix: self.sim_df no longer exists by @RaulFD-creator in #68
• 🪲 Bug fix: Substitute distance for sim_function for 'embeddings' sim by @RaulFD-creator in #69
• 🛠️🪲: Multiple bug fixes and minor code developments by @RaulFD-creator in #70
• 🪲 Bug fix: pointer in similarity calculation needs to depend on ta… by @RaulFD-creator in #71
• 🪲 Bug fix: Minor bug fixes for Lipinski similarity by @RaulFD-creator in #72
• 🧹 Tidy code: Avoid problem when jaccard is used with ecfp by @RaulFD-creator in #73
• 🏎️ Optim: Optimized bulk similarities by @RaulFD-creator in #74
• 🏎️ Optim: ccpart algorithm, slightly improved by @RaulFD-creator in #75
• 🪲 Bug fix: Apply distance to similarity transformation for distance by @RaulFD-creator in #76
• 🛠️ Code-dev: Substitute gzip for pickle for saving partitions by @RaulFD-creator in #77
• Minor 🧹 Tidy code and 📝 Documentation updates by @RaulFD-creator in #78
• 🪲🧹 Minor bug fix with needle function and tidier code by @RaulFD-creator in #79
• 🪲 Bug fix: MACCS keys with not RDKit distance by @RaulFD-creator in #80

Full Changelog: v.0.0.34...v.0.0.35

v.0.0.34

What's Changed

• 🛠️ Code-dev: Add support for peptides similarity in HDG by @RaulFD-creator in #65
• 🪲 Bug fix: Normal alignment int for mmseqs_v by @RaulFD-creator in #66

Full Changelog: v.0.0.33...v.0.0.34

v.0.0.33

What's Changed

What's Changed

• 🛠️ Code-dev: Added support for filtering within sim_df2mtx by @RaulFD-creator in #58
• Prepare version 0.0.32 by @RaulFD-creator in #59
• 🛠️ Code-dev: Substitute calculate_similarity for specialised functions by @RaulFD-creator in #60
• 🛠️ Code-dev: Implemented #33. AU-GOOD for arbitrary target distribution by @RaulFD-creator in #61
• 🛠️ Code-dev: Added supprot to needle similarity by @RaulFD-creator in #62
• 📝 Docs: Updated documentation by @RaulFD-creator in #63

Full Changelog: v.0.0.31...v.0.0.33

v.0.0.32

What's Changed

• 🛠️ Code-dev: Added support for filtering within sim_df2mtx by @RaulFD-creator in #58
• Prepare version 0.0.32 by @RaulFD-creator in #59
• 🛠️ Code-dev: Substitute calculate_similarity for specialised functions by @RaulFD-creator in #60
• 🛠️ Code-dev: Implemented #33. AU-GOOD for arbitrary target distribution by @RaulFD-creator in #61
• 🛠️ Code-dev: Added supprot to needle similarity by @RaulFD-creator in #62
• 📝 Docs: Updated documentation by @RaulFD-creator in #63

Full Changelog: v.0.0.31...v.0.0.32

v.0.0.31

What's Changed

• 🪲 Bug fix: Improved output for fingerprint alignment by @RaulFD-creator in #49
• 🛠️ Code-dev: min_threshold partition calculation to 0. by @RaulFD-creator in #52
• 🛠️ Code-dev: Revisions to similarity and clustering algorithms by @RaulFD-creator in #53
• 🪲 Bug fix: Embeddings query not queries by @RaulFD-creator in #54
• 🛠️ Code-dev: Optimised memory use for fingerprint_alignment by @RaulFD-creator in #55
• 🛠️ Code-dev: Optimised sim_df2mtx by @RaulFD-creator in #56
• 🛠️ Code-dev: Added support for filtering within sim_df2mtx by @RaulFD-creator in #57

Full Changelog: v.0.0.30...v.0.0.31

v.0.0.30

What's Changed

• 🪲 Bug fix: Similarity arguments does not overrule parameters by @RaulFD-creator in #45
• 🛠️ Code-dev: change default settings for mmseqs alignment by @RaulFD-creator in #46
• 🛠️ Code-dev: Multiple foldseek metrics by @RaulFD-creator in #47
• 🛠️ Code-dev: Only import wilcoxon when needed by @RaulFD-creator in #48

Full Changelog: v.0.0.29...v.0.0.30

v.0.0.29

What's Changed

• 🪲 Bug fix: self.df should have been self.data by @RaulFD-creator in #43
• 🚀 Release: v.0.0.29 by @RaulFD-creator in #44

Full Changelog: v.0.0.28...v.0.0.29

v.0.0.28

What's Changed

• Several small updates by @RaulFD-creator in #37
• Quality of life improvements to calculate_similarity input format by @RaulFD-creator in #38
• 🪲 Bug fix fd7aab7: FP name change to… by @RaulFD-creator in #40
• 🛠️ Code-dev: Minor improvements to FP alignment by @RaulFD-creator in #41
• Small changes and bug fixes by @RaulFD-creator in #42

Full Changelog: v.0.0.27...v.0.0.28