**Major Release:**
We refactored the whole code into a modular version and implemented four ready to use probe design pipeline.
The modularized version now allows to plug different processing steps together to implement new oligo design pipelines eifficently. Furthermore, we have an underlying data structure that connects all modules via the same API. The new modules decsribe the different processing steps of oligo design pipeline, i.e. Property Filters, Specificity Filters, Scorings and Set Selection.
The new pipelines are: Scrinshot (modularized), Merfish, SeqFish+ and Oligo-Seq experiments
We also added tests for all implemented functionalities as well as integration tests for each pipeline, included into GitHub Actions.
In addition, we added an exhaustive documentation on the framework, installation, how to build custom pipelines and each offered ready to use pipeline.
What's Changed
* Add functionality to _ftp_loader.py by chelseabright96 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/8
* Add functionality to data_parser.py by chelseabright96 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/10
* Pre filters by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/12
* Unit tests by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/13
* Probesets by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/15
* Update README.md by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/17
* Joblib by chelseabright96 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/14
* Padlock pipeline by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/19
* docs update by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/20
* Test docs by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/21
* Databse split by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/22
* Tutorial fix by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/23
* Refactoring by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/24
* Padlock pipeline by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/25
* Gff parser fix by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/29
* Feature/new property filters by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/33
* Cross hybrid by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/35
* Feature/refactor property filter by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/37
* Database refactor by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/36
* Feature/refactor_property_filter by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/38
* Update specificity by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/34
* 39 integrate exact match filter into cross hybridization filter by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/48
* Bugfix/test errors by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/45
* AI-filters by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/54
* 49 exact match filter by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/55
* 46 oligo database attributes class by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/51
* Changed instances of dictionaries to LRUDDBDict by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/56
* Update tests by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/57
* 52 oligo scoring functions by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/60
* Oligo-seq-pipeline by francesco-campi in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/63
* 53 scrinshot pipeline by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/64
* Implemented heterodimer filter by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/65
* Enhance database loading by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/67
* remove Bio package for blast and turn into subprocess by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/68
* 62 seqfish pipeline by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/78
* 69 filter for isoform consensus by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/73
* 71 utr sequence by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/74
* 75 exon junction computation by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/76
* 72 database table output by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/85
* 77 filter for exon number by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/79
* 81 intergenic sequence computation by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/84
* 80 update pytests by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/87
* Faster heuristic method to generate non-overlapping sets by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/86
* Start split tutorial (1-4) by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/90
* Add links in doc by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/91
* 82 documentation by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/88
* 89 refactor pipelines by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/92
* New version of Oligo Designer Toolsuite by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/93
* Docs by IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/95
* Update README.md by lisa-sousa in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/97
New Contributors
* chelseabright96 made their first contribution in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/8
**Full Changelog**: https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/compare/v0.1.3...v1.0.0