Pyomic

Install

- fix the error of pip in install

bulk2single module

- Change the `deep-forest` of `Single2Spatial` to `Neuron Network` to perform classification task
- The entire Single2Spatial inference process is accelerated using the GPU, and can be estimated at the batch level by modifying the set `predicted_size`, the original author's function is estimated spot by spot, which is very inefficient
- Update the logical of `Single2Spatial.load` to accelerate model loading

single module:

- Add `pyVIA` module include `run`, `plot_piechart_graph`, `plot_stream`, `plot_trajectory_gams`, `plot_lineage_probability`, `plot_gene_trend`, `plot_gene_trend_heatmap`, `plot_clustergraph`
- Fix the error of warning of `utils.pyomic_plot_set`
- Update the requirements included `pybind11`, `hnswlib`, `termcolor`, `pygam`, `pillow`, `gdown`

single module:

- Add `pySCSA` module included `cell_anno`, `cell_anno_print`, `cell_auto_anno`, `get_model_tissue`
- Update the pySCSA tutorial that can be found at [here](https://pyomic.readthedocs.io/en/latest/Tutorials-single/t_cellanno/)
- Add filter the doublets cells of `single.scanpy_lazy`
- Add `single.scanpy_cellanno_from_dict` to annotate easier
- Updated the database of SCSA from [CellMarker2.0](http://bio-bigdata.hrbmu.edu.cn/CellMarker/)
- Fix the error database key `Ensembl_HGNC` and `Ensembl_Mouse` of SCSA

Update bulk and bulk2single code reference

bulk module:

- Fix the `cutoff` parameter non-vaild on `bulk.geneset_enrichment`
- Add `pyPPI`,`pyGSEA`,`pyWGCNA`,`pyTCGA`,`pyDEG` module.

bulk2single module:

- Add the `bulk2single.save` to save model by manual

Update all code reference

- Fix the parameter non-vaild on `single.mofa.mofa_run` function
- Add the layer raw count addition on `single.scanpy_lazy` function
- Add `utils.plot_boxplot` to plot the box plot with jittered points.
- Add `bulk.pyDEseq.plot_boxplot` to plot the box plot with jittered points of specific Genes.

bulk2single module:

- Add the `bulk2single` module
- Fix the model load error from bulk2space
- Fix the early stop from bulk2space
- Add more friendly input method and visualisation
- Add the loss history visualisation

utils module:

- Add the `pyomic_palette` in plot module