v0.9.17

Fixed a Dragon LIONESS bug

Ticino release, v 0.9.16

• COBRA has been added to the zoo!
• igraph has been updated. Beware of stochastic algorithms like clustering.
• Dependencies and bug fixes

franklin

Franklin release, v 0.9.15

• Added mc-pvalues for dragon
• Patches for pandas deprecated funcions
• Documentation patch

0.9.14

• add Zenodo DOI

0.9.13

• We have added some options to LIONESS: single lioness files can be saved in HDF (fmt='h5') which saves a lot of time and memory. By passing ignore_final to lioness (with save_single_lioness) each lioness is discarded after being saved, hence you won't have all lioness networks in memory at the same time.
• PANDA can be run with_header from CLI
• Added pytables/tables in dependencies.

0.9.12

• We are changing the PANDA outputs and default flags. For now we are updating the command line
  call only, behavior is kept as in 0.9.11 for the internal functions. By passing old_compatible = False
  the final output will always have column headers and indices.
• PUMA and PANDA do not save_tmp as default.
• lioness for puma has been fixed
• Fixed PANDA data preprocessing bug

0.9.11

• Added LIONESS for DRAGON with tests
• PANDA preprocessing expression: In Panda preprocessing there was a problem with indices. Using gene2idx.get(x, 0) always give you the index 0 if x is missing from gene2idx.get (like a gene in gene expression and not in motif, since gene2idx is build on top of the intersection of expression and motif). Now we use gene_names to both create the indices for self.expression and to access with .loc[] the expression data frame self.expression_data - New PANDA tests - Updated LIONESS start and end parameters so that they are independent of the background. Example: One can now run panda on 100 samples and then apply LIONESS on only the first 10.
• Added LIONESS subset parameter: passing subset parameters (a list of indices or sample names, [1,2,10]) allows to run LIONESS only on specific samples. This parameter has priority over the start and end parameters.

0.9.10

0.9.10 (2022-10-28)

Fixing single/double precision for GPU
Clearing GPU after computation to free more memory

0.9.9

0.9.9 (2022-10-21)

• added the case for square nonsymmetric matrices for normalization in panda
• Updated tests for panda and lioness to match MATLAB
• Fixed Panda-Lioness GPU inconsistencies
• Forcing igraph<0.10, otherwise condor community assignment results change. This will need further investigation in the future.
• Fixed lioness GPU export (now lioness allows to save the full matrix, with explicit edge and sample names).

0.9.8

Bump version: 0.9.7 → 0.9.8