InMoose release changelog

[0.7.4-dev]

• fix single sample clustering error, changing cluster consensus to nan
• improve pyDESeq2 documentation

[0.7.3]

• fix dispersion estimation and MAD computation in deseq2 module
• improve GLM fit in deseq2 module
• create cohort_qc module with CohortMetric and QCReport classes to
  evaluate dataset quality after batch effect correction
• improve cohort_qc module when the number of covariates is 0 or 1
• improve documentation for diffexp module
• improve documentation for consensus_clustering module
• batch effect correction functions now accept AnnData as input
• fix p-value adjustment in deseq2 module
• add logos and badges in the README

[0.7.2]

• opt out of numpy 2.1.0 until statsmodels supports it
• fix an array indexing bug in function meta_de
• function meta_de is now robust to NaN p-values
• allow arbitrary types for batch and group arguments in function
  sim_rnaseq

[0.7.1]

• fix a bug when splicing a DEResults
• fix coverage report upload in CI/CD pipeline
• improve documentation landing page and references
• use a package-specific logger

[0.7.0]

• harmonize differential expression analysis results across deseq2, edgepy
  and limma modules
• add a meta-analysis feature for differential expression

[0.6.0]

• move most of C++ code to Python and Cython
• compatibility with numpy 2.0.0

[0.5.1]

• fix pycombat covariates action remove with count dataframe output

[0.5.0]

• add experimental support for MSVC compiler
• add R-like functions for fitting linear models in module utils
• add a function to compute natural cubic spines basis in module utils
• add tmixture functions from R package limma
• add linear model fit functions from R package limma
• add functions handling duplicated probes from R package limma
• lint code with ruff
• add a "differential expression analysis" section to the doc

[0.4.1]

• fix an incorrect github action version number

[0.4.0]

• support for Python 3.12
• bump github actions versions
• publish coverage report to coveralls.io
• port edgeR functions for differential expression to inmoose
• Modifiy clustering stability plot
• remove many (not all) warnings

[0.3.1]

• Fix issue #25 and #10 related to counts parameter data format check and gestion (when it's a pandas dataframe)
• add DESeq2 variance stabilizing transformation to the deseq2 package
• improve the error message for confounding variable in pycombat package
• fix build on readthedocs

[0.3.0]

• add and optimize a few functions in the utils.stats module
• add a module featuring a port of the DESeq2 R package

[0.2.4]

• add a data module, with two RNA-Seq datasets: pasilla and airway
• fix build on readthedocs
• updated bibliography with our BMC Bioinformatics paper
• add verbose to consensus clustering computation
• add a utility class VirtualCohortInput to better check the well definition
  of inputs to the batch effect correction routines

[0.2.3]

• fix syntax-impairing typos in pyproject.toml

[0.2.2]

• proper documentation for the sim module
• code is now formatted with black
• add a link to the documentation in the README file
• better handling of covariates in pycombat module

[0.2.1]

• add a function to generate simulated RNA-Seq and scRNA-Seq data
• drop support of Python 3.8 due to memory management issues in extensions
• add a module to perform consensus clustering and select the optimal number of
  clusters

[0.2.0]

• inmoose now requires Python >= 3.8
• reorganize tests directory
• refactor module for batch effect correction. It is now named pycombat
  (instead of batch), and the function to correct batch effect on microarray
  data is now pycombat_norm (instead of pycombat).
• refactor design matrix computation, to share the code between pycombat_norm
  and pycombat_seq
• batch effect correction functions now accept both numpy arrays and pandas
  dataframes as input for the counts matrix
• improved logging: no more prints, better log formatting
• inmoose doc is now on readthedocs.org

[0.1.1]

• upgrade to Cython 3.0.0b2
• fix C++ extension loading on Linux
• add CI/CD to build, test and publish distributions

[0.1.0]

Initial release