AttributeError: Module 'scipy' has no attribute 'random'

[ahucke]

I am running into an issue when trying to follow the tutorial provided by the creator. It states that "AttributeError: Module 'scipy' has no attribute 'random'".

This are my python configurations: python: /miniconda3/envs/mofa/bin/python libpython: /miniconda3/envs/mofa/lib/libpython3.11.so pythonhome: /miniconda3/envs/mofa:/miniconda3/envs/mofa version: 3.11.0 | packaged by conda-forge | (main, Jan 14 2023, 12:27:40) [GCC 11.3.0] numpy: /miniconda3/envs/mofa/lib/python3.11/site-packages/numpy numpy_version: 1.24.2

And this is my code:

----message=FALSE------------------------------------------------------------

library(data.table) library(MOFA2) library(reticulate)

Sys.setenv(OMP_NUM_THREADS="1") reticulate::use_condaenv('/miniconda3/envs/mofa/') reticulate::py_config()

-----------------------------------------------------------------------------

data <- make_example_data( n_views = 2, n_samples = 200, n_features = 1000, n_factors = 10 )[[1]]

lapply(data,dim)

----message=FALSE------------------------------------------------------------

MOFAobject <- create_mofa(data)

-----------------------------------------------------------------------------

plot_data_overview(MOFAobject)

----message=FALSE------------------------------------------------------------

N = ncol(data[[1]]) groups = c(rep("A",N/2), rep("B",N/2))

MOFAobject <- create_mofa(data, groups=groups)

-----------------------------------------------------------------------------

plot_data_overview(MOFAobject)

-----------------------------------------------------------------------------

filepath <- system.file("extdata", "test_data.RData", package = "MOFA2") load(filepath)

head(dt)

-----------------------------------------------------------------------------

MOFAobject <- create_mofa(dt) print(MOFAobject)

----out.width = "80%"--------------------------------------------------------

plot_data_overview(MOFAobject)

-----------------------------------------------------------------------------

data_opts <- get_default_data_options(MOFAobject) head(data_opts)

-----------------------------------------------------------------------------

model_opts <- get_default_model_options(MOFAobject) model_opts$num_factors <- 10 head(model_opts)

-----------------------------------------------------------------------------

train_opts <- get_default_training_options(MOFAobject) train_opts

----message=FALSE------------------------------------------------------------

MOFAobject <- prepare_mofa( object = MOFAobject, data_options = data_opts, model_options = model_opts, training_options = train_opts )

-----------------------------------------------------------------------------

outfile = file.path("/MOFA/model.hdf5") MOFAobject.trained <- run_mofa(MOFAobject, outfile)

-----------------------------------------------------------------------------

sessionInfo()

This is the result of sessionInfo: R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default BLAS: /usr/lib64/libblas.so.3.4.2 LAPACK: /usr/lib64/liblapack.so.3.4.2

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] BiocManager_1.30.19 RColorBrewer_1.1-3 tibble_3.1.8 ggrepel_0.9.2 dplyr_1.0.10 tidyr_1.2.1
[7] ggplot2_3.4.0 readxl_1.4.1 reticulate_1.28-9000 data.table_1.14.6 MOFA2_1.4.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.10 here_1.0.1 dir.expiry_1.2.0 lattice_0.20-45 png_0.1-8 assertthat_0.2.1
[7] rprojroot_2.0.3 utf8_1.2.2 R6_2.5.1 cellranger_1.1.0 plyr_1.8.8 stats4_4.1.2
[13] pillar_1.8.1 basilisk_1.6.0 rlang_1.0.6 rstudioapi_0.14 S4Vectors_0.32.4 Matrix_1.5-3
[19] Rtsne_0.16 stringr_1.4.1 pheatmap_1.0.12 munsell_0.5.0 uwot_0.1.14 DelayedArray_0.20.0 [25] HDF5Array_1.22.1 compiler_4.1.2 pkgconfig_2.0.3 BiocGenerics_0.40.0 tidyselect_1.2.0 IRanges_2.28.0
[31] matrixStats_0.62.0 fansi_1.0.3 withr_2.5.0 rhdf5filters_1.6.0 basilisk.utils_1.6.0 grid_4.1.2
[37] jsonlite_1.8.4 gtable_0.3.1 lifecycle_1.0.3 DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
[43] cli_3.4.1 stringi_1.7.8 farver_2.1.1 reshape2_1.4.4 filelock_1.0.2 generics_0.1.3
[49] vctrs_0.5.2 cowplot_1.1.1 Rhdf5lib_1.16.0 tools_4.1.2 forcats_0.5.2 glue_1.6.2
[55] purrr_1.0.1 MatrixGenerics_1.9.1 parallel_4.1.2 colorspace_2.0-3 rhdf5_2.38.1 corrplot_0.92

Previously, I ran into an issue that said that I should use the most recent version of mofapy2 (0.6.4) while I was trying to use mofapy2 (0.6.7). I solved this by force installing the requested version with py_install("mofapy2 == 0.6.4").

Thanks for the help!