environment.yml

# Dev Environment
name: pimms
channels:
  - conda-forge
  - pytorch
  - nvidia
  - fastai # fastchan
  - bioconda
  - plotly
dependencies:
  - python>=3.9,<=3.12
  - numpy
  - pandas>=1
  - scipy>=1.6
  # plotting
  - matplotlib>=3.4
  - python-kaleido
  - plotly
  - seaborn
  - pip
  # ML
  - pytorch #=1.13.1=py3.8_cuda11.7_cudnn8_0
  # - pytorch-cuda
  - scikit-learn
  - fastai
  - torchvision
  # - cudatoolkit #=11.7
  # - tensorboard
  - umap-learn
  # stats
  - pingouin
  - statsmodels
  # other
  - tqdm # progress bars
  - xmltodict # configs
  - openpyxl # xml
  - omegaconf
  - plac>=1.0
  # snakemake
  - snakemake-minimal #<7.26
  # jupyter
  - ipykernel
  - ipython
  - ipywidgets
  - jupyterlab # standalone jupyter installation
  # - jupyter_contrib_nbextensions # delete configuration file if you see an error: https://github.com/jupyter/nbconvert/issues/526#issuecomment-277552771
  - jupyter-dash
  - papermill # execute ipynb's
  # R packages (listed in NAGuideR)
  - r-base
  - r-devtools # is it needed for source installs on windows server?
  - r-irkernel
  - r-reshape2
  - r-stringi # + rmarkdown hack for reshape2
  - r-stringr # reshape2
  - r-tidyverse
  - r-gdata
  - r-glmnet
  - r-e1071
  # - r-norm
  - r-missforest
  # - r-vim
  # - r-mice
  - r-cluster
  - r-mvtnorm
  # - r-rrcov
  - r-gmm
  - r-tmvtnorm
  - r-igraph
  # - bioconductor-biocinstaller
  # - r-imputelcmd # bioconda
  # - bioconductor-impute
  # - bioconductor-pcamethods
  # - rrcovNA, GMSimpute
  # SeqKnn, pcaMethods, DreamAI # bioconductor
  # dev
  - pytest
  - pytest-cov
  # - jupytext
  # - flake8
  # - flake8-bugbear
  # - build
  # - pre-commit
  # - jupyterlab_code_formatter
  # - jupyterlab-git
  - pip:
      - -e .
      - mrmr-selection
      - njab