neuroconda_basepackages.yml

name: neuroconda_build
channels:
  - conda-forge
  - r
dependencies:
  - altair
  - black
  - bokeh
  - cookiecutter
  - datashader
  - dask
  - dask-jobqueue
  - dcm2niix
  - dipy
  - fsleyes
  - fsleyes-props
  - fsleyes-widgets
  - fslpy
  - git
  - git-annex
  - gitpython
  - graphviz
  - hdf5
  - indexed_gzip
  - ipython
  - jupyter
  - jupyter_console
  - jupyterlab
  - jupyterlab_server
  - matplotlib
  - msgpack-python
  - nbconvert
  - nbformat
  - nibabel
  - nilearn
  - nipype
  - numpy
  - pandas
  - pandoc
  - perl
  - pillow
  - pip
  - prov
  - pygithub
  - pymc3
  - pytest
  - pytest-runner
  - pytest-cov
  - python>=3.6
  - r-stringi
  - r-abind
  - r-afex
  - r-assertthat
  - r-backports
  - r-base
  - r-base64enc
  - r-bayesfactor
  - r-bayesplot
  - r-bh
  - r-bindr
  - r-bindrcpp
  - r-bit
  - r-bit64
  - r-bitops
  - r-blob
  - r-boot
  - r-bridgesampling
  - r-brms
  - r-brobdingnag
  - r-broom
  - r-callr
  - r-car
  - r-cardata
  - r-caret
  - r-catools
  - r-cellranger
  - r-checkmate
  - r-class
  - r-cli
  - r-clipr
  - r-cluster
  - r-coda
  - r-codetools
  - r-colorspace
  - r-colourpicker
  - r-config
  - r-contfrac
  - r-crayon
  - r-crosstalk
  - r-curl
  - r-cvst
  - r-data.table
  - r-dbi
  - r-dbplyr
  - r-ddalpha
  - r-deoptimr
  - r-desc
  - r-desolve
  - r-digest
  - r-dimred
  - r-dplyr
  - r-drr
  - r-dt
  - r-dygraphs
  - r-elliptic
  - r-essentials
  - r-evaluate
  - r-fansi
  - r-forcats
  - r-foreach
  - r-foreign
  - r-forge
  - r-formatr
  - r-fs
  - r-future
  - r-generics
  - r-geometry
  - r-ggplot2
  - r-ggridges
  - r-gistr
  - r-glmnet
  - r-globals
  - r-glue
  - r-gower
  - r-gridextra
  - r-gtable
  - r-gtools
  - r-haven
  - r-hexbin
  - r-highr
  - r-hms
  - r-htmltools
  - r-htmlwidgets
  - r-httpuv
  - r-httr
  - r-hypergeo
  - r-igraph
  - r-inline
  - r-ipred
  - r-irdisplay
  - r-irkernel
  - r-iterators
  - r-jsonlite
  - r-kernlab
  - r-kernsmooth
  - r-knitr
  - r-labeling
  - r-later
  - r-lattice
  - r-lava
  - r-lavaan
  - r-lazyeval
  - r-listenv
  - r-lme4
  - r-lmertest
  - r-loo
  - r-lubridate
  - r-magic
  - r-magrittr
  - r-maps
  - r-maptools
  - r-markdown
  - r-mass
  - r-matrix
  - r-matrixmodels
  - r-matrixstats
  - r-memoise
  - r-mgcv
  - r-mime
  - r-miniui
  - r-minqa
  - r-mnormt
  - r-modelmetrics
  - r-modelr
  - r-mongolite
  - r-munsell
  - r-mvtnorm
  - r-nleqslv
  - r-nlme
  - r-nloptr
  - r-nnet
  - r-numderiv
  - r-odbc
  - r-openssl
  - r-openxlsx
  - r-packrat
  - r-pbapply
  - r-pbdzmq
  - r-pbivnorm
  - r-pbkrtest
  - r-pillar
  - r-pkgbuild
  - r-pkgconfig
  - r-pki
  - r-plogr
  - r-pls
  - r-plyr
  - r-prettyunits
  - r-processx
  - r-prodlim
  - r-profvis
  - r-progress
  - r-promises
  - r-pryr
  - r-ps
  - r-psych
  - r-purrr
  - r-quantmod
  - r-quantreg
  - r-r.methodss3
  - r-r.oo
  - r-r.utils
  - r-r2d3
  - r-r6
  - r-randomforest
  - r-rappdirs
  - r-rbokeh
  - r-rcolorbrewer
  - r-rcpp
  - r-rcppeigen
  - r-rcpproll
  - r-rcurl
  - r-readr
  - r-readxl
  - r-recipes
  - r-recommended
  - r-rematch
  - r-repr
  - r-reprex
  - r-reshape2
  - r-rio
  - r-rjava
  - r-rjdbc
  - r-rjsonio
  - r-rlang
  - r-rmarkdown
  - r-robustbase
  - r-rpart
  - r-rprojroot
  - r-rsconnect
  - r-rsqlite
  - r-rstan
  - r-rstantools
  - r-rstudioapi
  - r-rvest
  - r-scales
  - r-selectr
  - r-sfsmisc
  - r-shiny
  - r-shinyjs
  - r-shinystan
  - r-shinythemes
  - r-sourcetools
  - r-sp
  - r-sparklyr
  - r-sparsem
  - r-spatial
  - r-squarem
  - r-stanheaders
  - r-stringi
  - r-stringr
  - r-survival
  - r-threejs
  - r-tibble
  - r-tidyr
  - r-tidyselect
  - r-tidyverse
  - r-timedate
  - r-tinytex
  - r-ttr
  - r-utf8
  - r-uuid
  - r-viridislite
  - r-whisker
  - r-withr
  - r-xfun
  - r-xml2
  - r-xtable
  - r-xts
  - r-yaml
  - r-zip
  - r-zoo
  - rstudio
  - scikit-image
  - scikit-learn
  - scipy
  - seaborn
  - simplegeneric
  - statsmodels
  - tensorflow
  - tensorflow-probability
  - theano
  - tqdm
  - xnat
  - cython
  - numba
  - jupyterlab_code_formatter
  - aniso8601
  - flask-restful
  - humanize
  - iso8601
  - itsdangerous
  - jsmin
  - keyrings.alt
  - monotonic
  - pathlib
  - patool
  - shapely
  - sqlalchemy
  - svgutils
  - transforms3d
  - whoosh
  - pyyaml
  - docopt
  - beautifulsoup4
  - httpretty
  - multidict
  - nose
  - vcrpy
  - wget
  - yarl
  - boto
  - fasteners
    #- mpi4py brainiak dependency
  - networkx=2.1 # one of the pip packages pins this
  - pigz
  - zarr
  - jax
  - pyarrow
  - filelock
  - rpy2
  - spyder
  - prefect
  - airflow-with-dask
  - pyvista
  - awscli
    # - napari needs newer qt than supported by other libraries (probably fsl)
  - pip:
    - bids-validator
    - ciftify
    - citeproc-py
    - datalad
    - datalad-container
    - datalad-hirni
    - datalad-metalad
    - datalad-neuroimaging
    - datalad-webapp
    - git+https://github.com/jooh/Dcm2Bids@0.4.0.1
    - dcmstack
    - duecredit
    - grabbit
    - heudiconv
      # - brainiak - skip, incompatible with new pip
    - neurodocker
    - niworkflows
    - num2words
    - pybids
    - pycortex
    - pydeface
    - python-xmp-toolkit
    - templateflow
    - transplant