Create conda environment.yml file to install most R deps

README.md

@@ -22,28 +22,47 @@ and a standardized "recipe" format to define the steps in our workflows.
 [Documentation](https://springtime.readthedocs.io/)
 
 <!--installation-start-->
-## Installation
+## Requirements
 
-To install springtime in your current environment, type
+This project requires python and R. To simplify installation of the (indirect) R
+depencencies you can create a Anaconda environment using [Mamba
+forge](https://github.com/conda-forge/miniforge#mambaforge) with:
+
+```shell
+mamba env create --file environment.yml
+conda activate springtime
+```
+
+## Install Python package with dependencies
+
+Once you have python and R, to install springtime in your current environment,
+type
 
 ```bash
 pip install git+https://github.com/phenology/springtime.git
 ```
 
-## R dependencies
-
-Some datasets use [R](https://www.r-project.org/) libraries.
+## Install R dependencies
 
-The R dependencies can be installed from R shell with
+Some datasets use [R](https://www.r-project.org/) libraries. The R dependencies
+can be installed with
 
-```R
-if(!require(devtools)){install.packages(devtools)}
-devtools::install_github("bluegreen-labs/[email protected]")
-install.packages("daymetr")
-devtools::install_github("ropensci/rppo")
+```bash
+Rscript -e 'devtools::install_github("bluegreen-labs/phenor")'
+Rscript -e 'devtools::install_github("ropensci/rppo")'
+Rscript -e 'install.packages("daymetr")'
 ```
 
-To complete installation you might need to install some OS dependencies.
+
+## Verify installation
+
+```bash
+python -m r2py.situation
+> ...
+> Calling `R RHOME`: /home/peter/miniconda3/envs/springtime/lib/R
+> Environment variable R_LIBS_USER: None
+> ...
+```
 <!--installation-end-->
 
 <!--illustration-start-->

environment.yml

@@ -0,0 +1,57 @@
+name: springtime
+channels:
+  - conda-forge
+dependencies:
+  - pip!=21.3
+  - python==3.10
+  - hatch
+  # R dependencies
+  - r-base >=4.2
+  # - r-BayesianTools   # not in any anconda channel
+  - r-ape
+  - r-changepoint
+  - r-class
+  - r-devtools
+  - r-doparallel
+  - r-expm
+  - r-filelock
+  - r-foreach
+  - r-gap
+  - r-GenSA
+  - r-getpass 
+  - r-ggplot2
+  - r-gmm
+  - r-httr
+  - r-idpmisc
+  - r-jsonlite
+  - r-keyring
+  - r-kernsmooth 
+  - r-lme4
+  - r-lmtest
+  - r-magrittr
+  - r-minqa
+  - r-msm
+  - r-ncdf4
+  - r-nloptr
+  - r-proxy
+  - r-qgam
+  - r-raster
+  - r-rcppeigen
+  # - r-rgenoud # is in r channel
+  - r-rvest
+  - r-sf
+  - r-snow
+  - r-sp
+  - r-sodium
+  - r-survival
+  - r-terra
+  - r-tibble
+  - r-tidyr
+  - r-tmvtnorm
+  - r-units
+  - r-wk
+  - r-xml2
+  - r-uuid
+  - r-zoo
+# TODO make list smaller by only listing most direct dependencies
+# this will make it easier to maintain the list

mkdocs.yml

@@ -8,7 +8,6 @@ nav:
       - Getting started: setup.md
   - User Guide:
       - Getting started: setup.md
-      - Conda installation: conda.md
       - CRIB installation: crib.md
   - Example notebooks: notebooks/pk_wishful_workflows.ipynb
   - Contributing guide: contributing.md