Devel 2.5.3 (#20)

* Fix docker build command

* Include conda env from antonio

* Added mamba doc for recipe

* Update dockerfile to 1.5.0

* Update README (conda as preferred install method)

* upgraded docker to 1.5.1 (added python packages)

* Added python dependencies and using mambabuild

* Change channel order in conda install command

Setting conda-forge as primary channel avoids conflicts with the default channel

* reduced meta.yml dependencies

* Update README.md

Include additional aid for jupyter notebook installation in new climate4r dedicated environments

* Update README.md

* Generated Dockerfile for 1.5.0

* updated conda to 1.5.1

* Updated README

* using r- packages instead of install.R

* The first release based only on conda packages

* Fix build string

* Relaxing R and Python version specification

* Preparing release v2.5.3

Co-authored-by: zequihg50 <[email protected]>
Co-authored-by: Jesus Fernandez <[email protected]>
Co-authored-by: Jesus Fernandez <[email protected]>
Co-authored-by: Joaquin Bedia <[email protected]>

Dockerfile

@@ -1,3 +1,13 @@
-FROM santandermetgroup/climate4r:1.4.1
+FROM jupyter/base-notebook:latest
 
-COPY --chown=jovyan:users notebooks /home/$NB_USER/notebooks
+USER root
+RUN apt-get update && apt-get install -y xorg git
+
+USER $NB_USER
+RUN conda install mamba -y -n base -c conda-forge && \
+    mamba install -y -c conda-forge -c r -c defaults -c santandermetgroup \
+                  r-climate4r=2.5.3 \
+                  xarray pandas matplotlib cartopy netcdf4 cftime dask iris \
+                  jupyter_contrib_nbextensions jupyter_nbextensions_configurator r-irkernel && \
+    chown -R jovyan:users /home/jovyan && \
+    R --vanilla -e 'IRkernel::installspec()'

README.md

@@ -48,8 +48,33 @@ Moreover, there is a [notebook repository](https://github.com/SantanderMetGroup/
 
 ## Installation
 
+The `climate4R` framework relies on a wealth of other R packages and bindings to third-party libraries. Therefore, the recommended installation is through the conda package below, which ensures the proper installation of all dependencies.
+
+### Installation using miniconda:
+
+[Miniconda](https://docs.conda.io/en/latest/miniconda.html) is a free minimal installer for conda. The [conda recipe](conda) installs an up-to-date version of the different packages composing the `climate4R` framework, along with the associated library dependencies (udunits, openjdk, netcdf Java etc.), avoiding potential problems like the R-java configuration etc. Note that the appropriate miniconda distribution must be installed (go to the [miniconda installers page](https://docs.conda.io/en/latest/miniconda.html)) before running the following commands. We recommend starting from a clean environment (named climate4R in this example):
+
+```bash
+conda create --name climate4R
+conda activate climate4R
+```
+
+In this environment, install `climate4R` by issuing:
+
+```bash
+conda install -c conda-forge -c r -c defaults -c santandermetgroup climate4r
+```
+
+Activate the conda environment to work with climate4R. Deactivate the environment with:
+
+```bash
+conda deactivate
+```
+
 ### Direct package installation from github:
 
+Individual packages can be installed directly from the github sources.
+
 ``` r
     > library(devtools)
     > install_github(c("SantanderMetGroup/loadeR.java",
@@ -60,26 +85,7 @@ Moreover, there is a [notebook repository](https://github.com/SantanderMetGroup/
                  "SantanderMetGroup/downscaleR"))
 ```
 
-### Installation using miniconda:
-
-[Miniconda](https://docs.conda.io/en/latest/miniconda.html) is a free minimal installer for conda. Using the [conda recipe](https://github.com/SantanderMetGroup/climate4R/tree/master/conda) it is possible to install an up-to-date version of the different packages composing the `climate4R` framework, and all the associated library dependencies (udunits, openjdk, netcdf Java etc.), avoiding some possible problems like the R-java configuration etc. Note that the appropriate miniconda distribution must be installed before running the command (go to the [miniconda installers page](https://docs.conda.io/en/latest/miniconda.html)):
-
-```bash
-# create a conda environment
-conda create --name nameofmycondaenvironment
-# activate the environment
-conda activate nameofmycondaenvironment
-# install climate4R
-conda install -c defaults -c r -c conda-forge -c santandermetgroup climate4r
-```
-Activate the conda environment to work with climate4R. To deactivate the environment run the following:
-
-```bash
-# deactivate the environment
-conda deactivate nameofmycondaenvironment
-```
-
-### NOTE: installation of specific package versions
+#### NOTE: installation of specific package versions
 
 In case a particular paper notebook is to be replicated, the installation of specific version tags can be done by just explicitly indicating the tag number in the repo name. For example:
 

conda/README.md

@@ -0,0 +1,43 @@
+# Conda recipe for climate4R metapackage
+
+## Installing climate4R conda metapackage
+
+```bash
+conda install -c conda-forge -c r -c defaults -c santandermetgroup  r-climate4r
+```
+
+***
+_Note for jupyter notebook users_: From a dedicated environment, to run notebooks using climate4R include it as:
+
+```bash
+conda install -c conda-forge -c r -c defaults -c santandermetgroup  r-climate4r
+ jupyter r-irkernel
+```
+
+in order to include jupyter notebooks in your newly created environment
+***
+
+## Building climate4R conda metapackage
+
+```bash
+conda build -c conda-forge -c r -c defaults -c santandermetgroup .
+anaconda login
+anaconda upload -u SantanderMetGroup PATH_TO_TAR_BZ2
+```
+
+## ToDo, explore mamba and boa
+
+[mamba](https://github.com/mamba-org/mamba) and [boa](https://github.com/mamba-org/boa)
+
+Install:
+
+```bash
+conda install mamba -n base -c conda-forge
+```
+
+Build:
+
+```bash
+rm -rf ${HOME}/miniconda3/conda-bld/src_cache
+conda mambabuild -c conda-forge -c r -c defaults -c santandermetgroup . &>log &
+```