From 63343e17736fa3829329c3f13aa18772b6205788 Mon Sep 17 00:00:00 2001
From: Stefan Verhoeven <stefan.verhoeven@gmail.com>
Date: Wed, 15 Feb 2023 13:50:54 +0100
Subject: [PATCH 1/4] Create conda environment.yml file to install most R deps

Refs #54
---
 README.md       |  8 ++++++++
 environment.yml | 53 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 61 insertions(+)
 create mode 100644 environment.yml

diff --git a/README.md b/README.md
index ca1f68a5..ce4b859c 100644
--- a/README.md
+++ b/README.md
@@ -45,3 +45,11 @@ install.packages("daymetr")
 ```
 
 To complete installation you might need to install some OS dependencies.
+
+The installation of the dependences of the R dependencies can be annoying. To simplify installation of the dependencies of the 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
+```
\ No newline at end of file
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 00000000..e989ee01
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,53 @@
+name: springtime
+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

From 6e9c3d683820cd29e0b703ac44e467b9aedeb8d3 Mon Sep 17 00:00:00 2001
From: Stefan Verhoeven <stefan.verhoeven@gmail.com>
Date: Wed, 15 Feb 2023 13:54:57 +0100
Subject: [PATCH 2/4] English

---
 README.md       | 9 +++++++--
 environment.yml | 2 ++
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index ce4b859c..c694d24f 100644
--- a/README.md
+++ b/README.md
@@ -46,10 +46,15 @@ install.packages("daymetr")
 
 To complete installation you might need to install some OS dependencies.
 
-The installation of the dependences of the R dependencies can be annoying. To simplify installation of the dependencies of the R depencencies you can create a Anaconda environment using
+The installation of the dependencies of the R dependencies can be cumbersome (takes a long time, lots of compilation with obscure errors, requires root access, etc.). To simplify installation of the dependencies of the 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
-```
\ No newline at end of file
+
+# Install 
+
+# Install Python code with
+hatch env create
+```
diff --git a/environment.yml b/environment.yml
index e989ee01..997b5621 100644
--- a/environment.yml
+++ b/environment.yml
@@ -51,3 +51,5 @@ dependencies:
   - 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

From 9c57bbea67f0ef873984184d9588ddb995fbb051 Mon Sep 17 00:00:00 2001
From: Stefan Verhoeven <stefan.verhoeven@gmail.com>
Date: Wed, 15 Feb 2023 13:55:33 +0100
Subject: [PATCH 3/4] Try to dry

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index c694d24f..e7f0b8ca 100644
--- a/README.md
+++ b/README.md
@@ -53,7 +53,7 @@ The installation of the dependencies of the R dependencies can be cumbersome (ta
 mamba env create --file environment.yml
 conda activate springtime
 
-# Install 
+# Install R dependencies as list above
 
 # Install Python code with
 hatch env create

From 9189c72c7373437e37b612e145f63e04f5215530 Mon Sep 17 00:00:00 2001
From: Stefan Verhoeven <s.verhoeven@esciencecenter.nl>
Date: Wed, 15 Feb 2023 14:29:50 +0100
Subject: [PATCH 4/4] Update environment.yml

Co-authored-by: Peter Kalverla <peter.kalverla@gmx.com>
---
 environment.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/environment.yml b/environment.yml
index 997b5621..a2a23a59 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,4 +1,6 @@
 name: springtime
+channels:
+  - conda-forge
 dependencies:
   - pip!=21.3
   - python==3.10