Python Snippet
-# Get list of run belonging to the workflow with `workflow_id` = '1000009172'
-response = requests.get(
- "http://pecan.localhost/api/runs/?workflow_id=1000009172",
- auth=HTTPBasicAuth('carya', 'illinois')
- )
-print(json.dumps(response.json(), indent=2))
# Get list of run belonging to the workflow with `workflow_id` = '1000009172'
+response = requests.get(
+ "http://pecan.localhost/api/runs/?workflow_id=1000009172",
+ auth=HTTPBasicAuth('carya', 'illinois')
+ )
+print(json.dumps(response.json(), indent=2))
## {
## "runs": [
## {
@@ -1792,12 +1790,12 @@
GET /api/runs/{run_id}
R Snippet
-
# Get details of run belonging with `id` = '99000000282'
-res <- httr::GET(
- "http://pecan.localhost/api/runs/99000000282",
- httr::authenticate("carya", "illinois")
- )
-print(jsonlite::fromJSON(rawToChar(res$content)))
+
# Get details of run belonging with `id` = '99000000282'
+res <- httr::GET(
+ "http://pecan.localhost/api/runs/99000000282",
+ httr::authenticate("carya", "illinois")
+ )
+print(jsonlite::fromJSON(rawToChar(res$content)))
## $runtype
## [1] "sensitivity analysis"
@@ -1861,12 +1859,12 @@
@@ -1935,22 +1933,22 @@
GET /api/runs/{run_id}/output/{filename}
R Snippet
-
# Download the '2002.nc' output file for the run with id = 99000000282
-res <- httr::GET(
- "http://pecan.localhost/api/runs/99000000282/output/2002.nc",
- httr::authenticate("carya", "illinois")
- )
-writeBin(res$content, "test.2002.nc")
+
# Download the '2002.nc' output file for the run with id = 99000000282
+res <- httr::GET(
+ "http://pecan.localhost/api/runs/99000000282/output/2002.nc",
+ httr::authenticate("carya", "illinois")
+ )
+writeBin(res$content, "test.2002.nc")
Python Snippet
-
# Download the '2002.nc' output file for the run with id = 99000000282
-response = requests.get(
- "http://pecan.localhost/api/runs/99000000282/output/2002.nc",
- auth=HTTPBasicAuth('carya', 'illinois')
- )
-with open("test.2002.nc", "wb") as file:
- file.write(response.content)
+
# Download the '2002.nc' output file for the run with id = 99000000282
+response = requests.get(
+ "http://pecan.localhost/api/runs/99000000282/output/2002.nc",
+ auth=HTTPBasicAuth('carya', 'illinois')
+ )
+with open("test.2002.nc", "wb") as file:
+ file.write(response.content)
@@ -1960,23 +1958,23 @@
GET /api/runs/{run_id}/graph/{year}/{y_var}
R Snippet
-
# Plot the Gross Primary Productivity vs Time for the run with ID `99000000282` for the year 2002
-res <- httr::GET(
- "http://pecan.localhost/api/runs/99000000282/graph/2002/GPP",
- httr::authenticate("carya", "illinois")
- )
-writeBin(res$content, "test.png")
+
# Plot the Gross Primary Productivity vs Time for the run with ID `99000000282` for the year 2002
+res <- httr::GET(
+ "http://pecan.localhost/api/runs/99000000282/graph/2002/GPP",
+ httr::authenticate("carya", "illinois")
+ )
+writeBin(res$content, "test.png")
Python Snippet
-
# Plot the Gross Primary Productivity vs Time for the run with ID `99000000282` for the year 2002
-response = requests.get(
- "http://pecan.localhost/api/runs/99000000282/graph/2002/GPP",
- auth=HTTPBasicAuth('carya', 'illinois')
- )
-with open("test.png", "wb") as file:
- file.write(response.content)
+
# Plot the Gross Primary Productivity vs Time for the run with ID `99000000282` for the year 2002
+response = requests.get(
+ "http://pecan.localhost/api/runs/99000000282/graph/2002/GPP",
+ auth=HTTPBasicAuth('carya', 'illinois')
+ )
+with open("test.png", "wb") as file:
+ file.write(response.content)
Importing Functions: Use Roxygen
PEcAn style is to import very few functions and instead use fully namespaced function calls (pkg::fn()) everywhere it’s practical to do so. In cases where double-colon notation would be especially burdensome, such as when importing custom binary operators like %>%, it’s acceptable to import specific functions into the package namespace. Do this by using Roxygen comments of the form #' @importFrom pkg function, not by hand-editing the NAMESPACE file.
If the import is only used in one or a few functions, use an @importFrom in the documentation for each function that uses it. If it is used all over the package, use a single @importFrom in the Roxygen documentation block for the whole package, which probably lives in a file called either zzz.R or <your_package_name>-package.R:
-#' What your package does
-#'
-#' Longer description of the package goes here.
-#' Probably with links to other resources about it, citations, etc.
-#'
-#' @docType package
-#' @name PEcAn.yourpkg
-#' @importFrom magrittr %>%
-NULL
#' What your package does
+#'
+#' Longer description of the package goes here.
+#' Probably with links to other resources about it, citations, etc.
+#'
+#' @docType package
+#' @name PEcAn.yourpkg
+#' @importFrom magrittr %>%
+NULL
Roxygen will make sure there’s only one NAMESPACE entry per imported function no matter how many importFrom statements there are, but please pick a scheme (either import on every usage or once for the whole package), stick with it, and do not make function x() rely on an importFrom in the comments above function y().
Please do not import entire package namespaces (#' @import pkg); it increases the chance of function name collisions and makes it much harder to understand which package a given function was called from.
A special note about importing functions from the tidyverse: Be sure to import from the package(s) that actually contain the functions you want to use, e.g. Imports: dplyr, magrittr, purrr / @importFrom magrittr %>% / purrr::map(...), not Imports: tidyverse / @importFrom tidyverse %>% / tidyverse::map(...). The package named tidyverse is just a interactive shortcut that loads the whole collection of constituent packages; it doesn’t export any functions in its own namespace and therefore importing it into your package doesn’t make them available.
diff --git a/develop/index.html b/develop/index.html
index 9b436af54..105515e9f 100644
--- a/develop/index.html
+++ b/develop/index.html
@@ -23,7 +23,7 @@
-
+
@@ -230,9 +230,8 @@
7.1 Additional web configuration
7.2 Settings-configured analyses
13 PEcAn workflow (web/workflow.R)
@@ -779,7 +777,7 @@ Example of a Dockerfile, in this case to build the ED2 model.
-ARG IMAGE_VERSION="latest"
-# ----------------------------------------------------------------------
-# BUILD MODEL BINARY
-# ----------------------------------------------------------------------
-FROM pecan/models:${IMAGE_VERSION} as model-binary
-
-# Some variables that can be used to set control the docker build
-ARG MODEL_VERSION=git
-
-# install dependencies
-RUN apt-get update \
- && apt-get install -y --no-install-recommends \
- build-essential \
- curl \
- gfortran \
- git \
- libhdf5-dev \
- libopenmpi-dev \
- && rm -rf /var/lib/apt/lists/*
-
-# download, unzip and build ed2
-WORKDIR /src
-RUN git -c http.sslVerify=false clone https://github.com/EDmodel/ED2.git \
- && cd ED2/ED/build \
- && curl -o make/include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.Linux \
- && if [ "${MODEL_VERSION}" != "git" ]; then git checkout ${MODEL_VERSION}; fi \
- && ./install.sh -g -p VM
-
-########################################################################
-
-# ----------------------------------------------------------------------
-# BUILD PECAN FOR MODEL
-# ----------------------------------------------------------------------
-FROM pecan/models:latest
-
-# ----------------------------------------------------------------------
-# INSTALL MODEL SPECIFIC PIECES
-# ----------------------------------------------------------------------
-
-RUN apt-get update \
- && apt-get install -y --no-install-recommends \
- libgfortran3 \
- libopenmpi2 \
- && rm -rf /var/lib/apt/lists/*
-
-# ----------------------------------------------------------------------
-# SETUP FOR SPECIFIC MODEL
-# ----------------------------------------------------------------------
-
-# Some variables that can be used to set control the docker build
-ARG MODEL_VERSION=git
-
-# Setup model_info file
-COPY models/ed/model_info.json /work/model.json
-RUN sed -i -e "s/@VERSION@/${MODEL_VERSION}/g" \
- -e "s#@BINARY@#/usr/local/bin/ed2.${MODEL_VERSION}#g" /work/model.json
-
-# COPY model binary
-COPY --from=model-binary /src/ED2/ED/build/ed_2.1-opt /usr/local/bin/ed2.${MODEL_VERSION}
ARG IMAGE_VERSION="latest"
+# ----------------------------------------------------------------------
+# BUILD MODEL BINARY
+# ----------------------------------------------------------------------
+FROM pecan/models:${IMAGE_VERSION} as model-binary
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=git
+
+# install dependencies
+RUN apt-get update \
+ && apt-get install -y --no-install-recommends \
+ build-essential \
+ curl \
+ gfortran \
+ git \
+ libhdf5-dev \
+ libopenmpi-dev \
+ && rm -rf /var/lib/apt/lists/*
+
+# download, unzip and build ed2
+WORKDIR /src
+RUN git -c http.sslVerify=false clone https://github.com/EDmodel/ED2.git \
+ && cd ED2/ED/build \
+ && curl -o make/include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.Linux \
+ && if [ "${MODEL_VERSION}" != "git" ]; then git checkout ${MODEL_VERSION}; fi \
+ && ./install.sh -g -p VM
+
+########################################################################
+
+# ----------------------------------------------------------------------
+# BUILD PECAN FOR MODEL
+# ----------------------------------------------------------------------
+FROM pecan/models:latest
+
+# ----------------------------------------------------------------------
+# INSTALL MODEL SPECIFIC PIECES
+# ----------------------------------------------------------------------
+
+RUN apt-get update \
+ && apt-get install -y --no-install-recommends \
+ libgfortran3 \
+ libopenmpi2 \
+ && rm -rf /var/lib/apt/lists/*
+
+# ----------------------------------------------------------------------
+# SETUP FOR SPECIFIC MODEL
+# ----------------------------------------------------------------------
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=git
+
+# Setup model_info file
+COPY models/ed/model_info.json /work/model.json
+RUN sed -i -e "s/@VERSION@/${MODEL_VERSION}/g" \
+ -e "s#@BINARY@#/usr/local/bin/ed2.${MODEL_VERSION}#g" /work/model.json
+
+# COPY model binary
+COPY --from=model-binary /src/ED2/ED/build/ed_2.1-opt /usr/local/bin/ed2.${MODEL_VERSION}
WARNING: Dockerfile environment variables set via ENV are assigned all at once; they do not evaluate successively, left to right.
Consider the following block:
-# Don't do this!
-ENV MODEL_TYPE="SIPNET" \
- MODEL_VERSION=136 \
- MODEL_TYPE_VERSION=${MODEL_TYPE}_${MODEL_VERSION} # <- Doesn't know about MODEL_TYPE or MODEL_VERSION!
# Don't do this!
+ENV MODEL_TYPE="SIPNET" \
+ MODEL_VERSION=136 \
+ MODEL_TYPE_VERSION=${MODEL_TYPE}_${MODEL_VERSION} # <- Doesn't know about MODEL_TYPE or MODEL_VERSION!
In this block, the expansion for setting MODEL_TYPE_VERSION is not aware of the current values of MODEL_TYPE or MODEL_VERSION, and will therefore be set incorrectly to just _ (unless they have been set previously, in which case it will be aware only of their earlier values).
As such, variables depending on other variables must be set in a separate, subsequent ENV statement than the variables they depend on.
Once the model has build and is working we can add it to the PEcAn stack and be able to use this model in the web interface. There are two methods to start this new model. First, we can add it to the docker-compose.yml file and start the container using docker-compose -p pecan -d up.
- sipnet:
- image: pecan/model-ed2-git
- networks:
- - pecan
- volumes:
- - pecan:/data
- depends_on:
- - rabbitmq
- restart: unless-stopped
sipnet:
+ image: pecan/model-ed2-git
+ networks:
+ - pecan
+ volumes:
+ - pecan:/data
+ depends_on:
+ - rabbitmq
+ restart: unless-stopped
Alternatively we can start the container manually using the following command.
-docker run \
- --detach \
- --rm \
- --name pecan-ed2-git \
- --networks pecan_pecan \
- --volume pecan_pecan:/data
- pecan/model-ed2-git
docker run \
+ --detach \
+ --rm \
+ --name pecan-ed2-git \
+ --networks pecan_pecan \
+ --volume pecan_pecan:/data
+ pecan/model-ed2-git