Merge branch 'develop' into convert-input

CONTRIBUTING.md

@@ -115,4 +115,4 @@ git push -u origin GH-issuenumber-title-of-issue
 - [Adding models to PEcAn](https://pecanproject.github.io/pecan-documentation/latest/adding-an-ecosystem-model.html)
 - [PEcAn configuration files](https://pecanproject.github.io/pecan-documentation/latest/pecan-xml-configuration.html)
 - [Development help](https://pecanproject.github.io/pecan-documentation/latest/developer-guide.html)
-- [PEcAn Code of Conduct](https://pecanproject.github.io/pecan-documentation/latest/contributor-covenant-code-of-conduct.html)
+- [PEcAn Code of Conduct](CODE_OF_CONDUCT.md)

book_source/03_topical_pages/92_workflow_modules.Rmd

@@ -5,7 +5,7 @@ NOTE: As of PEcAn 1.2.6 -- needs to be updated significantly
 <!--NEEDS TO BE UPDATED SIGNIFICANTLY-->
 ## Overview
 
-Workflow inputs and outputs (click to open in new page, then zoom). Code used to generate this image is provided in [qaqc/vignettes/module_output.Rmd](https://github.com/PecanProject/pecan/blob/main/qaqc/vignettes/module_output.Rmd)
+Workflow inputs and outputs (click to open in new page, then zoom). Code used to generate this image is provided in [base/qaqc/vignettes/module_output.Rmd](https://github.com/PecanProject/pecan/blob/master/base/qaqc/vignettes/module_output.Rmd)
 
 [![PEcAn Workflow](http://isda.ncsa.illinois.edu/~kooper/EBI/workflow.svg)](http://isda.ncsa.illinois.edu/~kooper/EBI/workflow.svg)
 

docker-compose.yml

@@ -99,7 +99,7 @@ services:
       - "traefik.http.services.bety.loadbalancer.server.port=8000"
       - "traefik.http.routers.bety.rule=Host(`${TRAEFIK_HOST:-pecan.localhost}`) && PathPrefix(`/bety/`)"
     healthcheck:
-      test: "curl --silent --fail http://localhost:8000/${RAILS_RELATIVE_URL_ROOT} > /dev/null || exit 1"
+      test: "curl --silent --fail http://localhost:8000/$${RAILS_RELATIVE_URL_ROOT} > /dev/null || exit 1"
       interval: 10s
       timeout: 5s
       retries: 5
@@ -190,7 +190,7 @@ services:
       - pecan:/data
       - pecan:/var/www/html/pecan/data
     healthcheck:
-      test: "curl --silent --fail http://localhost/pecan/ > /dev/null || exit 1"
+      test: "curl --silent --fail http://localhost:8080/pecan > /dev/null || exit 1"
       interval: 10s
       timeout: 5s
       retries: 5
@@ -218,7 +218,7 @@ services:
     volumes:
       - pecan:/data
     healthcheck:
-      test: "curl --silent --fail http://localhost:9999/monitor/ > /dev/null || exit 1"
+      test: "curl --silent --fail http://localhost:9999 > /dev/null || exit 1"
       interval: 10s
       timeout: 5s
       retries: 5
@@ -354,7 +354,7 @@ services:
       - "traefik.http.routers.dbsync.middlewares=dbsync-stripprefix"
       - "traefik.http.middlewares.dbsync-stripprefix.stripprefix.prefixes=/monitor"
     healthcheck:
-      test: "curl --silent --fail http://localhost/dbsync/ > /dev/null || exit 1"
+      test: "curl --silent --fail http://localhost:3838 > /dev/null || exit 1"
       interval: 10s
       timeout: 5s
       retries: 5
@@ -386,7 +386,7 @@ services:
     volumes:
       - pecan:/data/
     healthcheck:
-      test: "curl --silent --fail http://localhost/api/ping > /dev/null || exit 1"
+      test: "curl --silent --fail http://localhost:8000/api/ping > /dev/null || exit 1"
       interval: 10s
       timeout: 5s
       retries: 5

docker/data/Dockerfile

@@ -18,4 +18,4 @@ RUN apk --no-cache add bash curl rsync postgresql-client unzip \
     && curl -s -o create_met_driver.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/create_met_driver.tar.gz
 
 COPY add-data.sh add.util.sh /work/
-CMD ["bash", "-c", "/work/add-data.sh"]
+CMD ["bash", "/work/add-data.sh"]

docker/docs/Dockerfile

@@ -28,6 +28,11 @@ RUN make build
 # ----------------------------------------------------------------------
 FROM httpd
 
+# need curl for health checks
+RUN apt-get update \
+    && apt-get install -y curl \
+    && rm -rf /var/lib/apt/lists/*
+
 COPY docker/docs/index.html /usr/local/apache2/htdocs/
 COPY --from=pecandocs /src/book_source/_book/ /usr/local/apache2/htdocs/docs/pecan/
 

modules/uncertainty/R/sensitivity.R

@@ -28,7 +28,6 @@
 ##' @export
 ##' @author Ryan Kelly, David LeBauer, Rob Kooper, Mike Dietze, Istem Fer
 #--------------------------------------------------------------------------------------------------#
-##' @author Ryan Kelly, David LeBauer, Rob Kooper, Mike Dietze
 read.sa.output <- function(traits, quantiles, pecandir, outdir, pft.name = "", 
                            start.year, end.year, variable, sa.run.ids = NULL, per.pft = FALSE) {
 

shiny/dbsync/Dockerfile

@@ -7,7 +7,7 @@ ENV PGHOST=postgres \
     GEOCACHE=/srv/shiny-server/geoip.json
 
 RUN apt-get update \
-    && apt-get -y install libpq-dev libssl-dev \
+    && apt-get -y install curl libpq-dev libssl-dev \
     && install2.r -e -s -n -1 curl dbplyr DT leaflet RPostgreSQL \
     && rm -rf /srv/shiny-server/* \
     && rm -rf /var/lib/apt/lists/*