Merge branch 'PecanProject:develop' into develop

.github/workflows/download-met-data.yml

@@ -0,0 +1,57 @@
+name : Test Data Download
+on :
+  # allow manual triggering
+  workflow_dispatch:
+
+  schedule:
+    # run Thursday 4:30 AM UTC
+  - cron: '30 4 * * 4'
+
+env:
+  R_LIBS_USER: /usr/local/lib/R/site-library
+  LC_ALL: en_US.UTF-8
+  NCPUS: 2
+  PGHOST: postgres
+  CI: true
+
+jobs:
+  met-data-download:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    services:
+      postgres:
+        image: mdillon/postgis:9.5
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
+    container: 
+      image: pecan/depends:R4.1
+
+    steps:
+    # checkout source code
+    - name: work around https://github.com/actions/checkout/issues/766
+      run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
+    - uses: actions/checkout@v4
+      with:
+        set-safe-directory: false
+
+    # install additional tools needed
+    - name: install utils
+      run: apt-get update && apt-get install -y postgresql-client qpdf
+    - name: install new dependencies
+      run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R
+
+    # initialize database
+    - name: db setup
+      uses: docker://pecan/db:ci
+    - name: add models to db
+      run: ./scripts/add.models.sh
+
+    # compile PEcAn code
+    - name: build
+      run: make -j1
+
+    - name: CRUNCEP
+      run: |
+        Rscript ./tests/test_met_downloads.R --settings ./tests/met_download_settings/docker.CRUNCEP.xml

Makefile.depends

@@ -18,13 +18,13 @@ $(call depends,models/fates): | .install/base/logger .install/base/remote .insta
 $(call depends,models/gday): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,models/jules): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
 $(call depends,models/ldndc): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere .install/modules/data.land
-$(call depends,models/linkages): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/linkages): | .install/base/db .install/base/logger .install/base/remote .install/base/utils .install/modules/data.land
 $(call depends,models/lpjguess): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,models/maat): | .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.atmosphere
 $(call depends,models/maespa): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
 $(call depends,models/preles): | .install/base/logger .install/base/utils .install/modules/data.atmosphere
-$(call depends,models/sibcasa): | .install/base/logger .install/base/utils
-$(call depends,models/sipnet): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/sibcasa): | .install/base/logger
+$(call depends,models/sipnet): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere .install/modules/data.land
 $(call depends,models/stics): | .install/base/logger .install/base/remote .install/base/settings .install/base/utils
 $(call depends,models/template): | .install/base/db .install/base/logger .install/base/utils
 $(call depends,modules/allometry): | .install/base/db

base/db/R/dbfiles.R

@@ -50,9 +50,8 @@ dbfile.input.insert <- function(in.path, in.prefix, siteid, startdate, enddate,
 
 
   # setup parent part of query if specified
-  if (is.na(parentid)) {
-    parent <- ""
-  } else {
+  parent <- ""
+  if (!is.na(parentid)) {
     parent <- paste0(" AND parent_id=", parentid)
   }
 
@@ -242,13 +241,13 @@ dbfile.input.check <- function(siteid, startdate = NULL, enddate = NULL, mimetyp
   formatid <- get.id(table = "formats", colnames = c("mimetype_id", "name"), values = c(mimetypeid, formatname), con = con)
 
   if (is.null(formatid)) {
-    invisible(data.frame())
+    return (invisible(data.frame()))
   }
 
   # setup parent part of query if specified
-  if (is.na(parentid)) {
-    parent <- ""
-  } else {
+  parent <- ""
+
+  if (!is.na(parentid)) {
     parent <- paste0(" AND parent_id=", parentid)
   }
 
@@ -450,7 +449,7 @@ dbfile.posterior.check <- function(pft, mimetype, formatname, con, hostname = PE
   # find appropriate pft
   pftid <- get.id(table = "pfts", values = "name", colnames = pft, con = con)
   if (is.null(pftid)) {
-    invisible(data.frame())
+    return (invisible(data.frame()))
   }
 
   # find appropriate format
@@ -461,7 +460,7 @@ dbfile.posterior.check <- function(pft, mimetype, formatname, con, hostname = PE
   formatid <- get.id(table = "formats", colnames = c("mimetype_id", "name"), values = c(mimetypeid, formatname), con = con)
 
   if (is.null(formatid)) {
-    invisible(data.frame())
+    return (invisible(data.frame()))
   }
 
   # find appropriate posterior
@@ -473,7 +472,7 @@ dbfile.posterior.check <- function(pft, mimetype, formatname, con, hostname = PE
     con = con
   )[["id"]]
   if (is.null(posteriorid)) {
-    invisible(data.frame())
+    return (invisible(data.frame()))
   }
 
   invisible(dbfile.check(type = "Posterior", container.id = posteriorid, con = con, hostname = hostname))
@@ -639,12 +638,12 @@ dbfile.file <- function(type, id, con, hostname = PEcAn.remote::fqdn()) {
 
   if (nrow(files) > 1) {
     PEcAn.logger::logger.warn("multiple files found for", id, "returned; using the first one found")
-    invisible(file.path(files[1, "file_path"], files[1, "file_name"]))
+    return(invisible(file.path(files[1, "file_path"], files[1, "file_name"])))
   } else if (nrow(files) == 1) {
-    invisible(file.path(files[1, "file_path"], files[1, "file_name"]))
+    return(invisible(file.path(files[1, "file_path"], files[1, "file_name"])))
   } else {
     PEcAn.logger::logger.warn("no files found for ", id, "in database")
-    invisible(NA)
+    return(invisible(NA))
   }
 }
 
@@ -662,7 +661,8 @@ dbfile.id <- function(type, file, con, hostname = PEcAn.remote::fqdn()) {
   # find appropriate host
   hostid <- db.query(query = paste0("SELECT id FROM machines WHERE hostname='", hostname, "'"), con = con)[["id"]]
   if (is.null(hostid)) {
-    invisible(NA)
+    PEcAn.logger::logger.warn("hostid not found in database")
+    return (invisible(NA))
   }
 
   # find file

base/db/tests/Rcheck_reference.log

@@ -62,8 +62,7 @@ The Date field is over a month old.
 * checking package directory ... OK
 * checking for future file timestamps ... OK
 * checking ‘build’ directory ... OK
-* checking DESCRIPTION meta-information ... NOTE
-License stub is invalid DCF.
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

base/qaqc/tests/Rcheck_reference.log

@@ -21,10 +21,6 @@
 * checking package directory ... OK
 * checking DESCRIPTION meta-information ... NOTE
 Malformed Description field: should contain one or more complete sentences.
-Authors@R field gives no person with name and roles.
-Authors@R field gives no person with maintainer role, valid email
-address and non-empty name.
-License stub is invalid DCF.
 * checking top-level files ... NOTE
 Non-standard file/directory found at top level:
   ‘README.Rmd’

base/remote/tests/Rcheck_reference.log

@@ -19,8 +19,7 @@
 * checking whether package ‘PEcAn.remote’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
-* checking DESCRIPTION meta-information ... NOTE
-License stub is invalid DCF.
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

base/settings/tests/Rcheck_reference.log

@@ -73,8 +73,7 @@ The Date field is over a month old.
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
-* checking DESCRIPTION meta-information ... NOTE
-License stub is invalid DCF.
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... NOTE
 Non-standard file/directory found at top level:
   ‘examples’

base/visualization/tests/Rcheck_reference.log

@@ -71,8 +71,7 @@ The Date field is over a month old.
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
-* checking DESCRIPTION meta-information ... NOTE
-License stub is invalid DCF.
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

base/workflow/DESCRIPTION

@@ -17,9 +17,6 @@ Authors@R: c(person("Mike", "Dietze", role = c("aut"),
              person("Shawn", "Serbin", role = c("aut"),
                      email = "[email protected]"),
              person("University of Illinois, NCSA", role = c("cph")))
-Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
-    Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin
-Maintainer: David LeBauer <[email protected]>
 Description: The Predictive Ecosystem Carbon Analyzer
     (PEcAn) is a scientific workflow management tool that
     is designed to simplify the management of model

base/workflow/tests/Rcheck_reference.log

@@ -62,15 +62,7 @@ The Date field is over a month old.
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
-* checking DESCRIPTION meta-information ... NOTE
-Author field differs from that derived from Authors@R
-  Author:    ‘David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin’
-  Authors@R: ‘Mike Dietze [aut], David LeBauer [aut, cre], Xiaohui Feng [aut], Dan Wang [aut], Carl Davidson [aut], Rob Kooper [aut], Shawn Serbin [aut], University of Illinois, NCSA [cph]’
-
-Maintainer field differs from that derived from Authors@R
-  Maintainer: ‘David LeBauer <[email protected]>’
-  Authors@R:  ‘David LeBauer <[email protected]>’
-License stub is invalid DCF.
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK