Merge branch 'develop' into use-pak-for-deps

Makefile

@@ -134,12 +134,6 @@ $(subst .doc/models/template,,$(MODELS_D)): .install/models/template
 ### Order-only dependencies
 # (i.e. prerequisites must exist before building target, but
 # target need not be rebuilt when a prerequisite changes)
-
-.doc/base/all: | $(ALL_PKGS_D)
-.install/base/all: | $(ALL_PKGS_I)
-.check/base/all: | $(ALL_PKGS_C)
-.test/base/all: | $(ALL_PKGS_T)
-
 include Makefile.depends
 
 clean:

base/all/DESCRIPTION

@@ -1,7 +1,6 @@
 Package: PEcAn.all
 Type: Package
-Title: PEcAn functions used for ecological forecasts and
-    reanalysis
+Title: PEcAn Functions Used for Ecological Forecasts and Reanalysis
 Version: 1.8.0.9000
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),
                      email = "[email protected]"),

base/all/R/pecan_version.R

@@ -55,23 +55,24 @@ pecan_version <- function(version = max(PEcAn.all::pecan_releases$version),
     all_pkgs <- sessioninfo::package_info(pkgs = "installed", dependencies = FALSE)
     our_pkgs <- all_pkgs[grepl("PEcAn", all_pkgs$package),]
 
+    # Why do we need this when `pkgs = "installed"` usually shows loaded too?
+    # Because there are times a package is loaded but not installed
+    # (e.g. notably during R CMD check)
     all_loaded <- sessioninfo::package_info(pkgs = "loaded", dependencies = FALSE)
     our_loaded <- all_loaded[grepl("PEcAn", all_loaded$package),]
 
-    unloaded <- our_pkgs[!our_pkgs$package %in% our_loaded$package,]
-    our_pkgs <- rbind(our_loaded, unloaded)
-    our_pkgs <- our_pkgs[order(our_pkgs$package),]
-
-
     # TODO: consider using package_info's callouts of packages where loaded and
     #   installed versions mismatch -- it's a more elegant version of what we
     #   were trying for with the "multiple rows for packages with multiple
     #   versions found" behavior.
-    our_pkgs$installed <- ifelse(
-      test = is.na(our_pkgs$loadedversion),
-      yes = our_pkgs$ondiskversion,
-      no = our_pkgs$loadedversion)
-    our_pkgs <- our_pkgs[, c("package", "installed", "source")]
+    our_pkgs <- merge(
+      x = our_pkgs[, c("package", "ondiskversion", "source")],
+      y = our_loaded[, c("package", "loadedversion", "source")],
+      by.x = c("package", "ondiskversion", "source"),
+      by.y = c("package", "loadedversion", "source"),
+      all = TRUE,
+      sort = TRUE)
+    colnames(our_pkgs) <- c("package", "installed", "source")
     our_pkgs$installed <- package_version(our_pkgs$installed)
 
   } else {
@@ -89,7 +90,8 @@ pecan_version <- function(version = max(PEcAn.all::pecan_releases$version),
       package = names(our_loaded),
       installed = sapply(our_loaded, `[[`, "Version"))
     our_loaded$installed <- package_version(our_loaded$installed)
-    our_pkgs <- merge(our_pkgs, our_loaded, all = TRUE)
+    our_pkgs <- merge(our_pkgs, our_loaded, all = TRUE, sort = TRUE)
+    our_pkgs <- our_pkgs[!duplicated(our_pkgs),]
   }
 
 

base/all/data/pecan_version_history.R

@@ -23,3 +23,8 @@ for (col in colnames(pecan_version_history)) {
       strict = strict)
   }
 }
+
+# Now remove local vars
+# Yes, this really is needed: _all_ objects left defined at end of script
+# will be added to the package data list!
+rm(strict, na_version, col)

base/all/tests/Rcheck_reference.log

@@ -14,38 +14,6 @@ New submission
 
 Version contains large components (1.7.2.9000)
 
-License components with restrictions and base license permitting such:
-  BSD_3_clause + file LICENSE
-File 'LICENSE':
-  University of Illinois/NCSA Open Source License
-
-  Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
-
-  Permission is hereby granted, free of charge, to any person obtaining
-  a copy of this software and associated documentation files (the
-  "Software"), to deal with the Software without restriction, including
-  without limitation the rights to use, copy, modify, merge, publish,
-  distribute, sublicense, and/or sell copies of the Software, and to
-  permit persons to whom the Software is furnished to do so, subject to
-  the following conditions:
-
-  - Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimers.
-  - Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimers in the
-    documentation and/or other materials provided with the distribution.
-  - Neither the names of University of Illinois, NCSA, nor the names
-    of its contributors may be used to endorse or promote products
-    derived from this Software without specific prior written permission.
-
-  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-  IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR
-  ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
-  CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-  WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
-
 Strong dependencies not in mainstream repositories:
   PEcAn.DB, PEcAn.settings, PEcAn.MA, PEcAn.logger, PEcAn.utils,
     PEcAn.uncertainty, PEcAn.data.atmosphere, PEcAn.data.land,
@@ -54,13 +22,6 @@ Strong dependencies not in mainstream repositories:
 Suggests or Enhances not in mainstream repositories:
   PEcAn.ED2, PEcAn.SIPNET, PEcAn.BIOCRO, PEcAn.DALEC, PEcAn.LINKAGES,
     PEcAn.allometry, PEcAn.photosynthesis
-
-The Title field should be in title case. Current version is:
-‘PEcAn functions used for ecological forecasts and reanalysis’
-In title case that is:
-‘PEcAn Functions Used for Ecological Forecasts and Reanalysis’
-
-The Date field is over a month old.
 * checking package namespace information ... OK
 * checking package dependencies ... NOTE
 Depends: includes the non-default packages:

book_source/01_introduction/01_project_overview.Rmd

@@ -2,7 +2,7 @@
 
 The Predictive Ecosystem Analyzer (PEcAn) is an integrated informatics toolbox for ecosystem modeling (Dietze et al. 2013, LeBauer et al. 2013). PEcAn consists of: 
 
-1. An application program interface (API) that encapsulates an ecosystem model, providing a common interface, inputs, and output.
+1. An application program interface (API) that encapsulates an ecosystem model, providing a common interface, inputs, and output
 2. Core utilities for handling and tracking model runs and the flows of information and uncertainties into and out of models and analyses
 3. An accessible web-based user interface and visualization tools
 4. An extensible collection of modules to handle specific types of analyses (sensitivity, uncertainty, ensemble), model-data syntheses (benchmarking, parameter data assimilation, state data assimilation), and data processing (model inputs and data constraints)

docker-compose.yml

@@ -2,6 +2,7 @@ services:
 
   # webserver to handle all traffic. This can use let's encrypt to generate a SSL cert.
   traefik:
+    hostname: traefik
     image: "traefik:v2.9"
     command:
       - --log.level=INFO
@@ -38,6 +39,7 @@ services:
 
   # rabbitmq to connect to extractors
   rabbitmq:
+    hostname: rabbitmq
     image: rabbitmq:3.8-management
     restart: unless-stopped
     networks:
@@ -64,6 +66,7 @@ services:
 
   # postgresql + postgis to hold all the data
   postgres:
+    hostname: postgres
     image: mdillon/postgis:9.5
     restart: unless-stopped
     networks:
@@ -80,6 +83,7 @@ services:
   # BETY rails frontend to the database
   # ----------------------------------------------------------------------
   bety:
+    hostname: bety
     image: pecan/bety:${BETY_VERSION:-latest}
     restart: unless-stopped
     networks:
@@ -108,6 +112,7 @@ services:
   # RStudio
   # ----------------------------------------------------------------------
   rstudio:
+    hostname: rstudio
     image: pecan/base:${PECAN_VERSION:-latest}
     command: /work/rstudio.sh
     restart: unless-stopped
@@ -151,6 +156,7 @@ services:
 
   # PEcAn documentation as well as PEcAn home page
   docs:
+    hostname: docs
     image: pecan/docs:${PECAN_VERSION:-latest}
     restart: unless-stopped
     networks:
@@ -167,6 +173,7 @@ services:
 
   # PEcAn web front end, this is just the PHP code
   pecan:
+    hostname: pecan-web
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/web:${PECAN_VERSION:-latest}
     restart: unless-stopped
@@ -197,6 +204,7 @@ services:
 
   # PEcAn model monitor
   monitor:
+    hostname: monitor
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/monitor:${PECAN_VERSION:-latest}
     restart: unless-stopped
@@ -225,6 +233,7 @@ services:
 
   # PEcAn executor, executes jobs. Does not the actual models
   executor:
+    hostname: executor
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/executor:${PECAN_VERSION:-latest}
     restart: unless-stopped
@@ -248,6 +257,7 @@ services:
   # ----------------------------------------------------------------------
   # PEcAn FATES model runner
   fates:
+    hostname: fates
     user: "${UID:-1001}:${GID:-1001}"
     image: ghcr.io/noresmhub/ctsm-api:latest
     restart: unless-stopped
@@ -263,6 +273,7 @@ services:
 
   # PEcAn basgra model runner
   basgra:
+    hostname: basgra
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-basgra-basgra_n_v1.0:${PECAN_VERSION:-latest}
     restart: unless-stopped
@@ -278,6 +289,7 @@ services:
 
   # PEcAn sipnet model runner
   sipnet:
+    hostname: sipnet-git
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-sipnet-git:${PECAN_VERSION:-latest}
     restart: unless-stopped
@@ -293,6 +305,7 @@ services:
 
   # PEcAn ED model runner
   ed2:
+    hostname: ed2-2_2_0
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-ed2-2.2.0:${PECAN_VERSION:-latest}
     restart: unless-stopped
@@ -308,6 +321,7 @@ services:
 
   # PEcAn MAESPA model runner
   maespa:
+    hostname: maespa-git
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-maespa-git:${PECAN_VERSION:-latest}
     restart: unless-stopped
@@ -323,6 +337,7 @@ services:
 
   # PEcAn BioCro model runner
   biocro:
+    hostname: biocro-0_95
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-biocro-0.95:${PECAN_VERSION:-latest}
     restart: unless-stopped
@@ -341,6 +356,7 @@ services:
   # ----------------------------------------------------------------------
   # PEcAn DB Sync visualization
   dbsync:
+    hostname: dbsync
     image: pecan/shiny-dbsync:${PECAN_VERSION:-latest}
     restart: unless-stopped
     networks:
@@ -363,6 +379,7 @@ services:
   # PEcAn API
   # ----------------------------------------------------------------------
   api:
+    hostname: api
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/api:${PECAN_VERSION:-latest}
     restart: unless-stopped