Merge branch 'develop' into basgra-yasso-pr

.github/labeler.yml

@@ -0,0 +1,57 @@
+#
+# Add project labels
+#
+
+# Add 'Documentation' label to any changes in the documentation
+
+'Documentation':
+  - book_source/**
+  - documentation/**
+  - CONTRIBUTING.md
+  - DEBUGING.md
+  - DEV-INTRO.md
+  - README.md
+
+# Add 'Dockerfile' label to any changes in the docker directory
+'Dockerfile':
+  - docker/**
+
+
+# Add 'Website' label to any changes in the web directory
+
+'Website':
+  - web/**
+
+# Add 'Base' label to any changes in the base directory
+
+'Base':
+  - base/**
+
+# Add 'Models' label to any changes in the models directory
+
+'Models':
+  - models/**
+
+# Add 'Modules' label to any changes in the modules directory
+
+'Modules':
+  - modules/**
+
+# Add 'GitHub Actions' label to any changes in the .github/workflows directory
+
+'GitHub Actions':
+  - .github/workflows/**
+
+# Add 'Scripts' label to any changes in the scripts directory
+
+'Scripts':
+  - scripts/**
+
+# Add 'Tests' label to any changes in the tests directory
+
+'Tests':
+  - tests/**
+  - '**/tests/**'
+  - '!**/tests/Rcheck_reference.log'
+
+

.github/settings.yml

@@ -0,0 +1,30 @@
+#Define the colour of labels over here
+
+labels:
+
+  - name: "Documentation"
+    color: a2dcf2
+
+  - name: "Dockerfile"
+    color: 0052CC
+
+  - name: "Website"
+    color: 84b6eb
+
+  - name: "Base"
+    color: 1ED626
+
+  - name: "Models"
+    color: C5DEF5
+
+  - name: "Modules"
+    color: FBCA04
+
+  - name: "GitHub Actions"
+    color: 84b6eb
+
+  - name: "Scripts"
+    color: 3B8924
+
+  - name: "Tests"
+    color: ff8c00

.github/workflows/prlabeler.yml

@@ -0,0 +1,22 @@
+# This workflow is based on github action official label action v4.
+# This workflow action is triggered on pull request event(on both fork & inside repo)
+# Labels will be applied based on filepath modification in PR.
+# This workflow uses a regex based labeling config file(.github/labeler.yml) to take labeling decision.
+
+name: "PR Labeler"
+on:
+  - pull_request_target
+jobs:
+  label:
+    permissions:
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/labeler@v4
+        with:
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+          configuration-path: ".github/labeler.yml"
+          sync-labels: false
+          dot: true

Makefile

@@ -153,7 +153,8 @@ clean:
 	+ ./scripts/time.sh "roxygen2 ${1}" Rscript -e ${SETROPTIONS} \
 		-e "if (!requireNamespace('roxygen2', quietly = TRUE)" \
 		-e "    || packageVersion('roxygen2') != '7.2.3') {" \
-		-e "  devtools::install_github('r-lib/[email protected]')" \
+		-e "  cran <- c(getOption('repos'), 'cloud.r-project.org')" \
+		-e "  remotes::install_version('roxygen2', '7.2.3', repos = cran, upgrade = FALSE)" \
 		-e "}"
 	$(eval INSTALLED_ROXYGEN_VERSION := 7.2.3)
 	echo `date` > $@

Makefile.depends

@@ -30,7 +30,7 @@ $(call depends,models/template): | .install/base/db .install/base/logger .instal
 $(call depends,modules/allometry): | .install/base/db
 $(call depends,modules/assim.batch): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/workflow .install/modules/benchmark .install/modules/emulator .install/modules/meta.analysis .install/modules/uncertainty
 $(call depends,modules/assim.sequential): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization .install/base/workflow .install/modules/benchmark .install/modules/data.land .install/modules/data.remote .install/modules/uncertainty
-$(call depends,modules/benchmark): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.land
+$(call depends,modules/benchmark): | .install/base/db .install/base/logger .install/base/settings .install/base/utils .install/modules/data.land
 $(call depends,modules/data.atmosphere): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils
 $(call depends,modules/data.hydrology): | .install/base/logger .install/base/utils
 $(call depends,modules/data.land): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization .install/modules/benchmark .install/modules/data.atmosphere

base/all/DESCRIPTION

@@ -64,13 +64,15 @@ Depends:
 Imports:
     utils
 Suggests:
+    mockery,
     PEcAn.ED2,
     PEcAn.SIPNET,
     PEcAn.BIOCRO,
     PEcAn.DALEC,
     PEcAn.LINKAGES,
     PEcAn.allometry,
     PEcAn.photosynthesis,
+    sessioninfo,
     testthat
 License: BSD_3_clause + file LICENSE
 Copyright: Authors

base/all/R/pecan_version.R

@@ -16,13 +16,16 @@
 #'  locations in `.libPaths()`, or if you've loaded a new version into your
 #'  current session by loading it from its source directory without installing
 #'  it to the R library.
-#' If you see multiple rows unexpectedly, try `find.package(<pkgname>, verbose = TRUE)` to see where each version was found.
+#' If you see multiple rows unexpectedly, try
+#'  `find.package(<pkgname>, verbose = TRUE)` to see where each version was found.
 #'
 #' @param version PEcAn release number to use for expected package versions
 #' @param exact Show only tags that exactly match `version`,
 #'  or all tags that have it as a substring?
 #' @return data frame with columns for package name, expected version(s),
-#'  and installed version
+#'  and installed version.
+#'  If the `sessioninfo` package is installed, a fourth column reports where
+#'  each package was installed from: local, github, CRAN, etc.
 #'
 #' @examples
 #' pecan_version()
@@ -35,25 +38,6 @@
 #' @export
 pecan_version <- function(version = max(PEcAn.all::pecan_releases$version),
                           exact = FALSE) {
-  all_pkgs <- as.data.frame(utils::installed.packages())
-  our_pkgs <- all_pkgs[
-    grepl("PEcAn", all_pkgs$Package),
-    c("Package", "Version")
-  ]
-  colnames(our_pkgs) <- c("package", "installed")
-  our_pkgs$installed <- package_version(our_pkgs$installed)
-
-  # Check in currently loaded packages too,
-  # add rows for any that differ from installed versions
-  sess <- utils::sessionInfo()
-  sess <- c(sess$otherPkgs, sess$loadedOnly)
-  our_loaded <- sess[grepl("PEcAn", names(sess))]
-  our_loaded <- data.frame(
-    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)
-
   if (!exact) {
     version <- sapply(
       X = version,
@@ -62,9 +46,58 @@ pecan_version <- function(version = max(PEcAn.all::pecan_releases$version),
     )
     version <- unique(unlist(version))
   }
+  cols_to_return <- c("package", version, "installed")
+
+
+  if (requireNamespace("sessioninfo", quietly = TRUE)) {
+    cols_to_return <- c(cols_to_return, "source")
+
+    all_pkgs <- sessioninfo::package_info(pkgs = "installed", dependencies = FALSE)
+    our_pkgs <- all_pkgs[grepl("PEcAn", all_pkgs$package),]
+
+    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$installed <- package_version(our_pkgs$installed)
+
+  } else {
+    all_pkgs <- as.data.frame(utils::installed.packages())
+    our_pkgs <- all_pkgs[
+      grepl("PEcAn", all_pkgs$Package),
+      c("Package", "Version")
+    ]
+    colnames(our_pkgs) <- c("package", "installed")
+    our_pkgs$installed <- package_version(our_pkgs$installed)
+    sess <- utils::sessionInfo()
+    sess <- c(sess$otherPkgs, sess$loadedOnly)
+    our_loaded <- sess[grepl("PEcAn", names(sess))]
+    our_loaded <- data.frame(
+      package = names(our_loaded),
+      installed = sapply(our_loaded, `[[`, "Version"))
+    our_loaded$installed <- package_version(our_loaded$installed)
+    our_pkgs <- merge(our_pkgs, our_loaded, all = TRUE)
+  }
+
 
-  res <- merge(our_pkgs, PEcAn.all::pecan_version_history, all = TRUE)
-  res <- res[, c("package", version, "installed")]
+  res <- merge(
+    x = our_pkgs,
+    y = PEcAn.all::pecan_version_history,
+    all = TRUE)
+  res <- res[, cols_to_return]
 
   drop_na_version_rows(res)
 }

base/all/tests/testthat/test-pecan_version.R

@@ -26,22 +26,22 @@ test_that("pecan_version", {
   # tags substring matched only when exact = FALSE
   expect_named(
     pecan_version("v1.5"),
-    c("package", paste0("v1.5.", 0:3), "installed")
+    c("package", paste0("v1.5.", 0:3), "installed", "source")
   )
   expect_error(
     pecan_version("v1.5", exact = TRUE),
     "undefined columns"
   )
   expect_named(
     pecan_version("v1.3", exact = TRUE),
-    c("package", "v1.3", "installed")
+    c("package", "v1.3", "installed", "source")
   )
 
   # returns current release if no args given
   noargs <- pecan_version()
   expected_tag <- tail(PEcAn.all::pecan_releases, 1)$tag
-  expect_length(noargs, 3)
-  expect_named(noargs, c("package", expected_tag, "installed"))
+  expect_length(noargs, 4)
+  expect_named(noargs, c("package", expected_tag, "installed", "source"))
 
   # Why the `any()`s below?
   # Because R CMD check runs tests with local test dir added to .libPaths,
@@ -67,3 +67,27 @@ test_that("pecan_version", {
     )
   )
 })
+
+
+test_that("pecan_version without sessioninfo", {
+
+  with_sessinfo <- pecan_version()
+
+  # make pecan_version think the sessioninfo package is unavailable
+  mockery::stub(pecan_version, 'requireNamespace', FALSE)
+  without_sessinfo <- pecan_version()
+
+  expect_length(with_sessinfo, 4)
+  expect_length(without_sessinfo, 3)
+  expect_equal(
+    with_sessinfo[, colnames(with_sessinfo) != "source"],
+    without_sessinfo)
+})
+
+# TODO: Would be nice to add a check here that will notice if the list of PEcAn
+# releases falls out of date, but it's not clear what other source of truth
+# to consult to determine that.
+#
+# The approach that failed just before I wrote this note:
+# No, the version of PEcAn.all (1.8.1.9000 today) is not reliably in sync with
+# the PEcAn version last tagged as a release (1.7.2 today).

base/workflow/DESCRIPTION

@@ -31,20 +31,21 @@ Description: The Predictive Ecosystem Carbon Analyzer
     that can be used to run the major steps of a PEcAn analysis.
 License: BSD_3_clause + file LICENSE
 Imports:
-  dplyr,
-	PEcAn.data.atmosphere,
-	PEcAn.data.land,
-	PEcAn.DB,
-	PEcAn.logger,
-	PEcAn.remote,
-	PEcAn.settings,
-	PEcAn.uncertainty,
-	PEcAn.utils,
-	purrr (>= 0.2.3),
-	XML
+    dplyr,
+    PEcAn.data.atmosphere,
+    PEcAn.data.land,
+    PEcAn.DB,
+    PEcAn.logger,
+    PEcAn.remote,
+    PEcAn.settings,
+    PEcAn.uncertainty,
+    PEcAn.utils,
+    purrr (>= 0.2.3),
+    XML
 Suggests:
-	testthat,
-    mockery
+    mockery,
+    testthat,
+    withr
 Copyright: Authors
 Encoding: UTF-8
 RoxygenNote: 7.2.3

base/workflow/R/start_model_runs.R

@@ -23,7 +23,7 @@ start_model_runs <- function(settings, write = TRUE, stop.on.error = TRUE) {
 
   run_file <- file.path(settings$rundir, "runs.txt")
   # check if runs need to be done
-  if (!file.exists(file.path(settings$rundir, "runs.txt"))) {
+  if (!file.exists(run_file)) {
     PEcAn.logger::logger.warn(
       "runs.txt not found, assuming no runs need to be done")
     return()

base/workflow/tests/testthat/test.start_model_runs.R

@@ -0,0 +1,20 @@
+test_that("`start_model_runs` throws a warning if runs.txt not provided", {
+  withr::with_tempdir({
+    PEcAn.logger::logger.setUseConsole(TRUE, FALSE)
+    on.exit(PEcAn.logger::logger.setUseConsole(TRUE, TRUE))
+    settings <- list(rundir = getwd())
+    expect_output(start_model_runs(settings), "runs.txt not found")
+  })
+})
+
+test_that("`start_model_runs` throws a warning if runs.txt is empty", {
+  withr::with_tempdir({
+    PEcAn.logger::logger.setUseConsole(TRUE, FALSE)
+    on.exit(PEcAn.logger::logger.setUseConsole(TRUE, TRUE))
+    settings <- list(rundir = getwd())
+    file_path <- file.path(getwd(), "runs.txt")
+    file.create(file_path)
+    expect_output(start_model_runs(settings), "runs.txt found, but is empty")
+  })
+})
+