Merge pull request #370 from DrylandEcology/feature_dbOutput_DataAccess

- new functions to deal with the output database:
  `dbOutput_add_calculated_field`, `dbOut_read_variables_from_scenario`
- new functions for circular arithmetic: `circ_add`, `circ_minus`
- other new functions: `trewartha_climate`, `rbind_2cols_nonoverlapping`
- upgraded to rSOILWAT2 v3.1.3
- several bug fixes
- upgraded to lintr v2.0.0

.Rbuildignore

@@ -14,3 +14,5 @@
 ^cran-comments\.md$
 ^NEWS\.md$
 
+^doc$
+^Meta$

.gitignore

@@ -35,3 +35,5 @@ src/*.o
 src/*.so
 src/*.dll
 .Rproj.user
+doc
+Meta

.lintr

@@ -1,21 +1,38 @@
 linters: with_defaults(
-  #--- DEFAULT LINTERS
-  # Default line length:
-  line_length_linter(80L),
+  #------ DEFAULT LINTERS
+  assignment_linter,
   closed_curly_linter(allow_single_line = TRUE),
-  # Turn off default linters for now:
+  commas_linter,
+  commented_code_linter,
+  equals_na_linter,
+  function_left_parentheses_linter,
+  infix_spaces_linter,
+  line_length_linter(80L),
+  no_tab_linter,
+  object_length_linter,
+  object_usage_linter,
+  open_curly_linter,
+  paren_brace_linter,
+  pipe_continuation_linter,
+  seq_linter,
+  single_quotes_linter,
+  spaces_inside_linter,
+  spaces_left_parentheses_linter,
+  trailing_blank_lines_linter,
+  trailing_whitespace_linter,
+  #--- Turn off default linters for now:
   object_name_linter = NULL,
-  #--- NON-DEFAULT LINTERS
-  # Not activated non-default linters:
+  cyclocomp_linter = NULL,
+  #------ NON-DEFAULT LINTERS
+  #--- Not activated non-default linters:
   #extraction_operator_linter,
   #implicit_integer_linter,
   #todo_comment_linter,
-  # Activated non-default linters:
-  T_and_F_symbol_linter,
+  #--- Activated non-default linters:
   absolute_path_linter(lax = TRUE),
+  T_and_F_symbol_linter,
   nonportable_path_linter(lax = TRUE),
   semicolon_terminator_linter(semicolon = c("compound", "trailing")),
-  seq_linter,
   undesirable_function_linter,
   undesirable_operator_linter,
   unneeded_concatenation_linter)

.travis.yml

@@ -14,6 +14,7 @@ env:
     - NOT_CRAN=false
     # secure `GITHUB_PAT` for drs to increase "GitHub API rate limit"
     - secure: "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"
+    - LINTR_COMMENT_BOT=false
 
 sudo: false
 cache: packages # sets `R_LIBS_USER`

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rSFSW2
 Title: Simulation Framework for SOILWAT2
-Version: 4.0.0
-Date: 2019-05-03
+Version: 4.1.0
+Date: 2019-10-18
 Authors@R: c(
   person("Daniel", "Schlaepfer", email = "daniel.schlaepfer@yale.edu",
     comment = c(ORCID = "0000-0001-9973-2065"), role = c("aut", "cre")),
@@ -14,7 +14,7 @@ Description: Setting up, carrying out, and analyzing ecosystem water balance
 Depends:
     R (>= 3.5.0)
 Imports:
-    rSOILWAT2 (>= 3.0.0),
+    rSOILWAT2 (>= 3.1.3),
     RSQLite (>= 2.1.1),
     DBI (>= 1.0),
     Rcpp (>= 0.12.12),
@@ -45,7 +45,7 @@ Suggests:
     spelling (>= 1.1),
     hunspell (>= 2.9),
     covr,
-    lintr (>= 1.0.3.9000),
+    lintr (>= 2.0.0),
     goodpractice
 Remotes:
     github::dschlaep/weathergen

NAMESPACE

@@ -22,6 +22,8 @@ export(check_monotonic_increase)
 export(check_outputDB_completeness)
 export(check_rSFSW2_project_input_data)
 export(check_weatherDB)
+export(circ_add)
+export(circ_minus)
 export(climscen_metadata)
 export(compare_test_output)
 export(compare_two_dbOutput)
@@ -32,11 +34,13 @@ export(crs_units)
 export(dbConnect2)
 export(dbExecute2)
 export(dbOut_check_values)
+export(dbOut_read_variables_from_scenario)
 export(dbOut_update_values)
 export(dbOutput_ListDesignTables)
 export(dbOutput_ListInternalTables)
 export(dbOutput_ListOutputTables)
 export(dbOutput_Tables_have_SoilLayers)
+export(dbOutput_add_calculated_field)
 export(dbOutput_subset)
 export(dbOutput_update_OverallAggregationTable)
 export(dbWork_Ntodo)
@@ -80,6 +84,7 @@ export(germination_wait_times)
 export(get.SeveralOverallVariables)
 export(get.SeveralOverallVariables_Ensemble)
 export(get.SeveralOverallVariables_Scenario)
+export(get.SeveralOverallVariables_Scenario_old)
 export(get.Table)
 export(get.Table_Ensemble)
 export(get.Table_Scenario)