Clean NEWS (#1470)

* Clean NEWS * 🤖 Update Core Files. * Update contribution section --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Open-Systems-Pharmacology · Jul 26, 2024 · 3b49493 · 3b49493
1 parent d62441d
commit 3b49493
Show file tree

Hide file tree

Showing 12 changed files with 61 additions and 77 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -1,31 +1,26 @@
 # ospsuite 12.1.0
 
-## New dependencies
-
-  - `{rSharp}`
-
-## New features
+## Major Changes
 
+  - The package fully supports Linux.
+  - The package loses dependency `{rClr}` and gains `{rSharp}`.
   - The package does not require a local installation of PK-Sim any more. All required 
   dependencies are shipped with the package.
-
-  - The package fully supports Linux.
-
-## Major Changes
-
-  - The package loses dependency `{rClr}`
 
 
 # ospsuite 12.0.0
 
-## New dependencies
 
-  - `{openxlsx}`
-  - `{lifecyle}`
+## Breaking Changes
 
+  - The single argument of the `getBaseUnit()` function is now named
+    `quantityOrDimension` (was `dimension` previously). It can now use objects
+    of class `Quantity` as inputs, to be consistent with the `toBaseUnit()`
+    function.
 
-## New features
+## Major Changes
 
+  - The package gains `{openxlsx}` and `{lifecyle}` dependencies.
   - Added a function `getSteadyState()` to calculate steady state values for
     simulations. This function is of particular use for models of endogenous
     substrates, where changing a parameter value (e.g., the production rate)
@@ -35,23 +30,9 @@
     where the rates of the processes do not (significantly) change. The
     steady-state is NOT analytically calculated or estimated in any other way
     than simulating for the given time.
-
   - Added a function `exportSteadyStateToXLS()` to export steady state values
     calculated for one simulation using the `getSteadyState()` to an Excel file
     that can be imported in MoBi.
-
-
-
-## Breaking Changes
-
-  - The single argument of the `getBaseUnit()` function is now named
-    `quantityOrDimension` (was `dimension` previously). It can now use objects
-    of class `Quantity` as inputs, to be consistent with the `toBaseUnit()`
-    function.
-
-
-## Major Changes
-
   - Lower limit of quantification (LLOQ) is plotted as dotted lines for
     `plotIndividualTimeProfile()` and `plotPopulationTimeProfile()`.
   - `plotPopulationTimeProfile()` provides two new aggregations methods:

diff --git a/README.Rmd b/README.Rmd
@@ -246,8 +246,8 @@ conduct](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CODE_OF_
 We encourage contribution to the Open Systems Pharmacology community.
 Before getting started please read the [contribution
 guidelines](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CONTRIBUTING.md).
-If you are contributing to the codebase, please be familiar with the [coding
-standards](https://github.com/Open-Systems-Pharmacology/developer-docs/blob/main/ospsuite-r-specifics/CODING_STANDARDS_R.md).
+If you are contributing to the codebase, please be familiar with the [R coding
+standards](https://dev.open-systems-pharmacology.org/r-development-resources/coding_standards_r) as well as the [collaboration guide](https://dev.open-systems-pharmacology.org/r-development-resources/collaboration_guide).
 
 # License
 

diff --git a/README.md b/README.md
@@ -116,23 +116,24 @@ files provided with the
 When installing from such files, the CRAN dependencies need to be
 installed manually first.
 
-    #> Warning: package 'pacman' was built under R version 4.2.3
-    # Install dependencies (e.g. R6) which are on CRAN
-    install.packages("data.table")
-    install.packages("dplyr")
-    install.packages("ggplot2")
-    install.packages("ggtext")
-    install.packages("jsonlite")
-    install.packages("lifecycle")
-    install.packages("openxlsx")
-    install.packages("patchwork")
-    install.packages("purrr")
-    install.packages("R6")
-    install.packages("readr")
-    install.packages("rlang")
-    install.packages("stringr")
-    install.packages("tidyr")
-    install.packages("xml2")
+``` r
+# Install dependencies (e.g. R6) which are on CRAN
+install.packages("data.table")
+install.packages("dplyr")
+install.packages("ggplot2")
+install.packages("ggtext")
+install.packages("jsonlite")
+install.packages("lifecycle")
+install.packages("openxlsx")
+install.packages("patchwork")
+install.packages("purrr")
+install.packages("R6")
+install.packages("readr")
+install.packages("rlang")
+install.packages("stringr")
+install.packages("tidyr")
+install.packages("xml2")
+```
 
 #### Install non-CRAN dependencies
 
@@ -227,9 +228,11 @@ conduct](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CODE_OF_
 We encourage contribution to the Open Systems Pharmacology community.
 Before getting started please read the [contribution
 guidelines](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CONTRIBUTING.md).
-If you are contributing to the codebase, please be familiar with the
-[coding
-standards](https://github.com/Open-Systems-Pharmacology/developer-docs/blob/main/ospsuite-r-specifics/CODING_STANDARDS_R.md).
+If you are contributing to the codebase, please be familiar with the [R
+coding
+standards](https://dev.open-systems-pharmacology.org/r-development-resources/coding_standards_r)
+as well as the [collaboration
+guide](https://dev.open-systems-pharmacology.org/r-development-resources/collaboration_guide).
 
 # License
 

diff --git a/inst/lib/ConsoleApp.deps.json b/inst/lib/ConsoleApp.deps.json
@@ -12,7 +12,7 @@
           "OSPSuite.R": "12.0.300",
           "OSPSuite.SimModel.Ubuntu22": "4.0.0.59",
           "OSPSuite.SimModelSolver_CVODES.Ubuntu22": "4.1.0.9",
-          "PKSim.R": "12.0.296"
+          "PKSim.R": "12.0.297"
         },
         "runtime": {
           "ConsoleApp.dll": {}
@@ -1336,7 +1336,7 @@
           "System.Xml.ReaderWriter": "4.3.0"
         }
       },
-      "PKSim.Assets/12.0.296": {
+      "PKSim.Assets/12.0.297": {
         "dependencies": {
           "OSPSuite.Assets": "12.0.300",
           "OSPSuite.Assets.Images": "12.0.300",
@@ -1346,7 +1346,7 @@
           "PKSim.Assets.dll": {}
         }
       },
-      "PKSim.Assets.Images/12.0.296": {
+      "PKSim.Assets.Images/12.0.297": {
         "dependencies": {
           "OSPSuite.Assets": "12.0.300",
           "OSPSuite.Assets.Images": "12.0.300",
@@ -1356,33 +1356,33 @@
           "PKSim.Assets.Images.dll": {}
         }
       },
-      "PKSim.CLI.Core/12.0.296": {
+      "PKSim.CLI.Core/12.0.297": {
         "dependencies": {
           "OSPSuite.Assets": "12.0.300",
           "OSPSuite.Core": "12.0.300",
           "OSPSuite.Utility": "4.1.0.6",
-          "PKSim.Core": "12.0.296"
+          "PKSim.Core": "12.0.297"
         },
         "runtime": {
           "PKSim.CLI.Core.dll": {}
         }
       },
-      "PKSim.Core/12.0.296": {
+      "PKSim.Core/12.0.297": {
         "dependencies": {
           "Newtonsoft.Json": "12.0.3",
           "OSPSuite.Assets": "12.0.300",
           "OSPSuite.Assets.Images": "12.0.300",
           "OSPSuite.Core": "12.0.300",
           "OSPSuite.Infrastructure.Import": "12.0.300",
           "OSPSuite.Utility": "4.1.0.6",
-          "PKSim.Assets": "12.0.296",
+          "PKSim.Assets": "12.0.297",
           "System.ComponentModel.Annotations": "4.7.0"
         },
         "runtime": {
           "PKSim.Core.dll": {}
         }
       },
-      "PKSim.Infrastructure/12.0.296": {
+      "PKSim.Infrastructure/12.0.297": {
         "dependencies": {
           "FluentNHibernate": "2.1.2",
           "LumenWorksCsvReader": "4.0.0",
@@ -1401,40 +1401,40 @@
           "OSPSuite.Infrastructure.Serialization": "12.0.300",
           "OSPSuite.Presentation.Serialization": "12.0.300",
           "OSPSuite.Utility": "4.1.0.6",
-          "PKSim.Assets": "12.0.296",
-          "PKSim.Core": "12.0.296",
-          "PKSim.Presentation": "12.0.296"
+          "PKSim.Assets": "12.0.297",
+          "PKSim.Core": "12.0.297",
+          "PKSim.Presentation": "12.0.297"
         },
         "runtime": {
           "PKSim.Infrastructure.dll": {}
         }
       },
-      "PKSim.Presentation/12.0.296": {
+      "PKSim.Presentation/12.0.297": {
         "dependencies": {
           "OSPSuite.Assets": "12.0.300",
           "OSPSuite.Core": "12.0.300",
           "OSPSuite.Presentation": "12.0.300",
           "OSPSuite.TeXReporting": "3.0.0.5",
           "OSPSuite.Utility": "4.1.0.6",
-          "PKSim.Assets": "12.0.296",
-          "PKSim.Assets.Images": "12.0.296",
-          "PKSim.Core": "12.0.296"
+          "PKSim.Assets": "12.0.297",
+          "PKSim.Assets.Images": "12.0.297",
+          "PKSim.Core": "12.0.297"
         },
         "runtime": {
           "PKSim.Presentation.dll": {}
         }
       },
-      "PKSim.R/12.0.296": {
+      "PKSim.R/12.0.297": {
         "dependencies": {
           "OSPSuite.Assets": "12.0.300",
           "OSPSuite.Core": "12.0.300",
           "OSPSuite.FuncParser": "4.0.0.59",
           "OSPSuite.SimModel": "4.0.0.59",
           "OSPSuite.SimModelSolver_CVODES": "4.1.0.9",
           "OSPSuite.Utility": "4.1.0.6",
-          "PKSim.CLI.Core": "12.0.296",
-          "PKSim.Core": "12.0.296",
-          "PKSim.Infrastructure": "12.0.296",
+          "PKSim.CLI.Core": "12.0.297",
+          "PKSim.Core": "12.0.297",
+          "PKSim.Infrastructure": "12.0.297",
           "System.Data.SQLite.Core": "1.0.118"
         },
         "runtime": {
@@ -2331,37 +2331,37 @@
       "path": "system.xml.xmldocument/4.3.0",
       "hashPath": "system.xml.xmldocument.4.3.0.nupkg.sha512"
     },
-    "PKSim.Assets/12.0.296": {
+    "PKSim.Assets/12.0.297": {
       "type": "project",
       "serviceable": false,
       "sha512": ""
     },
-    "PKSim.Assets.Images/12.0.296": {
+    "PKSim.Assets.Images/12.0.297": {
       "type": "project",
       "serviceable": false,
       "sha512": ""
     },
-    "PKSim.CLI.Core/12.0.296": {
+    "PKSim.CLI.Core/12.0.297": {
       "type": "project",
       "serviceable": false,
       "sha512": ""
     },
-    "PKSim.Core/12.0.296": {
+    "PKSim.Core/12.0.297": {
       "type": "project",
       "serviceable": false,
       "sha512": ""
     },
-    "PKSim.Infrastructure/12.0.296": {
+    "PKSim.Infrastructure/12.0.297": {
       "type": "project",
       "serviceable": false,
       "sha512": ""
     },
-    "PKSim.Presentation/12.0.296": {
+    "PKSim.Presentation/12.0.297": {
       "type": "project",
       "serviceable": false,
       "sha512": ""
     },
-    "PKSim.R/12.0.296": {
+    "PKSim.R/12.0.297": {
       "type": "project",
       "serviceable": false,
       "sha512": ""

diff --git a/inst/lib/ConsoleApp.dll b/inst/lib/ConsoleApp.dll
diff --git a/inst/lib/PKSim.Assets.Images.dll b/inst/lib/PKSim.Assets.Images.dll
diff --git a/inst/lib/PKSim.Assets.dll b/inst/lib/PKSim.Assets.dll
diff --git a/inst/lib/PKSim.CLI.Core.dll b/inst/lib/PKSim.CLI.Core.dll
diff --git a/inst/lib/PKSim.Core.dll b/inst/lib/PKSim.Core.dll
diff --git a/inst/lib/PKSim.Infrastructure.dll b/inst/lib/PKSim.Infrastructure.dll
diff --git a/inst/lib/PKSim.Presentation.dll b/inst/lib/PKSim.Presentation.dll
diff --git a/inst/lib/PKSim.R.dll b/inst/lib/PKSim.R.dll