Merge branch 'dev' of github.com:KineticPreProcessor/KPP into dev

- pull before commit.

.ci-pipelines/ci-manual-cleanup-script.sh

@@ -5,15 +5,15 @@
 ### NOTE: This script runs CI-tests manually (for testing/debugging) ###
 ########################################################################
 
-# List of tests (add more as necessary; separate each with a space)
-all_tests="radau90 rk rktlm ros ros_split rosadj rosenbrock90 rostlm saprc2006 sd sdadj small_f90 ros_upcase ros_minver small_strato seulex90 ros_autoreduce"
+# Get the list of CI test folders in ALL_TESTS
+source ./ci-testing-list.sh
 
 # Current directory
 this_dir=$(pwd -P)
 
 # Run each test
 # Check status of each individual operation and exit if any do not complete
-for this_test in $all_tests; do
+for this_test in $ALL_TESTS; do
 
     cd ../ci-tests/$this_test
     [ $? -ne 0 ] && exit 1

.ci-pipelines/ci-manual-testing-script.sh

@@ -5,12 +5,11 @@
 ### NOTE: This script runs CI-tests manually (for testing/debugging) ###
 ########################################################################
 
-# List of tests (add more as necessary; separate each with a space)
-all_tests="radau90 rk rktlm ros ros_split rosadj rosenbrock90 rostlm saprc2006 sd sdadj small_f90 ros_upcase small_strato seulex90 ros_autoreduce"
+# Get the list of CI test folders in $ALL_TESTS
+source ./ci-testing-list.sh
 
-# Run each test
 # Check status of each individual operation and exit if any do not complete
-for this_test in $all_tests; do
+for this_test in $ALL_TESTS; do
 
     cd ../ci-tests/$this_test
     [ $? -ne 0 ] && exit 1
@@ -41,24 +40,6 @@ for this_test in $all_tests; do
 
 done
 
-# Run the ros_minver test, which tests if KPP will fail when the
-# current version is older than the version specified #MINVERSION.
-# NOTE: This test succeeds when KPP fails, so run it separately!
-for this_test in "ros_minver"; do
-
-    cd ../ci-tests/$this_test
-    [ $? -ne 0 ] && exit 1
-
-    echo ""
-    echo ">>>>>>>> Generating $this_test mechanism with KPP <<<<<<<<"
-    echo ""
-    ../../bin/kpp $this_test.kpp
-    [ $? -eq 0 ] && exit 1
-
-    cd ..
-
-done
-
 # Return w/ success
 echo ""
 echo ">>>>>>>> All tests finished succesfully! <<<<<<<<"

.ci-pipelines/ci-testing-list.sh

@@ -0,0 +1,27 @@
+########################################################################
+### List of C-I test folders for KPP (edit as necessary!)            ###
+########################################################################
+
+ALL_TESTS="C_rk
+C_rosadj
+C_sd
+C_sdadj
+C_small_strato
+F90_lsode
+F90_radau
+F90_rk
+F90_rktlm
+F90_ros
+F90_rosadj
+F90_ros_autoreduce
+F90_rosenbrock
+F90_ros_split
+F90_rostlm
+F90_ros_upcase
+F90_saprc_2006
+F90_sd
+F90_sdadj
+F90_seulex
+F90_small_strato
+X_minver"
+

.ci-pipelines/ci-testing-script.sh

@@ -4,12 +4,12 @@
 ### CI tests for github.com/KineticPreProcessor/KPP                  ###
 ########################################################################
 
-# List of tests (add more as necessary; separate each with a space)
-all_tests="radau90 rk rktlm ros rosadj rosenbrock90 rostlm saprc2006 sd sdadj small_f90 ros_upcase small_strato seulex90 ros_autoreduce"
+# Get the list of CI test folders in ALL_TESTS
+source ./ci-testing-list.sh
 
 # Run each test
 # Check status of each individual operation and exit if any do not complete
-for this_test in $all_tests; do
+for this_test in $ALL_TESTS; do
 
     cd /kpp/ci-tests/$this_test
     [ $? -ne 0 ] && exit 1
@@ -38,24 +38,6 @@ for this_test in $all_tests; do
 
 done
 
-# Run the ros_minver test, which tests if KPP will fail when the
-# current version is older than the version specified #MINVERSION.
-# NOTE: This test succeeds when KPP fails, so run it separately!
-for this_test in "ros_minver"; do
-
-    cd /kpp/ci-tests/$this_test
-    [ $? -ne 0 ] && exit 1
-
-    echo ""
-    echo ">>>>>>>> Generating $this_test mechanism with KPP <<<<<<<<"
-    echo ""
-    ../../bin/kpp $this_test.kpp
-    [ $? -eq 0 ] && exit 1
-
-    cd ..
-
-done
-
 # Return w/ success
 echo ""
 echo ">>>>>>>> All tests finished succesfully! <<<<<<<<"

.zenodo.json

@@ -14,15 +14,15 @@
 	},
 	{
 	    "name": "Michael Long",
-	    "affiliation": "Harvard University"
+	    "affiliation": "Renaissance Fiber, LLC, North Carolina, USA"
 	},
 	{
 	    "name": "Robert Yantosca",
-	    "affiliation": "Harvard University"
+	    "affiliation": "Harvard University, Cambridge, MA, USA"
 	},
 	{
 	    "name": "Haipeng Lin",
-	    "affiliation": "Harvard University"
+	    "affiliation": "Harvard University, Cambridge, MA, USA"
 	}
     ],
     "description": "The Kinetic Pre-Processor (KPP)",
@@ -34,6 +34,6 @@
 	"climate-modeling",
 	"fortran-90"
     ],
-    "license": "GNU GPLv3",
+    "license": "GNU General Public License v2.0 or later",
     "upload_type": "software"
 }

AUTHORS.txt

@@ -1,10 +1,9 @@
-Authors for KPP (19 Apr 2022)
+Authors for KPP (30 Jun 2022)
 
 Name            Github handle
 -----           -------------
 Adrian Sandu    @adrian-sandu
 Rolf Sander     @RolfSander
-Josue Bock      @JosueBock
 Michael Long    @msl3v
 Bob Yantosca    @yantosca
 Haipeng Lin     @jimmielin

CHANGELOG.md

@@ -7,6 +7,27 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Unreleased
 
+### Added
+
+- C-lanugage updates
+  - Restored driver programs `general.c` and `general_adj.c`
+  - Updated rate-law functions in `util/UserRateLaws.c`
+  - Added C-I tests for C-language integrators (using the
+    `small_strato` mechanism 
+  - Now use `//` instead of `/* */` comment strings 
+- ReadTheDocs documentation updates:
+  - Authors in the reference page are now listed alphabetically
+  - In-text citations now use the :cite:t style (e.g. "Smith et al [2000]")
+  - Corrected several omissions
+  - Removed table numbers from tables (to reduce confusion)
+- Added a C-I test for `rosenbrock_autoreduce`
+
+### Changed
+
+- Renamed CI-test folders for clarity
+- DOUBLE_COMPLEX is now replaced by COMPLEX(kind=dp)
+- Fixed incorrect license string in .zenodo.json
+
 ## [2.6.0]
 
 ### Added

CONTRIBUTING.md

@@ -4,21 +4,24 @@ Thank you for looking into contributing to KPP!  KPP is an open-source
 package that relies on contributions from community members
 like you. Whether you're a new or longtime KPP user, you're a
 valued member of the community, and we want you to feel empowered to
-contribute. 
+contribute.
 
 #### We use GitHub and ReadTheDocs
-We use GitHub to host the KPP source code, to track issues, user questions, and feature requests, and to accept pull requests: [https://github.com/KineticPreProcessor/KPP](https://github.com/KineticPreProcessor/KPP). Please help out as you can in response to issues and user questions.
+We use GitHub to host the KPP source code, to track issues, user
+questions, and feature requests, and to accept pull requests:
+[https://github.com/KineticPreProcessor/KPP](https://github.com/KineticPreProcessor/KPP). Please
+help out as you can in response to issues and user questions.
 
 We use ReadTheDocs to host the KPP user documentation: [https://kpp.readthedocs.io](https://kpp.readthedocs.io).
 
 #### How to submit changes
 We use [GitHub
-Flow](https://guides.github.com/introduction/flow/index.html),  so all changes happen through pull requests. This 
+Flow](https://guides.github.com/introduction/flow/index.html),  so all changes happen through pull requests. This
 workflow is described here: [GitHub
 Flow](https://guides.github.com/introduction/flow/index.html). If your
 change affects multiple submodules, submit a pull request for each
 submodule with changes, and link to these submodule pull requests in
-your main pull request. 
+your main pull request.
 
 As the author you are responsible for:
 - Testing your changes
@@ -32,7 +35,12 @@ inconsistent conventions are inevitable, but we ask that you do your
 best to be consistent with nearby code.
 
 #### How to request an enhancement
-We accept feature requests through issues on GitHub. To request a new feature, [open a new issue](https://github.com/KineticPreProcessor/KPP/issues/new/choose) and select the feature request template. Please include all the information that might be relevant, including the motivation for the feature.
+We accept feature requests through issues on GitHub. To request a new
+feature, [open a new
+issue](https://github.com/KineticPreProcessor/KPP/issues/new/choose)
+and select the feature request template. Please include all the
+information that might be relevant, including the motivation for the
+feature. 
 
 #### How to report a bug
 Please see "Support Guidelines".

README.md

@@ -10,4 +10,7 @@ This is the repository for the The Kinetic PreProcessor (KPP) source code.
 KPP is distributed under [GPLv3, the general public license](https://github.com/KineticPreProcessor/KPP/blob/main/LICENSE.txt).
 
 ## Documentation
-Please see our comprehensive KPP User's Guide (https://kpp.readthedocs.io) for installation and usage instructions.
+Please see our comprehensive KPP User's Guide
+([html](https://kpp.readthedocs.io),
+[pdf](https://kpp.readthedocs.io/_/downloads/en/latest/pdf/)) for
+installation and usage instructions.

SUPPORT.md

@@ -7,10 +7,17 @@ We track bugs, user questions, and feature requests through GitHub issues.
 Please help out as you can in response to issues and user questions.
 
 #### How to report a bug
-We use GitHub to track issues. To report a bug, [open a new issue](https://github.com/KineticPreProcessor/KPP/issues/new/choose) and select the "report a bug" template.  Please include all the information that might be relevant, including instructions for reproducing the bug.  
+We use GitHub to track issues. To report a bug, [open a new
+issue](https://github.com/KineticPreProcessor/KPP/issues/new/choose)
+and select the "report a bug" template.  Please include all the
+information that might be relevant, including instructions for
+reproducing the bug.
 
 #### Where can I ask for help?
-We use GitHub issues to support user questions. To ask a question, [open a new issue](https://github.com/KineticPreProcessor/KPP/issues/new/choose) and select the "ask a question" template.
+We use GitHub issues to support user questions. To ask a question,
+[open a new
+issue](https://github.com/KineticPreProcessor/KPP/issues/new/choose)
+and select the "ask a question" template.
 
 #### How to submit changes
 Please see "Contributing Guidelines".

ci-tests/C_rk/C_rk.kpp

@@ -0,0 +1,4 @@
+#MODEL      small_strato
+#INTEGRATOR runge_kutta
+#LANGUAGE   C
+#DRIVER     general

ci-tests/C_rosadj/C_rosadj.kpp

@@ -0,0 +1,4 @@
+#MODEL      small_strato
+#INTEGRATOR rosenbrock_adj
+#LANGUAGE   C
+#DRIVER     general_adj

ci-tests/C_sd/C_sd.kpp

@@ -0,0 +1,4 @@
+#MODEL      small_strato
+#INTEGRATOR sdirk
+#LANGUAGE   C
+#DRIVER     general

ci-tests/C_sdadj/C_sdadj.kpp

@@ -0,0 +1,4 @@
+#MODEL      small_strato
+#INTEGRATOR sdirk_adj
+#LANGUAGE   C
+#DRIVER     general_adj

ci-tests/C_small_strato/C_small_strato.kpp

@@ -0,0 +1,10 @@
+#MODEL      small_strato
+#LANGUAGE   C
+#DOUBLE     ON
+#INTEGRATOR rosenbrock
+#DRIVER     general
+#JACOBIAN   SPARSE_LU_ROW
+#HESSIAN    ON
+#STOICMAT   ON
+
+{This is the small_strato example from Chapter 2 of the KPP manual}

docs/source/bibtex.json

@@ -1,36 +1,38 @@
 {
     "cited": {
         "getting_started/00_revision_history": [
-            "2004:IUPAC",
-            "2005:Sander_et_al",
+            "Atkinson_et_al._2004",
+            "Sander_et_al._2005",
         ],
         "using_kpp/04_input_for_kpp": [
-            "1996:Sandu_et_al",
+            "Sandu_et_al._2006",
         ],
         "using_kpp/05_output_from_kpp": [
-            "1996:Sandu_et_al",
+            "Sandu_et_al._2006",
         ],
         "tech_info/06_numerical_methods": [
-            "1989:VODE",
-	    "1991:Hairer_and_Wanner",
-	    "1993:Hairer_Norsett_and_Wanner",
-            "1996:Sandu_et_al",
-            "1997:Sandu_et_al_2",
-            "1997:Verwer",
+            "Brown_Byrne_and_Hindmarsh_1989",
+	    "Hairer_and_Wanner_1991",
+	    "Hairer_Norsett_and_Wanner_1993",
+            "Sandu_et_al._1996",
+            "Sandu_et_al._1997b",
+            "Verwer_et_al._1999",
+	    "Lin_et_al._2022",
         ],     
         "citations/09_acknowledgments": [
-            "1996:Damian-Iordache",
+            "Damian-Iordache_1996",
         ],
         "citations/10_kpp_references": [
-            "1989:VODE",
-	    "1991:Hairer_and_Wanner",
-	    "1993:Hairer_Norsett_and_Wanner",
-            "1996:Damian-Iordache",
-            "1996:Sandu_et_al",
-            "1997:Sandu_et_al_2",
-            "1997:Verwer",
-            "2004:IUPAC",
-            "2005:Sander_et_al",
+            "Brown_Byrne_and_Hindmarsh_1989",
+	    "Hairer_and_Wanner_1991",
+	    "Hairer_Norsett_and_Wanner_1993",
+            "Damian-Iordache_1996",
+            "Sandu_et_al._1996",
+            "Sandu_et_al._1997b",
+            "Verwer_et_al._1999",
+            "Atkinson_et_al._2004",
+            "Sander_et_al._2005",
+	    "Lin_et_al._2022",	    
         ],
     }
 }