Merge pull request #533 from SuperDARN/release/rst-5.0

Release RST 5.0

.github/PULL_REQUEST_TEMPLATE/release_template.md

@@ -35,6 +35,7 @@ Please comment in the Pull Request conversation if you need additional time to t
 - [ ] Update hardware files (if required)
 - [ ] Update `.rst.version`
 - [ ] Update author list in `.zenodo.json`
+- [ ] Update author list in `AUTHORS.md`
 
 ## Extra Notes
 
@@ -51,4 +52,4 @@ If you found no bugs during testing, please *approve* the PR:
 1. Click on `files changed` top right
 2. Click on `start review` green top right  button
 3. In the comment box, state which operating system you used for testing, and any other helpful information
-4. Select `approve` and `submit review`
+4. Select `approve` and `submit review`

.gitignore

@@ -2,22 +2,24 @@
 *.so
 *.o
 *~
-bin/
-build/bin/
-build/include/
-build/lib/
-dlm/
-/doc/
-/idl/
-/include/
-lib/
-log/
+
+bin
+/build/include
+/build/lib
+/dlm
+/doc
+/idl
+/include
+/lib
+/log
 
 codebase/general/src.lib/stdkey.1.5/src/make_palette
 
 *errstr.h
 *hlpstr.h
 *version.h
+!fitacfversion.h
+
 site/
 docs/xml
 docs/latex/

.profile/superdarn.bash

@@ -4,6 +4,7 @@
 export ISTP_PATH="/data/istp"
 
 export SD_HDWPATH="${RSTPATH}/tables/superdarn/hdw/"
+export SD_TDIFFPATH="${RSTPATH}/tables/superdarn/tdiff/"
 export SD_RADAR="${RSTPATH}/tables/superdarn/radar.dat"
 
 export AACGM_DAT_PREFIX=${RSTPATH}"/tables/analysis/aacgm/aacgm_coeffs"

.profile/superdarn.tcsh

@@ -4,6 +4,7 @@
 setenv ISTP_PATH "/data/istp"
 
 setenv SD_HDWPATH "${RSTPATH}/tables/superdarn/hdw/"
+setenv SD_TDIFFPATH "${RSTPATH}/tables/superdarn/tdiff/"
 setenv SD_RADAR "${RSTPATH}/tables/superdarn/radar.dat"
 
 setenv AACGM_DAT_PREFIX ${RSTPATH}"/tables/analysis/aacgm/aacgm_coeffs"

.rst.version

@@ -1 +1 @@
-4.7
+5.0

.zenodo.json

@@ -1,38 +1,50 @@
 {
+    "title": "SuperDARN Radar Software Toolkit (RST) 5.0",
+
     "creators":[
         {
             "name": "SuperDARN Data Analysis Working Group"
         },
-        {
-            "affiliation": "Naval Research Laboratory",
-            "name": "Burrell, A.G.",
-            "orcid": "0000-0001-8875-9326"
-        },
         {
             "affiliation": "Dartmouth College",
             "name": "Thomas, E.G.",
             "orcid": "0000-0001-8036-8793"
         },
         {
             "affiliation": "University of Saskatchewan",
-            "name": "Schmidt, M.T.",
-            "orcid": "0000-0002-3265-977X"
+            "name": "Reimer, A.S.",
+            "orcid": "0000-0002-4621-3453"
         },
         {
-            "affiliation": "The Unviersity Centre in Svalbard",
+            "affiliation": "The University Centre in Svalbard",
             "name": "Bland, E.C.",
             "orcid": "0000-0002-0252-0400"
         },
         {
-            "affiliation": "Istituto Nazionale di Geofisica e Vulcanologia",
-            "name": "Coco, I.",
-            "orcid": "0000-0003-4070-6828"
+            "affiliation": "Naval Research Laboratory",
+            "name": "Burrell, A.G.",
+            "orcid": "0000-0001-8875-9326"
+        },
+        {
+            "affiliation": "Lancaster University",
+            "name": "Grocott, A.",
+            "orcid": "0000-0002-6489-095X"
         },
         {
             "affiliation": "University of Saskatchewan",
             "name": "Ponomarenko, P.V.",
             "orcid": "0000-0001-8407-0193"
         },
+        {
+            "affiliation": "University of Saskatchewan",
+            "name": "Schmidt, M.T.",
+            "orcid": "0000-0002-3265-977X"
+        },
+        {
+            "affiliation": "Dartmouth College",
+            "name": "Shepherd, S.G.",
+            "orcid": "0000-0003-1992-4118"
+        },
         {
             "affiliation": "Virginia Tech",
             "name": "Sterne, K.T.",

AUTHORS.md

@@ -16,19 +16,20 @@ The original RST package is credited to:
 The RST is now maintained collaboratively by the SuperDARN Data Analysis Working Group (DAWG). Members of the international SuperDARN community have contributed to the RST by adding new features, writing documentation, improving modularity, refactoring, fixing bugs, and testing the software. These contributions are credited to:
 
 - D.D. Billett, documentation, testing, enhancements
-- E.C. Bland, DAWG Co-Chair (2019-), fit_speck_removal, documentation, testing
+- E.C. Bland, DAWG Co-Chair (2019-2022), fit_speck_removal, documentation, testing
 - A.G. Burrell, documentation, bugfixes, testing
 - I. Coco, testing
 - E.D.P. Cousins, CS10 and PSR10 convection models
+- A. Grocott, DAWG Co-Chair (2022-), testing
 - K. Kotyk, FITACF_v3
-- P.V. Ponomarenko, DAWG Chair (2013-2019), FITACF_v2, FITACF_v3, data simulator library
-- A.S. Reimer, refactorization, documentation, bugfixes
-- A.J. Ribeiro, FITEX2, LMFIT, data simulator library
+- P.V. Ponomarenko, DAWG Chair (2013-2019), FitACF 2.0, FitACF 3.0, data simulator library
+- A.S. Reimer, LMFit 2.0, refactorization, documentation, bugfixes
+- A.J. Ribeiro, FitEX 2.0, LMFit, data simulator library
 - M.T. Schmidt, refactorization, documentation, enhancements, bugfixes
 - S.G. Shepherd, AACGM_v2, MLT_v2, IGRF_v2, elevation_v2, TS18 convection model
 - K.T. Sterne, DAWG Co-Chair (2019-), code comments, documentation
-- E.G. Thomas, TS18 convection model, IDL gridding library, sounding library, refactorization, modularization, code comments
+- E.G. Thomas, TS18 convection model, Christmas Valley virtual height model, IDL gridding library, sounding library, fitacfclientgui, refactorization, modularization, code comments, bug fixes
 - M.-T. Walach, bugfixes, testing, documentation
-- C.L. Waters, FITACF_v2
+- C.L. Waters, FitACF 2.0
 
 Please help us make this list as complete as possible! Suggestions for updates should be directed to the Data Analysis Working Group <darn-dawg@isee.nagoya-u.ac.jp>.

README.md

@@ -25,9 +25,7 @@ Installation guide for:
 
 ## How to cite the RST
 
-Instructions for citing the RST are available on Zenodo. Click on DOI badge:
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.801458.svg)](https://doi.org/10.5281/zenodo.801458)
-Scroll to the bottom and copy the *Share Cite as* text or download the citation in your prefered format under *Export*.
+Instructions for citing the RST are available on [Zenodo](https://doi.org/10.5281/zenodo.801458). Scroll to the end of the page and choose your perferred citation format.
 
 ## Data access and usage policy
 
@@ -47,7 +45,6 @@ For more information, please read [citing SuperDARN data](https://radar-software
 
 The DAWG welcomes new testers and developers to join the team. Here are some ways to contribute:
 
-  - Test pull requests: to determine which [pull requests](https://github.com/SuperDARN/rst/pulls) need to be tested right away, filter them by their milestones
-  - Get involved in projects: the [projects](https://github.com/SuperDARN/rst/projects) page is used to organize our priority areas. Each project board shows items which are in progress, ready for testing/review, and completed.
+ - Test pull requests: to determine which [pull requests](https://github.com/SuperDARN/rst/pulls) need to be tested right away, filter them by their milestones
  - Discuss [issues](https://github.com/SuperDARN/rst/issues) and answer questions
  - Become a developer: if you would like to contribute code to the RST, please submit a new [issue](https://github.com/SuperDARN/rst/issues) on Github, or contact us at darn-dawg *at* isee *dot* nagoya-u *dot* ac *dot* jp.

build/make/makebin.darwin

@@ -7,7 +7,7 @@
 # Darwin (GCC)
 #
 
-CFLAGS = -Wall -pedantic -O3 -D_GNU_SOURCE -D_DARWIN -I/opt/local/include
+CFLAGS = -Wall -pedantic -O3 -D_GNU_SOURCE -D_DARWIN -I$(XPATH)/include
 
 ifdef XPATH
   ifdef XLIB
@@ -27,7 +27,7 @@ endif
 CFLAGS += $(INCLUDE)
 
 LFLAGS =  -Wl,-rpath,@loader_path/../lib/ -Wl,-rpath,@loader_path/../../lib/ \
-          -L/opt/local/lib -L$(LIBPATH)
+          -L$(XPATH)/lib -L$(LIBPATH)
 
 .c.o:
 	$(CC) $(CFLAGS) -c $<    

codebase/analysis/src.lib/aacgm_v2/aacgm.1.0/include/aacgmlib_v2.h

@@ -64,6 +64,9 @@ int AACGM_v2_SetDateTime(int year, int month, int day,
 int AACGM_v2_GetDateTime(int *year, int *month, int *day,
                          int *hour, int *minute, int *second, int *dayno);
 int AACGM_v2_SetNow(void);
+int AACGM_v2_Lock(void);
+int AACGM_v2_Unlock(void);
+int AACGM_v2_Locked(void);
 
 #endif
 

codebase/analysis/src.lib/aacgm_v2/aacgm.1.0/src/aacgmlib_v2.c

@@ -37,6 +37,9 @@
 ; AACGM_v2_SetDateTime
 ; AACGM_v2_GetDateTime
 ; AACGM_v2_SetNow
+; AACGM_v2_Lock
+; AACGM_v2_Unlock
+; AACGM_v2_Locked
 ; AACGM_v2_errmsg
 ;
 
@@ -69,7 +72,8 @@ static struct {
   int second;
   int dayno;
   int daysinyear;
-} aacgm_date = {-1,-1,-1,-1,-1,-1,-1,-1};
+  int locked;
+} aacgm_date = {-1,-1,-1,-1,-1,-1,-1,-1,0};
 
 static int myear = 0;       /* model year: 5-year epoch */
 static double fyear = 0.;   /* floating point year */
@@ -1016,7 +1020,7 @@ int AACGM_v2_Convert(double in_lat, double in_lon, double height,
 
   /* height > 2000 km not allowed for coefficients */
   if (height > MAXALT && !(code & (TRACE|ALLOWTRACE|BADIDEA))) {
-    fprintf(stderr, "ERROR: coefficients are not valid for altitudes "
+    fprintf(stderr, "AACGM-v2 ERROR: coefficients are not valid for altitudes "
                     "above %d km: %lf.\n", MAXALT, height);
     fprintf(stderr, "       You must either use field-line tracing "
                     "(TRACE or ALLOWTRACE) or\n"
@@ -1207,6 +1211,80 @@ int AACGM_v2_SetNow(void)
   return err;
 }
 
+/*-----------------------------------------------------------------------------
+;
+; NAME:
+;       AACGM_v2_Lock
+;
+; PURPOSE:
+;       Function to set lock, which will prevent extra date and time checks
+;       when performing MLT_v2 conversions.
+;
+; CALLING SEQUENCE:
+;       err = AACGM_v2_Lock();
+;
+;     Return Value:
+;       error code
+;
+;+-----------------------------------------------------------------------------
+*/
+
+int AACGM_v2_Lock(void)
+{
+  aacgm_date.locked = 1;
+
+  return 0;
+}
+
+/*-----------------------------------------------------------------------------
+;
+; NAME:
+;       AACGM_v2_Unlock
+;
+; PURPOSE:
+;       Function to remove lock, which will enforce date and time checks when
+;       performing MLT_v2 conversions (default behavior).
+;
+; CALLING SEQUENCE:
+;       err = AACGM_v2_Unlock();
+;
+;     Return Value:
+;       error code
+;
+;+-----------------------------------------------------------------------------
+*/
+
+int AACGM_v2_Unlock(void)
+{
+  aacgm_date.locked = 0;
+
+  return 0;
+}
+
+/*-----------------------------------------------------------------------------
+;
+; NAME:
+;       AACGM_v2_Locked
+;
+; PURPOSE:
+;       Function to get lock status, which can be used to either enforce or
+;       prevent extra date and time checks when performing MLT_v2 conversions.
+;
+; CALLING SEQUENCE:
+;       locked = AACGM_v2_Locked();
+;
+;     Return Value:
+;       lock status
+;
+;+-----------------------------------------------------------------------------
+*/
+
+int AACGM_v2_Locked(void)
+{
+  return (aacgm_date.locked);
+}
+
+
 /*-----------------------------------------------------------------------------
 ;
 ; NAME:

codebase/analysis/src.lib/mlt_v2/mlt.1.0/src/mlt_v2.c

@@ -100,7 +100,7 @@ double MLTConvert_v2(int yr, int mo, int dy, int hr, int mt ,int sc,
     /* AACGM date/time not set so set it to the date/time passed in */
     err = AACGM_v2_SetDateTime(yr,mo,dy,hr,mt,sc);
     if (err != 0) return (err);
-  } else {
+  } else if (!AACGM_v2_Locked()) {
     /* If date/time passed into function differs from AACGM data/time by more
      * than 30 days, recompute the AACGM-v2 coefficients */
     ajd = TimeYMDHMSToJulian(ayr,amo,ady,ahr,amt,asc);

codebase/analysis/src.lib/mpfit/mpfit.1.2/include/mpfit.h → codebase/analysis/src.lib/mpfit/mpfit.1.4/include/mpfit.h

@@ -10,12 +10,10 @@
  *   (comparable to IDL fitting routine MPFIT
  *    see http://cow.physics.wisc.edu/~craigm/idl/idl.html)
  */
-/*
- $Log: mpfit.c.h,v $
- Revision 1.17 2009/02/18 23:08:49 craigm Exp
- just downloaded.
-
 
+/* Header file defining constants, data structures and functions of
+   mpfit library 
+   $Id$
 */
 
 #ifndef MPFIT_H
@@ -27,7 +25,7 @@ extern "C" {
 #endif
 
 /* MPFIT version string */
-#define MPFIT_VERSION "1.2"
+#define MPFIT_VERSION "1.4"
 
 /* Definition of a parameter constraint structure */
 struct mp_par_struct {
@@ -76,12 +74,13 @@ struct mp_config_struct {
   double epsfcn;  /* Finite derivative step size               Default: MP_MACHEP0 */
   double stepfactor; /* Initial step bound                     Default: 100.0 */
   double covtol;  /* Range tolerance for covariance calculation Default: 1e-14 */
-  int maxiter;    /* Maximum number of iterations.  If maxiter == 0,
+  int maxiter;    /* Maximum number of iterations.  If maxiter == MP_NO_ITER,
                      then basic error checking is done, and parameter
                      errors/covariances are estimated based on input
                      parameter values, but no fitting iterations are done. 
 		     Default: 200
 		  */
+#define MP_NO_ITER (-1) /* No iterations, just checking */
   int maxfev;     /* Maximum number of function evaluations, or 0 for no limit
 		     Default: 0 (no limit) */
   int nprint;     /* Default: 1 */