Changes

Summary

1. CHG: Need to link GMT differently and add more libraries to distributable
2. CHG: Need to link GMT differently and add more libraries to distributable
3. CHG: minor typo in path
4. CHG: minor, adding larsen to default machine when using interpAdusumilli, RignotMeltRate and SeaRISE
5. CHG: Adjusted tolerances
6. CHG: Adjusted tolerances
7. CHG: Forgot to change back to patch
8. CHG: Corrected configs; list of files to sign
9. CHG: Removed --memory-init-file (no longer supported)
10. CHG: Added comment about needing symlink
11. CHG: Cleanup
12. CHG: Cleanup
13. CHG: Upgrade Linux builds to PETSc 3.20, GMT 6.5
14. CHG: archive 4001 for new MITgcm version (68i)
15. CHG: Adjusted tolerances; svn bug fixes
16. CHG: Modified test suites; svn bug fixes
17. CHG: Modified test suites
18. CHG: Modified test suites
19. CHG: Modified test suites
20. CHG: Modified test suites
21. CHG: Modified test suites
22. CHG: Modified test suites
23. CHG: Modified test suites
24. NEW: added distinguishable_colors.m
25. CHG: Modified test suites; corrected patch and config for GMT
26. CHG: Issues with whitespace in patch; path to config files; adjusted tolerances
27. CHG: Issues with whitespace in patch; path to config files
28. ADD: interpolate dHdt map of Greenland
29. CHG: Corrected paths to config files
30. CHG: Support for macOS distributable configurations for both Intel and Silicon
31. CHG: minor
32. moving from MITgcm checkpoint 68h to 68i, which includes options file for mac silicone compilation
33. CHG: Need to deepcopy model; clean up
34. BUG: fixing uninitialized i
35. CHG: Adjusted tolerances
36. CHG: edit GetGroundedPart functions in c/classes/Elements/ to accomodate sub-element melt parameterization when using IntrusionMelt module
37. CHG: Adjusted tolerances
38. CHG: Adjusted tolerances
39. CHG: Adjusted tolerances; modified test suites
40. CHG: Exporting LIBRARY_PATH from m4 does not seem to work for some reason
41. CHG: Adjusted test suites and tolerances
42. CHG: Adjusted test suites
43. CHG: Adjusted tolerances
44. CHG: Adjusted tolerances; modified test suites; bad variable name
45. CHG: Add supplied Fortran dir to library path
46. CHG: better error message if 2 different versions of ISSM are being used
47. CHG: Need to set LDFLAGS under macOS if it is unset
48. CHG: Bad replacement of tabs on copy/paste
49. CHG: Missed some changes to install scripts
50. CHG: For some reason, need to pass in exported LDFLAGS to config for Silicon
51. CHG: No longer need separate PETSc install scripts for Intel and Silicon
52. CHG: Corrected path to libgfortran
53. CHG: Fixes for latest version of Xcode
54. ADD: a function to merge multiple exp files to a single one
55. CHG: allow to swap edges
56. ADD: Latest version of PETSc for Intel-based Macs
57. ADD: Patch for Intel-based Macs and latest version of Xcode/Command Line Tools linker
58. CHG: Updating Gmsh 4 to latest version
59. CHG: Corrected test suite
60. CHG: Exporting *_NROPTIONS and MATLAB_PATH from complete packaging wrapper scripts
61. CHG: Forgot to add new method for getting all available test IDs
62. CHG: Corrections to how test suites are parsed under Python
63. CHG: Test suite adjustments
64. CHG: Adjusted tolerances; test suite adjustments; clean up
65. CHG: Adjusted tolerances; exclude Dakota tests from basic Python run
66. BUG: Corrected bad paths
67. CHG: Reducing external packages
68. CHG: Corrected path to libgfortran et al
69. CHG: Not patching file correctly
70. CHG: Bad config
71. CHG: Bypassing test456 (for now); added macOS Silicon Python build to quickly determine if test is failing because of architecture or API
72. CHG: mostly cosmetics
73. CHG: Add python and javascript fields related to IntrusionMelt
74. CHG: Missing Python 3 packager
75. CHG: Need to patch static copy of GMT on Silicon
76. NEW: Add IntrusionMelt module to include melt under grounding zones, edits after Robel, Wilson, Seroussi TC (2022)
77. CHG: Correcting paths
78. CHG: Generalizing packaging scripts for macOS
79. CHG: Typo
80. CHG: Adjusted tolerances
81. ADD: Needed to modify permissions
82. DEL: Need to modify permissions
83. CHG: Modifying binaries packaging for macOS to allow for Intel and Silicon variants
84. BUG: fixing memory leak
85. CHG: Adjusted tolerances
86. CHG: Adjusted tolerances
87. CHG: Reverting last commit for now
88. update to PDD factor calculation
89. CHG: added accumulated SMB to pdd
90. BUG: check that observations are in chronological order
91. NEW: speedup isoline if edges are provided (and return edges optionally)
92. CHG: do not error out when calling log with 0 speed, just spit out a warning
93. CHG: minor
94. BUG: fixing library problems on totten
95. CHG: add P2 element support for FS in Tria.cpp. Use P1 projection of the velocity for interpolation when we compute db/dt and ds/dt, ignore the contribution from the edges.
96. CHG: Adjusted tolerances
97. CHG: do not include free surface solver everytime
98. CHG: adding constraints to free surfaces as a temporary hack
99. CHG: fixing issues with type casts in love_core capability.
100. CHG: Adjusted tolerances
101. CHG: adding dpsimplify.m to simplify profiles
102. CHG: Adjusted tolerances
103. BUG: Corrected patch
104. CHG: taking care of MOLHO when extracting models
105. CHG: now returns ocean_levelset and not md
106. CHG: no options to pass on to exp_ginput
107. CHG: Silence output of `which`; define AR and RANLIB
108. BUG: Name conflict (will fix later)
109. CHG: Generalized m1qn3 makefile and config to allow for shared and static builds; cleanup of Triangle makefiles/configs
110. BUG: Need to recommit with execution bit on
111. BUG: Need to recommit with execution bit on
112. CHG: Generalized m1qn3 makefile and config to allow for shared and static builds; cleanup of Triangle makefiles/configs
113. BUG: archiver flags were not being applied
114. CHG: Reverting m1qn3 patch to work on errors
115. CHG: Updated m1qn3 to overcome warnings with modern Fortran compilers
116. CHG: Adjusted tolerances
117. CHG: interpISMIP6AntarcticaOcn.m and interpISMIP6AntarcticaSMB.m: generalize to address bugs in locating the data files for certain models
118. CHG: cleaning up GEMB if statement time step calculation for thermo
119. CHG: Adjusted tolerances
120. CHG: Adjusted tolerances
121. CHG: relax tols for GEMB
122. CHG: update GEMB archives for jenkins
123. CHG: update tol for GEMB
124. CHG: GEMB carry surface melt every timestep, restrict case 4 and 5 densification schemes
125. CHG: minor comments for GEMB
126. CHG: interpISMIP6 function inputs define model with single string, simplify nc file identification
127. CHG: Adjusted tolerances
128. CHG: fixing some stuff
129. NEW: adding vz to SIA
130. CHG: Adjusted tolerances
131. CHG: Adjusted tolerances
132. CHG: Adjusted tolerances
133. CHG: Adjusted tolerances
134. CHG: Adjusted tolerances; updated test suites
135. CHG: Updated config for new MATLAB version
136. CHG: Updated MATLAB, OS, build configs
137. CHG: fixing case issues with ISMIP6 forcings
138. CHG: Updated JRE, MATLAB, OS, build configs
139. NEW: interpolation for new Stal antarctic geothermal flux
140. CHG: Adjusted tolerances
141. CHG: GlaDS- new input parameter rheology_B_base and new optional output HydrologySheetDischarge added to hydrology model
142. CHG: MATLAB > Python; clean up
143. CHG: Handle cases where PYTHONPATH already has a value; updating config for netcdf-python for machines where we do not want to install via pip
144. CHG: Adding packages to UB CCR config to help with debugging
145. CHG: Adding packaged to UB CCR config to help with debugging
146. CHG: Updating UB CCR config enable debugging
147. CHG: deal with negative log scale
148. CHG: Updating UB CCR config to compile Python wrappers for debugging submit
149. CHG: Updating UB CCR config to compile Python wrappers for debugging submit
150. CHG: Updating UB CCR config to compile Python wrappers for debugging submit
151. NEW: added ISMIP6 Antarctica forcings, still need to be fully tested
152. NEW: extended CalvingMIP to 3d Penta
153. CHG: Cleanup of chaco and semic from build configs where appropriate
154. CHG: Cleanup of chaco and semic from build configs where appropriate
155. CHG: The SMBsemic module uses the surface mass balance = SMB_ice + SMB_snow, not solely SMB_ice. Also, the term "SurfaceMassBalanceSemicEnum" is removed from Enum field.
156. Added a utility function to mask out unwatnted groups of elements and unit test
157. CHG: Added install scripts specific to Ghub Workspace 10 env; path corrections
158. CHG: Added install scripts specific to Ghub Workspace 10 env; path corrections
159. ADD: Jenkins config for Ghub Workspace 10 env
160. NEW: added petsc 3.20 install for mac
161. CHG: MATLAB -> Python; cleanup
162. CHG: Cleanup
163. CHG: MATLAB -> Python
164. CHG: Generic ar and ranlib
165. bug fix: time(1) and time(end) outside observation time works now
166. CHG: fix bug in classes/SMBsemic.py and synchronize classes/SMBsemic for python and matlab.
167. BUG: fix NaN index when using overlay
168. CHG: make the function to work for 2D grid as well