Changes

Summary

1. Update README.md (commit: fa5aabb) (details)
2. Update README.md (commit: a330354) (details)
3. CHG: adding other way to download ISSM from GitHub (commit: 48a9b97) (details)
4. CHG: Updating paths to Python installation (now using venv) (commit: 1eecdda) (details)
5. CHG: Adjusted tolerances (commit: 7c9d257) (details)
6. Delete README (commit: f722f58) (details)
7. CHG: upgrading to latest PETSc version (commit: f90c46a) (details)
8. BUG: Path to libgfortran (commit: df2b7bd) (details)
9. CHG: Need libgcc in package (commit: 8728b60) (details)
10. BUG: Path fixes (commit: dbaaac8) (details)
11. BUG: Not catching runme error; 'exclude_name' option no longer exists (commit: fdf735f) (details)
12. CHG: svn -> git; uncommitted cluster class; clean up of devpath from when we couldn't compile native Silicon MEX-files (commit: 0ab2011) (details)
13. BUG: Incorrect file name (commit: 00e5cd2) (details)
14. CHG: Virtual environment not preserved in called script (commit: 5bca2aa) (details)
15. CHG: removing old scripts (commit: e6392fa) (details)
16. CHG: moved up one directory and removed  from version check (commit: ce3c9bb) (details)
17. CHG: adding more files to gitignore (commit: 01ce958) (details)
18. CHG: Adjusted tolerances (commit: 64353b1) (details)
19. CHG: Minor changes to test fixes to GitHub Webhook -> Jenkins (commit: 67730b9) (details)
20. CHG: removing reference to cshrc, replacing by zshrc (commit: efea8d3) (details)
21. CHG: Adjusted tolerances (commit: e8a3cb5) (details)
22. CHG: Removing Cmake to avoid conflicts with standalone copy (commit: 4fa30f1) (details)
23. BUG: Removed 'command' (commit: 361128b) (details)
24. ADD: Missing empty Models/ dir (commit: 16ff615) (details)
25. Update of .gitignore. (commit: a28a358) (details)
26. Moved all CoDiPack specific functions to CoDiPackGlobal.h. (commit: 0316be7) (details)
27. CHG: Add default location for libgfortran on Mac to rpath (commit: 84ea771) (details)
28. CHG: adaptive time stepping needs vz in 3d (commit: 861dc45) (details)
29. CHG: throw error message if FCT in 3d (commit: 35053c5) (details)
30. CHG: Use git now to get changes and determine installation type (commit: 4599fe3) (details)
31. CHG: minor, testing to see if jenkins will recompile (commit: 520a010) (details)
32. CHG: forgot to change path to m/mesh/planet (commit: 727459b) (details)
33. CHG: Additions to ignore list (commit: 4378483) (details)
34. Create codeql.yml (commit: 0cb8aca) (details)
35. Bump the npm_and_yarn group across 1 directory with 2 updates (commit: a4e0257) (details)
36. CHG: Fixes for gfortran path in rpath; new config for CodeQL (commit: 1e3507d) (details)
37. Update codeql.yml (commit: 1dab3bf) (details)
38. Update codeql.yml (commit: 0b666a6) (details)
39. Update codeql.yml (commit: f1d20f2) (details)
40. Update codeql.yml (commit: f53e75a) (details)
41. CHG: Disabling wrappers on CodeQL build (commit: b5f1b8f) (details)
42. CHG: Correcting handling of git commit and changes when fetch has not been used (commit: c0b9d49) (details)
43. Delete codeql.yml (commit: ebaf87e) (details)
44. CHG: Adding whitespace and rerunning jobs (commit: fa36bf7) (details)
45. CHG: removing double blank lines (commit: 0586570) (details)
46. CHG: Adjusted tolerances (commit: 6e744f2) (details)
47. CHG: Updates to UB CCR config; changed path of gmshplanet.py (commit: d9a0c8b) (details)
48. CHG: do not rotate matrices if no node is rotated (breaking a golden rule here: this change is NOT tested yet, sorry if I am breaking anything (commit: c02b705) (details)
49. CoDiPack type can be defined during the configuration. (commit: 52173da) (details)
50. BUG: Need to update previous commit every time we run (commit: 7fb17d4) (details)
51. CHG: Outstanding commit and test fix to git change polling (commit: 9870579) (details)
52. Extracted common computation from StressbalanceAnalysis.cpp. (commit: 173984e) (details)
53. Added Preaccumulation helper for sparse row assembly. (commit: a7ae0dd) (details)
54. BUG: Fix for rpath anb libgfortran on Mac; no effect, but make sure MSYS2 is set correctly (commit: b2271bf) (details)
55. CHG: vertical speed needs md.basalforcings.perturbation_melting_rate (commit: 8d4bb33) (details)
56. CHG: vertical speed needs md.basalforcings.perturbation_melting_rate (commit: 7541e0c) (details)
57. CHG: missing -fPIC install-linux.sh (commit: 1ea61ca) (details)
58. CHG: macOS now only provides python3 and not python, and header files are now in the Headers directory (commit: bf9c1e1) (details)
59. CHG: removing SLEPSC and ADIC2 that we have never used (commit: 938aaa9) (details)
60. CHG: adding common factor to KMatrices StressBalance (commit: 31753cc) (details)
61. CHG: do not extrude lat/lon if undefined (commit: fe118e0) (details)
62. CHG: refine should deal with lat/long as well (commit: b6eb641) (details)
63. BUG: output is md2 and not md (commit: 53a5f78) (details)
64. CHG: if no observations are provided, we can still use md.initialization.vx/vy to set new spc's (commit: 81a688b) (details)
65. CHG: New cluster class for submitting jobs to UB CCR; typos (commit: 7885d2b) (details)
66. CHG: adding factors to analysis (commit: 44d1c2c) (details)
67. CHG: added Data directory for examples (commit: 19b70db) (details)
68. CHG: adding factors in analysis (commit: 3a66e7c) (details)
69. CHG: added factors in analysis (commit: 1644d52) (details)
70. CHG: fixed problem with Glads (commit: 2063a05) (details)
71. BUG: MPI_Wait should wait for the cpu that is receiving for once, which created seg faults with AD (commit: d04ef90) (details)
72. CHG: renaming Viscous Budd (commit: 36ebee1) (details)
73. CHG: Adjusted tolerances (commit: 49f94dd) (details)
74. CHG: multithreading ContourToNodes (commit: 1e79391) (details)
75. BUG: mexPrintf is NOT thread safe and crashes. Replace by printf (commit: 9474be9) (details)
76. CHG: Temporary fix for not being able to connect via port 22 (commit: a83fea6) (details)
77. CHG: Need P instead of p option (commit: cf35b4b) (details)
78. CHG: added PROJ_LIB env variable to make sure proj.db is found. There are sometimes conflicts with MATLAB's libraries which must be taken care of (commit: a75b963) (details)
79. CHG: minor changed ISSM description (commit: bdd72f6) (details)
80. CHG: ITS_LIVE annual velocity updated to v02, data avaliable from 1985 to 2022. The .nc files are in netCDF4 format, to load in Matlab, we need to use `h5read` (commit: 43146cb) (details)
81. ADD: interpolate from MEaSUREs monthly averaged velocity Mosaic (2014-2023) : https://doi.org/10.5067/EGKZX6FXXM4P (commit: dbcc688) (details)
82. CHG: use mapping toolbox map if Googlemaps is not available (commit: d980ed3) (details)
83. CHG: fixed zoom level option (commit: 83cdc8c) (details)
84. CHG: adjusted tolerances (commit: 86dd813) (details)
85. CHG: added interactive to disp: (commit: 23bf349) (details)
86. Added time and memory output for CoDiPack. (commit: 31dab70) (details)
87. Make preaccumulation configurable. (commit: b741196) (details)
88. Create c-cpp.yml (commit: 8d1129b) (details)
89. Update c-cpp.yml (commit: 57e71e6) (details)
90. CHG: changed checks on flags (commit: 8a0fac6) (details)
91. CHG: need to initialize as 0 (commit: 1c719e0) (details)
92. Update c-cpp.yml (commit: c6b61c1) (details)
93. Update c-cpp.yml (commit: 533d30c) (details)
94. Update c-cpp.yml (commit: 5a3ec47) (details)
95. Update c-cpp.yml (commit: 571d041) (details)
96. Update c-cpp.yml, add matlab (commit: 2f464c6) (details)
97. Update c-cpp.yml (commit: b78ae06) (details)
98. Update c-cpp.yml (commit: df8b3b6) (details)
99. Create github_linux_basic (commit: 5b34d72) (details)
100. Update c-cpp.yml (commit: d3045ed) (details)
101. Update c-cpp.yml (commit: 42c18ea) (details)
102. change the directory for CI files (commit: 13f902e) (details)
103. Update README.md (commit: cc2ad67) (details)
104. Update README.md (commit: a1131fe) (details)
105. create badge for CI, add it to README (commit: 684ad98) (details)
106. CHG: minor (commit: 9092bf4) (details)
107. BUG: forgot to close parenthesis (commit: 2e01ed8) (details)
108. CHG: upgrading PETSc in order to find latest ZLIB (commit: b3dbeeb) (details)
109. FIX: calculation of VAF based on mask in Tria.cpp (commit: 1f9cd7f) (details)
110. CHG: trying to simplify CI (commit: f1e8d22) (details)
111. CHG: trying to simplify CI (commit: db0c094) (details)
112. CHG: getting PETSc from apt-get (commit: 4fbda8b) (details)
113. CHG: PETSc needs to be installed manually, but we can skip autotools and cmake (commit: 5059e9c) (details)
114. BUG: fixing CI problem (commit: 8350f08) (details)
115. CHG: trying to fix CI (commit: 65c0f6e) (details)
116. CHG: trying to fix CI (commit: 2ed9f19) (details)
117. CHG: trying to fix CI (commit: b6cd13d) (details)
118. CHG: trying to fix CI (commit: 2e0f8b8) (details)
119. Update README.md (commit: 9661eba) (details)
120. NEW: added option 'quitonerror' for GitHub's CI (commit: cc5f201) (details)
121. CHG: fixing matlab tests in GitHub CI (commit: 246bda2) (details)
122. CHG: trying to fix CI with MATLAB (commit: 7f9ba8b) (details)
123. CHG: trying to debug CI (commit: c4ee45e) (details)
124. CHG: trying to add MATLAB tests (commit: 031c116) (details)
125. CHG: fixing MATLAB (commit: a979171) (details)
126. load matlab action manually (commit: 0bc0f3c) (details)
127. FIX: updated archive 540 (commit: 2ba99c0) (details)
128. CHG: checking env (commit: 2538728) (details)
129. CHG: checking env (commit: a359b8b) (details)
130. CHG: checking env (commit: f597fb4) (details)
131. CHG: checking env (commit: ce37a17) (details)
132. CHG: checking env (commit: d5f69f3) (details)
133. CHG: checking env (commit: d2964e7) (details)
134. set environment before running matlab (commit: 76e3036) (details)
135. Update c-cpp.yml (commit: e30c029) (details)
136. Update c-cpp.yml (commit: 7b61081) (details)
137. Update c-cpp.yml (commit: 168094e) (details)
138. Update c-cpp.yml (commit: 21920c7) (details)
139. CHG: fixed typo (commit: 70b01e1) (details)
140. NEW: added a function that reads a geotiff and outputs x,y,data (commit: d78e873) (details)
141. CHG: better check on METIS header (commit: 05cd86f) (details)
142. CHG: removing PETSc from installation (commit: 8eceb90) (details)
143. CHG: install openMPI (commit: df04386) (details)
144. CHG: figuring out open MPI (commit: f6e9ef8) (details)
145. CHG: mpi-include does not need -I (commit: 44a9842) (details)
146. CHG: scalapack is installed as part of open MPI (commit: dc05929) (details)
147. CHG: do not assume that ParMETIS is installed if MUMPS is provided (commit: a31e6d3) (details)
148. CHG: do not preload petsc files if petsc is not installed (commit: 0a97081) (details)
149. CHG: reverting to installing PETSc (commit: d0fde5f) (details)
150. CHG: simplifying workflow and scripts (commit: 382596b) (details)
151. CHG: change name (commit: 54b070a) (details)
152. CHG: removing MPICH from PETSc to speed up CI (commit: 2f9390b) (details)
153. CHG: adding more libs to mpi (commit: 15d7142) (details)
154. CHG: forgot to change LD_PRELOAD (commit: 7c3cac2) (details)
155. CHG: adding flag to mpiexec to avoid openmpi error message about 'There are not enough slots available' (commit: 48737e1) (details)
156. CHG: do not make MeshPartition a template (commit: 6bfebab) (details)
157. CHG: added example (commit: c8b520e) (details)
158. BUG: do not initialize codi_global if autodiff is false (commit: 4dc2ae2) (details)
159. CHG: Added packages to UB CCR installation; do not compile MeshPartition if METIS is not available (commit: 787af96) (details)
160. try to set two steps for the CI (commit: f400850) (details)
161. try to add cache (commit: ad75a7b) (details)
162. try to set the path for cache (commit: 6ed91f0) (details)
163. try again with env variable (commit: 750c718) (details)
164. update download path in artifact (commit: 13af998) (details)
165. try to also cache matlab (commit: 5de8374) (details)
166. change mpi back to petsc version (commit: 4e142f4) (details)
167. no need to cache matlab (commit: 239ff87) (details)
168. cache matlab (commit: f6f2916) (details)
169. try the uncompress path again (commit: a175878) (details)
170. download to /root (commit: 03b51c1) (details)
171. try to use relative path (commit: 8f3ee6d) (details)
172. add relative path (commit: fa1031b) (details)
173. change relative path again (commit: 91d425f) (details)
174. typo fixed (commit: 1fe7196) (details)
175. update working dir (commit: 1be644a) (details)
176. activate compile (commit: 64d3590) (details)
177. put test back (commit: 8cd2297) (details)
178. remove apt-get installed mpi (commit: 45287e7) (details)
179. try to create a matrix of test (commit: 7baf86f) (details)
180. try matrix with string variables (commit: 6fc2d49) (details)
181. add codipack in CI (commit: 909790b) (details)
182. try to fix codipack configure (commit: 093a11e) (details)
183. add gsl (commit: 884b5f0) (details)
184. seperate basic and codipack (commit: 7283804) (details)
185. Update common-workflow.yml (commit: 0ce30b9) (details)
186. only include ad tests for ccdipack (commit: 92c4d5e) (details)
187. fix bug in main-ci (commit: e2e12b5) (details)
188. set different names for different runs (commit: 0bde952) (details)
189. add type of input.os (commit: bb088f1) (details)
190. try to cache src/c (commit: 1df6ca5) (details)
191. fix error in the test job (commit: 63ba042) (details)
192. remove cache src/c (commit: e253f84) (details)
193. try petsc-3.20 for ad (commit: 69212ab) (details)
194. try to use env to set the id of cache (commit: b7973ce) (details)
195. try github.env (commit: 1e05474) (details)
196. try to fix bugs when using inputs in cache id (commit: 18ac845) (details)
197. fix bug in the if condition (commit: 1f4a9f4) (details)
198. fix codipack (commit: fae90a5) (details)
199. try ad again (commit: 66e4f82) (details)
200. CHG: added error message instead of just bypassing (commit: 1aa4555) (details)
201. CHG: for macOS we now also need to add  -commons use_dylibs (commit: eddbc51) (details)
202. BUG: need to provide specific LD_FLAGS and tweak setCompiler.py to make it work on Sonoma (commit: 2364937) (details)
203. CHG: cleanup (commit: 14d761f) (details)
204. remove with-petsc in codipack (commit: b35a114) (details)
205. reduce matrix size for tests (commit: 4671a46) (details)
206. check spaces (commit: 5ccd274) (details)
207. turn off codipack tests (commit: 3f44b86) (details)
208. do not compress petsc/src/ to decrease the size of the artifact (commit: 38f993e) (details)
209. try to exclude petsc/src (commit: 29dbe16) (details)
210. add gsl to codipack version (commit: 8bb700f) (details)
211. CHG: calving rate in CalvingMIP use normal vector from the levelset (commit: 8b089ab) (details)
212. Update README.md (commit: 81ee094) (details)
213. Update README.md (commit: d3c04a9) (details)
214. Update action badge in README.md (commit: ba30c85) (details)
215. CHG: default md.levelset.reinit_frequency=10. Add more description to stabilization (commit: b5d77dd) (details)
216. CHG: make two CIs separately for Ubuntu basic and codipack (commit: 2b5a6ff) (details)
217. CHG: Update test540, due to update default reinit_frequency (commit: 3e9e691) (details)
218. change the way to reuse workflow (commit: 1e8a29b) (details)
219. hard code the version of configure ISSM for now (commit: 80151a8) (details)
220. BUG: fix CalvingCalvingMIP in Penta (commit: b2de648) (details)
221. fix bugs in action.yml (commit: 830d14b) (details)
222. separate prepare externalpackes and build (commit: d8e2dd1) (details)
223. test ISSM_DIR (commit: fa789b6) (details)
224. Update action.yml (commit: 5aa39ba) (details)
225. fix ISSM_DIR issue (commit: 8bd8575) (details)
226. rerun CI, make input name shorter (commit: ca8a4ee) (details)
227. fix bug in action.yml (commit: 73c3538) (details)
228. CHG: update Archive540 (commit: 8c4f19d) (details)
229. rerun full CI (commit: 886c972) (details)
230. fix bug in uploading artifact (commit: c64a63f) (details)
231. BUG: fix CalvingCalvingMIP (commit: d8bbe33) (details)
232. BUG: recompile ISSM, update test540 Archive (commit: bdff019) (details)
233. CHG: update Archive affected by levelset.reinit_frequency=10 (commit: 96b1b80) (details)
234. add badges for Ubuntu Basic and CodiPack (commit: a79de1e) (details)
235. CHG: MATLAB -> Python and Javascript (commit: 6a2b0e0) (details)
236. NEW: Add contrib/poinelli folder and include Paolo2023 interpolation script (commit: 3875940) (details)
237. CHG: 1st edit of interpPaolo2023 (commit: 266f7ef) (details)
238. CHG: taking care of paths with white spaces (commit: b801141) (details)
239. CHG: relaxed tolerances for test 541 (commit: 74b8289) (details)
240. CHG: Cleanup (commit: 5495d62) (details)
241. CHG: update to GEMB merge layers to parallel matlab version updates (commit: e068d33) (details)
242. CHG: update GEMB tols for latest commit (commit: 1b6b531) (details)
243. CHG: update remaining tols in windows and on git for GEMB (commit: a727659) (details)
244. CHG: Cleanup of configuration options (commit: 2561795) (details)
245. BUG: Needed closing ;; (commit: bdf2ded) (details)
246. CHG: Removing support for Android (commit: 0db7fc2) (details)
247. CHG: Synchronized enums after pull and merge (commit: 8d404e5) (details)
248. BUG: Cleaned up configs (commit: 9655481) (details)
249. BUG: Correcting env var substitution (commit: 3148eb2) (details)
250. CHG: Cleanup (commit: 36c824f) (details)
251. CHG: Cleanup (commit: fd4f45b) (details)
252. CHG: Moving standard env vars to issm_options for MSYS2 builds (commit: 4977f2a) (details)
253. CHG: Cleanup; missing env var for Javascript build (commit: 53ee210) (details)
254. BUG: Fix for MSYS2 build (commit: 3a68cbf) (details)
255. merge actions to the workflow file (commit: 64ffe94) (details)
256. use multiple lines for the yml (commit: 254f18b) (details)
257. try to set matlab outside (commit: 6d03ef5) (details)
258. fix missing type of common-workflow.yml (commit: 58fd525) (details)
259. fix bug in setting matlab root (commit: bb0d287) (details)
260. if cache not hit, then recompile (commit: f16e34a) (details)
261. CHG: added check to tell useers they cannot use both PETSc and CoDiPack (commit: c88b7a0) (details)
262. BUG: Need to check if supplied gfortran and other libs are files for binaries builds (commit: 5a5c9ed) (details)
263. CHG: added some explanation (commit: b2f314e) (details)
264. BUG: compute calving rate after extrapolation, so that the direction can be correctly computated in the inactive elements (commit: b256810) (details)
265. BUG: update archive 540,541,542 (commit: b3a4f1b) (details)
266. update 806,812 (commit: 65c5aa9) (details)
267. BUG: update archive 3203 (commit: 8a2b0db) (details)
268. CHG: Consolidation of C*OPTFLAGS to C*FLAGS; missing parmetis option (commit: ed36509) (details)
269. BUG: Missing commit from pristine copy (commit: d808565) (details)
270. BUG: CXXFLAGS is not empty by default under clang (commit: bf3a691) (details)
271. BUG: Bad path to gfortran (commit: 4157c9d) (details)
272. use json to handle matrix strategy (commit: 2850cf1) (details)
273. CHG: Standardizing MATLAB and Python wrapper makefiles; adding more possible NumPy header file locations (commit: 0f0b973) (details)
274. BUG: fixed memory leak (commit: 9f57800) (details)
275. BUG: Reverting changes for now to get versioned code working (commit: 1b3278c) (details)
276. CHG: Standardizing MATLAB and Python wrapper makefiles (commit: c11a839) (details)
277. BUG: Reverting (again, sigh) (commit: fe24717) (details)
278. add \' in common_workflow (commit: bca13c6) (details)
279. Update common-workflow.yml (commit: f7c3b4e) (details)
280. Update common-workflow.yml (commit: 14a21f6) (details)
281. Update common-workflow.yml (commit: 7755735) (details)
282. update workflow using one file for one case (commit: c286907) (details)
283. CHG: MATLAB -> Python wrapper Makrfile.am; upgraded nodes to NumPy 2 (commit: 3197af5) (details)
284. ADD: output melt rate and its components in SHAKTI hydrology (commit: eb104ba) (details)
285. CHG: removing unused options (commit: 179c0e1) (details)
286. CHG: Removed HTTPS protocol as checkout option; added troubleshooting note about HTTPS protocol error (commit: edf3382) (details)
287. CHG: More clarification about HTTPS vs SSH (commit: 04c2e18) (details)
288. NEW: added file to interpolate undercutting forcings from ISMIP6 data files (commit: e67508f) (details)
289. CHG: added ref (commit: a1b5485) (details)
290. CHG: moving file to a better directory (commit: 534d762) (details)
291. CHG: update ICESat2 ATL14/15 to version 4 (commit: 303c711) (details)
292. CHG: closed contour should be option #1 (commit: ea7f3f6) (details)
293. CHG: minor estetics (commit: 3533cfa) (details)
294. CHG:update script for TACC Frontera (commit: f98ea83) (details)
295. NEW: add option to include subglacial hydrology layer thickness in driving stress calculation of the SSA (commit: 65a0dde) (details)
296. CHG: include stressbalance hydrology layer capability in python (commit: f91a234) (details)
297. BUG: fix loading MEaSUREs velocity for individual glaciers (commit: 5149a85) (details)
298. CHG: update Jakobshavn MEaSUREs velocity to 2024 (commit: c05462e) (details)
299. BUG: add if for more general model results (commit: cce08d8) (details)
300. BUG: generalize analyzeCalvingfront function (commit: 2b89286) (details)
301. CHG: second iteration of interpPaolo2023- add interpolation routine (commit: 368b7a0) (details)
302. CHG: include temporal component in Paolo2023 melt rate (commit: 681261f) (details)
303. NEW: added error message if cxxoptflags is provided (commit: 27d598e) (details)
304. BUG: python should not need MEXLIB, this introduces dependencies that are problematic (commit: 43afcce) (details)
305. BUG: bad python syntax (commit: 13ff1be) (details)
306. CHG: simplifying hydro slope code (commit: f5fe9bf) (details)
307. NEW: nightly run test for stressbalance hydrology layer (commit: 63801ab) (details)
308. CHG: add interpolated dates as output (commit: 05a3bc3) (details)
309. CHG: do not use configure.py in installation script, call configure directly (commit: 88caf6f) (details)
310. CHG: fixed RHS (commit: 2412ce3) (details)
311. ADD: stanage cluster settings for Sheffield University Stanage HPC cluster (commit: ee8d2e1) (details)
312. BUG: ocean-averaged sea level loads (commit: 40790d0) (details)
313. NEW: retrieving change in gravitational acceleration from ESA solver (commit: 7bb99ab) (details)
314. CHG: fixed bad character from Surendra's commit (commit: 1744867) (details)
315. CHG: fixing NR (commit: 58c5d9f) (details)
316. CHG: make python test identical to MATLAB test (commit: 8f25deb) (details)
317. CHG: making python test identical to MATLAB (commit: 2adee40) (details)
318. ESA nightly updated with a new diagostic (commit: 52f6f6b) (details)
319. CHG: relaxing tolerances (commit: 45900e6) (details)
320. CHG: relaxing tolerances (commit: 298cb7b) (details)
321. CHG: relaxing tolerances (commit: ec666e0) (details)
322. CHG: New archives; changes to ext pkg install scripts and Makefiles as needed to account for new changes to macOS linker (commit: 0eae8ab) (details)
323. Update .gitignore (commit: edf75a0) (details)
324. CHG: Updated PETSc version (commit: 6c1248e) (details)
325. CHG: Renaming of GDAL install scripts (commit: b3c0a8b) (details)
326. CHG: Fixes for latest PETSc version install script (commit: c15f2a6) (details)
327. BUG: Corrected install script (commit: 487471c) (details)
328. CHG: Adjusted tolerances (commit: 486465f) (details)
329. CHG: Disabling test 362 for Silicon-based Mac as it has large errors (commit: 1a65809) (details)
330. CHG: Adjusted tolerances (commit: 8921351) (details)
331. CHG: Adjusted tolerances (commit: 3553fe3) (details)
332. CHG: Corrected install script name (commit: 7a19986) (details)
333. Update .gitignore (commit: dab7cb3) (details)
334. CHG: moving functions around (commit: c285b96) (details)
335. ADD: mac basic CI (commit: 42d81d1) (details)
336. CHG: Love core accuracy and stability improved. NEW: Complex solution enabled (commit: 3083c90) (details)
337. CHG: Love core accuracy and stability improved. NEW: Complex solution enabled (commit: 1c6ce92) (details)
338. fixing merging error in Makefile.am (commit: 9a7c619) (details)
339. CHG:cleaned up Love core for final version (commit: 1044ddf) (details)
340. FIX: fixing recast of int/double to double precision for some compilers in Love core (commit: ac99ef7) (details)
341. FIX: cleaning up love core (commit: f3f84ba) (details)
342. CHG: Bug in Python wrapper; cleanup (commit: 5ee7514) (details)
343. CHG: Updated gitignore; removed test 362 from test suite for distributables on Silicon-based Macs (commit: ebebeee) (details)
344. CHG: Committing local changes from UB CCR (commit: 6447d8a) (details)
345. Update test2085.m (commit: 2733d6e) (details)
346. Update test2084.m (commit: ce8285b) (details)
347. CHG: minor edit, include larsen-thwaites hosts to interpStal2020 (commit: 86a3b91) (details)
348. CHG: Older versions of PETSc use config/configure.py (may need to change others) (commit: 4edb121) (details)
349. CHG: Updates for saving model for JavaScript (commit: 9d324ae) (details)
350. CHG: Disabling guts of some savemodeljs methods until they are added to issm.js (commit: 4631b66) (details)
351. CHG: Turning off development mode so we can generate new binaries automatically for use on VESL (commit: 457cb9e) (details)
352. CHG: Fixes for JavaScript API and Emscripten compilation (commit: 150ded5) (details)
353. CHG: no error compiler flag still needed (commit: bfe4006) (details)
354. CHG: More JavaScript API fixes; compiler options to disable wasm (commit: 7393150) (details)
355. CHG: Make sure optimization is use for JavaScript binaries, but that certain functions are not optimized out (commit: 3a60c66) (details)
356. CHG: Emscripten does not like opt flag (commit: a1fa7c0) (details)
357. BUG: Issue was missing quote, not flag (commit: 4fa7540) (details)
358. CHG: Added missing exported functions for JavaScript binaries (commit: 6cbf657) (details)
359. CHG: Adjusted tolerances (commit: 933c33c) (details)
360. CHG: Fixes for outputting transient class to JavaScript model (commit: 6e9dbd7) (details)
361. BUG: gmsl was not the same as bslc. Now fixed. test2011 modified. (commit: 63f13df) (details)
362. CHG: Updated archives (commit: 58d0ba8) (details)
363. FIX: Bug in frequency love number output format when np>1; CHG: updated love core tests and archives (commit: e8b3f46) (details)
364. FIX: love core: recast some integers to doubletype to help some mac compilers (commit: 6f59af1) (details)
365. FIX: Missing synched enum files for Love core update (commit: 2e0d421) (details)
366. Update test2075.m (commit: f463f88) (details)
367. Update test2071.m (commit: 825cf18) (details)
368. CHG: Adjusted tolerances (commit: 8b7ecfc) (details)
369. CHG: Fixes for love numbers and related tests under Python API (commit: 90fe3da) (details)
370. BUG: Fixed parens (commit: 4d9897d) (details)
371. CHG: Do not assume that system/subprocess call will use bash as shell; cleanup (commit: 369a51b) (details)
372. CHG: Translated test2085 from MATLAB -> Python (commit: 9634a49) (details)
373. fix penta section normals and remove duplicate code (commit: efde1a9) (details)
374. fix indentation (commit: 4586e1c) (details)
375. CHG: Adjusted tolerances; do not run test 2085 on Silicon (commit: 9b45c84) (details)
376. CHG: Adjusted tolerances (commit: 08469f9) (details)
377. remove unused indices in  Tria::NormalTop (commit: 21dcef2) (details)
378. CHG: Updated path to gfortran (commit: 70147fb) (details)
379. CHG: extract AD cost functions (commit: d03a573) (details)
380. CHG: Modified all basic external package installation scripts to use developers' download links, where possible (commit: 0e1d4f4) (details)
381. CHG: Check if LDFLAGS is set (commit: c8c5fd8) (details)
382. CHG: Updated all install scripts for external packages needed for extended capabilities (commit: 3918dec) (details)
383. CHG: Uploading Chaco source to repository as it does not download properly from Sandia's GitHub repo (commit: 2c403f6) (details)
384. CHG: Moved Adjoinable MPI source to repo because developer's Mercurial repo appears to be down (commit: 951d8ba) (details)
385. CHG: More external package fixes (commit: 79fcea5) (details)
386. CHG: Adjusted tolerances (commit: 2e6f604) (details)
387. CHG: Need to ignore download script in directory to properly download datasets (commit: db7f6b2) (details)
388. CHG: Rolling back to HDF5 1.14.3 as newer versions do not properly compile on Intel-based Macs (known issue) (commit: c432a9f) (details)
389. BUG: Expode hidden NumPy symbols in newer versions; cleanup (commit: fd275dd) (details)
390. CHG: Adjusted tolerances (commit: 473a8bf) (details)
391. CHG: Fix bug in src/c/analyses/SmbAnalysis.cpp (commit: fed894b) (details)
392. CHG: Update SmbSEMIC modules (commit: 111e86f) (details)
393. ADD: MATLAB - interpolate netcdf file with using xarray in python. (commit: daf8293) (details)
394. CHG: Resolve memory leakage in SEMIC. (commit: 5bec532) (details)
395. CHG: model.refine MATLAB -> Python; clean up (commit: 70cadb9) (details)
396. BUG: Bad indexing of bamgmesh out (commit: 617fa79) (details)
397. CHG: Catch unsupported draw function; clean up (commit: a5470e5) (details)
398. CHG: Adjusted tolerances (commit: 750f4b7) (details)
399. FIX: Output of Tidal love numbers in Love core (commit: 5bbf926) (details)
400. CHG: do not assume hemisphere (commit: 29e26a7) (details)
401. BUG: if minor version of python is greater than 9 the last digit was removed. Now fixed (commit: 734d71a) (details)
402. CHG: Fix SEMIC enables to run surface mass and energy balance with albedo scheme of Alex. Fix Documentation for SMBsemic with albedo scheme of Denby and ISBA. (commit: 3c778b7) (details)
403. ADD: flag `with_matlab` in CI with matlab (commit: a1d0fbe) (details)
404. CHG: input.with_matlab -> input.interface (commit: bd92bb5) (details)
405. ADD: ubuntu python test (commit: 14fe0b8) (details)
406. ADD: install python-dev (commit: c23fa5e) (details)
407. ADD: python tests (commit: 00193b4) (details)
408. BUG: fix .yml (commit: 2d40145) (details)
409. CHG: python path for CI (commit: 0776a0a) (details)
410. BUG: fix python path (commit: 9cd4b54) (details)
411. CHG: get python path from python action (commit: eac81c0) (details)
412. CHG: use env (commit: 9e781b9) (details)
413. Update ubuntu-python.yml (commit: 6b751ae) (details)
414. CHG: output python path after setup (commit: cc03516) (details)
415. change to v5 python action (commit: 6012a64) (details)
416. update python path (commit: 79a9ec3) (details)
417. fix bug in python_version (commit: 10e0102) (details)
418. CHG: wrong place holder for string (commit: 2c7f585) (details)
419. currentlt test with only python (commit: 2722bc2) (details)
420. add libpython (commit: 49c8613) (details)
421. update CI (commit: 74f450e) (details)
422. update CI (commit: 6073f89) (details)
423. set python path (commit: 0d924c2) (details)
424. update numpy path (commit: e33ed82) (details)
425. check the folder (commit: 51346a8) (details)
426. add path to numpy (commit: 89950de) (details)
427. add path to numpy (commit: 7e617b9) (details)
428. update numpy (commit: a16ee76) (details)
429. add test numpy (commit: c7ff259) (details)
430. print more (commit: 93fc7cc) (details)
431. look into _core (commit: f1b7cf4) (details)
432. add python to test (commit: 67a6f83) (details)
433. add netCDF4 (commit: be2d32c) (details)
434. add source ISSM (commit: 2e5bf2e) (details)
435. ADD: ubuntu python CI test (commit: 14b7eaa) (details)
436. Revert "add python CI" (commit: 1861be8) (details)
437. Revert "Revert "add python CI"" (commit: 830f9fd) (details)
438. CHG: Eased tolerances (commit: 56a15f2) (details)
439. CHG: Moving certain external packages to new repo (commit: a178c10) (details)
440. ADD: `cutoff` option in flowlines.m (commit: d0b3440) (details)
441. BUG: revert issmscpin to previous version (commit: 3cb91ea) (details)
442. CHG: adding dynamic function name (commit: caad0b5) (details)
443. CHG: automatically remove checkpoint file once done to save disk space (commit: b73355e) (details)
444. CHG: Cleanup; MATLAB -> Python; documentation (commit: c8d98c1) (details)
445. CHG: Merging Inwoo's fix for MATLAB + Python APIs with minor changes (commit: 3fc67bb) (details)

Update README.md
 (commit: fa5aabb)

Update README.md
 (commit: a330354)

CHG: adding other way to download ISSM from GitHub
 (commit: 48a9b97)

CHG: Updating paths to Python installation (now using venv)
 (commit: 1eecdda)

CHG: Adjusted tolerances
 (commit: 7c9d257)

Delete README
 (commit: f722f58)

CHG: upgrading to latest PETSc version
 (commit: f90c46a)

BUG: Path to libgfortran
 (commit: df2b7bd)

CHG: Need libgcc in package
 (commit: 8728b60)

BUG: Path fixes
 (commit: dbaaac8)

BUG: Not catching runme error; 'exclude_name' option no longer exists
 (commit: fdf735f)

CHG: svn -> git; uncommitted cluster class; clean up of devpath from when we couldn't compile native Silicon MEX-files
 (commit: 0ab2011)

BUG: Incorrect file name
 (commit: 00e5cd2)

CHG: Virtual environment not preserved in called script
 (commit: 5bca2aa)

CHG: removing old scripts
 (commit: e6392fa)

CHG: moved up one directory and removed  from version check
 (commit: ce3c9bb)

CHG: adding more files to gitignore
 (commit: 01ce958)

CHG: Adjusted tolerances
 (commit: 64353b1)

CHG: Minor changes to test fixes to GitHub Webhook -> Jenkins
 (commit: 67730b9)

CHG: removing reference to cshrc, replacing by zshrc
 (commit: efea8d3)

CHG: Adjusted tolerances
 (commit: e8a3cb5)

CHG: Removing Cmake to avoid conflicts with standalone copy
 (commit: 4fa30f1)

BUG: Removed 'command'
 (commit: 361128b)

ADD: Missing empty Models/ dir
 (commit: 16ff615)

Update of .gitignore.
 (commit: a28a358)

Moved all CoDiPack specific functions to CoDiPackGlobal.h.
 (commit: 0316be7)

CHG: Add default location for libgfortran on Mac to rpath
 (commit: 84ea771)

CHG: adaptive time stepping needs vz in 3d
 (commit: 861dc45)

CHG: throw error message if FCT in 3d
 (commit: 35053c5)

CHG: Use git now to get changes and determine installation type
 (commit: 4599fe3)

CHG: minor, testing to see if jenkins will recompile
 (commit: 520a010)

CHG: forgot to change path to m/mesh/planet
 (commit: 727459b)

CHG: Additions to ignore list
 (commit: 4378483)

Create codeql.yml

Adding code scanning for security vulnerabilities
 (commit: 0cb8aca)

Bump the npm_and_yarn group across 1 directory with 2 updates

Bumps the npm_and_yarn group with 2 updates in the /jenkins/javascript/karma directory: [karma](https://github.com/karma-runner/karma) and [mathjs](https://github.com/josdejong/mathjs).


Updates `karma` from 0.13.22 to 6.4.3
- [Release notes](https://github.com/karma-runner/karma/releases)
- [Changelog](https://github.com/karma-runner/karma/blob/master/CHANGELOG.md)
- [Commits](https://github.com/karma-runner/karma/compare/v0.13.22...v6.4.3)

Updates `mathjs` from 3.20.2 to 13.0.0
- [Changelog](https://github.com/josdejong/mathjs/blob/develop/HISTORY.md)
- [Commits](https://github.com/josdejong/mathjs/compare/v3.20.2...v13.0.0)

---
updated-dependencies:
- dependency-name: karma
  dependency-type: direct:development
  dependency-group: npm_and_yarn
- dependency-name: mathjs
  dependency-type: direct:development
  dependency-group: npm_and_yarn
...

Signed-off-by: dependabot[bot] <support@github.com>
 (commit: a4e0257)

CHG: Fixes for gfortran path in rpath; new config for CodeQL
 (commit: 1e3507d)

Update codeql.yml
 (commit: 1dab3bf)

Update codeql.yml
 (commit: 0b666a6)

Update codeql.yml
 (commit: f1d20f2)

Update codeql.yml
 (commit: f53e75a)

CHG: Disabling wrappers on CodeQL build
 (commit: b5f1b8f)

CHG: Correcting handling of git commit and changes when fetch has not been used
 (commit: c0b9d49)

Delete codeql.yml

Deleting for now until external packages can be offloaded to package managers.
 (commit: ebaf87e)

CHG: Adding whitespace and rerunning jobs
 (commit: fa36bf7)

CHG: removing double blank lines
 (commit: 0586570)

CHG: Adjusted tolerances
 (commit: 6e744f2)

CHG: Updates to UB CCR config; changed path of gmshplanet.py
 (commit: d9a0c8b)

CHG: do not rotate matrices if no node is rotated (breaking a golden rule here: this change is NOT tested yet, sorry if I am breaking anything
 (commit: c02b705)

CoDiPack type can be defined during the configuration.
 (commit: 52173da)

BUG: Need to update previous commit every time we run
 (commit: 7fb17d4)

CHG: Outstanding commit and test fix to git change polling
 (commit: 9870579)

Extracted common computation from StressbalanceAnalysis.cpp.
 (commit: 173984e)

Added Preaccumulation helper for sparse row assembly.
 (commit: a7ae0dd)

BUG: Fix for rpath anb libgfortran on Mac; no effect, but make sure MSYS2 is set correctly
 (commit: b2271bf)

CHG: vertical speed needs md.basalforcings.perturbation_melting_rate
 (commit: 8d4bb33)

CHG: vertical speed needs md.basalforcings.perturbation_melting_rate
 (commit: 7541e0c)

CHG: missing -fPIC install-linux.sh
 (commit: 1ea61ca)

CHG: macOS now only provides python3 and not python, and header files are now in the Headers directory
 (commit: bf9c1e1)

CHG: removing SLEPSC and ADIC2 that we have never used
 (commit: 938aaa9)

CHG: adding common factor to KMatrices StressBalance
 (commit: 31753cc)

CHG: do not extrude lat/lon if undefined
 (commit: fe118e0)

CHG: refine should deal with lat/long as well
 (commit: b6eb641)

BUG: output is md2 and not md
 (commit: 53a5f78)

CHG: if no observations are provided, we can still use md.initialization.vx/vy to set new spc's
 (commit: 81a688b)

CHG: New cluster class for submitting jobs to UB CCR; typos
 (commit: 7885d2b)

CHG: adding factors to analysis
 (commit: 44d1c2c)

CHG: added Data directory for examples
 (commit: 19b70db)

CHG: adding factors in analysis
 (commit: 3a66e7c)

CHG: added factors in analysis
 (commit: 1644d52)

CHG: fixed problem with Glads
 (commit: 2063a05)

BUG: MPI_Wait should wait for the cpu that is receiving for once, which created seg faults with AD
 (commit: d04ef90)

CHG: renaming Viscous Budd
 (commit: 36ebee1)

CHG: Adjusted tolerances
 (commit: 49f94dd)

CHG: multithreading ContourToNodes
 (commit: 1e79391)

BUG: mexPrintf is NOT thread safe and crashes. Replace by printf
 (commit: 9474be9)

CHG: Temporary fix for not being able to connect via port 22
 (commit: a83fea6)

CHG: Need P instead of p option
 (commit: cf35b4b)

CHG: added PROJ_LIB env variable to make sure proj.db is found. There are sometimes conflicts with MATLAB's libraries which must be taken care of
 (commit: a75b963)

CHG: minor changed ISSM description
 (commit: bdd72f6)

CHG: ITS_LIVE annual velocity updated to v02, data avaliable from 1985 to 2022. The .nc files are in netCDF4 format, to load in Matlab, we need to use `h5read`
 (commit: 43146cb)

ADD: interpolate from MEaSUREs monthly averaged velocity Mosaic (2014-2023) : https://doi.org/10.5067/EGKZX6FXXM4P
 (commit: dbcc688)

CHG: use mapping toolbox map if Googlemaps is not available
 (commit: d980ed3)

CHG: fixed zoom level option
 (commit: 83cdc8c)

CHG: adjusted tolerances
 (commit: 86dd813)

CHG: added interactive to disp:
 (commit: 23bf349)

Added time and memory output for CoDiPack.
 (commit: 31dab70)

Make preaccumulation configurable.
 (commit: b741196)

Create c-cpp.yml
 (commit: 8d1129b)

Update c-cpp.yml
 (commit: 57e71e6)

CHG: changed checks on flags
 (commit: 8a0fac6)

CHG: need to initialize as 0
 (commit: 1c719e0)

Update c-cpp.yml
 (commit: c6b61c1)

Update c-cpp.yml
 (commit: 533d30c)

Update c-cpp.yml
 (commit: 5a3ec47)

Update c-cpp.yml
 (commit: 571d041)

Update c-cpp.yml, add matlab
 (commit: 2f464c6)

Update c-cpp.yml
 (commit: b78ae06)

Update c-cpp.yml
 (commit: df8b3b6)

Create github_linux_basic
 (commit: 5b34d72)

Update c-cpp.yml
 (commit: d3045ed)

Update c-cpp.yml
 (commit: 42c18ea)

change the directory for CI files
 (commit: 13f902e)

Update README.md
 (commit: cc2ad67)

Update README.md
 (commit: a1131fe)

create badge for CI, add it to README
 (commit: 684ad98)

CHG: minor
 (commit: 9092bf4)

BUG: forgot to close parenthesis
 (commit: 2e01ed8)

CHG: upgrading PETSc in order to find latest ZLIB
 (commit: b3dbeeb)

FIX: calculation of VAF based on mask in Tria.cpp
 (commit: 1f9cd7f)

CHG: trying to simplify CI
 (commit: f1e8d22)

CHG: trying to simplify CI
 (commit: db0c094)

CHG: getting PETSc from apt-get
 (commit: 4fbda8b)

CHG: PETSc needs to be installed manually, but we can skip autotools and cmake
 (commit: 5059e9c)

BUG: fixing CI problem
 (commit: 8350f08)

CHG: trying to fix CI
 (commit: 65c0f6e)

CHG: trying to fix CI
 (commit: 2ed9f19)

CHG: trying to fix CI
 (commit: b6cd13d)

CHG: trying to fix CI
 (commit: 2e0f8b8)

Update README.md

Added commit notes (and testing fixes for Jenkins workflow)
 (commit: 9661eba)

NEW: added option 'quitonerror' for GitHub's CI
 (commit: cc5f201)

CHG: fixing matlab tests in GitHub CI
 (commit: 246bda2)

CHG: trying to fix CI with MATLAB
 (commit: 7f9ba8b)

CHG: trying to debug CI
 (commit: c4ee45e)

CHG: trying to add MATLAB tests
 (commit: 031c116)

CHG: fixing MATLAB
 (commit: a979171)

load matlab action manually

as suggested https://github.com/matlab-actions/run-command/issues/53
 (commit: 0bc0f3c)

FIX: updated archive 540
 (commit: 2ba99c0)

CHG: checking env
 (commit: 2538728)

CHG: checking env
 (commit: a359b8b)

CHG: checking env
 (commit: f597fb4)

CHG: checking env
 (commit: ce37a17)

CHG: checking env
 (commit: d5f69f3)

CHG: checking env
 (commit: d2964e7)

set environment before running matlab
 (commit: 76e3036)

Update c-cpp.yml
 (commit: e30c029)

Update c-cpp.yml
 (commit: 7b61081)

Update c-cpp.yml
 (commit: 168094e)

Update c-cpp.yml
 (commit: 21920c7)

CHG: fixed typo
 (commit: 70b01e1)

NEW: added a function that reads a geotiff and outputs x,y,data
 (commit: d78e873)

CHG: better check on METIS header
 (commit: 05cd86f)

CHG: removing PETSc from installation
 (commit: 8eceb90)

CHG: install openMPI
 (commit: df04386)

CHG: figuring out open MPI
 (commit: f6e9ef8)

CHG: mpi-include does not need -I
 (commit: 44a9842)

CHG: scalapack is installed as part of open MPI
 (commit: dc05929)

CHG: do not assume that ParMETIS is installed if MUMPS is provided
 (commit: a31e6d3)

CHG: do not preload petsc files if petsc is not installed
 (commit: 0a97081)

CHG: reverting to installing PETSc
 (commit: d0fde5f)

CHG: simplifying workflow and scripts
 (commit: 382596b)

CHG: change name
 (commit: 54b070a)

CHG: removing MPICH from PETSc to speed up CI
 (commit: 2f9390b)

CHG: adding more libs to mpi
 (commit: 15d7142)

CHG: forgot to change LD_PRELOAD
 (commit: 7c3cac2)

CHG: adding flag to mpiexec to avoid openmpi error message about 'There are not enough slots available'
 (commit: 48737e1)

CHG: do not make MeshPartition a template
 (commit: 6bfebab)

CHG: added example
 (commit: c8b520e)

BUG: do not initialize codi_global if autodiff is false
 (commit: 4dc2ae2)

CHG: Added packages to UB CCR installation; do not compile MeshPartition if METIS is not available
 (commit: 787af96)

try to set two steps for the CI
 (commit: f400850)

try to add cache
 (commit: ad75a7b)

try to set the path for cache
 (commit: 6ed91f0)

try again with env variable
 (commit: 750c718)

update download path in artifact
 (commit: 13af998)

try to also cache matlab
 (commit: 5de8374)

change mpi back to petsc version
 (commit: 4e142f4)

no need to cache matlab
 (commit: 239ff87)

cache matlab
 (commit: f6f2916)

try the uncompress path again
 (commit: a175878)

download to /root
 (commit: 03b51c1)

try to use relative path
 (commit: 8f3ee6d)

add relative path
 (commit: fa1031b)

change relative path again
 (commit: 91d425f)

typo fixed
 (commit: 1fe7196)

update working dir
 (commit: 1be644a)

activate compile
 (commit: 64d3590)

put test back
 (commit: 8cd2297)

remove apt-get installed mpi
 (commit: 45287e7)

try to create a matrix of test
 (commit: 7baf86f)

try matrix with string variables
 (commit: 6fc2d49)

add codipack in CI
 (commit: 909790b)

try to fix codipack configure
 (commit: 093a11e)

add gsl
 (commit: 884b5f0)

seperate basic and codipack
 (commit: 7283804)

Update common-workflow.yml
 (commit: 0ce30b9)

only include ad tests for ccdipack
 (commit: 92c4d5e)

fix bug in main-ci
 (commit: e2e12b5)

set different names for different runs
 (commit: 0bde952)

add type of input.os
 (commit: bb088f1)

try to cache src/c
 (commit: 1df6ca5)

fix error in the test job
 (commit: 63ba042)

remove cache src/c
 (commit: e253f84)

try petsc-3.20 for ad
 (commit: 69212ab)

try to use env to set the id of cache
 (commit: b7973ce)