Changes

Summary

1. Update README.md (details)
2. Update README.md (details)
3. CHG: adding other way to download ISSM from GitHub (details)
4. CHG: Updating paths to Python installation (now using venv) (details)
5. CHG: Adjusted tolerances (details)
6. Delete README (details)
7. CHG: upgrading to latest PETSc version (details)
8. BUG: Path to libgfortran (details)
9. CHG: Need libgcc in package (details)
10. BUG: Path fixes (details)
11. BUG: Not catching runme error; 'exclude_name' option no longer exists (details)
12. CHG: svn -> git; uncommitted cluster class; clean up of devpath from when we couldn't compile native Silicon MEX-files (details)
13. BUG: Incorrect file name (details)
14. CHG: Virtual environment not preserved in called script (details)
15. CHG: removing old scripts (details)
16. CHG: moved up one directory and removed  from version check (details)
17. CHG: adding more files to gitignore (details)
18. CHG: Adjusted tolerances (details)
19. CHG: Minor changes to test fixes to GitHub Webhook -> Jenkins (details)
20. CHG: removing reference to cshrc, replacing by zshrc (details)
21. CHG: Adjusted tolerances (details)
22. CHG: Removing Cmake to avoid conflicts with standalone copy (details)
23. BUG: Removed 'command' (details)
24. ADD: Missing empty Models/ dir (details)
25. Update of .gitignore. (details)
26. Moved all CoDiPack specific functions to CoDiPackGlobal.h. (details)
27. CHG: Add default location for libgfortran on Mac to rpath (details)
28. CHG: adaptive time stepping needs vz in 3d (details)
29. CHG: throw error message if FCT in 3d (details)
30. CHG: Use git now to get changes and determine installation type (details)
31. CHG: minor, testing to see if jenkins will recompile (details)
32. CHG: forgot to change path to m/mesh/planet (details)
33. CHG: Additions to ignore list (details)
34. Create codeql.yml (details)
35. Bump the npm_and_yarn group across 1 directory with 2 updates (details)
36. CHG: Fixes for gfortran path in rpath; new config for CodeQL (details)
37. Update codeql.yml (details)
38. Update codeql.yml (details)
39. Update codeql.yml (details)
40. Update codeql.yml (details)
41. CHG: Disabling wrappers on CodeQL build (details)
42. CHG: Correcting handling of git commit and changes when fetch has not been used (details)
43. Delete codeql.yml (details)
44. CHG: Adding whitespace and rerunning jobs (details)
45. CHG: removing double blank lines (details)
46. CHG: Adjusted tolerances (details)
47. CHG: Updates to UB CCR config; changed path of gmshplanet.py (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 (details)
49. CoDiPack type can be defined during the configuration. (details)
50. BUG: Need to update previous commit every time we run (details)
51. CHG: Outstanding commit and test fix to git change polling (details)
52. Extracted common computation from StressbalanceAnalysis.cpp. (details)
53. Added Preaccumulation helper for sparse row assembly. (details)
54. BUG: Fix for rpath anb libgfortran on Mac; no effect, but make sure MSYS2 is set correctly (details)
55. CHG: vertical speed needs md.basalforcings.perturbation_melting_rate (details)
56. CHG: vertical speed needs md.basalforcings.perturbation_melting_rate (details)
57. CHG: missing -fPIC install-linux.sh (details)
58. CHG: macOS now only provides python3 and not python, and header files are now in the Headers directory (details)
59. CHG: removing SLEPSC and ADIC2 that we have never used (details)
60. CHG: adding common factor to KMatrices StressBalance (details)
61. CHG: do not extrude lat/lon if undefined (details)
62. CHG: refine should deal with lat/long as well (details)
63. BUG: output is md2 and not md (details)
64. CHG: if no observations are provided, we can still use md.initialization.vx/vy to set new spc's (details)
65. CHG: New cluster class for submitting jobs to UB CCR; typos (details)
66. CHG: adding factors to analysis (details)
67. CHG: added Data directory for examples (details)
68. CHG: adding factors in analysis (details)
69. CHG: added factors in analysis (details)
70. CHG: fixed problem with Glads (details)
71. BUG: MPI_Wait should wait for the cpu that is receiving for once, which created seg faults with AD (details)
72. CHG: renaming Viscous Budd (details)
73. CHG: Adjusted tolerances (details)
74. CHG: multithreading ContourToNodes (details)
75. BUG: mexPrintf is NOT thread safe and crashes. Replace by printf (details)
76. CHG: Temporary fix for not being able to connect via port 22 (details)
77. CHG: Need P instead of p option (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 (details)
79. CHG: minor changed ISSM description (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` (details)
81. ADD: interpolate from MEaSUREs monthly averaged velocity Mosaic (2014-2023) : https://doi.org/10.5067/EGKZX6FXXM4P (details)
82. CHG: use mapping toolbox map if Googlemaps is not available (details)
83. CHG: fixed zoom level option (details)
84. CHG: adjusted tolerances (details)
85. CHG: added interactive to disp: (details)
86. Added time and memory output for CoDiPack. (details)
87. Make preaccumulation configurable. (details)
88. Create c-cpp.yml (details)
89. Update c-cpp.yml (details)
90. CHG: changed checks on flags (details)
91. CHG: need to initialize as 0 (details)
92. Update c-cpp.yml (details)
93. Update c-cpp.yml (details)
94. Update c-cpp.yml (details)
95. Update c-cpp.yml (details)
96. Update c-cpp.yml, add matlab (details)
97. Update c-cpp.yml (details)
98. Update c-cpp.yml (details)
99. Create github_linux_basic (details)
100. Update c-cpp.yml (details)
101. Update c-cpp.yml (details)
102. change the directory for CI files (details)
103. Update README.md (details)
104. Update README.md (details)
105. create badge for CI, add it to README (details)
106. CHG: minor (details)
107. BUG: forgot to close parenthesis (details)
108. CHG: upgrading PETSc in order to find latest ZLIB (details)
109. FIX: calculation of VAF based on mask in Tria.cpp (details)
110. CHG: trying to simplify CI (details)
111. CHG: trying to simplify CI (details)
112. CHG: getting PETSc from apt-get (details)
113. CHG: PETSc needs to be installed manually, but we can skip autotools and cmake (details)
114. BUG: fixing CI problem (details)
115. CHG: trying to fix CI (details)
116. CHG: trying to fix CI (details)
117. CHG: trying to fix CI (details)
118. CHG: trying to fix CI (details)
119. Update README.md (details)
120. NEW: added option 'quitonerror' for GitHub's CI (details)
121. CHG: fixing matlab tests in GitHub CI (details)
122. CHG: trying to fix CI with MATLAB (details)
123. CHG: trying to debug CI (details)
124. CHG: trying to add MATLAB tests (details)
125. CHG: fixing MATLAB (details)
126. load matlab action manually (details)
127. FIX: updated archive 540 (details)
128. CHG: checking env (details)
129. CHG: checking env (details)
130. CHG: checking env (details)
131. CHG: checking env (details)
132. CHG: checking env (details)
133. CHG: checking env (details)
134. set environment before running matlab (details)
135. Update c-cpp.yml (details)
136. Update c-cpp.yml (details)
137. Update c-cpp.yml (details)
138. Update c-cpp.yml (details)
139. CHG: fixed typo (details)
140. NEW: added a function that reads a geotiff and outputs x,y,data (details)
141. CHG: better check on METIS header (details)
142. CHG: removing PETSc from installation (details)
143. CHG: install openMPI (details)
144. CHG: figuring out open MPI (details)
145. CHG: mpi-include does not need -I (details)
146. CHG: scalapack is installed as part of open MPI (details)
147. CHG: do not assume that ParMETIS is installed if MUMPS is provided (details)
148. CHG: do not preload petsc files if petsc is not installed (details)
149. CHG: reverting to installing PETSc (details)
150. CHG: simplifying workflow and scripts (details)
151. CHG: change name (details)
152. CHG: removing MPICH from PETSc to speed up CI (details)
153. CHG: adding more libs to mpi (details)
154. CHG: forgot to change LD_PRELOAD (details)
155. CHG: adding flag to mpiexec to avoid openmpi error message about 'There are not enough slots available' (details)
156. CHG: do not make MeshPartition a template (details)
157. CHG: added example (details)
158. BUG: do not initialize codi_global if autodiff is false (details)
159. CHG: Added packages to UB CCR installation; do not compile MeshPartition if METIS is not available (details)
160. try to set two steps for the CI (details)
161. try to add cache (details)
162. try to set the path for cache (details)
163. try again with env variable (details)
164. update download path in artifact (details)
165. try to also cache matlab (details)
166. change mpi back to petsc version (details)
167. no need to cache matlab (details)
168. cache matlab (details)
169. try the uncompress path again (details)
170. download to /root (details)
171. try to use relative path (details)
172. add relative path (details)
173. change relative path again (details)
174. typo fixed (details)
175. update working dir (details)
176. activate compile (details)
177. put test back (details)
178. remove apt-get installed mpi (details)
179. try to create a matrix of test (details)
180. try matrix with string variables (details)
181. add codipack in CI (details)
182. try to fix codipack configure (details)
183. add gsl (details)
184. seperate basic and codipack (details)
185. Update common-workflow.yml (details)
186. only include ad tests for ccdipack (details)
187. fix bug in main-ci (details)
188. set different names for different runs (details)
189. add type of input.os (details)
190. try to cache src/c (details)
191. fix error in the test job (details)
192. remove cache src/c (details)
193. try petsc-3.20 for ad (details)
194. try to use env to set the id of cache (details)
195. try github.env (details)
196. try to fix bugs when using inputs in cache id (details)
197. fix bug in the if condition (details)
198. fix codipack (details)
199. try ad again (details)
200. CHG: added error message instead of just bypassing (details)
201. CHG: for macOS we now also need to add  -commons use_dylibs (details)
202. BUG: need to provide specific LD_FLAGS and tweak setCompiler.py to make it work on Sonoma (details)
203. CHG: cleanup (details)
204. remove with-petsc in codipack (details)
205. reduce matrix size for tests (details)
206. check spaces (details)
207. turn off codipack tests (details)
208. do not compress petsc/src/ to decrease the size of the artifact (details)
209. try to exclude petsc/src (details)
210. add gsl to codipack version (details)
211. CHG: calving rate in CalvingMIP use normal vector from the levelset (details)
212. Update README.md (details)
213. Update README.md (details)
214. Update action badge in README.md (details)
215. CHG: default md.levelset.reinit_frequency=10. Add more description to stabilization (details)
216. CHG: make two CIs separately for Ubuntu basic and codipack (details)
217. CHG: Update test540, due to update default reinit_frequency (details)
218. change the way to reuse workflow (details)
219. hard code the version of configure ISSM for now (details)
220. BUG: fix CalvingCalvingMIP in Penta (details)
221. fix bugs in action.yml (details)
222. separate prepare externalpackes and build (details)
223. test ISSM_DIR (details)
224. Update action.yml (details)
225. fix ISSM_DIR issue (details)
226. rerun CI, make input name shorter (details)
227. fix bug in action.yml (details)
228. CHG: update Archive540 (details)
229. rerun full CI (details)
230. fix bug in uploading artifact (details)
231. BUG: fix CalvingCalvingMIP (details)
232. BUG: recompile ISSM, update test540 Archive (details)
233. CHG: update Archive affected by levelset.reinit_frequency=10 (details)
234. add badges for Ubuntu Basic and CodiPack (details)
235. CHG: MATLAB -> Python and Javascript (details)
236. NEW: Add contrib/poinelli folder and include Paolo2023 interpolation script (details)
237. CHG: 1st edit of interpPaolo2023 (details)
238. CHG: taking care of paths with white spaces (details)
239. CHG: relaxed tolerances for test 541 (details)
240. CHG: Cleanup (details)
241. CHG: update to GEMB merge layers to parallel matlab version updates (details)
242. CHG: update GEMB tols for latest commit (details)
243. CHG: update remaining tols in windows and on git for GEMB (details)
244. CHG: Cleanup of configuration options (details)
245. BUG: Needed closing ;; (details)
246. CHG: Removing support for Android (details)
247. CHG: Synchronized enums after pull and merge (details)
248. BUG: Cleaned up configs (details)
249. BUG: Correcting env var substitution (details)
250. CHG: Cleanup (details)
251. CHG: Cleanup (details)
252. CHG: Moving standard env vars to issm_options for MSYS2 builds (details)
253. CHG: Cleanup; missing env var for Javascript build (details)
254. BUG: Fix for MSYS2 build (details)
255. merge actions to the workflow file (details)
256. use multiple lines for the yml (details)
257. try to set matlab outside (details)
258. fix missing type of common-workflow.yml (details)
259. fix bug in setting matlab root (details)
260. if cache not hit, then recompile (details)
261. CHG: added check to tell useers they cannot use both PETSc and CoDiPack (details)
262. BUG: Need to check if supplied gfortran and other libs are files for binaries builds (details)
263. CHG: added some explanation (details)
264. BUG: compute calving rate after extrapolation, so that the direction can be correctly computated in the inactive elements (details)
265. BUG: update archive 540,541,542 (details)
266. update 806,812 (details)
267. BUG: update archive 3203 (details)
268. CHG: Consolidation of C*OPTFLAGS to C*FLAGS; missing parmetis option (details)
269. BUG: Missing commit from pristine copy (details)
270. BUG: CXXFLAGS is not empty by default under clang (details)
271. BUG: Bad path to gfortran (details)
272. use json to handle matrix strategy (details)
273. CHG: Standardizing MATLAB and Python wrapper makefiles; adding more possible NumPy header file locations (details)
274. BUG: fixed memory leak (details)
275. BUG: Reverting changes for now to get versioned code working (details)
276. CHG: Standardizing MATLAB and Python wrapper makefiles (details)
277. BUG: Reverting (again, sigh) (details)
278. add \' in common_workflow (details)
279. Update common-workflow.yml (details)
280. Update common-workflow.yml (details)
281. Update common-workflow.yml (details)
282. update workflow using one file for one case (details)
283. CHG: MATLAB -> Python wrapper Makrfile.am; upgraded nodes to NumPy 2 (details)
284. ADD: output melt rate and its components in SHAKTI hydrology (details)
285. CHG: removing unused options (details)
286. CHG: Removed HTTPS protocol as checkout option; added troubleshooting note about HTTPS protocol error (details)
287. CHG: More clarification about HTTPS vs SSH (details)
288. NEW: added file to interpolate undercutting forcings from ISMIP6 data files (details)
289. CHG: added ref (details)
290. CHG: moving file to a better directory (details)
291. CHG: update ICESat2 ATL14/15 to version 4 (details)
292. CHG: closed contour should be option #1 (details)
293. CHG: minor estetics (details)
294. CHG:update script for TACC Frontera (details)
295. NEW: add option to include subglacial hydrology layer thickness in driving stress calculation of the SSA (details)
296. CHG: include stressbalance hydrology layer capability in python (details)
297. BUG: fix loading MEaSUREs velocity for individual glaciers (details)
298. CHG: update Jakobshavn MEaSUREs velocity to 2024 (details)
299. BUG: add if for more general model results (details)
300. BUG: generalize analyzeCalvingfront function (details)
301. CHG: second iteration of interpPaolo2023- add interpolation routine (details)
302. CHG: include temporal component in Paolo2023 melt rate (details)
303. NEW: added error message if cxxoptflags is provided (details)
304. BUG: python should not need MEXLIB, this introduces dependencies that are problematic (details)
305. BUG: bad python syntax (details)
306. CHG: simplifying hydro slope code (details)
307. NEW: nightly run test for stressbalance hydrology layer (details)
308. CHG: add interpolated dates as output (details)
309. CHG: do not use configure.py in installation script, call configure directly (details)
310. CHG: fixed RHS (details)
311. ADD: stanage cluster settings for Sheffield University Stanage HPC cluster (details)
312. BUG: ocean-averaged sea level loads (details)
313. NEW: retrieving change in gravitational acceleration from ESA solver (details)
314. CHG: fixed bad character from Surendra's commit (details)
315. CHG: fixing NR (details)
316. CHG: make python test identical to MATLAB test (details)
317. CHG: making python test identical to MATLAB (details)
318. ESA nightly updated with a new diagostic (details)
319. CHG: relaxing tolerances (details)
320. CHG: relaxing tolerances (details)
321. CHG: relaxing tolerances (details)
322. CHG: New archives; changes to ext pkg install scripts and Makefiles as needed to account for new changes to macOS linker (details)
323. Update .gitignore (details)
324. CHG: Updated PETSc version (details)
325. CHG: Renaming of GDAL install scripts (details)
326. CHG: Fixes for latest PETSc version install script (details)
327. BUG: Corrected install script (details)
328. CHG: Adjusted tolerances (details)
329. CHG: Disabling test 362 for Silicon-based Mac as it has large errors (details)
330. CHG: Adjusted tolerances (details)
331. CHG: Adjusted tolerances (details)
332. CHG: Corrected install script name (details)
333. Update .gitignore (details)
334. CHG: moving functions around (details)
335. ADD: mac basic CI (details)
336. CHG: Love core accuracy and stability improved. NEW: Complex solution enabled (details)
337. CHG: Love core accuracy and stability improved. NEW: Complex solution enabled (details)
338. fixing merging error in Makefile.am (details)
339. CHG:cleaned up Love core for final version (details)
340. FIX: fixing recast of int/double to double precision for some compilers in Love core (details)
341. FIX: cleaning up love core (details)
342. CHG: Bug in Python wrapper; cleanup (details)
343. CHG: Updated gitignore; removed test 362 from test suite for distributables on Silicon-based Macs (details)
344. CHG: Committing local changes from UB CCR (details)
345. Update test2085.m (details)
346. Update test2084.m (details)
347. CHG: minor edit, include larsen-thwaites hosts to interpStal2020 (details)
348. CHG: Older versions of PETSc use config/configure.py (may need to change others) (details)
349. CHG: Updates for saving model for JavaScript (details)
350. CHG: Disabling guts of some savemodeljs methods until they are added to issm.js (details)
351. CHG: Turning off development mode so we can generate new binaries automatically for use on VESL (details)
352. CHG: Fixes for JavaScript API and Emscripten compilation (details)
353. CHG: no error compiler flag still needed (details)
354. CHG: More JavaScript API fixes; compiler options to disable wasm (details)
355. CHG: Make sure optimization is use for JavaScript binaries, but that certain functions are not optimized out (details)
356. CHG: Emscripten does not like opt flag (details)
357. BUG: Issue was missing quote, not flag (details)
358. CHG: Added missing exported functions for JavaScript binaries (details)
359. CHG: Adjusted tolerances (details)
360. CHG: Fixes for outputting transient class to JavaScript model (details)
361. BUG: gmsl was not the same as bslc. Now fixed. test2011 modified. (details)
362. CHG: Updated archives (details)
363. FIX: Bug in frequency love number output format when np>1; CHG: updated love core tests and archives (details)
364. FIX: love core: recast some integers to doubletype to help some mac compilers (details)
365. FIX: Missing synched enum files for Love core update (details)
366. Update test2075.m (details)
367. Update test2071.m (details)
368. CHG: Adjusted tolerances (details)
369. CHG: Fixes for love numbers and related tests under Python API (details)
370. BUG: Fixed parens (details)
371. CHG: Do not assume that system/subprocess call will use bash as shell; cleanup (details)
372. CHG: Translated test2085 from MATLAB -> Python (details)
373. fix penta section normals and remove duplicate code (details)
374. fix indentation (details)
375. CHG: Adjusted tolerances; do not run test 2085 on Silicon (details)
376. CHG: Adjusted tolerances (details)
377. remove unused indices in  Tria::NormalTop (details)
378. CHG: Updated path to gfortran (details)
379. CHG: extract AD cost functions (details)
380. CHG: Modified all basic external package installation scripts to use developers' download links, where possible (details)
381. CHG: Check if LDFLAGS is set (details)
382. CHG: Updated all install scripts for external packages needed for extended capabilities (details)
383. CHG: Uploading Chaco source to repository as it does not download properly from Sandia's GitHub repo (details)
384. CHG: Moved Adjoinable MPI source to repo because developer's Mercurial repo appears to be down (details)
385. CHG: More external package fixes (details)
386. CHG: Adjusted tolerances (details)
387. CHG: Need to ignore download script in directory to properly download datasets (details)
388. CHG: Rolling back to HDF5 1.14.3 as newer versions do not properly compile on Intel-based Macs (known issue) (details)
389. BUG: Expode hidden NumPy symbols in newer versions; cleanup (details)
390. CHG: Adjusted tolerances (details)
391. CHG: Fix bug in src/c/analyses/SmbAnalysis.cpp (details)
392. CHG: Update SmbSEMIC modules (details)
393. ADD: MATLAB - interpolate netcdf file with using xarray in python. (details)
394. CHG: Resolve memory leakage in SEMIC. (details)
395. CHG: model.refine MATLAB -> Python; clean up (details)
396. BUG: Bad indexing of bamgmesh out (details)
397. CHG: Catch unsupported draw function; clean up (details)
398. CHG: Adjusted tolerances (details)
399. FIX: Output of Tidal love numbers in Love core (details)
400. CHG: do not assume hemisphere (details)
401. BUG: if minor version of python is greater than 9 the last digit was removed. Now fixed (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. (details)
403. ADD: flag `with_matlab` in CI with matlab (details)
404. CHG: input.with_matlab -> input.interface (details)
405. ADD: ubuntu python test (details)
406. ADD: install python-dev (details)
407. ADD: python tests (details)
408. BUG: fix .yml (details)
409. CHG: python path for CI (details)
410. BUG: fix python path (details)
411. CHG: get python path from python action (details)
412. CHG: use env (details)
413. Update ubuntu-python.yml (details)
414. CHG: output python path after setup (details)
415. change to v5 python action (details)
416. update python path (details)
417. fix bug in python_version (details)
418. CHG: wrong place holder for string (details)
419. currentlt test with only python (details)
420. add libpython (details)
421. update CI (details)
422. update CI (details)
423. set python path (details)
424. update numpy path (details)
425. check the folder (details)
426. add path to numpy (details)
427. add path to numpy (details)
428. update numpy (details)
429. add test numpy (details)
430. print more (details)
431. look into _core (details)
432. add python to test (details)
433. add netCDF4 (details)
434. add source ISSM (details)
435. ADD: ubuntu python CI test (details)
436. Revert "add python CI" (details)
437. Revert "Revert "add python CI"" (details)
438. CHG: Eased tolerances (details)
439. CHG: Moving certain external packages to new repo (details)
440. ADD: `cutoff` option in flowlines.m (details)
441. BUG: revert issmscpin to previous version (details)
442. CHG: adding dynamic function name (details)
443. CHG: automatically remove checkpoint file once done to save disk space (details)
444. CHG: Cleanup; MATLAB -> Python; documentation (details)
445. CHG: Merging Inwoo's fix for MATLAB + Python APIs with minor changes (details)
446. BUG: should not capitalize Matlab and Python so that they can be picked up by modules (details)
447. BUG: Lowercasing JavaScript (details)

Update README.md

Update README.md

CHG: adding other way to download ISSM from GitHub

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

CHG: Adjusted tolerances

Delete README

CHG: upgrading to latest PETSc version

BUG: Path to libgfortran

CHG: Need libgcc in package

BUG: Path fixes

BUG: Not catching runme error; 'exclude_name' option no longer exists

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

BUG: Incorrect file name

CHG: Virtual environment not preserved in called script

CHG: removing old scripts

CHG: moved up one directory and removed  from version check

CHG: adding more files to gitignore

CHG: Adjusted tolerances

CHG: Minor changes to test fixes to GitHub Webhook -> Jenkins

CHG: removing reference to cshrc, replacing by zshrc

CHG: Adjusted tolerances

CHG: Removing Cmake to avoid conflicts with standalone copy

BUG: Removed 'command'

ADD: Missing empty Models/ dir

Update of .gitignore.

Moved all CoDiPack specific functions to CoDiPackGlobal.h.

CHG: Add default location for libgfortran on Mac to rpath

CHG: adaptive time stepping needs vz in 3d

CHG: throw error message if FCT in 3d

CHG: Use git now to get changes and determine installation type

CHG: minor, testing to see if jenkins will recompile

CHG: forgot to change path to m/mesh/planet

CHG: Additions to ignore list

Create codeql.yml

Adding code scanning for security vulnerabilities

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>

CHG: Fixes for gfortran path in rpath; new config for CodeQL

Update codeql.yml

Update codeql.yml

Update codeql.yml

Update codeql.yml

CHG: Disabling wrappers on CodeQL build

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

Delete codeql.yml

Deleting for now until external packages can be offloaded to package managers.

CHG: Adding whitespace and rerunning jobs

CHG: removing double blank lines

CHG: Adjusted tolerances

CHG: Updates to UB CCR config; changed path of gmshplanet.py

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

CoDiPack type can be defined during the configuration.

BUG: Need to update previous commit every time we run

CHG: Outstanding commit and test fix to git change polling

Extracted common computation from StressbalanceAnalysis.cpp.

Added Preaccumulation helper for sparse row assembly.

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

CHG: vertical speed needs md.basalforcings.perturbation_melting_rate

CHG: vertical speed needs md.basalforcings.perturbation_melting_rate

CHG: missing -fPIC install-linux.sh

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

CHG: removing SLEPSC and ADIC2 that we have never used

CHG: adding common factor to KMatrices StressBalance

CHG: do not extrude lat/lon if undefined

CHG: refine should deal with lat/long as well

BUG: output is md2 and not md

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

CHG: New cluster class for submitting jobs to UB CCR; typos

CHG: adding factors to analysis

CHG: added Data directory for examples

CHG: adding factors in analysis

CHG: added factors in analysis

CHG: fixed problem with Glads

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

CHG: renaming Viscous Budd

CHG: Adjusted tolerances

CHG: multithreading ContourToNodes

BUG: mexPrintf is NOT thread safe and crashes. Replace by printf

CHG: Temporary fix for not being able to connect via port 22

CHG: Need P instead of p option

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

CHG: minor changed ISSM description

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`

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

CHG: use mapping toolbox map if Googlemaps is not available

CHG: fixed zoom level option

CHG: adjusted tolerances

CHG: added interactive to disp:

Added time and memory output for CoDiPack.

Make preaccumulation configurable.

Create c-cpp.yml

Update c-cpp.yml

CHG: changed checks on flags

CHG: need to initialize as 0

Update c-cpp.yml

Update c-cpp.yml

Update c-cpp.yml

Update c-cpp.yml

Update c-cpp.yml, add matlab

Update c-cpp.yml

Update c-cpp.yml

Create github_linux_basic

Update c-cpp.yml

Update c-cpp.yml

change the directory for CI files

Update README.md

Update README.md

create badge for CI, add it to README

CHG: minor

BUG: forgot to close parenthesis

CHG: upgrading PETSc in order to find latest ZLIB

FIX: calculation of VAF based on mask in Tria.cpp

CHG: trying to simplify CI

CHG: trying to simplify CI

CHG: getting PETSc from apt-get

CHG: PETSc needs to be installed manually, but we can skip autotools and cmake

BUG: fixing CI problem

CHG: trying to fix CI

CHG: trying to fix CI

CHG: trying to fix CI

CHG: trying to fix CI

Update README.md

Added commit notes (and testing fixes for Jenkins workflow)

NEW: added option 'quitonerror' for GitHub's CI

CHG: fixing matlab tests in GitHub CI

CHG: trying to fix CI with MATLAB

CHG: trying to debug CI

CHG: trying to add MATLAB tests

CHG: fixing MATLAB

load matlab action manually

as suggested https://github.com/matlab-actions/run-command/issues/53

FIX: updated archive 540

CHG: checking env

CHG: checking env

CHG: checking env

CHG: checking env

CHG: checking env

CHG: checking env

set environment before running matlab

Update c-cpp.yml

Update c-cpp.yml

Update c-cpp.yml

Update c-cpp.yml

CHG: fixed typo

NEW: added a function that reads a geotiff and outputs x,y,data

CHG: better check on METIS header

CHG: removing PETSc from installation

CHG: install openMPI

CHG: figuring out open MPI

CHG: mpi-include does not need -I

CHG: scalapack is installed as part of open MPI

CHG: do not assume that ParMETIS is installed if MUMPS is provided

CHG: do not preload petsc files if petsc is not installed

CHG: reverting to installing PETSc

CHG: simplifying workflow and scripts

CHG: change name

CHG: removing MPICH from PETSc to speed up CI

CHG: adding more libs to mpi

CHG: forgot to change LD_PRELOAD

CHG: adding flag to mpiexec to avoid openmpi error message about 'There are not enough slots available'

CHG: do not make MeshPartition a template

CHG: added example

BUG: do not initialize codi_global if autodiff is false

CHG: Added packages to UB CCR installation; do not compile MeshPartition if METIS is not available

try to set two steps for the CI

try to add cache

try to set the path for cache

try again with env variable

update download path in artifact

try to also cache matlab

change mpi back to petsc version

no need to cache matlab

cache matlab

try the uncompress path again

download to /root

try to use relative path

add relative path

change relative path again

typo fixed

update working dir

activate compile

put test back

remove apt-get installed mpi

try to create a matrix of test

try matrix with string variables

add codipack in CI

try to fix codipack configure

add gsl

seperate basic and codipack

Update common-workflow.yml

only include ad tests for ccdipack

fix bug in main-ci

set different names for different runs

add type of input.os

try to cache src/c

fix error in the test job

remove cache src/c

try petsc-3.20 for ad

try to use env to set the id of cache

try github.env

try to fix bugs when using inputs in cache id

fix bug in the if condition

fix codipack

try ad again

CHG: added error message instead of just bypassing

CHG: for macOS we now also need to add  -commons use_dylibs

BUG: need to provide specific LD_FLAGS and tweak setCompiler.py to make it work on Sonoma

CHG: cleanup

remove with-petsc in codipack

reduce matrix size for tests

check spaces

turn off codipack tests

do not compress petsc/src/ to decrease the size of the artifact

try to exclude petsc/src

add gsl to codipack version

CHG: calving rate in CalvingMIP use normal vector from the levelset

Update README.md

Testing Jenkins status badge

Update README.md

Update action badge in README.md

CHG: default md.levelset.reinit_frequency=10. Add more description to stabilization

CHG: make two CIs separately for Ubuntu basic and codipack

CHG: Update test540, due to update default reinit_frequency

change the way to reuse workflow

hard code the version of configure ISSM for now

BUG: fix CalvingCalvingMIP in Penta

fix bugs in action.yml

separate prepare externalpackes and build

test ISSM_DIR