Fixup/merge 803 into next

Merge the 8.0.3 release into next, fixing conflicts. Replaces discussion PR #251

• Make sure we respect read-only petsc vectors

• Update doi in README

  Note: this is now the "all versions" doi, rather than the "latest version". The all versions link resolves to the latest version on Zenodo, but the link won't need updating when new versions are released.

• Add explicit targets to the generated source files

  This helps avoid issues when the dependency file exists but the $(GENERATED_SRC_DIR) doesn't. For example if a user has done make clean cleandirs, prior to this patch a subsequent make gs2 would fail (if not using ONE_STEP_PP).

• Avoid requiring SLEPC_ARCH to be set for eigensolver builds.

  This is a non-standard flag that is used where PETSC_ARCH should really be used. In the future we can remove references to SLEPC_ARCH, but we keep for now to maintain compatibility.

• Bug fix for fortdep -- allow it to recognise abstract interface

• gs2_save.fpp edited online with Bitbucket to fix bug in gs2_save -- restart files incorrectly tried to save and restore the last but two timestep size, resulting in potentially undefined coefficients for restarted runs.

• Allow OpenMPI to oversubscribe on GitLab CI

• Make smart default for write_fluxes

• Ensure we increment nout before leaving the diagnostics routine

  This fixes a bug with runs that disable the majority of the diagnostic output. The time dimension was remaining length 1, meaning the always present time dependent data only ever contained the last time point.

• Pull out formatting of git log into separate function

• Generalise the changelog generator to work between any two commits

• Fix Jenkins checkout due to update of plugin

• Minor bug fix, ensures that building auxiliary programs (such as dump_response etc.) will create bin (or more strictly $(BINDIR) ) if it doesn’t exist.

• Bug fix for dump_response program

• Ensure dump_response has the fft dependency

• Use default exit reason

• Merged in bugfix/stop-file-test-exit-code (pull request #204)

  Use exit code in job manage test

  Approved-by: Peter Hill peter.hill@york.ac.uk Approved-by: David Dickinson d.dickinson@york.ac.uk (cherry picked from commit 795a1610f7d4546e6cd5d562a265b73df526a3dd)

• Ensure exit_reason file is removed before test

• Manipulate exit_reason file on proc0 only

• Allow checkstop to manipulate state%exit_code

• Provide exit code for exiting normally on completing nsteps

• Fix style

• Make coment FORD style

• Append, not overwirte, the exit_reason file

• Change EXIT_NO_REASON to EXIT_NOT_REQUESTED

• Merged in bugfix/fix_jenkins_netcdf_dependency_changing (pull request #238)

  Try switching netcdf source to github from unidata ftp

  • Try switching netcdf source to github from unidata ftp

  • Fix directory names

  • Remove erroneous v

  • Fix other builds

  • Try updating to the latest netcdf versions

  • Revert "Try updating to the latest netcdf versions"

    This reverts commit fd3f8de2261e1528d8a46475ae4ccdbd067af74e.

    Requires changes to Jenkins makefile etc. which we can reserve for a more significant release.

  Approved-by: Joseph Parker joseph.parker@stfc.ac.uk Approved-by: David Dickinson d.dickinson@york.ac.uk

• Add smart default for write_nl_flux in old diagnostics

• Don't try to specify the exit_reason syntax

• Update the utils version

• Move test to after simulation finished

• Replace system with execute_command_line in tests

• Rename theta_grid:eps to theta_grid:eps_trapped to distinguish this from the related theta_grid_params:eps used by the s-alpha model

• Update netcdf output with eps_trapped

• Add long_name attribute for eps in netcdf output

• Update new diagnostics for change of name from eps to eps_trapped

• Fix typo in attribute

  skip ci

• Correct typo "CPP Plasma" to "CCP Plasma"

• Reorder statements to ensure we set variables based on the input values rather than the default values

  Both fft_use_wisdom and fft_measure_plan are set in the init_gs2_layouts call

  Backport from PR #164

• Update for changes in utils

• Update 8.0.3-RC latest versions of externals

  This commit updates utils to include:

  • bugfix/single-precision-timing (pull request #30)

  • feature/write-exit-reason (pull request #32)

  • bugfix/guard_against_empty_send_in_redistribute (pull request #31)

  and Makefiles to include:

  • bugfix/marconi-hdf5 (pull request #30)

  • bugfix/archer-build_gs2 (pull request #31)

  • fedora_makefile_parallelnetcdf_fix (pull request #29)

• feature/store-verbosity-backwards-compatible (pull request #36)

• feature/update-exit-codes (pull request #33)

• Update CITATION.cff and README for 8.0.3

• Update to release versions of utils and Makefiles

• Fix job manage test for changes in exit_code

• Update utils again to include the updated changelog

• Update CHANGELOG.md

• Update changelog

• Put 8.0.3 in RELEASE file and make sure Makefile parses this as a string

• Release date: 10/02/20