Keeping branch78 up-to-date

* Removing --dereference stuff in tar creation (#78)

* Printing profiler_hash_ for debugging (#78)

* Turning tests off temporarily (#78)

* Seeing if profiler entry exists after emplace (#78)

* Adding debug flags to system test compile step (#78)

* Trying different emplace method (#78)

* Replacing emblace with insert (#78)

* Running system tests inside build workflow (#78)

* Reverting previous change and adding sudo installs back to system.yml (#78)

* Adding sudo installs to build.yml too (#78)

* Testing alternative runner version (#78)

* Changing compiler version in system.yml (#78)

* Explicitly setting c++ standard to 17 (#78)

* Correcting job dependencies in cov.yml (#78)

* Putting lcov install before build in cov.yml (#78)

* Syntax error in yml (#78)

* Invalid line i cov.yml (#78)

* Specifying bash shell when installing lcov (#78)

* Adding conda init line - getting shell related error (#78)

* Trying to restart shell from command line (#78)

* Slight change to conda syntax (#78)

* Different command for installing lcov (#78)

* Testing to see if just g++ command works when compiling sys test (#78)

* Syntax error in cmake config (#78)

* Erroneous " (#78)

* Adding checkout step (#78)

* Specifing BUILD_TYPE env variable (#78)

* Grouping lcov/genhtml commands and specifying shell (#78)

* Testing activating conda inside lcov step (#78)

* Changing how lcov is used and adding deactivate step (#78)

* Re-trying conda activate (#78)

* Adding conda activate to lcov run step (#78)

* Testing pip install of Lcov (#78)

* Removing conda commands (#78)

* Separating out lcov commands (#78)

* Ensuring correct python version before pip install (#78)

* Altering python/pip/lcov syntax (#78)

* Removing python -m from lcov run step (#78)

* Using python module venv (#78)

* Missing flag from conda install (#78)

* Adding ls to find where lcov installed (#78)

* Trying a pip install over conda (#78)

* Error in pip install syntx (#78)

* Adding shell to install lcov step (#78)

* Added shell specification to wrong step (#78)

* Removing error prone line from install step (#78)

* Re-trying conda (#78)

* Removing reduntant comments (#78)

* Too many hyphones in conda flag (#78)

* Altering conda flag order (#78)

* Specifying where conda can find lcov (#78)

* Adding shell keyword to lcov step (#78)

* Running conda init after lcov install (#78)

* Activating env using source (#78)

* Trying conda init before conda activate (#78)

* Using a second conda init (#78)

* Finding base conda env (#78)

* Running source on conda.sh before activating (#78)

* Uncommenting rest of workflow (#78)

* Installing/using lcov in same step (#78)

* Changing name of coverage report artifact (#78)

* Deploying to pages from gh-pages branch (#78)

* Adding git config info (#78)

* Adding '-a' to git commit (#78)

* Deploying from actions (#78)

* Deploying from branch again, and creating conda env from-file (#78)

* Extra steps in push (#78)

* Changing environment.yml to a .txt (#78)

* Mistake in conda create line (#78)

* Specifying lcov dependency in conda create line rather than in environment file (#78)

* Ammending conda crate command (#78)

* Adding ls and git status steps to debug empty commits (#78)

* Re-writing push step in cov.yml (#78)

* Forgot remote update command (#78)

* Trying to print coverage overview upon PR creation (#78)

* Trying to use GD.pm library (#78)

* Adding GD download step (#78)

* Changing ubuntu version (#78)

* Switching to gcovr over lcov

* Yaml syntax error when declaring step envs at gcovr stage (#78)

* Changing filename to index.html (#78)

* Using rm not git-rm (#78)

* Updating push to gh-pages step (#78)

* Removing env variables from gcovr step (#78)

* Adding 'a' flag to git commit (#78)

* Trying git-rm aswell as rm (#78)

* Specifying gcov version in gcovr command (#78)

* Adding in another 'git reset' (#78)

* Running git-rm again before rm (#78)

* Updating git rm command (#78)

* Explicitly setting obj dir path for gcovr (#78)

* Error in gcovr syntax (#78)

* Using correct gcovr flags (#78)

* Removing build type from cmake steps (#78)

* Setting default g++ version to 11 to hopefully match gcov (#78)t:

* Removing initial 'sudo update-alternatives' (#78)

* Only specifying g++-11 as opposed to 11.2.0 (#78)

* Changing to g++-10 and remove alternatives command (#78)

* REverting back to g++-11 (#78)

* Adding update-alternatives command back in to set default to already-installed 10.3.0 (#78)

* Seeing if runner accepts g++-9/10 path (#78)

* Removing one of alternatives lines (#78)

* Adding gcov under slave flag (#78)

* Update comments and properly set flags (#78)

* Printing summary on PR comments (#78)

* printing text summary to pull request comments

* printing text summary to pull request comments

* Comment/documentation changes and adding -s flag to html-output gcovr step (#78)

* Format changes and adding env.CXX back to doc workflow (#78)

* adding covereage badge to README

* Adding steps to automatically push README changes (#78)

* Adding full path to brief-summary.txt (#78)

* trying again with redirecting --print-summary to a .txt

* Touching brief-summary.txt first (#78)

* Was putting info into brief-summary.txt in the wrong step (#78)

* Syntax error in sed command (#78)

* Update README.md

* Adding {} around BADGE_URL and WORKFLOW_URL (#78)

* Update README.md

* Removing quotation marks around BADGE declaration (#78)

* Update README.md

* Defining BADGE with env: syntax (#78)

* Added single quotes around BADGE (#78)

* Using different syntax to correctly determine colour of badge (#78)

* Changing sed delimiter to # to avoid multiple '/' confusion (#78)

* Update README.md

* Using '>=' over '-ge' in determine-colour step (#78)

* Update README.md

* New coverage workflow with neater overall structure (#78)

* Missing out cov.txt [temporairly a .txt] from prev commit (#78)

* Update README.md

* new coverage workflow that splits into 3 seperate jobs (#78)

* Syntax error in if statement (#78)

* typo (working-directiry) (#78)

* Activating correct conda environment (#78)

* fixing gcovr output flag (#78)

* correcting path to html artifact (#78)

* Calling checkout action in all subsequent jobs (#78)

* Update README.md

* Creating build directory in deploy_pages job

* Update README.md

* Workflow test branch (#9)

* added title to PR comment

* Update README.md

* fixing path to report.txt

* restructuring setup of OPTIONAL_ARGS

* removing plastic style from coverage badge

---------

Co-authored-by: github-actions[bot] <github-actions[bot]>

* Update README.md

* Update README.md

* Seperating install step into different workflow (#78)

* Making install step depend on build (#78)

* Adding build type environment variable to install workflow (#78)

* Running ls in system.yml after download to see what files were found (#78)

* Fixing tar's file not found error (#78)

* Moving install tar to build dir before unzipping (#78)

* Unzipping install tar in root dir instead of build (#78)

* seeing if mpi/omp install is required before system tests (#78)

* adding clang compiler (#78)

* error in yaml syntax (#78)

* adding default shell to individual jobs (#78)

* changing name of 'artifact' matrix (#78)

* Update test.yml

* Update system.yml

* Update test.yml

* removed dyn-build and sta-build env variables (#78)

* ammending build directory name declaration at start of build (#78)

* ammending build directory name declaration at start of build again (#78)

* Running ls before unzipping artifact (#78)

* Different command for unzipping all tar.gz in current dir (#78)

* Adding -n1 flag to xargs tar step (#78)

* Install workflow finished off and testing subsequent download in system.yml (#78)

* Fixing yaml syntax errors and ammending one of the input descriptions (#78)

* Reordering flags at cmake install step (#78)

* Switching to find's -exec -c instead of xargs (#78)

* Explicitly setting default shell to bash (#78)

* Running tar from root dir in install workflow (#78)

* Compiling and running system test using both compilers (#78)

* Updating ld path before system testing (#78)

* Updating system test permissions before running (#78)

* Compiler config done at new top-level workflow (#78)

* Fixing 'aritfact' typo

* Adding checkout actioin to unit.yml (#78)

* Artifact upload failure, retrying

* Additional workflow that calls top.yml (#78)

* Changed input. to inputs.[] (#78)

* Nesting workflows within each other (#78)

* Moving system to avoid exceeding nest limit (#78)

* Removing artifact inputs from build.yml (#78)

* Fixing working dir when running ctest (#78)

* New deploy_tests.yml and recallables altered accordingly (#78)

* Changing 'bool' to 'boolean' (#78)

* Fixing wrong inputs to system (#78)

* Fixing formatting of matrix environment variables (#78)

* Fixing formatting of matrix environment variables again(#78)

* Trying again with matrix env variables (#78)

* Adding appropriate backslashes to json env variable (#78)

* Removing fromJson function from matrix setting (#78)

* Trying single quotes around matrix declarations (#78)

* Returning to fromjson method for matrix parsing (#78)

* Reformatting json matrix declaration (#78)

* Testing if only having matrix defined solves json parse problem (#78)

* Using single quotes around the compiler and libs matrices (#78)

* Definding compiler and libs matrices in job instead of as environment variables (#78)

* Update deploy_tests.yml

* Putting Json into variable before github output (#78)

* Altering set-output step (#78)

* Potential fix if problem is caused by multi-line github outputs (#78)

* Removing json stuff to test general workflow (#78)

* Typo in install.yml (#78)

* Removing redundant xargs command (#78)

* Adding verbose flag to cmake (#78)

* Removing config cmake flag for now (#78)

* Trying 'make install' over 'cmake --install' (#78)

* Running ls at cmake install step (#78)

* Merging build and install workflows (#78)

* Removing install from dependency from system test job (#78)

* Adding ls before and after tar step in system.yml (#78)

* Unzipping tar in correct place in system.yml (#78)

* Erroneous line in system (#78)

* Changing system to ubuntu latest (#78)

* Correcting path to profiler libs in system test (#78)

* Adding PROF path to ld lib path and adding echo sanity check (#78)

* Showing contents of installed dirs in system.yml (#78)

* Removing leading '/' from install dir path (#78)

* Adding leading fowardslashes back to install path (#78)

* Adding '-C /' when unzipping install dir and trying ternary in job name (#78)

* Updating ld path before compiling system test (#78)

* Updating name of system test job too (#78)

* Adding omp lib install before system testing (#78)

* Fixing unit.yml unzip step (#78)

* Printing cpp compiler version before sys test (#78)

* Adding verbose compilation for system tst (#78)

* Trying env variable matrix trick again (#78)

* Defining matrices with text not json (#78)

* Dynamic matrix method with no | in env variable (#78)

* Removing coverage and doc changes from this issue (#78)

* Fixing workflow depedencies at top level (#78)

* Adding fortran system test (#78)

* Adjusting system tests and associated workflow (#78)

* Adding f90 sys test (#78)

* Adding verbose output to mpif90 (#78)

* Changing to mpifort (#78)

* Specifying compiler in mpicxx and mpifort commands (#78)

* Fixing yml syntax error in system.yml (#78)

* Tidying up comments (#78)

* Added draft readme for the system testing (#78)

* Finishing touches to new readme (#78)

* Removing -lprofiler flag from f90 sys test (#78)

* Seeing if lprofiler_c needed (#78)

* Reording flag when compiling sys test (#78)

---------

Co-authored-by: github-actions[bot] <github-actions[bot]>

… in different branch (#78)

…o mpifort (#78)

…iable (#78)