* Add a Dockerfile for testing
* Switch to FETK 1.8.1 and cleanup of FETK build
* New versions of geoflow and pb_solvers for testing
* Simplified Dockerfile
* Fixing a bug for getting FETK in windows
* A little more cleanup
* Update Geoflow git tag for new release
* Test building static libs
* Update pb_solvers commit to most recent release
* Update to the latest release of pb_solvers
* Separate configure/build stage for linux and mac
* Update the build script
* Update .build.sh
* Add libopenblas-dev to the linux dependencies
* Add tmate session to debug windows packing issue
* Debugging the windows packaging failure
* Maybe it's a shell problem?
* A little more debugging of the windows cpack failure
* Separate package creation for windows to get around the cmake/chocolatey conflict
* Best if I use the proper syntax . . .
* Typo fix
* Remove debugging modifications
* Cleanup of the build workflow
* Removing AppVeyor build and badge (Windows build is now done in GitHub Actions)
* Update .build.sh
* Update index.rst
* Use software-properties-common to get python3 in the Dockerfile
* Change directory into build before running tests
* Tests don't need to be their own project
* Turning off testing and building in the build script for GHA test purposes
* Check that the geoflow tests are working with this dev branch of geoflow
* Updated to released version of Geoflow
* First attempt at a test job
* Added required dependencies for apbs linkages
Added running of an example
* Fix directory
* Fixing the path to the downloaded artifacts
* Testing for mac and windows requirements
* Syntax fix
* Mod to check mac prereqs; note about windows prereqs
* (temporarily) remove some slow tests
* Add mac prereqs for test job
* Add component specification to all install lines and use to control the package creation
* Add tmate back in for now
* Enable the build of iAPBS, with a few changes to how it's done to make sure it links into apbs
* Minor logic fix
* Removed the include/Eigen directory. It seemed to be confusing the Windows build.
* APBS needs to know where Eigen3 is
* Geoflow updated to deconflict class name with FETK/mc. Build of Geoflow updated, with APBS dependency moved into APBS. Build in src is updated accordingly.
* Updating Geoflow to the new release
* Move configure_file for apbscfg.h down in the CMakeLists.txt so that it has all of the necessary info
* Enable tmate session in windows to check linking for a successful windows test
* Potential fix to incorrect arguments in calls to preRefineFE and postRefineFE
* tmate session on test job failure
* Temporarily include headers and libraries in the zip file
* Remove hardcoded apbscfg.h and maloccf.h
* Add windows dependencies to the test run
* echo the PATH variable so we can check to see if the vcpkg libraries are findable
* Add the vcpkg bin directory to the path
* Use variable ENABLE_FETK instead of FETK_ENABLED to control building with FETK
* Renaming some build variables, per some TODOs in apbscfg.h.in
* Switch use tests to using run_selected_tests.sh
* Forgot to include the script to run
* Fix permissions for the examples scripts by using the USE_SOURCE_PERMISSIONS argument
* Added CHANGELOG.md and .extract_section.sh script (copied from FETK implementation)
* Add release.yaml and release artifacts (copied implementation from FETK)
* Update version to 3.3.0.alpha
* Fix variable for tag name
* Move release of artifacts to a separate job
* Was missing the step id
* Also had the wrong id here
* Oy, hopefully the last thing I missed
* Fixing the logic of having a separate publish release job
* Reworking how the package filenames are handled
* Trigger a new build
* Attempting fix to issue with retrieving and storing the zip file name
* Use expression instead of shell expansion
* Workflow cleanup
* Back-filling the changelog's previous entries from the GitHub Releases
* Git tags are prepended with a v
* Consolidating cmake settings
* Turn PYGBE on, and a couple of associated fixes
* Stripping out Tinker support
* Enable debugging in workflows
* Add python3 to mac and linux dependencies
* Shouldn't need `vcpkg integrate install` in the use test
* Need the python library in linux
* Update .extract_section.sh to handle the rst file releases.rst
* Test conversion of release rst to md
* Oops, docker actions are linux only
* One more linux-only restriction
* Build directory and install directory check for already-set values in .build.sh
* Do initial work to accommodate building the NSIS file
* Fixing typos from the last commit
* Actually process and attempt to use the NSIS file
* Separate NSIS build into a separate step to see what's causing the job to hang
* Fixing step id
* Move release extraction to release.yaml and use setup-python@v2 for python installation
* Setup to do a little debugging
* Removing the use of git submodule updating in the build
* Remove NSIS use test for now
* Removing the use of NSIS packaging
* Setup a tmate session for container testing
* Do a test of running a windows container
* Another container test
* One more docker container attempt
* Some documentation updates
* Return to the regular build
* Copying in dependency libraries
* Fixing a library name
* Option for a fully static build (does not work when OpenMP is used)
* Try out a fully static build without OpenMP
* Working on diagnosing static build
* Two bug fixes
* Using a test version of FETK to try a static build
* YAML fix
* Not sure why it's behaving as if a git hash matches a version tag, but for now we'll force it to use the git hash FETK download
* Compile flag needed for linux, at least
* Modifying dependencies that are installed
* Updated pb_solvers for testing the use of the pbsolvers namespace; Fixed inclusion of BLAS.
* Try removing specification of compiler
* Update pb_solvers for wrapping fixes
* Enable tmate on failure
* Another pb_solvers update
* Remove openmp; I think it's screwing up finding OpenBLAS on Ubuntu
* Missing headers were causing a problem on macos
* Let's see if using libopenblas-serial-dev fixes the finding-openblas problem on linux
* Avoid some cmake warnings and use an updated pb_solvers
* Maybe the final fix to have things working? Updating pb_solvers.
* New version of FETK
* Including some dependencies
* Added finding AMD
* git-ignore all directories that start with build
* FETK is now treated as a required dependency, much earlier in the build
* These find modules are now handled by FETK
* Updating how dependencies are searched for and handled
* Use GNU standard install directories
* Getting things in the right order
* Remove the use of EXECUTABLE_OUTPUT_PATH and LIBRARY_OUTPUT_PATH
* I think we deleted nanoshaper when we cleared the temp directory, so don't do this
* Install metis manually on mac and linux to get static libs
* Separate tar and gunzip calls
* Sudo make install on linux
* Fixing the TABIPB library install location and NanoShaper duplicate install issues.
* Adding Python for linux
* Add a global static-build option and set the MSVC runtime library variable to hopefully perform a static build in windows
* Run tmate for windows to check linking
* Some anticipation of the types of jobs that will be run
* Adapt to changes in FETK
* Update FETK hash
* Remove extra line and print umfpack libraries
* Verbose build, for now
* Debugging messages
* Update FETK
* Need libumfpack for the windows use tests. And use tmate if the build fails.
* Remove the link search variables
* Enable PYGBE in Windows and add Python to use tests in all builds
* Fix copying of dlls into the Windows zip package
* Attempt at providing a windows equivalent of the use of dirname in main.c
* Typo
* We shouldn't need the installed prereqs in Windows (libraries should come with the zip file)
* Need to get rid of the extension
* Use 7z instead of zip/unzip
* Fixing the path to the package
* Need to specify the python version to CMake
* Min and max python versions
* Treat version numbers as strings until they're into CMake
* Fix python version variable
* Add ldd step for debugging windows use test
* Let's see if it's just Python/PYGBE causing problems on the windows build
* Let's see if it's the python linking or the PYGBE-enabled code is causing the Windows use test problem
* Fixing the declaration of mol_dirname for the Windows build and re-enabling the use of PYGBE
* Some documentation updates
* Try including PYGBE without doing _splitpath
* Get tmate in windows after build
* Specify Python architecture
* Revert tmate to on failure after build
* [skip ci]
Test skipping the CI process, and also minor docs update
* Retesting with all selected examples enabled
* Remove examples that fail
* Added comments on CMake policy choices
* New FETK version
* Cleanup
* Re-enable examples to check current status
* [skip ci] Updated current status of examples in run_selected_examples.sh.
* Add metis build to the Dockerfile
* Update FETK version in the Dockerfile
* Replace pbsam-auto with pbsam in a couple of examples
* Updated run_selected_examples.sh with gdb bt of geoflow/glycerol.in example
* [skip ci] Updated releases.rst
* Fixing the logic for recognizing version numbers. The key was to put the FETK_IMPORT_VERSION variable in brackets in the if() statement.
* Fixing issues in the running and wrapping of geoflow:
* The molecule index used when calling runGeometricFlowWrapAPBS is taken from the configuration `mol` value instead of hardcoded
* The input geoflow parameters (in struct of type GeometricFlowInput) are passed by pointer instead of as a struct
* PBAM and PBSAM are now disabled by default pending further development work on their integration
* Added notes for the failure of the born/apbs-mol-fem-extmesh.in example. Update FETK to fix the failure.
* Enable maximum verbosity in ctest to try to diagnose the weirdness in the windows ctest run
* Fix logic around finding python for cmake <v3.19 and for only having a minimum version defined
* Report test failures with raised exceptions
* See if the Windows test failures are a shell-related issue
* Adding some missing newlines
* Trying to sort the install dir for mac and linux
* Don't clean the install and build dirs. Let cmake take care of what it needs to take care of. And rm -rf'ing a directory passed to a script without any validation is scary.
* I do, in fact, need to create the build dir
* Un-verbose the linux and mac build
* Relative install dir
* Same thing, this time in linux too
* Non-verbose makefile in windows
* Install PYGBE if enabled
* Install in the build directory, not build/build
* Include bin directory in path for tests
* hyphens, not minuses. fixed spaces in names
* Parse before printing
* Debugging messages for python version
* Set path to include location of libumfpack
* Fix directory name in windows
* Prevent checking of uninitialized array
* Remove the PYGBE example
* Some CMake/Python debugging
* Set swap space in Windows to handle memory-intensive tests
* Instead of setting the swap space, set the pagefile size
* Add the large-address-aware option to the linker flags under Windows
* Print the execution log on failure
* Enter tmate in windows during the build job
* Use RELEASE_TYPE variable instead of hardcoding configuration name
* Switch to debug build for debugging
* Try to catch windows build failure
* Try to resolve the python debug library issue using Python_LIBRARY_RELEASE
* Use Python3_FIND_ABI to specify non-debug library
* Undo the python ABI thing
* Test hack to get around python debug library
* Add a temporary debugging tmate session
* Let's try debugging with the mac build
* For now, just build linux and mac
* Go back to a release build to try to replicate the crashes we saw before
* Make sure all arrays get some sort of initialization
* Call destructors if pointers aren't NULL
* FETK now on 1.9.0
* Updating FETK version to 1.9.1
* Cleanup and docs updates
* Exit the build script with an error when the build fails
* Use FETK v1.9.2
* Remove -fPIE option in a strange place
* Verbose build for debug
* Skip RPATH for static builds?
* Try FETK source build instead of release download
* Switch default FETK version to the git hash at v1.9.2 (causes source build instead of binary install)
* Remove verbosity from build script
* Cleanup
* Tweaking the docs
* Updating the check for a linux build
Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov>
Co-authored-by: Darren Curtis <Darren.Curtis@pnnl.gov>
Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov>
Co-authored-by: Darren Curtis <Darren.Curtis@pnnl.gov>
* Added support and examples for PYGBE
* Changed absolute path
* Try to please flake8
* Fixed tests, Python parser for pygbe, and added documentation
* Reduce generated artifacts
* noci Attempt to fix Appveyor
* noci Attempt 2 to fix Appveyor
* noci Updating CMake files to version 3
* noci Update CMake in externals
* updating submodule to latest
* noci update appveyor
* Figure out testing for protein-rna
* Skipping protein-rna testing
* Hardcode CMake install directory for include files
* Turn on verbose CMake output
* noci Turn on verbose CMake output
* noci Fix program files path
* noci Fix cmake path
* noci chore Adding script to test examples
* noci chore Update build scripts
Co-authored-by: Darren Curtis <intendo23@gmail.com>
