Nsoblath/issue 198#199

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nsoblath wants to merge 280 commits intomaster_unused_delete_me_March_2022from nsoblath/issue_198

+1,787-83,701

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Commits on Sep 25, 2021

Trying to fix the use of vcpkg-installed packages
Noah Oblath
committed
Problem with splitting command on multiple lines
Noah Oblath
committed
Again with the multiline thing
Noah Oblath
committed
Reverting previous change
Noah Oblath
committed

Commits on Sep 27, 2021

Switch Windows build to 32-bit (x86). Use FETK v1.8.0
Noah Oblath
committed

Commits on Sep 28, 2021

Switch back to main branch for FETK
Noah Oblath
committed
Put FETK variables in one place and fix typo
Noah Oblath
committed

Commits on Sep 29, 2021

Remove trace expand for easier debugging. Change build logic to get different build commands for FETK under windows vs mac+linux
Noah Oblath
committed
Install FETK after build, and minor cleanup
Noah Oblath
committed
Update cmake args for geoflow
Noah Oblath
committed
Add tmate session for potential debugging
Noah Oblath
committed
Reverting a change
Noah Oblath
committed
Hopefully fixing cmake commands for geoflow, pbam, and pbsam under windows
Noah Oblath
committed

Commits on Sep 30, 2021

Expect same libraries now in Windows
Noah Oblath
committed
Dev branch of geoflow and attempt to build as a subdirectory
Noah Oblath
committed
Geoflow updates
Noah Oblath
committed
Set Geoflow-enabling option
Noah Oblath
committed
Turn off within-build submodule update
Noah Oblath
committed

Commits on Oct 1, 2021

Attempting to deal with the installed name of the umfpack library
Noah Oblath
committed
Adapt to different blas libraries in windows vs linux/mac
Noah Oblath
committed
Try out switching FETK build/installation to using ExternalProject
Noah Oblath
committed
Don't need to specify platform or architecture in the external project's config options
Noah Oblath
committed
Sorting out source directories
Noah Oblath
committed
Specify all the necessary directories, and do it better this time
Noah Oblath
committed
Trying to fix the binary directory
Noah Oblath
committed
Another attempt to fix the external project directories
Noah Oblath
committed
Correctly set the FETK_INSTALL_PREFIX
Noah Oblath
committed
Include the toolchain file if it's defined
Noah Oblath
committed
Some debugging for the windows build.
Noah Oblath
committed

Commits on Oct 2, 2021

Add FindUMFPACK.cmake and use it
Noah Oblath
committed

Commits on Oct 4, 2021

Don't specify BLAS vendor for maximum flexibility
Noah Oblath
committed
Explicitly search for libumfpack because Windows
Noah Oblath
committed
Cleaning up the main CMakeLists.txt file
Noah Oblath
committed
Removing fetk submodule
Noah Oblath
committed
Cache repo version is now v0.4.0
Noah Oblath
committed
Recursive checkout instead of checkout then submodule update in build workflow
Noah Oblath
committed
Doc updates for FETK now being available in Windows
Noah Oblath
committed
Re-enable the mac build to see if we can get that working
Noah Oblath
committed
Trying to clean up the linux and mac dependencies
Noah Oblath
committed

Commits on Oct 5, 2021

Updated but development commit for pb_sovers
Noah Oblath
committed
pb_solvers update
Noah Oblath
committed
Sorting out the PBAM/PBSAM build
Noah Oblath
committed

Commits on Oct 7, 2021

Commits on Oct 8, 2021

Debugging artifact building
Noah Oblath
committed
Integrate BEM build (BEM wrap code now built in APBS). Turn on BEM build.
Noah Oblath
committed
Testing a parallel build
Noah Oblath
committed

Commits on Oct 9, 2021

Start switch to FetchContent from git submodules
Noah Oblath
committed
Remove submodule bem
Noah Oblath
committed
Remove submodule geoflow_c
Noah Oblath
committed
Remove submodule pb_s_am
Noah Oblath
committed
Switching from the submodule build to the FetchContent build for dependencies
Noah Oblath
committed
Comment out tmate session
Noah Oblath
committed

Commits on Oct 13, 2021

Add a Dockerfile for testing
Noah Oblath
committed
Switch to FETK 1.8.1 and cleanup of FETK build
Noah Oblath
committed
New versions of geoflow and pb_solvers for testing
Noah Oblath
committed
Simplified Dockerfile
Noah Oblath
committed
Fixing a bug for getting FETK in windows
Noah Oblath
committed
A little more cleanup
Noah Oblath
committed
Update Geoflow git tag for new release
Noah Oblath
committed
Test building static libs
Noah Oblath
committed

Commits on Oct 22, 2021

Update pb_solvers commit to most recent release
Noah Oblath
committed

Commits on Oct 29, 2021

Update to the latest release of pb_solvers
Noah Oblath
committed
Separate configure/build stage for linux and mac
Noah Oblath
committed
Update the build script
Noah Oblath
committed

Commits on Oct 30, 2021

Update .build.sh
Darren Curtis
authored

Commits on Nov 1, 2021

Add libopenblas-dev to the linux dependencies
Noah Oblath
committed
Add tmate session to debug windows packing issue
Noah Oblath
committed
Debugging the windows packaging failure
Noah Oblath
committed
Maybe it's a shell problem?
Noah Oblath
committed

Commits on Nov 2, 2021

A little more debugging of the windows cpack failure
Noah Oblath
committed
Separate package creation for windows to get around the cmake/chocolatey conflict
Noah Oblath
committed
Best if I use the proper syntax . . .
Noah Oblath
committed
Typo fix
Noah Oblath
committed
Remove debugging modifications
Noah Oblath
committed
Cleanup of the build workflow
Noah Oblath
committed
Merge branch 'master' into nsoblath/issue_163
Noah Oblath
committed
Removing AppVeyor build and badge (Windows build is now done in GitHub Actions)
Noah Oblath
committed

Commits on Nov 3, 2021

Update .build.sh
Darren Curtis
authored
Update index.rst
Darren Curtis
authored

Commits on Nov 4, 2021

Use software-properties-common to get python3 in the Dockerfile
Noah Oblath
committed
Change directory into build before running tests
Noah Oblath
committed
Tests don't need to be their own project
Noah Oblath
committed
Merge branch 'nsoblath/issue_163' of github.com:Electrostatics/apbs into nsoblath/issue_163
Noah Oblath
committed
Turning off testing and building in the build script for GHA test purposes
Noah Oblath
committed
Check that the geoflow tests are working with this dev branch of geoflow
Noah Oblath
committed
Updated to released version of Geoflow
Noah Oblath
committed
First attempt at a test job
Noah Oblath
committed
Added required dependencies for apbs linkages
Noah Oblath
committed

Commits on Nov 5, 2021

Fix directory
Noah Oblath
committed
Fixing the path to the downloaded artifacts
nsoblath
authored
Testing for mac and windows requirements
Noah Oblath
committed
Syntax fix
Noah Oblath
committed
Mod to check mac prereqs; note about windows prereqs
Noah Oblath
committed
(temporarily) remove some slow tests
Noah Oblath
committed
Add mac prereqs for test job
Noah Oblath
committed

Commits on Nov 6, 2021

Add component specification to all install lines and use to control the package creation
Noah Oblath
committed
Add tmate back in for now
Noah Oblath
committed

Commits on Nov 29, 2021

Enable the build of iAPBS, with a few changes to how it's done to make sure it links into apbs
Noah Oblath
committed
Minor logic fix
Noah Oblath
committed
Removed the include/Eigen directory. It seemed to be confusing the Windows build.
Noah Oblath
committed
APBS needs to know where Eigen3 is
Noah Oblath
committed
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.
Noah Oblath
committed
Updating Geoflow to the new release
Noah Oblath
committed

Commits on Nov 30, 2021

Move configure_file for apbscfg.h down in the CMakeLists.txt so that it has all of the necessary info
Noah Oblath
committed
Enable tmate session in windows to check linking for a successful windows test
Noah Oblath
committed
Potential fix to incorrect arguments in calls to preRefineFE and postRefineFE
Noah Oblath
committed
tmate session on test job failure
Noah Oblath
committed
Temporarily include headers and libraries in the zip file
Noah Oblath
committed
Remove hardcoded apbscfg.h and maloccf.h
Noah Oblath
committed

Commits on Dec 1, 2021

Add windows dependencies to the test run
Noah Oblath
committed
echo the PATH variable so we can check to see if the vcpkg libraries are findable
Noah Oblath
committed
Add the vcpkg bin directory to the path
Noah Oblath
committed
Use variable ENABLE_FETK instead of FETK_ENABLED to control building with FETK
Noah Oblath
committed
Renaming some build variables, per some TODOs in apbscfg.h.in
Noah Oblath
committed
Switch use tests to using run_selected_tests.sh
Noah Oblath
committed
Forgot to include the script to run
Noah Oblath
committed
Fix permissions for the examples scripts by using the USE_SOURCE_PERMISSIONS argument
Noah Oblath
committed
Added CHANGELOG.md and .extract_section.sh script (copied from FETK implementation)
Noah Oblath
committed
Add release.yaml and release artifacts (copied implementation from FETK)
Noah Oblath
committed
Update version to 3.3.0.alpha
Noah Oblath
committed
Fix variable for tag name
Noah Oblath
committed
Move release of artifacts to a separate job
Noah Oblath
committed
Was missing the step id
Noah Oblath
committed
Also had the wrong id here
Noah Oblath
committed
Oy, hopefully the last thing I missed
Noah Oblath
committed
Fixing the logic of having a separate publish release job
Noah Oblath
committed

Commits on Dec 2, 2021

Reworking how the package filenames are handled
Noah Oblath
committed
Trigger a new build
Noah Oblath
committed
Attempting fix to issue with retrieving and storing the zip file name
Noah Oblath
committed
Use expression instead of shell expansion
Noah Oblath
committed
Workflow cleanup
Noah Oblath
committed
Back-filling the changelog's previous entries from the GitHub Releases
Noah Oblath
committed
Git tags are prepended with a v
Noah Oblath
committed

Commits on Dec 4, 2021

Consolidating cmake settings
Noah Oblath
committed

Commits on Dec 6, 2021

Turn PYGBE on, and a couple of associated fixes
Noah Oblath
committed
Stripping out Tinker support
Noah Oblath
committed
Enable debugging in workflows
Noah Oblath
committed

Commits on Dec 7, 2021

Add python3 to mac and linux dependencies
Noah Oblath
committed
Shouldn't need vcpkg integrate install in the use test
Noah Oblath
committed
Need the python library in linux
Noah Oblath
committed
Update .extract_section.sh to handle the rst file releases.rst
Noah Oblath
committed
Test conversion of release rst to md
Noah Oblath
committed
Oops, docker actions are linux only
Noah Oblath
committed
One more linux-only restriction
Noah Oblath
committed
Build directory and install directory check for already-set values in .build.sh
Noah Oblath
committed
Do initial work to accommodate building the NSIS file
Noah Oblath
committed
Fixing typos from the last commit
Noah Oblath
committed
Actually process and attempt to use the NSIS file
Noah Oblath
committed
Separate NSIS build into a separate step to see what's causing the job to hang
Noah Oblath
committed
Fixing step id
Noah Oblath
committed

Commits on Dec 8, 2021

Move release extraction to release.yaml and use setup-python@v2 for python installation
Noah Oblath
committed
Setup to do a little debugging
Noah Oblath
committed
Removing the use of git submodule updating in the build
Noah Oblath
committed
Remove NSIS use test for now
Noah Oblath
committed

Commits on Dec 9, 2021

Removing the use of NSIS packaging
Noah Oblath
committed
Setup a tmate session for container testing
Noah Oblath
committed

Commits on Dec 10, 2021

Do a test of running a windows container
Noah Oblath
committed
Another container test
Noah Oblath
committed
One more docker container attempt
Noah Oblath
committed
Some documentation updates
Noah Oblath
committed
Return to the regular build
Noah Oblath
committed
Copying in dependency libraries
Noah Oblath
committed
Fixing a library name
Noah Oblath
committed
Option for a fully static build (does not work when OpenMP is used)
Noah Oblath
committed
Try out a fully static build without OpenMP
Noah Oblath
committed
Working on diagnosing static build
Noah Oblath
committed

Commits on Dec 11, 2021

Two bug fixes
Noah Oblath
committed

Commits on Dec 15, 2021

Using a test version of FETK to try a static build
Noah Oblath
committed
YAML fix
Noah Oblath
committed
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
Noah Oblath
committed
Compile flag needed for linux, at least
Noah Oblath
committed
Modifying dependencies that are installed
Noah Oblath
committed

Commits on Dec 16, 2021

Updated pb_solvers for testing the use of the pbsolvers namespace; Fixed inclusion of BLAS.
Noah Oblath
committed
Try removing specification of compiler
Noah Oblath
committed
Update pb_solvers for wrapping fixes
Noah Oblath
committed
Enable tmate on failure
Noah Oblath
committed
Another pb_solvers update
Noah Oblath
committed
Remove openmp; I think it's screwing up finding OpenBLAS on Ubuntu
Noah Oblath
committed
Missing headers were causing a problem on macos
Noah Oblath
committed
Let's see if using libopenblas-serial-dev fixes the finding-openblas problem on linux
Noah Oblath
committed
Avoid some cmake warnings and use an updated pb_solvers
Noah Oblath
committed
Maybe the final fix to have things working? Updating pb_solvers.
Noah Oblath
committed

Commits on Dec 17, 2021

New version of FETK
Noah Oblath
committed
Including some dependencies
Noah Oblath
committed
Added finding AMD
Noah Oblath
committed

Commits on Dec 20, 2021

git-ignore all directories that start with build
Noah Oblath
committed
FETK is now treated as a required dependency, much earlier in the build
Noah Oblath
committed
These find modules are now handled by FETK
Noah Oblath
committed
Updating how dependencies are searched for and handled
Noah Oblath
committed
Use GNU standard install directories
Noah Oblath
committed

Commits on Dec 21, 2021

Getting things in the right order
Noah Oblath
committed
Remove the use of EXECUTABLE_OUTPUT_PATH and LIBRARY_OUTPUT_PATH
Noah Oblath
committed
I think we deleted nanoshaper when we cleared the temp directory, so don't do this
Noah Oblath
committed
Install metis manually on mac and linux to get static libs
Noah Oblath
committed
Separate tar and gunzip calls
Noah Oblath
committed
Sudo make install on linux
Noah Oblath
committed
Fixing the TABIPB library install location and NanoShaper duplicate install issues.
Noah Oblath
committed
Adding Python for linux
Noah Oblath
committed
Add a global static-build option and set the MSVC runtime library variable to hopefully perform a static build in windows
Noah Oblath
committed
Run tmate for windows to check linking
Noah Oblath
committed
Some anticipation of the types of jobs that will be run
Noah Oblath
committed
Adapt to changes in FETK
Noah Oblath
committed
Update FETK hash
Noah Oblath
committed
Remove extra line and print umfpack libraries
Noah Oblath
committed
Verbose build, for now
Noah Oblath
committed
Debugging messages
Noah Oblath
committed
Update FETK
Noah Oblath
committed

Commits on Dec 22, 2021

Need libumfpack for the windows use tests. And use tmate if the build fails.
Noah Oblath
committed
Remove the link search variables
Noah Oblath
committed
Enable PYGBE in Windows and add Python to use tests in all builds
Noah Oblath
committed
Fix copying of dlls into the Windows zip package
Noah Oblath
committed
Attempt at providing a windows equivalent of the use of dirname in main.c
Noah Oblath
committed
Typo
Noah Oblath
committed
We shouldn't need the installed prereqs in Windows (libraries should come with the zip file)
Noah Oblath
committed
Need to get rid of the extension
Noah Oblath
committed
Use 7z instead of zip/unzip
Noah Oblath
committed

Commits on Dec 23, 2021

Fixing the path to the package
Noah Oblath
committed
Need to specify the python version to CMake
Noah Oblath
committed
Min and max python versions
Noah Oblath
committed
Treat version numbers as strings until they're into CMake
Noah Oblath
committed
Fix python version variable
Noah Oblath
committed

Commits on Dec 24, 2021

Add ldd step for debugging windows use test
Noah Oblath
committed
Let's see if it's just Python/PYGBE causing problems on the windows build
Noah Oblath
committed
Let's see if it's the python linking or the PYGBE-enabled code is causing the Windows use test problem
Noah Oblath
committed

Commits on Dec 31, 2021

Fixing the declaration of mol_dirname for the Windows build and re-enabling the use of PYGBE
Noah Oblath
committed
Some documentation updates
Noah Oblath
committed
Try including PYGBE without doing _splitpath
Noah Oblath
committed

Commits on Jan 1, 2022

Get tmate in windows after build
Noah Oblath
committed
Specify Python architecture
Noah Oblath
committed
Revert tmate to on failure after build
Noah Oblath
committed

Commits on Jan 2, 2022

[skip ci]
Noah Oblath
committed
Retesting with all selected examples enabled
Noah Oblath
committed
Remove examples that fail
Noah Oblath
committed

Commits on Jan 3, 2022

Added comments on CMake policy choices
Noah Oblath
committed
New FETK version
Noah Oblath
committed
Cleanup
Noah Oblath
committed
Re-enable examples to check current status
Noah Oblath
committed
[skip ci] Updated current status of examples in run_selected_examples.sh.
Noah Oblath
committed

Commits on Jan 4, 2022

Add metis build to the Dockerfile
Noah Oblath
committed
Update FETK version in the Dockerfile
Noah Oblath
committed
Replace pbsam-auto with pbsam in a couple of examples
Noah Oblath
committed
Updated run_selected_examples.sh with gdb bt of geoflow/glycerol.in example
Noah Oblath
committed
[skip ci] Updated releases.rst
Noah Oblath
committed
Comment out non-running examples
Noah Oblath
committed