* Break user guide into parts
* Break up file I missed
* Add basic .gitignore to suit out-of-tree builds in build, build1, build2 ... build9
* Small changes to autonumber.py for doc compilation
This is a small change designed not to fix the incorrect logic of
autonumber.py, but just to get the docs compiling. While assigning
numbers, the code now just ignores the autonumber_by_chapter
setting for a particular object if it can't find the appropriate
section in section_numbers. This is a temporary fix!
* Include part and chapter in autonumbered objects
* Fix autonumber.py to correctly reference autonumber roles in file-level sections
* Unify and simplify styling across documentation
* Break dev docs down into individual chapter-files
* Correct absolute links to relative
* Disable browser suggestions for lunrsearch box in API docs
* Remove part name from chapter 2.1
* Rename ambiguous 'Home' link to OpenMM.org
* Typo
* Minor fixes and reversions
Reverts some changes I had made and later thought better of,
and fixes some recurring typos across the documentation.
* Number developers guide chapters
* Fix responsiveness
* Remove header.rst and center captions
* Add a level of depth to main TOC and styling to accomodate
* Add third level to Part-level TOCs
* Use :numref: instead of :ref: to number links to sections
* Continuously number chapters in user guide
* navbar links to other docs relative, not absolute
* Improve navbar spacing with new template
* Fix sidebar while allowing it to scroll
* Hard -> Soft links for navigation.html template
* Add navigation.html template to cmakelists
* Add another level of .. to relative links
* Fix flex on C++ and remove layer of ..
* Began converting AMOEBA to common platform
* Beginning of OpenCL platform for AMOEBA
* Converted AmoebaVdwForce to common platform
* Cleaned up reference AMOEBA tests
* Began converting AmoebaMultipoleForce to common platform
* Continue converting AmoebaMultipoleForce to common platform
* Bug fixes
* Bug fix
* Continue converting AmoebaMultipoleForce to common platform
* Converting AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce to common platform
* Converting AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce to common platform
* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce
* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce
* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce
* Converted arrays from real3 to real
* Bug fix to OpenCL AmoebaGeneralizedKirkwoodForce
* Fixes for AMD GPUs
* Began converting HippoNonbondedForce to common platform
* Continuing to convert HippoNonbondedForce to common platform
* Continuing to convert HippoNonbondedForce to common platform
* Working on unifying PME kernels
* Fixed error on devices without 64 bit atomics
* Unified PME kernels
* Converted HippoNonbondedForce to common platform
* Creating OpenCL implementation of HippoNonbondedForce
* Continuing OpenCL implementation of HippoNonbondedForce
* Mostly finished OpenCL implementation of HippoNonbondedForce
* Eliminated three component vector types in host code
* Fix errors on CPU OpenCL
* Skip double precision tests for AMOEBA on OpenCL
* Bug fixes
* Bug fixes
* Fixed compilation error
* Add draft GHA-based CI for Linux
* Fix events
* Dup key
* Fix path
* Update env vars
* More fixes
* Fix env vars again
* add doxygen
* add sudo
* Typo
* upgrade CUDA
* escape newlines
* more backslashes
* fix CUDA_APT
* more env vars fixes
* fix missing file
* acumulate env_vars
* build python wrappers only if requested
* add pytest
* use $GITHUB_ENV
https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-commands-for-github-actions#environment-files
* use ${GITHUB_WORKSPACE}
* Pin older gromacs
* add windows
* Provide default values for unbound vars
* fixes
* this is powershell not cmd
* update envs
* win fix
* make windows use cmd
* Change install prefix
* fixes
* better env files
* Increase timeout threshold
* set xcode to 10.x
* specify action version
* fix sdk in macos
* split jobs a bit more
* build wrappers even if tests failed for core
* revert & resort build/test
* fix run logic?
* install envs in D:\
* add more cudas
* allow longer test times
* sudo that
* fix cuda ver checks
* another little fix
* one more
* missing package
* missing dev packages
* missing backslash
* add nvprof
* factor scripts out
* export CUDA_PATH
* no quotes in env var
* add more cudas
* fix ci name
* fix flags
* typo
* missing parenthesis
* add cuda 11.2 urls
* add retry loops for online installations
* add library existence tests
* verbose
* fix sets
* CPU and PME are not built in GPU variants; do not test for those
* quote?
* fix windows checks
* add macos opencl
* disable opencl tests on macos (but build anyway)
* add docs
* cd into build for docs!
* install then cd
* pin sphinxcontrib-bibtex
* we need tex in the system
* split docs into a separate job
* simplify retrying
* simplify retrying 2
* do install
* fix tlmgr installation
* more tex packages
* one more
* one more
* add textcomp to docs
* usepackage[utf8]{inputenc}
* switch to xelatex?
* add xetex
* more fonts
* do not use xindy
* tables can't contain blocks and use tabularcolumns at the same time
https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html?highlight=tabular#directive-tabularcolumns
* build libs in docs too
* update docs deps; bring in pdfs
* kill server after 404 checks
* chage 404 checker
* explicit locations needed
* cumulative exit codes
* override set -e
* update README badges
* add ppc / arm
* missing vbar
* not it
* one too many extensions
* do not test gromacs
* manage workspace
* source conda.sh
* add python version to matrix vars
* source first thing
* disable unbound checks
* add compilers
* some more cuda stuff
* add CPU only ppc64le
* link through stubs
* One more way to obtain HOST_USER_ID?
* let cmake find cf's opencl
* Try with GCC7
* add timeouts for docker based runs
* add several attempts for stochastic failures
* add tests with conda forge compilers
* do not parallelize pytest in docker runs
* exclude some known slow tests
* enable ccache
* forgot conda shell
* No need for macos sdk retries
* \ -> ^
* fix timestampt windows
* export env vars for current step too
* unneeded quotes windows?
* disable compression on windows?
* add ccache in docker too
* group commands
* fix syntax error
* fix version spec
* Increase timeout in Docker runs
* heh, it's double colon
* fix cache timestamp in windows
* escape % with %%
* ccache in docs too
* don't use wrapper package in windows; call vcvarsall directly
* More docker variants
* Handle ccache env vars in yaml
* Re-enable parallel pytest in Docker runs
* Delete unwanted azure ymls that I didn't end up using
* add some comments
* Update badge URL
* is that path messing with windows ccache?
* add CI-README
* Reduce CI matrix
* increase timeouts
* Add GCC7 on PPC QEmu again (temporarily, just for debugging)
* add docker instructions for local debugging
* fix start_docker_locally
* skip some url checks in docs
* Use new package name
* update link
* Updated to latest values for physical constants
* Updated documentation on physical constants
* Updated Python unit definitions
* Fixed constants in test case
* Added a comment
* Began creating common compute framework to unify code between CUDA and OpenCL
* Began OpenCL implementation of common compute framework
* Common implementation of CMMotionRemover
* CUDA implementation of common compute interface
* Converted HarmonicBondForce to common compute API
* Converted standard bonded forces to common compute API
* Converted ExpressionUtilities to common compute API
* Created ComputeParameterSet
* Converted custom bonded forces to common compute API
* Converted CustomCentroidBondForce to common compute API
* Converted CustomManyParticleForce to common compute API
* Moved lots of duplicate code from CudaContext and OpenCLContext to ComputeContext
* Converted GayBerneForce to common compute API
* Removed obsolete kernels
* Converted verlet integrators to common compute API
* Converted Langevin and Brownian integrators to common compute API
* Converted CustomIntegrator to common compute API
* Converted CustomNonbondedForce to common compute API
* Removed uses of a deprecated API
* Fixed failing test cases
* Converted GBSAOBCForce to common compute API
* Began converting CustomGBForce to common compute API
* Finished converting CustomGBForce to common compute API
* Merged duplicated code in CudaIntegrationUtilities and OpenCLIntegrationUtilities
* Converted RMSDForce and AndersenThermostat to common compute API
* Converted CustomHbondForce to common compute API
* Merged scripts for encoding kernel sources
* Converted Drude plugin to common compute API
* Fixed errors in CMake scripts
* Attempt at fixing errors on Windows
* Added discussion of common compute API to developer guide
* Added Windows export macro for common classes
* Fixed error in CMMotionRemover
* Ubdated travis to newer Ubuntu version
* Fixed errors on CPU OpenCL
* Fixed Windows linking errors
* Added missing pragma for 32 bit atomics
* Replaced long long with mm_long
* More fixes to Windows linking
* Bug fix
