GitLab

* addHydrogens() allows specifying exactly what hydrogens to add

* Prevent CI from using numpy 2.0

* Revised code from installing CUDA on CI

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Remove support for Gromacs implicit solvent

* Removed tests of implicit solvent

* Always use nvrtc for compilation

* Install nvrtc on CI

* Workaround for compiler error

* Set empty values for deprecated properties

* update to use newer openmm-torch version

* openmm8 rc1 envs

* forgot to bump nnpops

* Attempt at fixing failing pypy build

* Try using mambaforge

* Debugging

* A different approach to using mambaforge

* Try a separate environment file for pypy

* add guide for dev builds

* hosted env file for openmm-8 beta

* explain how to host an env

* add a namespace to support different os

* pin all the versions

* add version pins and env name

* Added pytest

* update envs

* add guide for dev builds

* hosted env file for openmm-8 beta

* explain how to host an env

* add a namespace to support different os

* pin all the versions

* add version pins and env name

* Added pytest

* add guide for dev builds

* hosted env file for openmm-8 beta

* explain how to host an env

* add a namespace to support different os

* Use PocketFFT instead of FFTW

* Minor cleanup

* Use PocketFFT instead of fftpack for reference platform

* Remove FFTW as a dependency

* Converted a test case to use PocketFFT

* Fixed an incorrect comment

* Update CUDA keys

* Fixed typo

* Optimized computing powers in CompiledExpression

* Fixed compilation error

* Attempt at fixing compilation error

* lets see what blows up!

* need to add env file, different name than normal

* lets see if setting an env will help it find the base

* try forcing the use of mamba

* this should break everything, but might make osx work

* lets see if this fixes the issue with the extension

* ci bump

* lets see if a different installer will work

* single thread build to see error better

* ci bump

* ci bump

* can't build opencl on m1

* add salt to url to prevent caching

* rename to reflect that we can just build CPU

* going to add a M1 x86_64 buld and an arm64 build

* lets see if I broke 86

* now lets see what happens with arm

* forgot to add new build files

* try older python version

* newer python?

* try mini forge

* ci bump

* unpin doxygen and remove gromacs as a dep

* double check where x86_64 libs are getting pulled in

* ci bump

* try and use conda compiler toolchain and set arch

* weird things happend with setting arch

* lets see what the arch the runner thinks it is using

* try printing arch again

* undo shell change

* remove changes to shell

* make sure I don't break other buikds

* fix syntax issue and add new label to actionlint

* ci bump

* ci bump

* lets focus on arm64 builds for now

* ci bump

* ci bump

* try setting arch to build with arch command

* split steps up so other builds don't break

* see if the cmake step is the only one we need to arch-ify

* cleaning things up

* cleaning things up

* set -j2 for make

* we can use the same build step as the otehr builds

* now lets see if it can install gromacs

* no gromacs, no problem?

* remove bit of logic stopping the build

* pin doxygen to 1.9.1

* try building openCL

* ci bump

* ci bump

* Adding support for new AMOEBA features

* Support modern method of specifying in-plane angles

* Implemented stretch-torsions

* Implemented angle-torsions

* More AMOEBA fixes

* Bug fix

* Converted AMOEBA 2018 force field

* Added documentation for AMOEBA 2018

* Added a missing file for tests

* Proof of concept matching current behaviour with Breathe

* Reorganise C++ API docs to work without autosummary

* Revert to Sphinx-native search

* Move remaining pip deps to conda

* Remove unnecessary lunrsearch templates

* Remove lunrsearch from cmake

* Tidy up layout of API docs

* Get code blocks to work with Breathe

Breathe doesn't seem to support the Doxygen <preformatted> tag.
It does support the <code> tag, but better yet it supports using
<verbatim> tags to embed rst into docstrings. This commit changes
all <pre> tags to use RST verbatim, and updates the Python
documentation machinery to support it too.

* Clarified some language

* Have doxygen exclude undocumented classes and have sphinx fail on warnings for C++ API docs

* List custom forces and integrators last

* Add breathe to documentation CI

* Typo

* Fix link to custom forces in extras.rst

* Have Breathe process only public classes

* Strip OpenMM:: prefix from rst files to avoid colons in links

* Remove existing private classes from EXCLUDE_SYMBOLS

* Add comment to C++ cmake describing why we promote warnings to errors

* Revise documentation build instructions for new dependencies

* Changes to work with recent versions of Sphinx

* Updated Sphinx version used for CI

* add docs for conda forge releases

* adapt to openmm git_url

* Use command line compiler if it is explicitly specified

* Don't set OPENMM_CUDA_COMPILER on Jenkins

* 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 c...

* Top level Python module is now "openmm"

* Updated module names in examples

* Updated module names in documentation

* Updated module in CI scripts

* Added deprecation warning

* Use list-comprehension in Python code

A minor change, but slighly easier to understand the initialization of
`parent_exclude_list` in my opinion.

* Implement __ne__ in Python classes that has __eq__

In Python 3, `__ne__` is automatically implemented as `not __eq__`.

However, in Python 2 it seems to be implemented as `not is` (so based on object
identity).

Based on setup.py [0] which says that "OpenMM requires Python 2.7 or better", it
should be useful to have better support for Python 2 :)

This was already done in 4 of the 12 classes that implements `__eq__`

```
>>> class WildCard(object):
...     def __eq__(self, other): return True

>>> w = WildCard()

>>> w == 42
True

>>> w != 42
True

>>> w != w
False
```

[0]: https://github.com/openmm/openmm/blob/5cef29ce8d4e17b6d0f9fd8a3c6cc1669ca0ba2b/wrappers/python/setup.py#L237

* Use umambiguous floor division for index calculations in Python

This makes the code work as intended if run...

I finally got nvidia-docker2 installed and actually working on my Gentoo
machine (I had to disable their restriction of using GPU devices to
users in the 'video' group, since the nvidia container runtime hook
didn't run as a user with those privileges, and I can't figure out what
user it was running as).

The other GPU-enabled node I added to the Jenkins array runs Ubuntu, and
that one already has nvidia-docker2 installed and running correctly on
it.

* Add a Jenkinsfile to drive a pipeline

* Also tweaks the installation script for Jenkins to be more amenable to
running other variants in parallel
* Restrict packaging script to only accept Python 2.7, since I think
that's long been the minimum supported Python version
* Allow run-ctest.py to run tests in parallel (and take advantage of
that in the Jenkins tests).

* CUDA -> CUDA_VERSION

* Jenkins will automatically post result back to GitHub.

Not need to have a separate step do that explicitly.

* Run as a login shell.

* Force looking for CUDA node.

* Make sure we load conda module.

* Start building in a docker slave -- much nicer!

* Try to fix up the installation a little.

* Fix more build issues.

* More build debugging.

* Oops -- recursive :-o

* Put opencl lib in library path

* Try 9.2

* Fix library path

* More updates to Jenkins build recipes.

* Try a new (simpler?) approach with building

* Oops...