GitLab

* Use newer docker container for PPC

* Try different syntax

* Properly handle duplicate atom type definitions without elements

* Correct the description of a test in a docstring

* Correctly handle existing type without element and duplicate type with element

* Try to update actions/cache to v4

* Use Intel OpenCL for CI

* Set environment variables

* Try to get CI to run

* Debugging

* Debugging

* Fixes for Intel OpenCL

* Updated Python versions for CI

* Install setuptools

* Use miniforge instead of mambaforge

* Fixed version number

* Try miniforge-variant

* CI build for HIP

* Removed some unneeded dependencies

* Fix test for which libraries are present

* Run Mac tests on ARM and Intel

* Added missing environment file

* Removed obsolete code for M1 runner

* Removed obsolete code for M1 runner

* Debug CI failures

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Removed build that was failing

* Fixed URL that had changed

* Revised code from installing CUDA on CI

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

Fix CI deprecation warnings

- Upgrade actions/checkout to v3 and actions/cache to v3.3.2 to address node.js 12 warnings
- https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
- Replace usages of set-output with `>> $GITHUB_OUTPUT` for Unix and `>> %GITHUB_OUTPUT` for Windows

* Always use nvrtc for compilation

* Install nvrtc on CI

* Workaround for compiler error

* Set empty values for deprecated properties

* Attempt at fixing failing pypy build

* Try using mambaforge

* Debugging

* A different approach to using mambaforge

* Try a separate environment file for pypy

* Ensure valid atom order after loading a checkpoint

* Run CI builds on Python 3.11

* Add library path with os.add_dll_directory()

* Update path for Visual Studio

* Try older miniforge version

Use miniforge version that was known to be working

* ci bump

* switch back to using latest miniforge3 + cleanup miniconda folder at the end of testing for the self-hosted runner'

* ci bump

* ci bump

* 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

* Accept relative links between documentation sites

* add glob to linkinator

* Recurse from index.html

* Path is relative to server-root

* Get all the dots and slashes just right

* Report only the broken links

* Treat linkinator's --skip argument as regex and skip the ks.uiuc.edu domain

* Increase linkinator timeout rather than skip ks.uiuc.edu

* typo

* another typo

* Delete .confirm_shortcut_change

* 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...