* run CI on new 0.10.x branch

* Update .github/workflows/CI.yaml

Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>

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Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>

* update comments

* bump ci

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Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* use python executable from env

* run tests using the shell

* parmed 4 seems to be giving us some issues

* actually I think we want the newer parmed

* pin pymbar for now

* ooof, parmed != pymbar

* add some more debugging to figure out how we are getting old parmed

* Update devtools/conda-envs/test_env.yaml

* see if shell=True fixes it

* removed parmed by mistake

* switch to using pymbar 3 & 4 support from openmmtools

* fix typo on import

* fix yaml

* switch to using pymbar 4

* missed a pymbar import

* missed another one

* bump ci

* missed a import

* go back to how it was

* Update devtools/conda-envs/test_env.yaml

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Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>

…ipeline (#1210)

* Initial and final topologies serialized per phase.

* Using properties instead of private attrs.

* Fix test

* Remove uneeded code/attributes

* bump ci

* Store phase topologies separately

* Fix tests. vacuum topologies expected.

* Better docstring.

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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* Added note about example for adding oe license

* make docker file much simpler

* build images in CI

* forgot to add conda-forge

* fix permissions on a step

* get oe_license file mounted in docker container

* mount path must be absolute

* setup singulairty to test + fix testing on docker image

* add some testing deps to the image

* add -v for tests, fix envar

* tests are failing, want to test rest of pipeline

* use latest openmm version

* hardcode perses version for now

* bump ci

* make sure we can make openeye dir

* support a dev build as well

* don't hardcode value

* fix name clash

* forgot to add conda-forge

* bump ci

* test docker image and fix missing deps

* install ps

* also push latest tag

* don't build on tag since the conda-forge package won't exist yet

* don't test the examples

* Remove docker deb build, we can do these ourselves

* better document container use

* build a latest version for apptainer

* build with 11.2 to make things more compatable

* skip docker test to see if other bits build okay

* see if I can get the step to fail if there is an error

* skip docker tests to make sure apptainer builds okay

* Add mpiplus and mpi4py to docker image

* give correct path to oe license

* add mpi stuff to docker

* clean up diskspace before build

* skip tests for singularity now that the only failures come from a package bug

* Improving examples dir structure and readme

* Adding Tyk2 CLI example

* removing new-cli/ripk2 example (deprecated)

* fix typo for link

* Clarify tyk2 cli example docs

* CI miscellaneous fixes (#1217)

* CI minor fixes. Allow codecov to fail.

* bump ci

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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* Changing offline freq default to checkpoint interval

* Fixing input yaml for example

* commenting offline-freq param

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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* peptide mutation MPI example added

* better documentation of motivation

* set cutoff distance in sterics_custom_nonbonded_force

* matching cutoff for custom forces. Improving logic.

* test for HTF nonbonded cutoff

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Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>

* CI miscellaneous fixes (#1217)

* CI minor fixes. Allow codecov to fail.

* bump ci

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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* added dels to contexts

* Update perses/app/setup_relative_calculation.py

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Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>

* fix spectator support. Enabling test.

* Test to run on GPU CI.