Merge pull request #1269 from Libensemble/release/v_1.2.2

Release/v 1.2.2

Author: shuds13

.github/workflows/basic.yml

@@ -167,4 +167,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.18.2
+        - uses: crate-ci/typos@v1.19.0

.github/workflows/extra.yml

@@ -250,4 +250,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.18.2
+        - uses: crate-ci/typos@v1.19.0

.wci.yml

@@ -16,8 +16,8 @@ description: |
 language: Python
 
 release:
-  version: 1.2.1
-  date: 2024-02-23
+  version: 1.2.2
+  date: 2024-03-21
 
 documentation:
   general: https://libensemble.readthedocs.io

CHANGELOG.rst

@@ -8,6 +8,30 @@ GitHub issues are referenced, and can be viewed with hyperlinks on the `github r
 
 .. _`github releases page`: https://github.com/Libensemble/libensemble/releases
 
+Release 1.2.2
+--------------
+
+:Date: March 21, 2024
+
+* Bugfix: Some `libE_specs` were not passed through correctly when added after ensemble initialization. #1264
+* `platform_specs` options are now merged with detected platforms, rather than replacing. #1265
+* Ensure simulation directories are created when `sim_input_dir` is specified, likewise for gen dirs. #1266
+
+Example user functions:
+
+* Improved structure of gpCAM generator. #1260
+
+:Note:
+
+* Tests were run on Linux and MacOS with Python versions 3.9, 3.10, 3.11, 3.12
+* Heterogeneous workflows tested on Frontier (OLCF), Polaris (ALCF), and Perlmutter (NERSC).
+* Note that tests have been recently run on Aurora (ALCF), but the system was unavailable at time of release.
+* Tests were also run on Bebop and Improv LCRC systems.
+
+:Known Issues:
+
+* See known issues section in the documentation.
+
 Release 1.2.1
 --------------
 

docs/data_structures/libE_specs.rst

@@ -128,6 +128,7 @@ libEnsemble is primarily customized by setting options within a ``LibeSpecs`` cl
 
                     **sim_input_dir** [str]:
                         Copy this directory's contents into the working directory upon calling the simulation function.
+                        Forms the base of a simulation directory.
 
                 .. tab-item:: Gens
 
@@ -145,6 +146,7 @@ libEnsemble is primarily customized by setting options within a ``LibeSpecs`` cl
 
                     **gen_input_dir** [str]:
                         Copy this directory's contents into the working directory upon calling the generator function.
+                        Forms the base of a generator directory.
 
         .. tab-item:: Profiling
 

docs/dev_guide/release_management/release_platforms/rel_spack.rst

@@ -5,13 +5,12 @@ A workflow for updating libEnsemble on Spack
 
 This assumes you have already:
 
- - made a PyPI package for new version of libEnsemble and
+ - made a PyPI package for the new libEnsemble version and
  - made a GitHub fork of Spack and cloned it to your local system.
 
 Details on how to create forks can be found at https://help.github.com/articles/fork-a-repo.
 
-You now have a configuration like that shown at (but without the upstream/local connection).
-https://stackoverflow.com/questions/6286571/are-git-forks-actually-git-clones.
+You now have a configuration like that shown at https://stackoverflow.com/a/6286877/6346040.
 
 Upstream, in this case, is the official Spack repository on GitHub. Origin is
 your fork on GitHub, and Local Machine is your local clone (from your fork).
@@ -33,7 +32,7 @@ To set upstream repo::
     git remote set-url --push upstream no_push
     git remote -v # Check for line: `upstream no_push (push)`
 
-Updating (the main develop branch)
+Updating (the develop branch)
 ----------------------------------
 
 You will now update your local machine from the upstream repo (if in doubt,
@@ -54,16 +53,17 @@ Fetch from the upstream repo::
 To update your local machine, you may wish to rebase or overwrite your local files.
 Select from the following:
 
-If you have local changes to go "on top" of latest code::
+Now make your local machine identical to the upstream repo (**WARNING:** Any local changes will be lost!)::
 
-    git rebase upstream/develop
+    git reset --hard upstream/develop
 
-Or to make your local machine identical to upstream repo (**WARNING:** Any local changes will be lost!)::
+Alternatively, if you have existing local changes to go "on top" of the latest
+code (usually we will make our release updates after this)::
 
-    git reset --hard upstream/develop
+    git rebase upstream/develop
 
 (Optional) You may want to update your forked (origin) repo on GitHub at this point.
-This may requires a forced push::
+This may require a forced push::
 
     git push origin develop --force
 
@@ -84,11 +84,11 @@ Quick example to update libEnsemble
 This will open the libEnsemble ``package.py`` file in your editor (given by
 environment variable ``EDITOR``)::
 
-    spack edit py-libensemble  # SPACK_ROOT must be set (see above) (python packages use "py-" prefix)
+    spack edit py-libensemble  # SPACK_ROOT must be set (see above) (Python packages use "py-" prefix)
 
 Or just open it manually: ``var/spack/repos/builtin/packages/py-libensemble/package.py``.
 
-Now get checksum for new lines:
+Now get the checksum for new lines:
 
 Get the tarball (see PyPI instructions), for the new release and use::
 
@@ -102,13 +102,13 @@ Check package::
 
      spack style
 
-This will install a few python spack packages and run style checks on just
+This will install a few Python Spack packages and run style checks on just
 your changes. Make adjustments if needed, until this passes.
 
 If okay - add, commit, and push to origin (forked repo). For example, if your version
-number is 0.9.1::
+number is 1.2.2::
 
-     git commit -am "libEnsemble: add v0.9.1"
+     git commit -am "libEnsemble: add v1.2.2"
      git push origin develop --force
 
 Once the branch is pushed to the forked repo, go to GitHub and do a pull request from this
@@ -117,7 +117,7 @@ branch on the fork to the develop branch on the upstream.
 Express Summary: Make Fork Identical to Upstream
 ------------------------------------------------
 
-Quick summary for bringing develop branch on forked repo up to speed with upstream
+Quick summary for bringing the develop branch on a forked repo up to speed with upstream
 (YOU WILL LOSE ANY CHANGES)::
 
     git remote add upstream https://github.com/spack/spack.git

docs/dev_guide/release_management/release_process.rst

@@ -29,6 +29,8 @@ Before release
 - ``MANIFEST.in`` is checked. Locally, try out ``python setup.py sdist`` and check created tarball.
   contains correct files and directories for PyPI package.
 
+- Locally check that the example code in the README works with both local comms and mpi4py.
+
 - Tests are run with source to be released (this may iterate):
 
   - On-line CI (GitHub Actions) tests must pass.

docs/platforms/bebop.rst

@@ -140,9 +140,9 @@ Additional Information
 See the LCRC Bebop docs here_ for more information about Bebop.
 
 .. _Anaconda: https://www.anaconda.com/
-.. _Bebop: https://www.lcrc.anl.gov/systems/resources/bebop/
+.. _Bebop: https://www.lcrc.anl.gov/systems/bebop
 .. _conda: https://conda.io/en/latest/
-.. _here: https://www.lcrc.anl.gov/for-users/using-lcrc/running-jobs/running-jobs-on-bebop/
+.. _here: https://docs.lcrc.anl.gov/bebop/running-jobs-bebop/
 .. _mpi4py: https://mpi4py.readthedocs.io/en/stable/
 .. _options: https://slurm.schedmd.com/srun.html
 .. _Slurm: https://slurm.schedmd.com/

docs/platforms/improv.rst

@@ -68,4 +68,4 @@ You can install mpi4py as usual having installed the Open-MPI module::
 Note if using ``mpi4py`` comms with Open-MPI, you may need to set ``export OMPI_MCA_coll_hcoll_enable=0``
 to prevent HCOLL warnings.
 
-.. _Improv: https://www.lcrc.anl.gov/for-users/using-lcrc/running-jobs/running-jobs-on-improv/
+.. _Improv: https://docs.lcrc.anl.gov/improv/running-jobs-improv/

docs/platforms/platforms_index.rst

@@ -42,7 +42,7 @@ On systems with a job scheduler, libEnsemble is typically run within a single
 :doc:`job submission<example_scripts>`. All user simulations will run on
 the nodes within that allocation.
 
-*How does libensemble know where to run tasks (user applications)?*
+*How does libEnsemble know where to run tasks (user applications)?*
 
 The libEnsemble :doc:`Executor<../executor/ex_index>` can be initialized from the user calling
 script, and then used by workers to run tasks. The Executor will automatically detect the nodes
@@ -221,7 +221,6 @@ libEnsemble on specific HPC systems.
     example_scripts
 
 .. _Balsam: https://balsam.readthedocs.io/en/latest/
-.. _Cooley: https://www.alcf.anl.gov/support-center/cooley
 .. _Globus Compute: https://www.globus.org/compute
 .. _Globus Compute endpoints: https://globus-compute.readthedocs.io/en/latest/endpoints.html
 .. _Globus: https://www.globus.org/