From 9c12c7ec324388abbfdf492c3b7fda2b6b2a33f8 Mon Sep 17 00:00:00 2001 From: jlnav Date: Mon, 31 Aug 2026 16:03:52 -0500 Subject: [PATCH 1/2] fix mpi4py link --- docs/introduction_latex.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/introduction_latex.rst b/docs/introduction_latex.rst index 512282dbf..72b3ab321 100644 --- a/docs/introduction_latex.rst +++ b/docs/introduction_latex.rst @@ -20,7 +20,7 @@ .. _libE_specs: https://libensemble.readthedocs.io/en/main/data_structures/libE_specs.html .. _manuscript: https://arxiv.org/abs/2104.08322 .. _mock: https://pypi.org/project/mock -.. _mpi4py: https://bitbucket.org/mpi4py/mpi4py +.. _mpi4py: https://mpi4py.readthedocs.io/en/stable/ .. _MPICH: http://www.mpich.org/ .. _mpmath: http://mpmath.org/ .. _NLopt documentation: https://nlopt.readthedocs.io/en/latest/NLopt_Installation/ From 1bd13052b5b659c53c2491115a0e3692b06eec23 Mon Sep 17 00:00:00 2001 From: jlnav Date: Tue, 1 Sep 2026 10:34:39 -0500 Subject: [PATCH 2/2] various link adjustments and fixes from pixi run -e docs sphinx-build -b linkcheck docs docs/_build/linkcheck, then gpt-luna fixing issues --- CONTRIBUTING.rst | 2 +- README.rst | 16 ++++++++-------- docs/FAQ.rst | 2 +- .../advanced_installation.rst | 6 +++--- .../release_platforms/rel_github.rst | 2 +- .../release_platforms/rel_spack.rst | 4 ++-- .../release_management/release_process.rst | 2 +- docs/examples/aposmm.rst | 2 +- docs/examples/gen_funcs.rst | 2 +- docs/executor/ex_overview.rst | 2 +- docs/introduction.rst | 4 ++-- docs/introduction_latex.rst | 12 ++++++------ docs/known_issues.rst | 2 +- docs/platforms/aurora.rst | 4 ++-- docs/platforms/bebop.rst | 2 +- docs/platforms/frontier.rst | 2 +- docs/platforms/perlmutter.rst | 2 +- docs/platforms/platforms_index.rst | 2 +- docs/platforms/polaris.rst | 6 +++--- docs/tutorials/aposmm_tutorial.rst | 2 +- docs/tutorials/executor_forces_tutorial.rst | 2 +- docs/tutorials/forces_gpu_tutorial.rst | 4 ++-- docs/tutorials/gpcam_tutorial.rst | 2 +- .../local_sine_tutorial/local_sine_tutorial.rst | 2 +- .../local_sine_tutorial_1.rst | 2 +- docs/welcome.rst | 4 ++-- libensemble/ensemble.py | 2 +- libensemble/gen_funcs/persistent_aposmm.py | 2 +- libensemble/libE.py | 4 ++-- libensemble/tools/tools.py | 2 +- 30 files changed, 52 insertions(+), 52 deletions(-) diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst index 6222c9ae6..212225eb0 100644 --- a/CONTRIBUTING.rst +++ b/CONTRIBUTING.rst @@ -24,7 +24,7 @@ Issues can be raised at Issues may include reporting bugs or suggested features. Administrators will add issues, as appropriate, to the project board at - https://github.com/Libensemble/libensemble/projects + https://github.com/orgs/Libensemble/projects By convention, user branch names should have a / format, where example types are feature, bugfix, testing, docs, and experimental. diff --git a/README.rst b/README.rst index 77f73518d..c593aec87 100644 --- a/README.rst +++ b/README.rst @@ -179,8 +179,8 @@ Resources :target: https://packages.spack.io/package.html?name=py-libensemble .. |Tests| image:: https://github.com/Libensemble/libensemble/actions/workflows/extra.yml/badge.svg?branch=main :target: https://github.com/Libensemble/libensemble/actions -.. |Coverage| image:: https://codecov.io/github/Libensemble/libensemble/graph/badge.svg - :target: https://codecov.io/github/Libensemble/libensemble +.. |Coverage| image:: https://app.codecov.io/github/Libensemble/libensemble/graph/badge.svg + :target: https://app.codecov.io/github/Libensemble/libensemble .. |Docs| image:: https://readthedocs.org/projects/libensemble/badge/?maxAge=2592000 :target: https://libensemble.readthedocs.org/en/latest/ :alt: Documentation Status @@ -195,7 +195,7 @@ Resources .. _conda-forge: https://conda-forge.org/ .. _Contributions: https://github.com/Libensemble/libensemble/blob/main/CONTRIBUTING.rst .. _docs: https://libensemble.readthedocs.io/en/main/advanced_installation.html -.. _gest-api: https://gest-api.readthedocs.io +.. _gest-api: https://gest-api.readthedocs.io/en/latest/ .. _GitHub: https://github.com/Libensemble/libensemble .. _libEnsemble mailing list: https://lists.mcs.anl.gov/mailman/listinfo/libensemble .. _libEnsemble Slack page: https://libensemble.slack.com @@ -203,20 +203,20 @@ Resources .. _mpmath: http://mpmath.org/ .. _PyPI: https://pypi.org .. _Quickstart: https://libensemble.readthedocs.io/en/main/introduction.html -.. _ReadtheDocs: http://libensemble.readthedocs.org/ +.. _ReadtheDocs: https://libensemble.readthedocs.io/en/latest/ .. _regression tests: https://github.com/Libensemble/libensemble/tree/main/libensemble/tests/regression_tests .. |Inline Example| image:: https://colab.research.google.com/assets/colab-badge.svg - :target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/readme_notebook.ipynb + :target: https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/readme_notebook.ipynb .. |Simple Ensemble| image:: https://colab.research.google.com/assets/colab-badge.svg - :target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/simple_sine/sine_tutorial_notebook.ipynb + :target: https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/simple_sine/sine_tutorial_notebook.ipynb .. |Ensemble with an MPI application| image:: https://colab.research.google.com/assets/colab-badge.svg - :target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/forces_with_executor/forces_tutorial_notebook.ipynb + :target: https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/forces_with_executor/forces_tutorial_notebook.ipynb .. |Optimization example| image:: https://colab.research.google.com/assets/colab-badge.svg - :target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/aposmm/aposmm_tutorial_notebook.ipynb + :target: https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/aposmm/aposmm_tutorial_notebook.ipynb .. |Surrogate Modeling| image:: https://colab.research.google.com/assets/colab-badge.svg :target: https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/gpcam_surrogate_model/gpcam.ipynb diff --git a/docs/FAQ.rst b/docs/FAQ.rst index 0339dbb68..931a2eda1 100644 --- a/docs/FAQ.rst +++ b/docs/FAQ.rst @@ -298,7 +298,7 @@ macOS and Windows Errors on our executables, then confirming the next alerts for the executable and ``mpiexec.hydra``. -.. _Installing PETSc On Microsoft Windows: https://petsc.org/release/install/windows/#recommended-installation-methods +.. _Installing PETSc On Microsoft Windows: https://petsc.org/release/install/windows/#installing-petsc-on-microsoft-windows .. _option to srun: https://docs.nersc.gov/systems/perlmutter/running-jobs/#single-gpu-tasks-in-parallel .. _Perlmutter: https://docs.nersc.gov/systems/perlmutter/architecture/ .. _Python multiprocessing docs: https://docs.python.org/3/library/multiprocessing.html diff --git a/docs/advanced_installation/advanced_installation.rst b/docs/advanced_installation/advanced_installation.rst index fc2e8546a..1bfc3767e 100644 --- a/docs/advanced_installation/advanced_installation.rst +++ b/docs/advanced_installation/advanced_installation.rst @@ -34,8 +34,8 @@ Globus Compute `Globus Compute`_ may be installed optionally to submit simulation function instances to remote Globus Compute endpoints. .. _Globus Compute: https://www.globus.org/compute -.. _Python: http://www.python.org -.. _NumPy: http://www.numpy.org +.. _Python: https://www.python.org/ +.. _NumPy: https://numpy.org/ .. _psutil: https://pypi.org/project/psutil/ -.. _pydantic: https://docs.pydantic.dev/1.10/ +.. _pydantic: https://pydantic.dev/docs/validation/latest/get-started/ .. _gest-api: https://github.com/campa-consortium/gest-api diff --git a/docs/dev_guide/release_management/release_platforms/rel_github.rst b/docs/dev_guide/release_management/release_platforms/rel_github.rst index 7398a2a55..ce88c868b 100644 --- a/docs/dev_guide/release_management/release_platforms/rel_github.rst +++ b/docs/dev_guide/release_management/release_platforms/rel_github.rst @@ -5,7 +5,7 @@ GitHub release The administrator should follow the GitHub instructions to draft a new release. These can currently be found at -https://help.github.com/en/articles/creating-releases. +https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository. Both the version and title will be of the form vX.Y.Z, for example, v0.5.0. diff --git a/docs/dev_guide/release_management/release_platforms/rel_spack.rst b/docs/dev_guide/release_management/release_platforms/rel_spack.rst index a7688ed72..33d875d13 100644 --- a/docs/dev_guide/release_management/release_platforms/rel_spack.rst +++ b/docs/dev_guide/release_management/release_platforms/rel_spack.rst @@ -8,7 +8,7 @@ This assumes you have already: - 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. +Details on how to create forks can be found at https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo. You now have a configuration like that shown at https://stackoverflow.com/a/6286877/6346040. @@ -130,5 +130,5 @@ Quick summary for bringing the develop branch on a forked repo up to speed with Reference: -.. _packaging: https://spack.readthedocs.io/en/latest/packaging_guide.html +.. _packaging: https://spack.readthedocs.io/en/latest/packaging_guide_creation.html .. _contribution: https://spack.readthedocs.io/en/latest/contribution_guide.html diff --git a/docs/dev_guide/release_management/release_process.rst b/docs/dev_guide/release_management/release_process.rst index 60d5b80cd..d988d16be 100644 --- a/docs/dev_guide/release_management/release_process.rst +++ b/docs/dev_guide/release_management/release_process.rst @@ -91,4 +91,4 @@ After release on the kanban project board (inc. the release checklist). Those that were already in *Done* should be archived. -.. _libE-Templater: https://github.com/Libensemble/libE-templater +.. _libE-Templater: https://github.com/Libensemble/libE-HPC-Templater diff --git a/docs/examples/aposmm.rst b/docs/examples/aposmm.rst index f5a7a2f11..969f6327d 100644 --- a/docs/examples/aposmm.rst +++ b/docs/examples/aposmm.rst @@ -65,5 +65,5 @@ LocalOptInterfacer .. _nlopt: https://nlopt.readthedocs.io/en/latest/ .. _petsc4py: https://bitbucket.org/petsc/petsc4py .. _SciPy: https://pypi.org/project/scipy -.. _PETSc/TAO: http://www.mcs.anl.gov/petsc +.. _PETSc/TAO: https://www.mcs.anl.gov/petsc/ .. _scipy.optimize: https://docs.scipy.org/doc/scipy/reference/optimize.html diff --git a/docs/examples/gen_funcs.rst b/docs/examples/gen_funcs.rst index 0bae6f764..6347d8bce 100644 --- a/docs/examples/gen_funcs.rst +++ b/docs/examples/gen_funcs.rst @@ -118,6 +118,6 @@ Modeling and Approximation .. _Surmise: https://surmise.readthedocs.io/en/latest/index.html .. _Tasmanian: https://github.com/ORNL/Tasmanian .. _user guide: https://libensemble.readthedocs.io/en/latest/programming_libE.html -.. _VTMOP: https://github.com/Libensemble/libe-community-examples#vtmop +.. _VTMOP: https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/generators.html#vtmop-link .. _WarpX: https://warpx.readthedocs.io/en/latest/ .. _ytopt: https://github.com/ytopt-team/ytopt diff --git a/docs/executor/ex_overview.rst b/docs/executor/ex_overview.rst index f53510b73..2cbbed265 100644 --- a/docs/executor/ex_overview.rst +++ b/docs/executor/ex_overview.rst @@ -156,4 +156,4 @@ which partitions resources among workers, ensuring that runs utilize different resources (e.g., nodes). Furthermore, the ``MPIExecutor`` offers resilience via the feature of re-launching tasks that fail to start because of system factors. -.. _concurrent futures: https://docs.python.org/library/concurrent.futures.html +.. _concurrent futures: https://docs.python.org/3/library/concurrent.futures.html diff --git a/docs/introduction.rst b/docs/introduction.rst index 0e1ebca6f..47c04f9fa 100644 --- a/docs/introduction.rst +++ b/docs/introduction.rst @@ -55,10 +55,10 @@ See the `user guide`_ for more information. .. _IPAC manuscript: https://doi.org/10.18429/JACoW-ICAP2018-SAPAF03 .. _NLopt: https://nlopt.readthedocs.io/en/latest/ .. _OPAL: http://amas.web.psi.ch/docs/opal/opal_user_guide-1.6.0.pdf -.. _PETSc/TAO: http://www.mcs.anl.gov/petsc +.. _PETSc/TAO: https://www.mcs.anl.gov/petsc/ .. _scipy.optimize: https://docs.scipy.org/doc/scipy/reference/optimize.html .. _Surmise: https://surmise.readthedocs.io/en/latest/index.html .. _Tasmanian: https://github.com/ORNL/Tasmanian .. _user guide: https://libensemble.readthedocs.io/en/latest/programming_libE.html -.. _VTMOP: https://github.com/Libensemble/libe-community-examples#vtmop +.. _VTMOP: https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/generators.html#vtmop-link .. _WarpX: https://warpx.readthedocs.io/en/latest/ diff --git a/docs/introduction_latex.rst b/docs/introduction_latex.rst index 72b3ab321..f1c5da96f 100644 --- a/docs/introduction_latex.rst +++ b/docs/introduction_latex.rst @@ -25,22 +25,22 @@ .. _mpmath: http://mpmath.org/ .. _NLopt documentation: https://nlopt.readthedocs.io/en/latest/NLopt_Installation/ .. _nlopt: https://nlopt.readthedocs.io/en/latest/ -.. _NumPy: http://www.numpy.org +.. _NumPy: https://numpy.org/ .. _OPAL: http://amas.web.psi.ch/docs/opal/opal_user_guide-1.6.0.pdf .. _petsc4py: https://bitbucket.org/petsc/petsc4py -.. _PETSc/TAO: http://www.mcs.anl.gov/petsc +.. _PETSc/TAO: https://www.mcs.anl.gov/petsc/ .. _poster: https://figshare.com/articles/libEnsemble_A_Python_Library_for_Dynamic_Ensemble-Based_Computations/12559520 .. _PSI/J: https://exaworks.org/psij .. _psi-j-python: https://github.com/ExaWorks/psi-j-python .. _psutil: https://pypi.org/project/psutil/ -.. _pydantic: https://pydantic-docs.helpmanual.io/ +.. _pydantic: https://pydantic.dev/docs/validation/latest/get-started/ .. _PyPI: https://pypi.org .. _pytest-cov: https://pypi.org/project/pytest-cov/ .. _pytest-timeout: https://pypi.org/project/pytest-timeout/ .. _pytest: https://pypi.org/project/pytest/ -.. _Python: http://www.python.org +.. _Python: https://www.python.org/ .. _Quickstart: https://libensemble.readthedocs.io/en/main/introduction.html -.. _ReadtheDocs: http://libensemble.readthedocs.org/ +.. _ReadtheDocs: https://libensemble.readthedocs.io/en/latest/ .. _SciPy: http://www.scipy.org .. _scipy.optimize: https://docs.scipy.org/doc/scipy/reference/optimize.html .. _setuptools: https://setuptools.pypa.io/en/latest/ @@ -52,6 +52,6 @@ .. _Tasmanian: https://github.com/ORNL/Tasmanian .. _tqdm: https://tqdm.github.io/ .. _user guide: https://libensemble.readthedocs.io/en/latest/programming_libE.html -.. _VTMOP: https://github.com/Libensemble/libe-community-examples#vtmop +.. _VTMOP: https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/generators.html#vtmop-link .. _WarpX: https://warpx.readthedocs.io/en/latest/ .. _xsdk: https://xsdk.info diff --git a/docs/known_issues.rst b/docs/known_issues.rst index a68f1bcf4..d5fb73e07 100644 --- a/docs/known_issues.rst +++ b/docs/known_issues.rst @@ -28,4 +28,4 @@ may occur when using libEnsemble. * We currently recommended running in Central mode on Bridges as distributed runs are experiencing hangs. -.. _pickle error: https://docs.nersc.gov/development/languages/python/using-python-perlmutter/#missing-support-for-matched-proberecv +.. _pickle error: https://docs.nersc.gov/development/languages/python/using-python-perlmutter/#known-issues diff --git a/docs/platforms/aurora.rst b/docs/platforms/aurora.rst index c29ed0bc0..660e36322 100644 --- a/docs/platforms/aurora.rst +++ b/docs/platforms/aurora.rst @@ -135,5 +135,5 @@ exception of different compiler options and numbers of workers (because the numbers of GPUs on a node differs). .. _ALCF: https://www.alcf.anl.gov/ -.. _Aurora: https://www.alcf.anl.gov/support-center/aurorasunspot/getting-started-aurora -.. _demonstration: https://youtu.be/H2fmbZ6DnVc +.. _Aurora: https://docs.alcf.anl.gov/aurora/getting-started-on-aurora/ +.. _demonstration: https://www.youtube.com/watch?v=H2fmbZ6DnVc&feature=youtu.be diff --git a/docs/platforms/bebop.rst b/docs/platforms/bebop.rst index 2682a5486..87779d646 100644 --- a/docs/platforms/bebop.rst +++ b/docs/platforms/bebop.rst @@ -94,6 +94,6 @@ See the LCRC Bebop docs here_ for more information about Bebop. .. _Anaconda: https://www.anaconda.com/ .. _Bebop: https://www.lcrc.anl.gov/systems/bebop -.. _conda: https://conda.io/en/latest/ +.. _conda: https://docs.conda.io/en/latest/ .. _here: https://docs.lcrc.anl.gov/bebop/running-jobs-bebop/ .. _mpi4py: https://mpi4py.readthedocs.io/en/stable/ diff --git a/docs/platforms/frontier.rst b/docs/platforms/frontier.rst index ef2251b32..79190ae5c 100644 --- a/docs/platforms/frontier.rst +++ b/docs/platforms/frontier.rst @@ -75,4 +75,4 @@ To see GPU usage, ssh into the node you are on in another window and run:: .. _Frontier: https://docs.olcf.ornl.gov/systems/frontier_user_guide.html .. _python_on_frontier: https://www.olcf.ornl.gov/wp-content/uploads/2-16-23_python_on_frontier.pdf -.. _demonstration: https://youtu.be/H2fmbZ6DnVc +.. _demonstration: https://www.youtube.com/watch?v=H2fmbZ6DnVc&feature=youtu.be diff --git a/docs/platforms/perlmutter.rst b/docs/platforms/perlmutter.rst index 7f6098657..f77c58232 100644 --- a/docs/platforms/perlmutter.rst +++ b/docs/platforms/perlmutter.rst @@ -188,7 +188,7 @@ Additional Information See the NERSC Perlmutter_ docs for more information about Perlmutter. -.. _conda: https://conda.io/en/latest/ +.. _conda: https://docs.conda.io/en/latest/ .. _mpi4py: https://mpi4py.readthedocs.io/en/stable/ .. _NERSC: https://www.nersc.gov/ .. _option to srun: https://docs.nersc.gov/systems/perlmutter/running-jobs/#single-gpu-tasks-in-parallel diff --git a/docs/platforms/platforms_index.rst b/docs/platforms/platforms_index.rst index d1de30c45..5983499ce 100644 --- a/docs/platforms/platforms_index.rst +++ b/docs/platforms/platforms_index.rst @@ -234,6 +234,6 @@ libEnsemble on specific HPC systems. example_scripts .. _Globus Compute: https://www.globus.org/compute -.. _Globus Compute endpoints: https://globus-compute.readthedocs.io/en/latest/endpoints.html +.. _Globus Compute endpoints: https://globus-compute.readthedocs.io/en/latest/endpoints/endpoint_examples.html .. _Globus: https://www.globus.org/ .. _handful of task-rate and data limits: https://globus-compute.readthedocs.io/en/latest/limits.html diff --git a/docs/platforms/polaris.rst b/docs/platforms/polaris.rst index 21518ccf4..08be1462c 100644 --- a/docs/platforms/polaris.rst +++ b/docs/platforms/polaris.rst @@ -85,8 +85,8 @@ GPU), see the :doc:`forces_gpu<../tutorials/forces_gpu_tutorial>` tutorial. A vi of this example is also available. .. _ALCF: https://www.alcf.anl.gov/ -.. _conda: https://conda.io/en/latest/ -.. _demonstration: https://youtu.be/Ff0dYYLQzoU +.. _conda: https://docs.conda.io/en/latest/ +.. _demonstration: https://www.youtube.com/watch?v=Ff0dYYLQzoU&feature=youtu.be .. _mpi4py: https://mpi4py.readthedocs.io/en/stable/ .. _Polaris: https://www.alcf.anl.gov/polaris -.. _Python for Polaris: https://docs.alcf.anl.gov/polaris/data-science-workflows/python/ +.. _Python for Polaris: https://docs.alcf.anl.gov/polaris/ diff --git a/docs/tutorials/aposmm_tutorial.rst b/docs/tutorials/aposmm_tutorial.rst index 7cc0d7b9f..09578ae1d 100644 --- a/docs/tutorials/aposmm_tutorial.rst +++ b/docs/tutorials/aposmm_tutorial.rst @@ -209,4 +209,4 @@ can be found in libEnsemble's `WarpX Scaling Test`_. .. _Six-Hump Camel function: https://www.sfu.ca/~ssurjano/camel6.html .. _WarpX Scaling Test: https://github.com/Libensemble/libe-community-examples/tree/main/warpx .. |Open in Colab| image:: https://colab.research.google.com/assets/colab-badge.svg - :target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/aposmm/aposmm_tutorial_notebook.ipynb + :target: https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/aposmm/aposmm_tutorial_notebook.ipynb diff --git a/docs/tutorials/executor_forces_tutorial.rst b/docs/tutorials/executor_forces_tutorial.rst index e1f7d4b81..37c0b8c57 100644 --- a/docs/tutorials/executor_forces_tutorial.rst +++ b/docs/tutorials/executor_forces_tutorial.rst @@ -467,4 +467,4 @@ to generator and simulator functions. .. _forces_simple_with_input_file: https://github.com/Libensemble/libensemble/tree/main/libensemble/tests/scaling_tests/forces/forces_simple_with_input_file .. _GitHub: https://github.com/Libensemble/libensemble/issues .. |Open in Colab| image:: https://colab.research.google.com/assets/colab-badge.svg - :target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/forces_with_executor/forces_tutorial_notebook.ipynb + :target: https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/forces_with_executor/forces_tutorial_notebook.ipynb diff --git a/docs/tutorials/forces_gpu_tutorial.rst b/docs/tutorials/forces_gpu_tutorial.rst index dc74ad215..fd0642a6c 100644 --- a/docs/tutorials/forces_gpu_tutorial.rst +++ b/docs/tutorials/forces_gpu_tutorial.rst @@ -308,6 +308,6 @@ where ``SLURM_EXACT`` is set to help prevent resource conflicts on each node. .. _forces_gpu: https://github.com/Libensemble/libensemble/blob/develop/libensemble/tests/scaling_tests/forces/forces_gpu .. _forces_gpu_var_resources: https://github.com/Libensemble/libensemble/blob/develop/libensemble/tests/scaling_tests/forces/forces_gpu_var_resources/run_libe_forces.py .. _forces_multi_app: https://github.com/Libensemble/libensemble/blob/develop/libensemble/tests/scaling_tests/forces/forces_multi_app/run_libe_forces.py -.. _Frontier: https://youtu.be/H2fmbZ6DnVc +.. _Frontier: https://www.youtube.com/watch?v=H2fmbZ6DnVc&feature=youtu.be .. _Perlmutter: https://www.youtube.com/watch?v=Av8ctYph7-Y -.. _Polaris: https://youtu.be/Ff0dYYLQzoU +.. _Polaris: https://www.youtube.com/watch?v=Ff0dYYLQzoU&feature=youtu.be diff --git a/docs/tutorials/gpcam_tutorial.rst b/docs/tutorials/gpcam_tutorial.rst index 190697374..3def3a97b 100644 --- a/docs/tutorials/gpcam_tutorial.rst +++ b/docs/tutorials/gpcam_tutorial.rst @@ -348,4 +348,4 @@ The plot should look similar to the following. .. _gpCAM: https://github.com/lbl-camera/gpCAM .. |Open in Colab| image:: https://colab.research.google.com/assets/colab-badge.svg - :target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/gpcam_surrogate_model/gpcam.ipynb + :target: https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/gpcam_surrogate_model/gpcam.ipynb diff --git a/docs/tutorials/local_sine_tutorial/local_sine_tutorial.rst b/docs/tutorials/local_sine_tutorial/local_sine_tutorial.rst index 8413c3de7..f1e392a0d 100644 --- a/docs/tutorials/local_sine_tutorial/local_sine_tutorial.rst +++ b/docs/tutorials/local_sine_tutorial/local_sine_tutorial.rst @@ -28,4 +28,4 @@ need to write a new allocation function. local_sine_tutorial_5 .. |Open in Colab| image:: https://colab.research.google.com/assets/colab-badge.svg - :target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/simple_sine/sine_tutorial_notebook.ipynb + :target: https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/simple_sine/sine_tutorial_notebook.ipynb diff --git a/docs/tutorials/local_sine_tutorial/local_sine_tutorial_1.rst b/docs/tutorials/local_sine_tutorial/local_sine_tutorial_1.rst index 5c5db2ec8..f0ebb4832 100644 --- a/docs/tutorials/local_sine_tutorial/local_sine_tutorial_1.rst +++ b/docs/tutorials/local_sine_tutorial/local_sine_tutorial_1.rst @@ -25,4 +25,4 @@ If your system doesn't allow you to perform these installations, try adding ``--user`` to the end of each command. .. _Matplotlib: https://matplotlib.org/ -.. _NumPy: https://www.numpy.org/ +.. _NumPy: https://numpy.org/ diff --git a/docs/welcome.rst b/docs/welcome.rst index 01fdef442..64ddfed17 100644 --- a/docs/welcome.rst +++ b/docs/welcome.rst @@ -17,8 +17,8 @@ .. image:: https://github.com/Libensemble/libensemble/actions/workflows/extra.yml/badge.svg?branch=main :target: https://github.com/Libensemble/libensemble/actions - .. image:: https://codecov.io/github/Libensemble/libensemble/graph/badge.svg - :target: https://codecov.io/github/Libensemble/libensemble + .. image:: https://app.codecov.io/github/Libensemble/libensemble/graph/badge.svg + :target: https://app.codecov.io/github/Libensemble/libensemble .. image:: https://readthedocs.org/projects/libensemble/badge/?maxAge=2592000 :target: https://libensemble.readthedocs.org/en/latest/ diff --git a/libensemble/ensemble.py b/libensemble/ensemble.py index 24b47d72b..dc2ac806c 100644 --- a/libensemble/ensemble.py +++ b/libensemble/ensemble.py @@ -142,7 +142,7 @@ class Ensemble: libEnsemble Executor instance for use within simulator functions or generators. - H0: `NumPy structured array `_, Optional + H0: `NumPy structured array `_, Optional A libEnsemble history to be prepended to this run's history :ref:`(example)`. diff --git a/libensemble/gen_funcs/persistent_aposmm.py b/libensemble/gen_funcs/persistent_aposmm.py index ac9a152ec..2ed26104a 100644 --- a/libensemble/gen_funcs/persistent_aposmm.py +++ b/libensemble/gen_funcs/persistent_aposmm.py @@ -113,7 +113,7 @@ def aposmm(H, persis_info, gen_specs, libE_info): .. seealso:: - `test_persistent_aposmm_scipy `_ + `test_persistent_aposmm_scipy `_ for basic APOSMM usage. .. seealso:: diff --git a/libensemble/libE.py b/libensemble/libE.py index 219e2cd8c..091a79e7f 100644 --- a/libensemble/libE.py +++ b/libensemble/libE.py @@ -191,7 +191,7 @@ def libE( Specifications for libEnsemble :doc:`(example)` - H0: `NumPy structured array `_, Optional + H0: `NumPy structured array `_, Optional A libEnsemble history to be prepended to this run's history :ref:`(example)` @@ -199,7 +199,7 @@ def libE( Returns ------- - H: `NumPy structured array `_ + H: `NumPy structured array `_ History array storing rows for each point. :ref:`(example)` diff --git a/libensemble/tools/tools.py b/libensemble/tools/tools.py index 859664f5d..c95be227e 100644 --- a/libensemble/tools/tools.py +++ b/libensemble/tools/tools.py @@ -95,7 +95,7 @@ def save_libE_output( Parameters ---------- - H: `NumPy structured array `_ + H: `NumPy structured array `_ History array storing rows for each point. :ref:`(example)`