Merge branch 'develop' into refactor/pathlib

.github/workflows/ci.yml

@@ -20,11 +20,11 @@ jobs:
                 include:
                     - os: macos-latest
                       python-version: 3.9
-                      mpi-version: "mpich"
+                      mpi-version: "mpich=4.0.3"
                       comms-type: m
                     - os: macos-latest
                       python-version: 3.9
-                      mpi-version: "mpich"
+                      mpi-version: "mpich=4.0.3"
                       comms-type: l
                     - os: ubuntu-latest
                       python-version: "3.10"

.readthedocs.yml

@@ -13,7 +13,7 @@ formats:
   - pdf
 
 python:
-    version: 3.7
+    version: 3.8
     install:
       - requirements: docs/requirements.txt
       - method: pip

README.rst

@@ -38,8 +38,8 @@ increased parallelism.
 libEnsemble aims for:
 
 • **Extreme scaling**: Run on or across_ laptops, clusters, and leadership-class machines.
-• **Dynamic Ensembles**: Generate new tasks on-the-fly based on previous computations.
-• **Dynamic Resource Management**: Reassign resource partitions of any size for tasks.
+• **Dynamic ensembles**: Generate new tasks on-the-fly based on previous computations.
+• **Dynamic resource management**: Reassign resource partitions of any size for tasks.
 • **Monitoring/killing of applications**: Ensemble members can poll or kill running apps.
 • **Resilience/fault tolerance**: libEnsemble can restart incomplete tasks or entire ensembles.
 • **Portability and flexibility**: Run identical libEnsemble scripts on different machines.

docs/conf.py

@@ -20,16 +20,11 @@
 import os
 import sys
 from datetime import datetime
+from unittest.mock import MagicMock
 
 exec(open("../libensemble/version.py").read())
 
 
-if sys.version_info >= (3, 3):
-    from unittest.mock import MagicMock
-else:
-    from mock import MagicMock
-
-
 class Mock(MagicMock):
     @classmethod
     def __getattr__(cls, name):
@@ -87,8 +82,7 @@ def __getattr__(cls, name):
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #
-needs_sphinx = "3.3"
-nitpicky = True
+needs_sphinx = "5.3"
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -102,6 +96,7 @@ def __getattr__(cls, name):
     "sphinx.ext.imgconverter",
     "sphinx.ext.mathjax",
     "sphinxcontrib.autodoc_pydantic",
+    "sphinx_design",
 ]
 bibtex_bibfiles = ["references.bib"]
 bibtex_default_style = "unsrt"
@@ -210,7 +205,7 @@ def __getattr__(cls, name):
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+# html_static_path = ["_static"]
 # html_static_path = []
 
 

docs/examples/alloc_funcs.rst

@@ -22,11 +22,7 @@ give_sim_work_first
   :members:
   :undoc-members:
 
-.. container:: toggle
-
-   .. container:: header
-
-      :underline:`give_sim_work_first.py`
+.. dropdown:: :underline:`give_sim_work_first.py`
 
    .. literalinclude:: ../../libensemble/alloc_funcs/give_sim_work_first.py
       :language: python
@@ -38,22 +34,12 @@ fast_alloc
   :members:
   :undoc-members:
 
-.. container:: toggle
-
-   .. container:: header
-
-      :underline:`fast_alloc.py`
+.. dropdown:: :underline:`fast_alloc.py`
 
    .. literalinclude:: ../../libensemble/alloc_funcs/fast_alloc.py
       :language: python
       :linenos:
 
-fast_alloc_to_aposmm
---------------------
-.. automodule:: fast_alloc_to_aposmm
-  :members:
-  :undoc-members:
-
 .. _start_only_persistent_label:
 
 start_only_persistent
@@ -62,11 +48,7 @@ start_only_persistent
   :members:
   :undoc-members:
 
-.. container:: toggle
-
-   .. container:: header
-
-      :underline:`start_only_persistent.py`
+.. dropdown:: :underline:`start_only_persistent.py`
 
    .. literalinclude:: ../../libensemble/alloc_funcs/start_only_persistent.py
       :language: python

docs/examples/sampling.rst

@@ -8,11 +8,7 @@ sampling
   :members:
   :undoc-members:
 
-.. container:: toggle
-
-   .. container:: header
-
-      :underline:`sampling.py`
+.. dropdown:: :underline:`sampling.py`
 
    .. literalinclude:: ../../libensemble/gen_funcs/sampling.py
       :language: python
@@ -24,11 +20,7 @@ persistent_sampling
   :members:
   :undoc-members:
 
-.. container:: toggle
-
-   .. container:: header
-
-      :underline:`persistent_sampling.py`
+.. dropdown:: :underline:`persistent_sampling.py`
 
    .. literalinclude:: ../../libensemble/gen_funcs/persistent_sampling.py
       :language: python

docs/examples/sim_funcs.rst

@@ -19,11 +19,7 @@ six_hump_camel
   :members:
   :undoc-members:
 
-.. container:: toggle
-
-   .. container:: header
-
-      :underline:`six_hump_camel.py`
+.. dropdown:: :underline:`six_hump_camel.py`
 
    .. literalinclude:: ../../libensemble/sim_funcs/six_hump_camel.py
       :language: python
@@ -41,11 +37,7 @@ noisy_vector_mapping
   :members:
   :undoc-members:
 
-.. container:: toggle
-
-   .. container:: header
-
-      :underline:`noisy_vector_mapping.py`
+.. dropdown:: :underline:`noisy_vector_mapping.py`
 
    .. literalinclude:: ../../libensemble/sim_funcs/noisy_vector_mapping.py
       :language: python
@@ -68,11 +60,7 @@ executor_hworld
 .. automodule:: executor_hworld
   :members:
 
-.. container:: toggle
-
-   .. container:: header
-
-      :underline:`executor_hworld.py`
+.. dropdown:: :underline:`executor_hworld.py`
 
    .. literalinclude:: ../../libensemble/sim_funcs/executor_hworld.py
       :language: python

docs/examples/tasmanian.rst

@@ -15,11 +15,7 @@ use either *venv* or *--user* install.
 .. role:: underline
     :class: underline
 
-.. container:: toggle
-
-   .. container:: header
-
-      :underline:`persistent_tasmanian.py`
+.. dropdown:: :underline:`persistent_tasmanian.py`
 
    .. literalinclude:: ../../libensemble/gen_funcs/persistent_tasmanian.py
       :language: python

docs/platforms/polaris.rst

@@ -22,11 +22,7 @@ To install further packages, including updating libEnsemble, you may either crea
 a virtual environment on top of this (if just using ``pip install``) or clone the base
 environment (if you need ``conda install``). More details at `Python for Polaris`_.
 
-.. container:: toggle
-
-   .. container:: header
-
-      Example of Conda + virtual environment
+.. dropdown:: Example of Conda + virtual environmentggle
 
    E.g.,~  to create a virtual environment that allows installation of further packages::
 

docs/requirements.txt

@@ -2,3 +2,4 @@ sphinx==5.3.0
 sphinxcontrib-bibtex
 ipykernel
 autodoc_pydantic
+sphinx-design

docs/running_libE.rst

@@ -139,11 +139,8 @@ a calling script in a familiar manner::
 
 This produces an initial ``my_calling_script.json`` serialization conforming to PSI/J's specification:
 
-.. container:: toggle
-
-    .. container:: header
-
-       ``my_calling_script.json``
+.. dropdown:: `my_calling_script.json``
+    :color: success
 
     .. code-block:: JSON
 
@@ -209,11 +206,8 @@ Results in::
 
 This also produces a Job-specific representation, e.g:
 
-.. container:: toggle
-
-    .. container:: header
-
-      ``8ba9de56.my_calling_script.json``
+.. dropdown:: ``8ba9de56.my_calling_script.json``
+    :color: success
 
     .. code-block:: JSON
 

docs/tutorials/executor_forces_tutorial.rst

@@ -144,11 +144,7 @@ Write an alternative Calling Script similar to above, but with the following dif
  3. Set :ref:`libEnsemble's logger<logger_config>` to print debug messages.
  4. Use the :meth:`save_libE_output()<tools.save_libE_output>` function to save the History array and ``persis_info`` to files after libEnsemble completes.
 
-.. container:: toggle
-
-   .. container:: header
-
-      **Click Here for Solution**
+.. dropdown:: **Click Here for Solution**
 
    .. code-block:: python
        :linenos:
@@ -357,11 +353,7 @@ These may require additional browsing of the documentation to complete.
      then reads the output ``.stat`` file, and calls :meth:`task.kill()<executor.Task.kill>` if the output file contains ``"kill\n"``
      or if ``task.runtime`` exceeds sixty seconds.
 
-.. container:: toggle
-
-   .. container:: header
-
-      **Click Here for Solution**
+.. dropdown:: **Click Here for Solution**
 
    .. code-block:: python
        :linenos:

docs/tutorials/local_sine_tutorial.rst

@@ -123,11 +123,7 @@ Exercise
 Write a simple generator function that instead produces random integers, using
 the ``numpy.random.Generator.integers(low, high, size)`` function.
 
-.. container:: toggle
-
-   .. container:: header
-
-      **Click Here for Solution**
+.. dropdown:: **Click Here for Solution**
 
    .. code-block:: python
        :linenos:
@@ -185,11 +181,7 @@ Exercise
 Write a simple simulator function that instead calculates the *cosine* of a received
 value, using the ``numpy.cos(x)`` function.
 
-.. container:: toggle
-
-   .. container:: header
-
-      **Click Here for Solution**
+.. dropdown:: **Click Here for Solution**
 
    .. code-block:: python
        :linenos:
@@ -353,11 +345,7 @@ Write a Calling Script with the following specifications:
   4. Set libEnsemble to stop execution after 160 *generations* using the ``gen_max`` key
   5. Print an error message if any errors occurred while libEnsemble was running
 
-.. container:: toggle
-
-   .. container:: header
-
-      **Click Here for Solution**
+.. dropdown:: **Click Here for Solution**
 
    .. code-block:: python
        :linenos:

install/environment.yml

@@ -4,4 +4,4 @@ channels:
 
 dependencies:
  - sphinxcontrib-bibtex
- - python>=3.7
+ - python>=3.8

install/testing_requirements.txt

@@ -6,3 +6,4 @@ pytest-timeout==2.1.0
 mock==4.0.3
 coveralls==3.3.1
 python-dateutil==2.8.2
+anyio==3.6.2