Merge pull request #175 from rosswhitfield/updates

Small documentation/code/testing updates

.github/workflows/conda_env/environment_dask_2.30.0.yml

@@ -1,8 +1,9 @@
+# same as NERSC Cori module python/3.8-anaconda-2020.11
 name: ips_test_dask_2.30
 channels:
 - conda-forge
 dependencies:
-- pytest-cov
+- pytest-cov<4
 - pytest-timeout
 - psutil
 - mpi4py

.github/workflows/conda_env/environment_dask_2.5.2.yml

@@ -1,8 +1,9 @@
+# same as NERSC Cori module python/3.7-anaconda-2019.10
 name: ips_test_dask_2.5
 channels:
 - conda-forge
 dependencies:
-- pytest-cov
+- pytest-cov<4
 - pytest-timeout
 - psutil
 - mpi4py

.github/workflows/conda_env/environment_dask_2022.7.0.yml

@@ -0,0 +1,13 @@
+# same as NERSC Perlmutter module python/3.9-anaconda-2021.11
+name: ips_test_dask_2022.7.0
+channels:
+- conda-forge
+dependencies:
+- pytest-cov<4
+- pytest-timeout
+- psutil
+- mpi4py
+- openmpi
+- dask=2022.7.0
+- coverage!=6.3
+- flask=2.2.2

.github/workflows/conda_env/environment_linux.yml

@@ -2,11 +2,12 @@ name: ips_test
 channels:
 - conda-forge
 dependencies:
-- pytest-cov
+- pytest-cov<4
 - pytest-timeout
 - psutil
 - mpi4py
-- dask=2022.08.1
+- openmpi
+- dask=2022.9.2
 - dakota
 - coverage!=6.3
 - flask=2.2.2

.github/workflows/conda_env/environment_macos.yml

@@ -2,7 +2,7 @@ name: ips_test
 channels:
 - conda-forge
 dependencies:
-- pytest-cov
+- pytest-cov<4
 - pytest-timeout
 - psutil
 - dask=2022.08.1

.github/workflows/conda_env/environment_minimal.yml

@@ -2,7 +2,7 @@ name: ips_test_minimal
 channels:
 - conda-forge
 dependencies:
-- pytest-cov
+- pytest-cov<4
 - pytest-timeout
 - psutil
 - coverage!=6.3

.github/workflows/conda_env/environment_static_analysis.yml

@@ -4,10 +4,10 @@ channels:
 dependencies:
 - python=3.8
 - flake8=5.0.4
-- pylint=2.15.0
+- pylint=2.15.3
 - bandit=1.7.4
 - codespell=2.2.1
-- dask=2022.08.1
+- dask=2022.9.2
 - pytest
 - flask=2.2.2
 - configobj

.github/workflows/workflows.yml

@@ -13,7 +13,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - uses: conda-incubator/setup-miniconda@v2
       with:
         auto-update-conda: true
@@ -45,22 +45,22 @@ jobs:
             conda_env: 'minimal'
           - os: ubuntu-latest
             python-version: 3.7
-            conda_env: 'dask_2.5.2' # same as NERSC Cori module python/3.7-anaconda-2019.10
+            conda_env: 'dask_2.5.2'
           - os: ubuntu-latest
             python-version: 3.8
-            conda_env: 'dask_2.30.0' # same as NERSC Cori module python/3.8-anaconda-2020.11
+            conda_env: 'dask_2.30.0'
           - os: ubuntu-latest
             python-version: 3.9
-            conda_env: 'linux'
+            conda_env: 'dask_2022.7.0'
           - os: ubuntu-latest
             python-version: "3.10"
-            conda_env: 'minimal'
+            conda_env: 'linux'
           - os: macos-latest
             python-version: 3.9
             conda_env: 'macos'
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - uses: conda-incubator/setup-miniconda@v2
       with:
         auto-update-conda: true
@@ -76,7 +76,7 @@ jobs:
     - name: Test with pytest
       run: python -m pytest --cov --cov-report=xml --cov-report=term --timeout=60
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
 
   tests-wsl:
 
@@ -87,7 +87,7 @@ jobs:
          shell: wsl-bash {0}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - run: wsl --set-default-version 1
       shell: cmd
     - uses: Vampire/setup-wsl@v1

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2006-2021, UT-Battelle, LLC. All rights reserved.
+Copyright 2006-2022, UT-Battelle, LLC. All rights reserved.
 
 Redistribution and use in source and binary forms, with or without 
 modification, are permitted provided that the following conditions 

doc/conf.py

@@ -1,5 +1,5 @@
 #-------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 #-------------------------------------------------------------------------------
 # -*- coding: utf-8 -*-
 #
@@ -43,7 +43,7 @@
 
 # General information about the project.
 project = u'Integrated Plasma Simulator (IPS)'
-copyright = u'2006-2021, UT-Battelle, LLC'
+copyright = u'2006-2022, UT-Battelle, LLC'
 
 from ipsframework._version import get_versions
 # The version info for the project you're documenting, acts as replacement for

doc/examples/component_skeleton.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-#  Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+#  Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 
 """

doc/examples/example_comp.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-#  Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+#  Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 
 """

doc/examples/skeleton_comp.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-#  Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+#  Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 
 """

doc/getting_started/getting_started.rst

@@ -19,9 +19,11 @@ The IPS code is currently located on the GitHub repository. In order to checkout
 Dependencies
 ------------
 
-**IPS Proper**
-
-The IPS framework is written in Python_, and requires Python 3.6+.  There are a few other packages that may be needed for certain components or utilities.  The framework does use the Python package ConfigObj_, however the source is already included and no package installation is necessary (likewise for Python 3.6 and the processing module).
+The IPS framework is written in Python_, and requires Python 3.6+.
+There are a few other packages that may be needed for certain
+components or utilities. The framework does use the Python package
+ConfigObj_, and urllib3_ is used to communicate with the
+:ref:`ips-portal`.
 
 Other Utilities
 ---------------
@@ -52,15 +54,18 @@ Other Utilities
 .. _Scipy: https://numpy.org
 .. _ConfigObj: http://configobj.readthedocs.io
 .. _Python: http://python.org
+.. _urllib3: https://urllib3.readthedocs.io
 
 .. _installing-ips:
 
 Building and Setting up Your Environment
 ========================================
 
-IPS itself doesn't have any dependencies to run except python version
-≥ 3.6. There is an optional dependency `Dask <https://dask.org>`_ that
-will enable Dask to be used for task pool scheduling, see
+IPS has two dependencies (ConfigObj_ and urllib3_) required to run in
+addition to python version ≥ 3.6. The dependencies will be
+automatically installed when you install ``ipsframework``. There is an
+optional dependency `Dask <https://dask.org>`_ that will enable Dask
+to be used for task pool scheduling, see
 :meth:`~ipsframework.services.ServicesProxy.submit_tasks`. IPS is
 tested to work with dask and distributed ≥ 2.5.2 but may work with
 earlier versions.

doc/user_guides/portal_guides.rst

@@ -1,3 +1,5 @@
+.. _ips-portal:
+
 ==========
 IPS Portal
 ==========

ipsframework/cca_es_spec.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 """
 The CCA event service, but without CCA-specific extensions:

ipsframework/component.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 """IPS Framework Component"""
 import sys

ipsframework/componentRegistry.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 import sys
 

ipsframework/configurationManager.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 import os
 import sys

ipsframework/convert_log_function.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 from ipsframework.utils import HTML
 

ipsframework/dakota_bridge.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 import os
 import sys

ipsframework/dataManager.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 import sys
 import os

ipsframework/debug.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 """
 This file writes debug messages to 'debug.out' file if the environment

ipsframework/eventService.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 """
 This file hosts the central event service and is not directly accessible to IPS.

ipsframework/eventServiceProxy.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 
 

ipsframework/ips.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 """
    The Integrated Plasma Simulator (IPS) Framework. This framework enables

ipsframework/ipsExceptions.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 
 

ipsframework/ips_dakota_client.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 
 import os

ipsframework/ips_dakota_dynamic.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 
 import os

ipsframework/ips_es_spec.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 from .cca_es_spec import EventListener, PublisherEventService, SubscriberEventService
 

ipsframework/ipsutil.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 import os
 import shutil

ipsframework/messages.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 
 

ipsframework/node_structure.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 """
 Node structures for RM are implemented here for convenience.

ipsframework/platformspec.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 import os
 import sys

ipsframework/portalBridge.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------
-# Copyright 2006-2021 UT-Battelle, LLC. See LICENSE for more information.
+# Copyright 2006-2022 UT-Battelle, LLC. See LICENSE for more information.
 # -------------------------------------------------------------------------------
 import re