Merge pull request #6 from NREL/dev

Merging dev changes to main

.github/workflows/test_pvade.yaml

@@ -0,0 +1,38 @@
+name: test_pvade
+
+on:
+  push:
+    branches: [ main, dev ]
+  pull_request:
+    branches: [ main, dev ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # Job 1 of 2 - run pytest on code
+  pytest:
+    name: Pytest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Build Conda environment
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: environment.yaml
+      - name: Run pytest
+        shell: bash -l {0}
+        run: pytest -sv pvade/tests/
+
+  # Job 2 of 2 - enforce Black formatting
+  formatting:
+    name: Black formatting
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable

.gitignore

@@ -0,0 +1,7 @@
+.*
+!/.gitignore
+!/.readthedocs.yaml
+*.pyc
+*.egg-info/
+
+docs/_build/

.readthedocs.yaml

@@ -0,0 +1,14 @@
+# .readthedocs.yaml
+
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "mambaforge-4.10"
+
+sphinx:
+  configuration: docs/conf.py
+
+conda:
+  environment: environment.yaml

README.md

@@ -1,9 +1,15 @@
-# PVOPT
-This project will develop an open source fluid-structure interaction model which can be used as part of a modeling chain to provide stressor inputs to mechanical module models to study the physics of failure for degradation mechanisms such as cell cracking, weathering of cracked cells, and glass breakage.
+# PVade
 
-https://github.nrel.gov/pages/warsalan/PVOPT/
+`PVade` is an open source fluid-structure interaction model which can be used to study wind loading and stability on solar-tracking PV arrays. `PVade` can be used as part of a larger modeling chain to provide stressor inputs to mechanical module models to study the physics of failure for degradation mechanisms such as cell cracking, weathering of cracked cells, and glass breakage. For more information, visit the [PVade Documentation](TODO).
+
+[![test_pvade](https://github.com/NREL/PVade/actions/workflows/test_pvade.yaml/badge.svg)](https://github.com/NREL/PVade/actions/workflows/test_pvade.yaml)
+
+## Getting Started
+
+New users are encouraged to review the [Getting Started](TODO) guide which describes how to create the Conda environment and run the example simulations.
+
+## Developer Quick Start
 
-# Getting Started
 1. To use this software, begin by creating a Conda environment using the provided `environment.yaml` file:
     ```bash
     conda env create -n my_env_name -f environment.yaml

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/background/index.rst

@@ -0,0 +1,20 @@
+Background
+==========
+
+A collection of resources for further reading on PVade topics and the theory and implementation for solver elements.
+
+Fluid Solver
+------------
+
+
+
+Structural Solver
+-----------------
+
+
+
+PV Wind Loading and Stability
+-----------------------------
+
+* E. Young, "Predicting wind loading and instability in solar tracking PV arrays", PV Reliability Workshop (2023), https://www.nrel.gov/docs/fy23osti/85567.pdf. 
+

docs/conf.py

@@ -0,0 +1,59 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../pvade"))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "PVade"
+copyright = "2023, Walid Arsalane, Ethan Young"
+author = "Walid Arsalane, Ethan Young"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosectionlabel",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
+
+# 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"]
+
+autoclass_content = "both"

docs/how_to_guides/getting_started.rst

@@ -0,0 +1,23 @@
+Getting Started
+===============
+
+Building Conda Environment
+--------------------------
+
+To use this software, begin by creating a Conda environment using the provided ``environment.yaml`` file::
+
+  conda env create -n my_env_name -f environment.yaml
+
+where ``my_env_name`` can be replaced with a short name for your Conda environment. When the environment finishes installing, activate it with::
+
+  conda activate my_env_name
+
+from within your activate Conda environment, a simulation can be executed with::
+
+  python main.py --command_line_arg value
+
+
+Running Examples
+----------------
+
+.. Fill in with walkthrough pointing to an example

docs/how_to_guides/hpc_jobs.rst

@@ -0,0 +1,4 @@
+HPC Jobs
+========
+
+.. Fill in with walkthrough pointing to an example

docs/how_to_guides/index.rst

@@ -0,0 +1,8 @@
+How To Guides
+=============
+
+.. toctree::
+   :maxdepth: 1
+
+   getting_started
+   hpc_jobs

docs/index.rst

@@ -0,0 +1,30 @@
+.. PVade documentation master file, created by
+   sphinx-quickstart on Fri Mar 10 11:27:06 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to PVade's documentation!
+=================================
+
+PVade is an open source fluid-structure interaction model which can be used to study wind loading and stability on solar-tracking PV arrays. PVade can be used as part of a larger modeling chain to provide stressor inputs to mechanical module models to study the physics of failure for degradation mechanisms such as cell cracking, weathering of cracked cells, and glass breakage.
+
+Organization
+------------
+
+Documentation is currently organized into three main categories:
+
+* :ref:`How to Guides`: User guides covering basic topics and use cases for the PVade software
+* :ref:`Technical Reference`: Programming details on the PVade API and functions
+* :ref:`Background`: Information and research sources for fluid and structural solvers and PV topics
+
+New users may find it helpful to review the :ref:`Getting Started` materials first.
+
+Contents
+--------
+
+.. toctree::
+   :maxdepth: 2
+
+   how_to_guides/index
+   technical_reference/index
+   background/index

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/technical_reference/data_stream.rst

@@ -0,0 +1,6 @@
+DataStream
+==========
+
+.. automodule:: pvade.DataStream
+   :members:
+   :private-members:

docs/technical_reference/domain_creation.rst

@@ -0,0 +1,6 @@
+DomainCreation
+==============
+
+.. automodule:: pvade.geometry.template.TemplateDomainCreation
+   :members:
+   :private-members:

docs/technical_reference/domain_creation_panels.rst

@@ -0,0 +1,6 @@
+DomainCreationPanels
+====================
+
+.. automodule:: pvade.geometry.panels.DomainCreation
+   :members:
+   :private-members:

docs/technical_reference/flow_manager.rst

@@ -0,0 +1,6 @@
+FlowManager
+===========
+
+.. automodule:: pvade.FlowManager
+   :members:
+   :private-members:

docs/technical_reference/index.rst

@@ -0,0 +1,14 @@
+Technical Reference
+===================
+
+.. toctree::
+   :maxdepth: 1
+
+   parameters
+   data_stream
+   domain_creation_panels
+   domain_creation
+   mesh_manager
+   mesh_manager_2d
+   mesh_manager_3d
+   flow_manager

docs/technical_reference/mesh_manager.rst

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+MeshManager
+===========
+
+.. automodule:: pvade.geometry.MeshManager
+   :members:
+   :private-members:

docs/technical_reference/mesh_manager_2d.rst

@@ -0,0 +1,6 @@
+MeshManager2D
+=============
+
+.. automodule:: pvade.geometry.MeshManager2d
+   :members:
+   :private-members:

docs/technical_reference/mesh_manager_3d.rst

@@ -0,0 +1,6 @@
+MeshManager3d
+=============
+
+.. automodule:: pvade.geometry.MeshManager3d
+   :members:
+   :private-members:

docs/technical_reference/parameters.rst

@@ -0,0 +1,6 @@
+Parameters
+==========
+
+.. automodule:: pvade.Parameters
+   :members:
+   :private-members:

environment.yaml

@@ -1,4 +1,4 @@
-name: pvopt-env
+name: pvade
 channels:
   - conda-forge  
   - defaults
@@ -10,13 +10,16 @@ dependencies:
   - jsonschema
   - jupyter
   - matplotlib
+  - meshio
   - pandas
   - pytest
   - python-gmsh
   - pyyaml
   - scipy
   - snakeviz
+  - sphinx
   - tqdm
   - pip
   - pip:
-    - -e . # Installs the pvopt package
+    - sphinx-rtd-theme
+    - -e . # Installs the pvade package