Doc updates

.gitignore

@@ -164,3 +164,4 @@ cython_debug/
 # Ignore rendered examples
 doc/source/examples/
 doc/source/API/_autosummary/
+doc/source/autoapi

doc/source/conf.py

@@ -33,7 +33,7 @@
 
 # Intersphinx mapping
 intersphinx_mapping = {
-    "python": ("https://docs.python.org/dev", None),
+    "python": ("https://docs.python.org/3", None),
     "numpy": ("https://numpy.org/devdocs", None),
     "matplotlib": ("https://matplotlib.org/stable", None),
     "imageio": ("https://imageio.readthedocs.io/en/stable", None),
@@ -50,7 +50,7 @@
     # general
     "GL06",  # Found unknown section
     "GL07",  # Sections are in the wrong order.
-    "GL08",  # The object does not have a docstring
+    # "GL08",  # The object does not have a docstring
     "GL09",  # Deprecation warning should precede extended summary
     "GL10",  # reST directives {directives} must be followed by two colons
     # Summary

doc/source/getting-started/index.rst

@@ -1,50 +1,71 @@
 Getting started
 ===============
 
+************
 Installation
-~~~~~~~~~~~~
+************
 
-This package is not yet available on the public PyPI, but you can still install
-it using ``pip`` from the private PyPI repository.
+Python module
+~~~~~~~~~~~~~
 
-The following on Windows:
+The ``ansys.dyna.core`` package currently supports Python 3.8 through
+Python 3.10 on Windows, Mac OS, and Linux.
 
-.. code::
+Install the latest release from 
+`PyPI <pydyna_pypi_>`_ with:
 
-   set PYANSYS_PYPI_PRIVATE_PAT=<REDACTED>
-   set INDEX_URL=https://%PYANSYS_PYPI_PRIVATE_PAT%@pkgs.dev.azure.com/pyansys/_packaging/pyansys/pypi/simple/
-   python -m pip install ansys-dyna-core --index-url %INDEX_URL%
+.. code:: console
 
-And if you are running Linux:
+   pip install ansys-dyna-core
 
-.. code::
+Alternatively, install the latest from 
+`PyDyna GitHub <pydyna_issues_>`_ via:
 
-   PYANSYS_PYPI_PRIVATE_PAT=<REDACTED>
-   export INDEX_URL='https://$PYANSYS_PYPI_PRIVATE_PAT@pkgs.dev.azure.com/pyansys/_packaging/pyansys/pypi/simple/'
-   python -m pip install ansys-dyna-core --index-url $INDEX_URL
+.. code:: console
+
+   pip install git+https://github.com/pyansys/pydyna.git
+
 
-Email your friendly PyAnsys team member for the ``PYANSYS_PYPI_PRIVATE_PAT``
-at `pyansys.core@ansys.com <mailto:pyansys.core@ansys.com>`_ or send a message via Teams.
+For a local *development* version, install with:
 
-**Installing from git**
+.. code:: console
 
-If you have ``git`` installed and want the bleeding edge version:
+   git clone https://github.com/pyansys/pydyna.git
+   cd pydyna
+   pip install -e .
 
-.. code::
+This allows you to install the ``ansys-dyna-core`` module
+and modify it locally and have the changes reflected in your setup
+after restarting the Python kernel.
 
-   pip install -U git+https://github.com/pyansys/pyDyna@main
+Offline installation
+~~~~~~~~~~~~~~~~~~~~
+If you lack an internet connection on your install machine, the recommended way
+of installing PyDyna is downloading the wheelhouse archive from the 
+`Releases Page <pydyna_releases_>`_ for your corresponding
+machine architecture.
 
-You need to be logged into GitHub locally and be a member of the `PyAnsys Organization <https://github.com/pyansys>`_.
+Each wheelhouse archive contains all the Python wheels necessary to install
+PyDyna from scratch on Windows and Linux for Python 3.8 through 3.11. You can install
+this on an isolated system with a fresh Python or on a virtual environment.
 
-Alternatively, if you need to modify the repository locally (or want to
-do local development), you can clone it and install it in "development" mode with:
+For example, on Linux with Python 3.8, unzip it and install it with the following:
 
-.. code::
+.. code:: console
 
-   git clone https://github.com/pyansys/pyDyna
-   cd pyDyna
-   pip install -e .
+   unzip ansys-dyna-core-v0.3.1-wheelhouse-ubuntu-latest-3.8.zip wheelhouse
+   pip install ansys-dyna-core -f wheelhouse --no-index --upgrade --ignore-installed
+
+If you're on Windows with Python 3.8, unzip to a ``wheelhouse`` directory and
+install using the preceding command.
+
+Consider installing using a `virtual environment <using_venv_>`_.
+
+.. include:: ../../../docker/pre/README.rst
+.. include:: ../../../docker/solver/README.rst
 
-Note the ``-e`` flag, which denotes that you are in development mode.
-You can make changes in the local ``pyDyna`` and have them reflected
-in your local install of PyDyna.
+.. LINKS
+.. _pydyna_pypi: https://pypi.org/projects/ansys-dyna-core/
+.. _pydyna_releases: https://github.com/ansys/pydyna/releases
+.. _pydyna_issues: https://github.com/ansys/pydyna/issues
+.. _using_venv: https://docs.python.org/3/library/venv.html

doc/source/user-guide/index.rst

@@ -26,12 +26,3 @@ leaving a Python environment.
 
 Visit the `DPF-Post Documentation <https://post.docs.pyansys.com>`_ for a
 detailed description of the package
-
-.. toctree::
-   :hidden:
-
-   pydyna_pre
-   pydyna_solver
-   pydyna_post
-
-

docker/pre/README.rst

@@ -1,43 +1,38 @@
-Create your own pydyna-pre service docker container
-===================================================
+Build pydyna-pre service docker container
+:::::::::::::::::::::::::::::::::::::::::
 
 The pydyna-pre service Docker containers can be easily built by following
 these steps.
 
-Inside this folder, the instructions (i.e. ``Dockerfile`` files) for
-building the pydyna-pre service Docker containers are made available. 
+To build the docker image you will need to clone pydyna repo locally:
 
-* ``Dockerfile``: this file builds the Linux-based Docker image.
+.. code:: console
+
+   git clone https://github.com/pyansys/pydyna.git
+   cd pydyna
+
+*  ``docker/pre/Dockerfile``: this file builds the Linux-based Docker image.
 
 Prerequisites
 ^^^^^^^^^^^^^
 
 * Ensure that ``docker`` is installed in your machine.
   If you do not have ``docker`` available, please refer to the
   `official Docker site <https://www.docker.com>`_.
-  Note that the container can also be started on Windows if the Docker Desktop has been installed.
-  How to install the Docker Desktop: https://docs.docker.com/desktop/install/windows-install/
 
-* Download the latest release artifacts. You can do this as follows:
+* Download the latest release artifacts for the Linux
+  Docker container. You can do this as follows:
 
   * Latest Linux artifacts: `linux-binaries.zip <https://github.com/ansys/pydyna/releases/download/v0.2.1/linux-binaries.zip>`_
 
-* Move these ``.zip`` files to the current location (i.e. ``<repository-root-folder>/docker/pre``).
-
-Starting the docker container
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-There are two ways to start docker container.
-
-1.bulid image and run container
->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+* Move these ``.zip`` files to the current location (i.e. ``<repository-root-folder>/docker``).
 
 Building the Docker images
-::::::::::::::::::::::::::
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 In order to build your images, follow the next instructions:
 
-* Locate yourself at ``<repository-root-folder>/docker/pre`` in your terminal.
+* Locate yourself at ``<repository-root-folder>/docker`` in your terminal.
 * Run the following Docker command:
 
   .. code:: bash
@@ -61,13 +56,13 @@ In order to build your images, follow the next instructions:
      >>> ......                                                   ......                             ............   ..............   ......
 
 Run the image as a container
-::::::::::::::::::::::::::::
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 * Run the following Docker command:
 
   .. code:: bash
 
-     docker run -d -p 50051:50051 ghcr.io/ansys/ls-pre
+     docker run -d -p 50051:50051 ghcr.io/ansys/ls-pre .
 
 * Check that the image has been created successfully.   
 
@@ -76,19 +71,4 @@ Run the image as a container
 
 
      >>> CONTAINER ID   IMAGE                  COMMAND                  CREATED         STATUS         PORTS                                           NAMES
-     >>> c77ffd67f9fa   ghcr.io/ansys/ls-pre   "python3 ./linux-bin…"   7 seconds ago   Up 7 seconds   0.0.0.0:50051->50051/tcp, :::50051->50051/tcp   hardcore_margulis
-
-
-2.Start the container from docker-compose.yml file
->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-Make sure the docker compose have been installed on your computer.
-For more information: https://docs.docker.com/compose/install/
-
-* Locate yourself at ``<repository-root-folder>/docker/pre`` in your terminal.
-* Run the following Docker command:
-
-  .. code:: bash
-
-     docker compose up -d
-
+     >>> c77ffd67f9fa   ghcr.io/ansys/ls-pre   "python3 ./linux-bin…"   7 seconds ago   Up 7 seconds   0.0.0.0:50051->50051/tcp, :::50051->50051/tcp   hardcore_margulis

docker/solver/Dockerfile

@@ -0,0 +1,87 @@
+FROM centos:7
+#
+# The order of the lines in here should be (as much as possible) in
+# an order that will create the same series of intermediate images
+# no mater what version of dyna we are using.  This will speed up
+# experiments when creating containers over and over.  Ordering the
+# commands this way makes the Dockerfile a bit more confusing, because
+# for example we make all the directories up top, but don't put things
+# in them until further down.  And some environment variables are near
+# the top, but others near the bottom
+
+LABEL "com.ansys.description"="Ansys MPPDYNA with gRPC server"
+
+# install some missing stuff we want/need
+
+RUN yum -y install openssh-clients openssh-server bind-utils sudo python3
+RUN python3 -m pip install --upgrade pip
+RUN python3 -m pip install grpcio
+RUN python3 -m pip install grpcio-tools
+#
+ENV USER mpirun
+ENV HOME /home/mpirun
+ENV LD_LIBRARY_PATH /ansys_inc/lib
+ENV LSTC_LICENSE network
+ENV LSTC_LICENSE_SERVER license
+ENV SSHDIR ${HOME}/.ssh/
+
+
+RUN groupadd ${USER}
+RUN useradd -g ${USER} -d ${HOME} ${USER} && \
+    echo "${USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+#
+RUN mkdir -p /ansys_inc/lib
+RUN mkdir -p /rundir
+RUN mkdir /var/run/sshd
+RUN mkdir -p ${SSHDIR}
+RUN chown -R ${USER}:${USER} /rundir
+RUN chmod -R 755 /rundir
+WORKDIR /rundir
+
+# set up the runtime environment variables for
+# dyna
+
+RUN echo "export LD_LIBRARY_PATH=/ansys_inc/lib:/opt/openmpi/lib" > ${HOME}/.bashrc
+# Adding these causes problems because they can't be overridden
+# via the "environment" attribute in a docker-compose file.
+# The ENV commands above come through as defaults, but can be
+# overridden (to use the ANSYS license, or a different license server)
+#
+# RUN echo "export LSTC_LICENSE=network" >> ${HOME}/.bashrc
+# RUN echo "export LSTC_LICENSE_SERVER=license" >> ${HOME}/.bashrc
+#
+# Get ssh properly set up
+#
+RUN sed -i 's/PermitRootLogin without-password/PermitRootLogin yes/' /etc/ssh/sshd_config
+# SSH login fix. Otherwise user is kicked off after login
+RUN sed 's@session\s*required\s*pam_loginuid.so@session optional pam_loginuid.so@g' -i /etc/pam.d/sshd
+#
+EXPOSE 22
+CMD ["/usr/sbin/sshd", "-D"]
+#
+# Everything above here should not depend on the version of DYNA or the MPI we are using
+# and so should behave nicely as regards the Docker image cache.  Below here not so much
+#
+ENV PATH /opt/openmpi/bin:${PATH}
+RUN echo "export PATH=/opt/openmpi/bin:\${PATH}" >> ${HOME}/.bashrc
+
+ADD ssh/config ${SSHDIR}/config
+ADD ssh/id_rsa ${SSHDIR}/id_rsa
+ADD ssh/id_rsa.pub ${SSHDIR}/id_rsa.pub
+ADD ssh/id_rsa.pub ${SSHDIR}/authorized_keys
+RUN ssh-keygen -A
+
+RUN chmod -R 600 ${SSHDIR}* && \
+    chown -R ${USER}:${USER} ${SSHDIR}
+
+RUN chown -R ${USER}:${USER} ${HOME}
+
+# Copy the openmpi libraries
+
+RUN mkdir -p /opt
+COPY mpi /opt/openmpi
+
+# The executable will go in /ansys_inc, and the
+# ifort runtime libraries in /ansys_inc/lib
+
+COPY docker_dir /ansys_inc

docker/solver/README.rst

@@ -0,0 +1,67 @@
+Build pydyna-solver service docker container
+::::::::::::::::::::::::::::::::::::::::::::
+
+The pydyna-solver service Docker containers can be easily built by following
+these steps.
+
+* ``docker/solver/Dockerfile``: this file builds the Linux-based Docker image.
+
+Prerequisites
+^^^^^^^^^^^^^
+
+* Ensure that ``docker`` is installed in your machine.
+  If you do not have ``docker`` available, please refer to the
+  `official Docker site <https://www.docker.com>`_.
+
+* If you are building the image on Windows, you will need to have 
+  Windows Subsystem for Linux (WSL) installed. The instructions for that can be found `here <https://learn.microsoft.com/en-us/windows/wsl/install>`
+
+* Download the latest release artifacts for the Linux
+  Docker container. You can do this as follows:
+
+  * Latest Linux artifacts: `mppdyna_docker_centos7.zip <https://github.com/ansys/pydyna/releases/download/v0.2.1/mppdyna_docker_centos7.zip>`_
+
+* Move these ``.zip`` files to a local directory ``local_image_build_dir``.
+
+Building the Docker images
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In order to build your images, follow the next instructions:
+
+* cd to ``local_image_build_dir``.
+* Run the following Docker command:
+
+  .. code:: bash
+
+     ./do_build 
+
+* Check that the image has been created successfully. You should see an output similar
+  to this one when running the following command:
+
+  .. code:: bash
+
+     docker images
+
+     >>> REPOSITORY                        TAG                                        IMAGE ID       CREATED          SIZE
+     >>> dyna_solver_v04                   latest                                     defbadbeee8e   16 minutes ago   730MB
+     >>> ......                                                   ......                             ............   ..............   ......
+
+Run the image as a container
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+* Edit the docker-compose.yml file and replace ``<license_server_name>`` with the correct license server hosting the DYNA license.
+  If you are using Ansy Flexlm license 
+
+* Run the following Docker command:
+
+  .. code:: bash
+
+     docker-compose up
+
+* Check that the image has been created successfully.   
+
+
+.. code:: bash
+
+     >>> CONTAINER ID   IMAGE             COMMAND                  CREATED          STATUS         PORTS                            NAMES
+     >>> be84c95db31d   dyna_solver_v04   "/ansys_inc/server.p…"   18 minutes ago   Up 8 seconds   22/tcp, 0.0.0.0:5000->5000/tcp   mppdyna_docker_centos7_dyna_1