complete the merge from develop

.readthedocs.yaml

@@ -14,6 +14,12 @@ build:
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: src/docs/sphinx/conf.py
+
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 # formats:
 #    - pdf
+
+# Set requirements required to build your docs
+python:
+  install:
+    - requirements: src/docs/sphinx/requirements.txt

CHANGELOG.md

@@ -11,7 +11,10 @@ and this project aspires to adhere to [Semantic Versioning](https://semver.org/s
 
 ### Added
 - Added parameters to control HDF5 compression options to the Relay Extract.
+- Added check to make sure all domain IDs are unique
 
+### Changed
+- Changed the Data Binning filter to accept a `reduction_field` parameter (instead of `var`), and similarly the axis parameters to take `field` (instead of `var`).  The `var` style parameters are still accepted, but deprecated and will be removed in a future release.
 
 ## [0.9.2] - Released 2023-06-30
 ### Preferred dependency versions for [email protected]

package.py

@@ -27,7 +27,7 @@ def create_package(output_file=None):
          suffix = "tar"
          t = datetime.datetime.now()
          output_file = "%s.%04d.%02d.%02d.%s" % (repo_name,t.year,t.month,t.day,suffix)
-    cmd = "python " + pkg_script + " --prefix=ascent " + output_file
+    cmd = "python3 " + pkg_script + " --prefix=ascent " + output_file
     print("[exe: {}]".format(cmd))
     subprocess.call(cmd,shell=True)
 

scripts/build_ascent/build_ascent.sh

@@ -169,7 +169,7 @@ if [ ! -d ${zlib_install_dir} ]; then
 if ${build_zlib}; then
 if [ ! -d ${zlib_src_dir} ]; then
   echo "**** Downloading ${zlib_tarball}"
-  curl -L https://www.zlib.net/zlib-${zlib_version}.tar.gz -o ${zlib_tarball}
+  curl -L https://github.com/madler/zlib/releases/download/v${zlib_version}/zlib-${zlib_version}.tar.gz -o ${zlib_tarball}
   tar -xzf ${zlib_tarball}
 fi
 

scripts/ci/docker/alpinedav_ubuntu_18.04_cuda_11.4.0_devel_tpls/build.sh

@@ -8,6 +8,6 @@ export TAG_BASE=alpinedav/ascent-ci:ubuntu-18.04-cuda-11.4.0-devel-tpls
 
 date
 
-python ../build_and_tag.py ${TAG_BASE}
+python3 ../build_and_tag.py ${TAG_BASE}
 
 date

scripts/ci/docker/alpinedav_ubuntu_20.04_cuda_12.1.1_devel_tpls/build.sh

@@ -8,6 +8,6 @@ export TAG_BASE=alpinedav/ascent-ci:ubuntu-20.04-cuda-12.1.1-devel-tpls
 
 date
 
-python ../build_and_tag.py ${TAG_BASE}
+python3 ../build_and_tag.py ${TAG_BASE}
 
 date

scripts/ci/docker/alpinedav_ubuntu_20.04_devel_tpls/build.sh

@@ -8,7 +8,7 @@ export TAG_BASE=alpinedav/ascent-ci:ubuntu-20.04-devel-tpls
 
 date
 
-python ../build_and_tag.py ${TAG_BASE}
+python3 ../build_and_tag.py ${TAG_BASE}
 
 date
 

scripts/ci/docker/alpinedav_ubuntu_20.04_rocm_5.1.3_devel_tpls/build.sh

@@ -8,6 +8,6 @@ export TAG_BASE=alpinedav/ascent-ci:ubuntu-20.04-rocm-5.1.3-devel-tpls
 
 date
 
-python ../build_and_tag.py ${TAG_BASE}
+python3 ../build_and_tag.py ${TAG_BASE}
 
 date

scripts/ci/docker/alpinedav_ubuntu_22.04_devel_tpls/build.sh

@@ -8,7 +8,7 @@ export TAG_BASE=alpinedav/ascent-ci:ubuntu-22.04-devel-tpls
 
 date
 
-python ../build_and_tag.py ${TAG_BASE}
+python3 ../build_and_tag.py ${TAG_BASE}
 
 date
 

scripts/ci/docker/build_and_tag.py

@@ -86,7 +86,7 @@ def main():
     os.chdir("../../../../")
 
     # get current copy of the ascent source
-    cmd ='python package.py {0}'
+    cmd ='python3 package.py {0}'
     sexe(cmd.format(pjoin(orig_dir, "ascent.docker.src.tar.gz")))
 
     # change back to orig working dir

src/docs/sphinx/Actions/Examples.rst

@@ -25,6 +25,8 @@ Resulting image:
 
 .. image:: examples/tout_render_3d_points_const_radius100.png
 
+.. _screen_annotations_off:
+
 An example of rendering with no screen annotations.
 ----------------------------------------------------
 
@@ -80,6 +82,8 @@ Resulting image:
 
 .. image:: examples/tout_vector_component100.png
 
+.. _world_annotations_off:
+
 An example of rendering with no world annotations.
 ---------------------------------------------------
 
@@ -718,6 +722,17 @@ Resulting image:
 
 .. image:: examples/tout_gradient_mag_braid100.png
 
+An example of data binning, binning spatially and summing a field.
+-------------------------------------------------------------------
+
+YAML actions:
+
+.. literalinclude:: examples/tout_binning_filter_bins100.yaml
+
+Resulting image:
+
+.. image:: examples/tout_binning_filter_bins100.png
+
 An example of using the log10 filter and clamping the min value. This can help when there are negative values present.
 -----------------------------------------------------------------------------------------------------------------------
 

src/docs/sphinx/Actions/Scenes.rst

@@ -395,7 +395,7 @@ parameters:
 - ``fg_color`` : an array of three floating point values that controls the foreground color. The foreground color is used to color annotations and mesh plot lines.
 - ``annotations`` : controls if annotations are rendered or not. Valid values are ``"true"`` and ``"false"``.
 - ``render_bg`` : controls if the background is rendered or not. If no background is rendered, the background will appear transparent. Valid values are ``"true"`` and ``"false"``.
-- ``dataset_bounds`` : controls the dimensions of the rendered bounding box around the dataset. This will overwrite the default bounding box based on the dataset's dimensions. A valid value is an array of six floats ([xMin,xMax,yMin,yMax,zMin,zMax]) that define dimensions larger than the default.  
+- ``dataset_bounds`` : controls the dimensions of the rendered bounding box around the dataset. This will overwrite the default bounding box based on the dataset's dimensions. A valid value is an array of six floats ([xMin,xMax,yMin,yMax,zMin,zMax]) that define dimensions larger than the default. Note: this does not control annotations. To turn off dataset annotations, see :ref:`world_annotations_off`. To turn off screen annotations, see :ref:`screen_annotations_off`.
 - ``color_bar_position`` : controls the position of 1 or more color bars. A valid value for positioning a single color bar is an array of four floats ([xMin,xMax,yMin,yMax]). A valid value for positioning N color bars is an array of 4*N floats ([xMin1_0,xMax1_0,yMin1_0,yMax1_0,...,xMin_n,xMax_n,yMin_n,yMax_n]). This repositioning is performed in Screen Space, so valid minimum and maximum values are limited to the range [-1,1] (i.e. the origin (0,0) is in the center of the image, (-1,-1) is the bottom-left corner, and (1,1) is the top-right corner). Note: Ascent does not check for correctness of user positioned color bars.
 
 
@@ -464,7 +464,7 @@ The code below creates a pipeline that first applies a contour filter and then a
     :align: center
 
     The camera placement chosen by the VQ metric DDS Entropy for this example.
-    This example and implementation of the other VQ metrics can be found in `auto_camera test <https://github.com/Alpine-DAV/ascent/blob/develop/src/tests/vtkh/t_vtk-h_auto_camera.cpp>`_.
+    This example and implementation of the other VQ metrics can be found in `auto_camera test <https://github.com/Alpine-DAV/ascent/blob/develop/src/tests/ascent/t_ascent_render_auto_camera.cpp>`_.
 
 .. _actions_cinema:
 

src/docs/sphinx/Actions/examples/tout_binning_filter_bins100.yaml

@@ -0,0 +1,38 @@
+#An example of data binning, binning spatially and summing a field.
+
+- 
+  action: "add_pipelines"
+  pipelines: 
+    pl1: 
+      f1: 
+        type: "binning"
+        params: 
+          reduction_op: "sum"
+          reduction_field: "braid"
+          output_field: "binning"
+          output_type: "bins"
+          axes: 
+            - 
+              field: "x"
+              num_bins: 10
+              min_val: -10.0
+              max_val: 10.0
+              clamp: 1
+            - 
+              field: "y"
+              num_bins: 10
+              clamp: 0
+            - 
+              field: "z"
+              num_bins: 10
+              clamp: 10
+- 
+  action: "add_scenes"
+  scenes: 
+    s1: 
+      plots: 
+        p1: 
+          type: "pseudocolor"
+          field: "binning"
+          pipeline: "pl1"
+      image_prefix: "/Users/harrison37/Work/alpine/ascent/build-debug/tests/_output/tout_binning_filter_bins"

src/docs/sphinx/Tutorial.rst

@@ -8,7 +8,7 @@
 Tutorial Overview
 ==================
 
-`Ascent Tutorial Intro Slides [pdf] <https://www.ascent-dav.org/tutorial/2022_08_23_ascent_intro.pdf>`_
+`Ascent Tutorial Intro Slides [pdf] <https://www.ascent-dav.org/tutorial/2023_08_22_ascent_intro.pdf>`_
 
 
 This tutorial introduces how to use Ascent, including basics about:
@@ -22,12 +22,11 @@ Ascent installs include standalone C++, Python, and Python-based Jupyter noteboo
 You can find the tutorial source code and notebooks in your Ascent install directory under ``examples/ascent/tutorial/ascent_intro/`` and the Cloverleaf3D demo files under ``examples/ascent/tutorial/cloverleaf_demos/``.
 
 
-Scheduled Tutorials:
 
+Tutorials:
+ * `In-Situ Analysis and Visualization with Ascent and ParaView Catalyst <https://sc23.supercomputing.org/presentation/?id=tut133&sess=sess211>`_ - November 2023, Denver, CO, USA
+ * `Introduction to Ascent, a Flyweight In Situ Visualization and Analysis for HPC Simulations @ LLNL's RADIUSS AWS Tutorial Series 2023 <https://software.llnl.gov/radiuss/event/2023/07/11/radiuss-on-aws/>`_ - August 2023, Virtual
  * `Introduction to Ascent, a Flyweight In Situ Visualization and Analysis for HPC Simulations @ LLNL's RADIUSS AWS Tutorial Series 2022 <https://software.llnl.gov/radiuss/event/2022/07/07/radiuss-on-aws/>`_ - August 2022, Virtual
-
-
-Past Tutorials:
  * `In Situ Analysis and Visualization with ParaView Catalyst and Ascent @ ISC 2022 <https://app.swapcard.com/widget/event/isc-high-performance-2022/planning/UGxhbm5pbmdfODYxMTUx>`_ - May 2022, Hamburg, Germany 
  * ECP 2022 Annual Meeting - May 2022, Virtual
  * `In Situ Analysis and Visualization with SENSEI and Ascent @ SC21 <https://sc21.supercomputing.org/presentation/?id=tut127&sess=sess190>`_ - Nov 2021, Virtual

src/docs/sphinx/Tutorial_Setup.rst

@@ -62,95 +62,95 @@ You can also launch the a Jupyter Notebook server from this image using the foll
 The url (http://localhost:8888) and password (``learn``) are the same as above.
 
 
-.. _tutorial_setup_public_installs:
-
-Using Public Installs of Ascent
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This section provides info about public installs we provide on several HPC machines.
-
-Additionally, here is a `link to the scripts used to build our public installs <https://github.com/Alpine-DAV/ascent/tree/develop/scripts/spack_install>`_ .
-
-OLCF Summit Installs
-+++++++++++++++++++++++
-
-
-* Build Details: gcc 9.3.0 with OpenMP and MPI support
-* Modules: ``gcc/9.3.0``
-* Location: ``/sw/summit/ums/ums010/ascent/current/summit/openmp/gnu/ascent-install/``
-
-You can copy the tutorial examples from this install and use them as follows:
-
-.. literalinclude:: tutorial_setup_olcf_summit_openmp_test.sh
-   :language: bash
-
-* Build Details: gcc 9.3.0 with CUDA 11.0.3 and MPI support
-* Modules: ``gcc/9.3.0`` ``cuda/11.0.3``
-* Location: ``/sw/summit/ums/ums010/ascent/current/summit/cuda/gnu/ascent-install/``
-
-You can copy the tutorial examples from this install and use them as follows:
-
-.. literalinclude:: tutorial_setup_olcf_summit_cuda_test.sh
-   :language: bash
-
-
-NERSC Perlmuter Install
-+++++++++++++++++++++++
-
-* Build Details: gcc 10.3.0 with CUDA 11.4.0 and MPI support
-* Modules: ``PrgEnv-gnu`` ``cpe-cuda/21.12``  ``cudatoolkit/21.9_11.4``
-* Location: ``/global/cfs/cdirs/alpine/software/ascent/current/perlmutter/cuda/gnu/ascent-install/``
-
-
-You can copy the tutorial examples from this install and use them as follows:
-
-.. literalinclude:: tutorial_setup_nersc_perlmutter_test.sh
-   :language: bash
-
-
-LLNL CZ TOSS 3 Install
-+++++++++++++++++++++++
-
-* Build Details: gcc 4.9.3 with OpenMP and MPI support
-* Modules: (none)
-* Location: ``/usr/gapps/conduit/software/ascent/current/toss_3_x86_64_ib/openmp/gnu/ascent-install/``
-
-You can copy the tutorial examples from this install and use them as follows:
-
-.. literalinclude:: tutorial_setup_llnl_pascal_openmp_test.sh
-   :language: bash
-
-
-Register Ascent's Python as a Jupyter Kernel
-+++++++++++++++++++++++++++++++++++++++++++++
-
-.. warning::
-    This works the LLNL LC TOSS3 CZ OpenMP install, we are working on recipes for other HPC centers.
-
-You can register Ascent's Python as a custom Jupyter kernel with Jupyter Hub.
-
-LLNL CZ TOSS 3 Jupyter Kernel Register Example:
-
-.. literalinclude:: tutorial_setup_llnl_pascal_openmp_jhub.sh
-   :language: bash
-
-After you register you will see an option to launch an Ascent kernel in Jupyter Hub:
-
-.. image:: images/llnl_jhub_kernel_select.png
-
-With this kernel you can access Ascent's Python modules or run the tutorial notebooks:
-
-.. image:: images/llnl_jhub_kernel_example.png
-
+.. .. _tutorial_setup_public_installs:
+..
+.. Using Public Installs of Ascent
+.. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+..
+.. This section provides info about public installs we provide on several HPC machines.
+..
+.. Additionally, here is a `link to the scripts used to build our public installs <https://github.com/Alpine-DAV/ascent/tree/develop/scripts/spack_install>`_ .
+..
+.. OLCF Summit Installs
+.. +++++++++++++++++++++++
+..
+..
+.. * Build Details: gcc 9.3.0 with OpenMP and MPI support
+.. * Modules: ``gcc/9.3.0``
+.. * Location: ``/sw/summit/ums/ums010/ascent/current/summit/openmp/gnu/ascent-install/``
+..
+.. You can copy the tutorial examples from this install and use them as follows:
+..
+.. .. literalinclude:: tutorial_setup_olcf_summit_openmp_test.sh
+..    :language: bash
+..
+.. * Build Details: gcc 9.3.0 with CUDA 11.0.3 and MPI support
+.. * Modules: ``gcc/9.3.0`` ``cuda/11.0.3``
+.. * Location: ``/sw/summit/ums/ums010/ascent/current/summit/cuda/gnu/ascent-install/``
+..
+.. You can copy the tutorial examples from this install and use them as follows:
+..
+.. .. literalinclude:: tutorial_setup_olcf_summit_cuda_test.sh
+..    :language: bash
+..
+..
+.. NERSC Perlmuter Install
+.. +++++++++++++++++++++++
+..
+.. * Build Details: gcc 10.3.0 with CUDA 11.4.0 and MPI support
+.. * Modules: ``PrgEnv-gnu`` ``cpe-cuda/21.12``  ``cudatoolkit/21.9_11.4``
+.. * Location: ``/global/cfs/cdirs/alpine/software/ascent/current/perlmutter/cuda/gnu/ascent-install/``
+..
+..
+.. You can copy the tutorial examples from this install and use them as follows:
+..
+.. .. literalinclude:: tutorial_setup_nersc_perlmutter_test.sh
+..    :language: bash
+..
+..
+.. LLNL CZ TOSS 3 Install
+.. +++++++++++++++++++++++
+..
+.. * Build Details: gcc 4.9.3 with OpenMP and MPI support
+.. * Modules: (none)
+.. * Location: ``/usr/gapps/conduit/software/ascent/current/toss_3_x86_64_ib/openmp/gnu/ascent-install/``
+..
+.. You can copy the tutorial examples from this install and use them as follows:
+..
+.. .. literalinclude:: tutorial_setup_llnl_pascal_openmp_test.sh
+..    :language: bash
 
-If you want to remove the registered kernel, you can use:
 
-.. code::
-  
-  # show list of registered kernels
-  jupyter kernelspec list
-  # remove our Ascent custom kernel
-  jupyter kernelspec uninstall ascent_kernel
+.. Register Ascent's Python as a Jupyter Kernel
+.. +++++++++++++++++++++++++++++++++++++++++++++
+..
+.. .. warning::
+..     This works the LLNL LC TOSS3 CZ OpenMP install, we are working on recipes for other HPC centers.
+..
+.. You can register Ascent's Python as a custom Jupyter kernel with Jupyter Hub.
+..
+.. LLNL CZ TOSS 3 Jupyter Kernel Register Example:
+..
+.. .. literalinclude:: tutorial_setup_llnl_pascal_openmp_jhub.sh
+..    :language: bash
+..
+.. After you register you will see an option to launch an Ascent kernel in Jupyter Hub:
+..
+.. .. image:: images/llnl_jhub_kernel_select.png
+..
+.. With this kernel you can access Ascent's Python modules or run the tutorial notebooks:
+..
+.. .. image:: images/llnl_jhub_kernel_example.png
+..
+..
+.. If you want to remove the registered kernel, you can use:
+..
+.. .. code::
+..
+..   # show list of registered kernels
+..   jupyter kernelspec list
+..   # remove our Ascent custom kernel
+..   jupyter kernelspec uninstall ascent_kernel
 
 ..
 .. SC19 Tutorial VM Option