Merge some bug fixes for windows

.github/workflows/draft-pdf.yml

@@ -2,6 +2,7 @@ on:
   push:
     branches: 
       - main
+      - development
 
 jobs:
   paper:

.github/workflows/minimal.yml

@@ -1,6 +1,9 @@
 name: Minimal
 
 on:
+  push:
+    branches:
+      - development
   pull_request:
     branches: 
       - main
@@ -13,8 +16,27 @@ on:
 
 jobs:
 
-  library:
-    name: "library" 
+  windows:
+    name: "windows"
+    runs-on: windows-latest
+    steps:
+    - uses: actions/checkout@v2      
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - name: Install dependencies
+      run: |
+          pip3 install click
+          pip3 install -r requirements/core.txt
+    - name: Run setup
+      run: |
+          python3 setup.py install --user
+    - name: Run tests
+      run: |
+          python3 tests/container/create.py
+
+  ubuntu: 
+    name: "ubuntu" 
     runs-on: ubuntu-latest
     steps:
     #- name: Login to Docker Hub

NOTICE

@@ -1,4 +1,4 @@
-Copyright (c) 2023 UChicago Argonne, LLC and contributors. All rights reserved.
+Copyright (c) 2023 UChicago Argonne LLC. All rights reserved.
 
 Title: BoxKit (SF-23-067)
 

bin/boost.py

@@ -21,7 +21,7 @@ def boost_build():
         "cd submodules/boost && ./bootstrap.sh"
         + f" --with-python-version={get_python_version()}"
         + " --with-toolset=gcc"
-        + f" --prefix={os.getenv('PWD')}/boxkit/depends/boost && ./b2 install",
+        + f" --prefix={os.getcwd()}/boxkit/depends/boost && ./b2 install",
         shell=True,
         check=True,
         executable="/bin/bash",
@@ -40,7 +40,7 @@ def boost_clean():
 
 def boost_install():
     """Install Boost library"""
-    if os.path.exists(os.getenv("PWD") + "/boxkit/depends/boost"):
+    if os.path.exists(os.getcwd() + "/boxkit/depends/boost"):
         subprocess.run(
             "mkdir -pv build/lib/boxkit/depends/boost/lib",
             shell=True,

bin/cbox.py

@@ -17,13 +17,13 @@
     "boost_version": "".join(sysconfig.get_python_version().split(".")),
     "python_include_path": sysconfig.get_python_inc(),
     "boost_include_path": (
-        os.getenv("PWD") + "/boxkit/depends/boost/include"
-        if os.path.exists(os.getenv("PWD") + "/boxkit/depends/boost")
+        os.getcwd() + "/boxkit/depends/boost/include"
+        if os.path.exists(os.getcwd() + "/boxkit/depends/boost")
         else os.getenv("BOOST_INCLUDE_DIR")
     ),
     "boost_lib_path": (
-        os.getenv("PWD") + "/boxkit/depends/boost/lib"
-        if os.path.exists(os.getenv("PWD") + "/boxkit/depends/boost")
+        os.getcwd() + "/boxkit/depends/boost/lib"
+        if os.path.exists(os.getcwd() + "/boxkit/depends/boost")
         else os.getenv("BOOST_LIB_DIR")
     ),
 }

boxkit/__meta__.py

@@ -1,8 +1,8 @@
 """Metadata for BoxKit package"""
 
 __pkgname__ = "BoxKit"
-__version__ = "2023.06.7"
+__version__ = "2023.9.1"
 __authors__ = "Akash Dhruv"
-__license__ = "Apache License"
-__copyright__ = "Copyright (c) Akash Dhruv 2023. All Rights Reserved."
+__license__ = "Apache Software License"
+__copyright__ = "Copyright (c) 2023 UChicago Argonne LLC and contributors. All Rights Reserved."
 __description__ = "BoxKit utility"

paper/paper.bib

@@ -5,16 +5,19 @@ @article{DUBEY2022
 	Pages = {101168},
 	Year = {2022},
 	issn = {2352-7110},
-	doi = {https://doi.org/10.1016/j.softx.2022.101168},
+	doi = {10.1016/j.softx.2022.101168},
 	url = {https://www.sciencedirect.com/science/article/pii/S2352711022001030},
 	Author = {Anshu Dubey and Klaus Weide and Jared O’Neal and Akash Dhruv and Sean Couch and J. Austin Harris and Tom Klosterman and Rajeev Jain and Johann Rudi and Bronson Messer and Michael Pajkos and Jared Carlson and Ran Chu and Mohamed Wahib and Saurabh Chawdhary and Paul M. Ricker and Dongwook Lee and Katie Antypas and Katherine M. Riley and Christopher Daley and Murali Ganapathy and Francis X. Timmes and Dean M. Townsley and Marcos Vanella and John Bachan and Paul M. Rich and Shravan Kumar and Eirik Endeve and W. Raphael Hix and Anthony Mezzacappa and Thomas Papatheodore}
 }
 
-@article{DHRUV2023,
-	Author = {Akash Dhruv},
-	Title = {A Vortex Damping Outflow Forcing for Multiphase Flows with Sharp Interfacial Jumps},
-	Year = {2023},
-	Journal = {Under Review}
+@misc{DHRUV2023,
+      title={A Vortex Damping Outflow Forcing for Multiphase Flows with Sharp Interfacial Jumps}, 
+      author={Akash Dhruv},
+      year={2023},
+      eprint={2306.10174},
+      archivePrefix={arXiv},
+      primaryClass={physics.flu-dyn},
+      url={https://arxiv.org/abs/2306.10174}
 }
 
 @dataset{HASSAN2023,
@@ -68,3 +71,8 @@ @misc{summit
   year = 2023,
   howpublished = {\url{https://www.olcf.ornl.gov/summit/}},
 }
+
+@misc{boxkit-performance,
+  title={{BoxKit Performance}},
+  howpublished= {\url{https://github.com/akashdhruv/boxkit-performance}},
+}

paper/paper.md

@@ -51,6 +51,12 @@ datasets (~10 GB) can leverage BoxKit to improve performance of offline training
 This mechanism is part of a broader workflow to  integrate simulations with machine 
 learning using a Fortran-Python bridge shown with dotted lines. \label{fig:workflow}](../media/workflow.png)
 
+Compared to existing data analysis packages like yt [@yt], BoxKit offers more intuitive 
+abstraction layers over AMR blocks through its metadata wrappers. This provides raw access 
+to simulation data allowing users to develop their own low-level methods for spatio-temporal 
+interpolation and stenciled computations. We aim for this library to complement existing
+packages rather than replace them.
+
 BoxKit also offers wrappers to scale the process of deploying workflows on NUMA and distributed
 computing architectures by providing decorators that can parallelize Python operations over a
 single data structure to operate over a list. This can be understood better using the 
@@ -68,7 +74,8 @@ def operation_on_block(block, *args):
     pass
 
 # Call the function with list of blocks as the first argument
-operation_on_block((block for block in list_of_blocks), *args)
+dset = boxkit.read_datset(...)
+operation_on_block((block for block in dset.blocklist), *args)
 ```
 
 The `Action` wrapper converts the function, `operation_on_block`, into a parallel method which 
@@ -107,16 +114,17 @@ increases.
 
 Mapping of AMR data to contingous arrays becomes important for applications
 where global operations in space are required. An example of this is SciKit's 
-``skimage_measure`` method, which can be used to measure bubble shape and size 
+``skimage.measure`` method, which can be used to measure bubble shape and size 
 for Flash-X boiling simulations. BoxKit improves performance of this operation 
-by ~5x.
+by ~5x. Data for these performance studies along with corresponding IPython 
+notebooks can be found in [@boxkit-performance].
 
 # Ongoing work
 
-Our ongoing work focuses on using BoxKit to improve performance of Scientific
+Our ongoing work focuses on developing BoxKit to improve performance of Scientific
 Machine Learning (SciML) applications and using it as part of a broader workflow 
 that integrates Fortran/C++ based applications with state-of-art machine learning 
-packages available in Python shown by dotted lines in \autoref{fig:workflow}.
+packages available in Python as highlighted in \autoref{fig:workflow}.
 
 # Acknowledgements
 

setup.py

@@ -4,6 +4,7 @@
 import os
 import sys
 import re
+import platform
 from setuptools import setup, find_packages
 
 sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
@@ -40,14 +41,19 @@
 # Call setup command with necessary arguments
 # replace existing build and develop commands
 # with custom commands defined in 'bin.cmd'
+if platform.system() == "Windows":
+    PACKAGE_DIR = ".\\"
+else:
+    PACKAGE_DIR = "./"
+
 setup(
     name=metadata["__pkgname__"],
     version=metadata["__version__"],
     author=metadata["__authors__"],
     description=metadata["__description__"],
     license=metadata["__license__"],
-    packages=find_packages(where="./"),
-    package_dir={"": "./"},
+    packages=find_packages(where=PACKAGE_DIR),
+    package_dir={"": PACKAGE_DIR},
     package_data={
         "": [
             "options.py",
@@ -58,7 +64,7 @@
     long_description=long_description,
     classifiers=[
         "Programming Language :: Python :: 3.8",
-        "License :: OSI Approved :: MIT License",
+        "License :: OSI Approved :: Apache Software License",
     ],
     install_requires=DEPENDENCIES,
     cmdclass={