Box-Tools · akashdhruv · Jun 17, 2023 · Dec 14, 2022 · Dec 14, 2022 · Dec 14, 2022
diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -0,0 +1,29 @@
+name: draft-pdf
+
+on:
+  pull_request:
+    branches: 
+      - main
+      - development
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf
diff --git a/.gitignore b/.gitignore
@@ -13,3 +13,4 @@ boxkit/depends/boost/*
 .sphinx/build/*
 !.sphinx/source/index.rst
 !README.rst
+!DESIGN.rst
diff --git a/.pylintrc b/.pylintrc
@@ -0,0 +1,3 @@
+[DESIGN]
+disable=
+    duplicate-code
diff --git a/DESIGN.rst b/DESIGN.rst
@@ -0,0 +1,30 @@
+##############################################
+ |icon| Software Design and Developer's Guide
+##############################################
+
+*****
+ API
+*****
+
+BoxKit API details here
+
+*********
+ Library
+*********
+
+BoxKit library details here
+
+*******
+ C-Box
+*******
+
+C++ backend detailes here
+
+***************
+ Miscellaneous
+***************
+
+Miscellaneous details about how to develop frontend methods, etc.
+
+.. |icon| image:: ./media/book.svg
+   :width: 25
diff --git a/README.rst b/README.rst
@@ -1,87 +1,113 @@
-.. |icon| image:: ./media/icon.svg
-  :width: 30
-
-=============
-|icon| BoxKit
-=============
+###############
+ |icon| BoxKit
+###############
 
 |Code style: black|
 
 |FlashX| |FlowX| |Minimal| |Publish|
 
-BoxKit is a library that provides building blocks to parallelize and scale data science, high performance computing, and machine learning applications for block-structured datasets. Spatial data from simulations and experiments can be accessed and managed using tools available in this library when working with more data analysis oriented packages like SciKit (https://github.com/scikit-learn/scikit-learn) and FlowNet (https://github.com/NVIDIA/flownet2-pytorch)
+BoxKit is a library that provides building blocks to parallelize and
+scale data science, high performance computing, and machine learning
+applications for block-structured datasets. Spatial data from
+simulations and experiments can be accessed and managed using tools
+available in this library when working with more data analysis oriented
+packages like SciKit (https://github.com/scikit-learn/scikit-learn) and
+FlowNet (https://github.com/NVIDIA/flownet2-pytorch)
 
-Installation
-============
+**************
+ Installation
+**************
 
-Stable releases of BoxKit are hosted on Python Package Index website (`<https://pypi.org/project/BoxKit/>`_) and can be installed by executing,
+Stable releases of BoxKit are hosted on Python Package Index website
+(https://pypi.org/project/BoxKit/) and can be installed by executing,
 
-::
+.. code::
 
    pip install BoxKit --user
-   
+
    export CXX=$(CPP_COMPILER)
    pip install BoxKit --user --install-option="--enable-testing" --install-option="--with-cbox"
-
-Note that ``pip`` should point to ``python3+`` installation package ``pip3``. 
 
-Upgrading and uninstallation is easily managed through this interface using,
+Note that ``pip`` should point to ``python3+`` installation package
+``pip3``.
+
+Upgrading and uninstallation is easily managed through this interface
+using,
 
-::
+.. code::
 
    pip install --upgrade BoxKit --user
    pip install --upgrade BoxKit --user --install-option="--enable-testing" --install-option="--with-cbox"
    pip uninstall BoxKit
 
-There maybe situations where users may want to install BoxKit in development mode $\\textemdash$ to design new features, debug, or customize classes/methods to their needs. This can be easily accomplished using the ``setup`` script located in the project root directory and executing,
+There maybe situations where users may want to install BoxKit in
+development mode $\\textemdash$ to design new features, debug, or
+customize classes/methods to their needs. This can be easily
+accomplished using the ``setup`` script located in the project root
+directory and executing,
 
-::
+.. code::
 
    ./setup develop
 
-Development mode enables testing of features/updates directly from the source code and is an effective method for debugging. Note that the ``setup`` script relies on ``click``, which can be installed using,
+Development mode enables testing of features/updates directly from the
+source code and is an effective method for debugging. Note that the
+``setup`` script relies on ``click``, which can be installed using,
 
-::
+.. code::
 
-  pip install click
-
-Usage
-=====
+   pip install click
 
-BoxKit is undergoing active development and therefore design changes are frequent, however, the library is divided into two broad categories:
+*******
+ Usage
+*******
 
-- **Create**: Containing interface for classes/methods to store spatial data in a rectangular/cubic frame, along with auxillary tools to manage irregular geometries composed of unstructured triangular mesh.
+BoxKit is undergoing active development and therefore design changes are
+frequent, however, the library is divided into two broad categories:
 
-- **Utilities**: Containing interface for classes/method to improve memory managment of data on NUMA nodes.
+-  **Create**: Containing interface for classes/methods to store spatial
+   data in a rectangular/cubic frame, along with auxillary tools to
+   manage irregular geometries composed of unstructured triangular mesh.
 
-We are currently setting up use cases for BoxKit, and will update this section when we are able to demonstrate proof-of-concept.
+-  **Utilities**: Containing interface for classes/method to improve
+   memory managment of data on NUMA nodes.
 
-Citation
-========
+We are currently setting up use cases for BoxKit, and will update this
+section when we are able to demonstrate proof-of-concept.
 
-::
+**********
+ Citation
+**********
 
-  @software{akash_dhruv_2022_7255632,
-    author       = {Akash Dhruv},
-    title        = {akashdhruv/BoxKit: October 2022},
-    month        = oct,
-    year         = 2022,
-    publisher    = {Zenodo},
-    version      = {22.10},
-    doi          = {10.5281/zenodo.7255632},
-    url          = {https://doi.org/10.5281/zenodo.7255632}
-  }
+.. code::
 
-Help & Support
-==============
+   @software{akash_dhruv_2022_7255632,
+     author       = {Akash Dhruv},
+     title        = {akashdhruv/BoxKit: October 2022},
+     month        = oct,
+     year         = 2022,
+     publisher    = {Zenodo},
+     version      = {22.10},
+     doi          = {10.5281/zenodo.7255632},
+     url          = {https://doi.org/10.5281/zenodo.7255632}
+   }
 
-Please file an issue on the repository page
+****************
+ Help & Support
+****************
 
+Please file an issue on the repository page
 
 .. |Code style: black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/psf/black
-   
+
 .. |FlashX| image:: https://github.com/akashdhruv/BoxKit/workflows/FlashX/badge.svg
+
 .. |FlowX| image:: https://github.com/akashdhruv/BoxKit/workflows/FlowX/badge.svg
+
 .. |Minimal| image:: https://github.com/akashdhruv/BoxKit/workflows/Minimal/badge.svg
+
 .. |Publish| image:: https://github.com/akashdhruv/BoxKit/workflows/Publish/badge.svg
+
+.. |icon| image:: ./media/icon.svg
+   :width: 30
diff --git a/boxkit/__meta__.py b/boxkit/__meta__.py
@@ -1,7 +1,7 @@
 """Metadata for BoxKit package"""
 
 __pkgname__ = "BoxKit"
-__version__ = "3.0"
+__version__ = "2023.06"
 __authors__ = "Akash Dhruv"
 __license__ = "Apache License"
 __copyright__ = "Copyright (c) Akash Dhruv 2021. All Rights Reserved."

diff --git a/boxkit/api/_mean.py b/boxkit/api/_mean.py
@@ -17,7 +17,7 @@ def mean_temporal(datasets, varlist, backend="serial", nthreads=1, monitor=False
     if isinstance(varlist, str):
         varlist = [varlist]
 
-    # TODO: Add more error handling here to account
+    # TODO: Add more error handling here to account # pylint: disable=fixme
     # for consistency between multiple datasets
     #
     # Handle errors, compute level of the first
@@ -33,6 +33,13 @@ def mean_temporal(datasets, varlist, backend="serial", nthreads=1, monitor=False
     # Create an mean dataset
     mean_dataset = datasets[0].clone(storage="numpy-memmap")
 
+    # loop over varlist append values to
+    # add it to the mean dataset and perform mean
+    for varkey in varlist:
+        mean_dataset.addvar(varkey)
+
+    sample_size = len(datasets)
+
     # Create a block list for reduction, first add
     # blocks from average_dataset and then loop over
     # datasets to add blocks from their respective blocklist
@@ -42,12 +49,8 @@ def mean_temporal(datasets, varlist, backend="serial", nthreads=1, monitor=False
         for block, blk_list in zip(dataset.blocklist, blk_reduce_list):
             blk_list.append(block)
 
-    # loop over varlist append values to
-    # add it to the mean dataset and perform mean
     for varkey in varlist:
-        mean_dataset.addvar(varkey)
 
-    for varkey in varlist:
         if monitor:
             time_reduction = library.Timer("[boxkit.mean_temporal.mean_blk_list]")
 
@@ -58,7 +61,9 @@ def mean_temporal(datasets, varlist, backend="serial", nthreads=1, monitor=False
             # pass list of parallel objects
             (blk_list for blk_list in blk_reduce_list),
             varkey,
+            sample_size,
         )
+
         if monitor:
             del time_reduction
 
@@ -68,12 +73,11 @@ def mean_temporal(datasets, varlist, backend="serial", nthreads=1, monitor=False
     return mean_dataset
 
 
-def mean_blk_list(blk_list, varkey):
+def mean_blk_list(blk_list, varkey, sample_size):
     """
     Reduce dataset / compute average
     """
     mean_blk = blk_list[0]
-    sample_size = len(blk_list[1:])
 
     for work_blk in blk_list[1:]:
         mean_blk[varkey] = mean_blk[varkey] + work_blk[varkey] / sample_size
diff --git a/boxkit/api/_mergeblocks.py b/boxkit/api/_mergeblocks.py
@@ -1,15 +1,13 @@
 """Module with implemenetation of api methods"""
 
-import sys
-
-from .. import library
-from .. import api
-from ..library import Action
+from boxkit import library  # pylint: disable=cyclic-import
+from boxkit import api  # pylint: disable=cyclic-import
+from boxkit.library import Action  # pylint: disable=cyclic-import
 
 
 def mergeblocks(
     dataset, varlist, nthreads=1, batch="auto", monitor=False, backend="serial"
-):
+):  # pylint: disable=too-many-arguments disable=too-many-locals
     """
     Reshaped dataset at a level
     """
@@ -34,9 +32,15 @@ def mergeblocks(
             )
 
     # Compute number of blocks in each direction
-    nblockx = int((dataset.xmax - dataset.xmin) / dataset.blocklist[0].dx / dataset.nxb)
-    nblocky = int((dataset.ymax - dataset.ymin) / dataset.blocklist[0].dy / dataset.nyb)
-    nblockz = int((dataset.zmax - dataset.zmin) / dataset.blocklist[0].dz / dataset.nzb)
+    nblockx = round(
+        (dataset.xmax - dataset.xmin) / dataset.blocklist[0].dx / dataset.nxb
+    )
+    nblocky = round(
+        (dataset.ymax - dataset.ymin) / dataset.blocklist[0].dy / dataset.nyb
+    )
+    nblockz = round(
+        (dataset.zmax - dataset.zmin) / dataset.blocklist[0].dz / dataset.nzb
+    )
 
     nblockx, nblocky, nblockz = [
         value if value > 0 else 1 for value in [nblockx, nblocky, nblockz]
@@ -76,10 +80,6 @@ def mergeblocks(
     if monitor:
         resources.display()
 
-        print(
-            f"[mem_dataset]: {round(sys.getsizeof(dataset._data.variables[varlist[0]][:])/(2**20),2)} MB"
-        )
-
     map_blk_to_merged_dset.nthreads = nthreads
     map_blk_to_merged_dset.monitor = monitor
     map_blk_to_merged_dset.backend = backend

diff --git a/boxkit/api/_read.py b/boxkit/api/_read.py
@@ -13,7 +13,7 @@ def read_dataset(
     force_memmap=False,
     nthreads=1,
     backend="serial",
-):
+):  # pylint: disable=too-many-arguments disable=too-many-locals
     """
     Create a dataset from a file
 

diff --git a/boxkit/api/_regionprops.py b/boxkit/api/_regionprops.py
@@ -3,8 +3,8 @@
 import itertools
 import skimage.measure as skimage_measure
 
-from .. import api
-from ..library import Action
+from boxkit import api  # pylint: disable=cyclic-import
+from boxkit.library import Action  # pylint: disable=cyclic-import
 
 
 def regionprops(dataset, lsetkey, backend="serial", nthreads=1, monitor=False):