Merge pull request #3 from Shimwell/develop

update to dockerfile

.github/workflows/docker_ci.yml

@@ -2,6 +2,7 @@
 name: docker based CI
 on:  
   pull_request:     
+
 jobs:  
   build:
     runs-on: ubuntu-latest

Dockerfile

@@ -31,13 +31,16 @@ RUN apt-get --yes install libeigen3-dev && \
     apt-get --yes install libtbb-dev && \
     apt-get --yes install libglfw3-dev && \
     apt-get --yes install cmake && \
+    apt-get --yes install g++ && \
     apt-get --yes install git
 
 # Clone and install MOAB
 RUN pip install --upgrade numpy cython
 RUN mkdir MOAB && \
     cd MOAB && \
-    git clone  --single-branch --branch 5.2.1 --depth 1 https://bitbucket.org/fathomteam/moab.git && \
+    git clone  --single-branch --branch 5.2.1 --depth 1 https://bitbucket.org/fathomteam/moab.git
+
+RUN cd MOAB && \
     mkdir build && \
     cd build && \
     cmake ../moab -DENABLE_HDF5=ON \
@@ -56,5 +59,16 @@ RUN mkdir MOAB && \
                   -DCMAKE_INSTALL_PREFIX=/MOAB && \
     make install && \
     cd pymoab && \
+    # not quite sure why these two lines are needed but it appears that pymoab
+    # is not available as "import pymoab" without them
     bash install.sh && \
     python setup.py install
+
+RUN pip install pytest-cov
+
+COPY setup.py setup.py
+COPY remove_dagmc_tags remove_dagmc_tags/
+COPY tests tests/
+COPY README.md README.md
+
+RUN python setup.py install

README.md

@@ -1,7 +1,12 @@
+[![N|Python](https://www.python.org/static/community_logos/python-powered-w-100x40.png)](https://www.python.org)
+[![docker based CI](https://github.com/Shimwell/remove_dagmc_tags/actions/workflows/docker_ci.yml/badge.svg)](https://github.com/Shimwell/remove_dagmc_tags/actions/workflows/docker_ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/remove-dagmc-tags?color=brightgreen&label=pypi&logo=grebrightgreenen&logoColor=green)](https://pypi.org/project/remove-dagmc-tags/)
+[![codecov](https://codecov.io/gh/shimwell/remove_dagmc_tags/branch/main/graph/badge.svg)](https://codecov.io/gh/shimwell/remove_dagmc_tags)
 
 This is a minimal Python package that provides both **command line** and **API** interfaces for removing **multiple** tags from a DAGMC h5m file.
 
-This is useful for preparing the h5m file for visulisation where it is desirable to remove reflecting surfaces, vacuum materials and the graveyard(s) region.
+This is useful for preparing the h5m file for visulisation where it is desirable to remove reflecting surfaces, vacuum materials and the graveyard(s) region
+from the geometry before viewing the vtk file.
 
 
 # Command line usage
@@ -12,19 +17,21 @@ remove-dagmc-tags -i dagmc.h5m -o dagmc_no_graveyard.h5m -t graveyard
 ```
 
 - the ```-i``` or ```--input``` argument specifies the input h5m file
-- the ```-o``` or ```--output``` argument specifies the output h5m file
+- the ```-o``` or ```--output``` argument specifies the output h5m or vtk filename
 - the ```-t``` or ```--tags``` argument specifies the tags to remove.
 - the ```-v``` or ```--verbose``` argument enables (true) or disables (false) the printing of additional details
 
-Multiple tags can also be removed. This example removes three tags from the dagmc.h5m file
+Multiple tags can also be removed and vtk files can be generated. This example
+removes three tags from the dagmc.h5m file and saves the result as a vtk file.
 
 ```bash
-remove-dagmc-tags -i dagmc.h5m -o dagmc_output.h5m -t mat:graveyard mat:vacuum reflective
+remove-dagmc-tags -i dagmc.h5m -o output.vtk -t mat:graveyard mat:vacuum reflective
 ```
 
 # Python API usage
 
 Removing a single tag called ```mat:graveyard``` from the dagmc.h5m file.
+
 ```python
 from remove_dagmc_tags import remove_tags
 
@@ -35,26 +42,45 @@ remove_tags(
 )
 ```
 
-Removing two tags called ```mat:graveyard``` and ```reflective``` from the dagmc.h5m file.
+Removing two tags called ```mat:graveyard``` and ```reflective``` from the
+dagmc.h5m file and saves the result as a vtk file and h5m file.
+
 ```python
 from remove_dagmc_tags import remove_tags
 
 remove_tags(
     input='dagmc.h5m',
-    output='output.h5m',
-    tags='reflective'
+    output=['output.vtk', 'output.h5m'],
+    tags=['reflective', 'mat:graveyard']
 )
 ```
 
 # Installation
 
+The recommended method of installing is via conda install as this is able to
+install all the dependencies including PyMoab.
+```bash
+conda install -c conda-forge remove_dagmc_tags
+```
+
+However the package is available via the PyPi package manager. In this case you
+will have to seperatly install PyMoab.
+
 ```bash
 pip install remove_dagmc_tags
 ```
 
 Some Python dependencies (such as Numpy) are installed during the ```pip install remove_dagmc_tags process```, however [PyMoab](https://bitbucket.org/fathomteam/moab/src/master/) needs to be installed seperatly to make full use of this package.
 
-One method of installing ```pymoab``` is to compile MOAB with pymoab enabled.
+
+One method of installing ```pymoab``` is to install MOAB via Conda which
+includes PyMoab.
+
+```bash
+conda install -c conda-forge moab
+```
+
+Another method of installing ```pymoab``` is to compile MOAB with pymoab enabled.
 
 ```bash
 mkdir MOAB

remove_dagmc_tags/__init__.py

@@ -0,0 +1,2 @@
+
+from .core import remove_tags, find_tags

remove_dagmc_tags/core.py

@@ -0,0 +1,137 @@
+
+import warnings
+from pathlib import Path
+from typing import List, Optional, Union
+
+import numpy as np
+from pymoab import core, types
+from pymoab.types import MBENTITYSET
+
+
+def create_moab_core(input):
+
+    moab_core = core.Core()
+    moab_core.load_file(str(input))
+
+    tag_name = moab_core.tag_get_handle(str(types.NAME_TAG_NAME))
+
+    tag_category = moab_core.tag_get_handle(str(types.CATEGORY_TAG_NAME))
+    root = moab_core.get_root_set()
+
+    # An array of tag values to be matched for entities returned by the
+    # following call.
+    group_tag_values = np.array(["Group"])
+
+    # Retrieve all EntitySets with a category tag of the user input value.
+    group_categories = list(moab_core.get_entities_by_type_and_tag(
+                            root, MBENTITYSET, tag_category, group_tag_values))
+
+    return moab_core, group_categories, tag_name
+
+
+def find_tags(
+    input: Optional[str] = 'dagmc.h5m',
+) -> List[str]:
+    """Removes a specific tag from a dagmc h5m file and saves the remaining
+    geometry as a new h5m file. Useful for visulising the geometry by removing
+    the graveyard tag and then the vtk file can be made without a bounding box
+    graveyard obstructing the view. Adapted from
+    https://github.com/svalinn/DAGMC-viz source code
+
+    Arguments:
+        input: The name of the h5m file to remove the dagmc tags from
+        output: The name of the outfile file(s) with the tags removed.
+            Supported extentions are .vtk and .h5m
+        tags: The tag or tags to remove.
+        verbose:
+
+    Returns:
+        filename of the new dagmc h5m file with the tags removed
+    """
+
+    moab_core, group_categories, tag_name = create_moab_core(input)
+
+    # Retrieve all EntitySets with a name tag.
+    group_names = moab_core.tag_get_data(tag_name, group_categories, flat=True)
+
+    return group_names
+
+
+def remove_tags(
+    input: Optional[str] = 'dagmc.h5m',
+    output: Optional[Union[str, List[str]]] = 'dagmc_removed_tag.vtk',
+    tags: Optional[Union[str, List[str]]] = 'graveyard',
+    verbose: Optional[bool] = False,
+):
+# -> List[List[str], List[str], List[str]]:
+    """Removes a specific tag from a dagmc h5m file and saves the remaining
+    geometry as a new h5m file. Useful for visulising the geometry by removing
+    the graveyard tag and then the vtk file can be made without a bounding box
+    graveyard obstructing the view. Adapted from
+    https://github.com/svalinn/DAGMC-viz source code
+
+    Arguments:
+        input: The name of the h5m file to remove the dagmc tags from
+        output: The name of the outfile file(s) with the tags removed.
+            Supported extentions are .vtk and .h5m
+        tags: The tag(S) to be removed.
+        verbose: Print out additional information (True) or not (False)
+
+    Returns:
+        filename(s) of the output files produced, names of tags removed, names
+        of all the tags available
+    """
+    if verbose is True:
+        print()
+        print('tags_to_remove', tags)
+
+    moab_core, group_categories, tag_name = create_moab_core(input)
+
+    group_names = find_tags(input=input)
+
+    if isinstance(tags, str):
+        tags_to_remove = [tags]
+    else:
+        tags_to_remove = tags
+
+    # Find the EntitySet whose name includes tag provided
+    sets_to_remove = []
+    names_to_remove = []
+    names_not_remove_removed = []
+
+    for group_set, name in zip(group_categories, group_names):
+        for tag_to_remove in tags_to_remove:
+            if tag_to_remove in str(name.lower()):
+                names_to_remove.append(name.lower())
+                sets_to_remove.append(group_set)
+            else:
+                names_not_remove_removed.append(name.lower())
+
+    names_to_remove = list(sorted(set(names_to_remove)))
+
+    if len(sets_to_remove) == 0:
+        warnings.warn('No tags removed.')
+
+    # prints out 
+    if verbose is True:
+        print()
+        for name in sorted(set(group_names)):
+            if str(name.lower()) in tags_to_remove:
+                print(str(name.lower()), ' --- >  Removing tag')
+            else:
+                print(str(name.lower()))
+        print()
+
+    # Remove the EntitySet from the data.
+    groups_to_write = [
+        group_set for group_set in group_categories if group_set not in sets_to_remove]
+
+    if isinstance(output, (str, Path)):
+        output = [output]
+
+    for out in output:
+        if verbose is True:
+            print('Writing', out)
+        moab_core.write_file(str(out), output_sets=groups_to_write)
+
+    return output, names_to_remove, sorted(set(group_names))

remove_dagmc_tags/remove-dagmc-tags

@@ -0,0 +1,45 @@
+#!/usr/bin/python
+
+from remove_dagmc_tags import remove_tags
+from pathlib import Path
+import argparse
+
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument(
+        '-t', '--tags',
+        nargs='*',
+        default=['graveyard'],
+        help="The tag or tags to remove."
+    )
+
+    parser.add_argument(
+        '-i', '--input',
+        type=Path, default=None,
+        help='Input h5m file',
+        required=True
+    )
+
+    parser.add_argument(
+        '-o', '--output',
+        type=Path, default='dagmc_removed_tag.h5m',
+        help='Output h5m file with removed tags'
+    )
+
+    parser.add_argument(
+        '-v', '--verbose',
+        type=bool, default=True,
+        help='Print additional details of the opperation'
+    )
+
+    args = parser.parse_args()
+
+    remove_tags(
+        input=args.input,
+        output=args.output,
+        tags=args.tags,
+        verbose=args.verbose
+    )

setup.py

@@ -0,0 +1,30 @@
+import setuptools
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name="remove_dagmc_tags",
+    version="0.0.2",
+    author="Jonathan Shimwell",
+    author_email="[email protected]",
+    description="A tool for selectively removing tags such as the graveyard from DAGMC h5m files.",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/shimwell/remove_dagmc_tags",
+    packages=setuptools.find_packages(),
+    zip_safe=True,
+    package_dir={"remove_dagmc_tags": "remove_dagmc_tags"},
+    scripts=['remove_dagmc_tags/remove-dagmc-tags'],
+    package_data={
+        "remove_dagmc_tags": [
+            "requirements.txt",
+            "README.md",
+            "LICENSE",
+        ]
+    },
+    tests_require=["pytest-cov"],
+    # install_requires=[
+    #     # 'pymoab' is is required for this package but is not available via pip install at the moment
+    # ],
+)