Merge pull request #30 from fusion-energy/develop

Patch release 0.2.3

.github/workflows/ci_with_install.yml

@@ -20,23 +20,28 @@ jobs:
   testing:
     runs-on: ubuntu-latest
     container:
-      # image: openmc/openmc:latest-dagmc is missing the dagmc universe
-      image: openmc/openmc:develop-dagmc
+      # image: continuumio/miniconda3:4.10.3
+      image: ghcr.io/openmc-data-storage/miniconda3_4.9.2_endfb-7.1_nndc_tendl_2019
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
 
+      - name: install dependancies
+        run: |
+          conda install -c conda-forge openmc
+
       - name: install package
         run: |
-          python setup.py install
+          pip install --upgrade pip
+          pip install .
+          python -c "import regular_mesh_plotter"
 
       - name: install packages for tests
         run: |
-          pip install -r requirements-test.txt 
+          pip install .[tests]
 
       - name: Run test_utils
         run: |
-          cp tests/example.stl .
           pytest tests/ -v --cov=regular_mesh_plotter --cov-append --cov-report term --cov-report xml
 
       - name: Upload to codecov

.gitignore

@@ -66,3 +66,6 @@ manifest_processed/
 # conda buid and dist dir
 build/
 dist/
+
+# python package version number
+_version.py

README.md

@@ -14,8 +14,7 @@
 pip install regular_mesh_plotter
 ```
 
-Mesh results in the form of Numpy arrays or OpenMC.tally objects can be plotted
-with a single API call.
+Mesh results in the form of at OpenMC.tally objects can be plotted with a single API call.
 
 A Matplotlib.pyplot object is returned by all functions so one can make changes
 to the legend, axis, colour map etc. However some key options are accessible
@@ -35,82 +34,41 @@ There are additional options that allow
 The resulting plots can be used to show dose maps, activation, reaction rate
 and other mesh tally results.
 
+The examples below require a mesh tally that can be read in with OpenMC in the following way.
 
-Example 1 shows a Numpy array plotted
 ```python
-from regular_mesh_plotter import plot_regular_mesh_values
-plot_regular_mesh_values(
-    values: np.ndarray,
-    filename: Optional[str] = None,
-    scale=None,  # LogNorm(),
-    vmin=None,
-    label="",
-    base_plt=None,
-    extent=None,
-    x_label="X [cm]",
-    y_label="Y [cm]",
-    rotate_plot: float = 0,
-)
-```
+import openmc
 
-Example 2 shows a Numpy array plotted with an underlying DAGMC geometry
-```python
-plot_regular_mesh_values_with_geometry(
-    values: np.ndarray,
-    dagmc_file_or_trimesh_object,
-    filename: Optional[str] = None,
-    scale=None,  # LogNorm(),
-    vmin=None,
-    label="",
-    extent=None,
-    x_label="X [cm]",
-    y_label="Y [cm]",
-    plane_origin: List[float] = None,
-    plane_normal: List[float] = [0, 0, 1],
-    rotate_mesh: float = 0,
-    rotate_geometry: float = 0,
-)
+# loads in the statepoint file containing tallies
+statepoint = openmc.StatePoint(filepath="statepoint.2.h5")
+
+# gets one tally from the available tallies
+my_tally = statepoint.get_tally(name="neutron_effective_dose_on_2D_mesh_xy")
 ```
 
-Example 3 shows a OpenMC tally plotted
+Example 1 shows a OpenMC tally plotted
 ```python
-plot_regular_mesh_tally(
-    tally,
-    dagmc_file_or_trimesh_object,
+
+import regular_mesh_plotter as rmp
+
+my_plot = rmp.plot_regular_mesh_tally(
+    tally=my_tally,
     std_dev_or_tally_value="tally_value",
-    filename: Optional[str] = None,
-    scale=None,  # LogNorm(),
-    vmin=None,
-    label="",
     x_label="X [cm]",
     y_label="Y [cm]",
-    plane_origin: List[float] = None,
-    plane_normal: List[float] = [0, 0, 1],
-    rotate_mesh: float = 0,
-    rotate_geometry: float = 0,
-    required_units=None,
-    source_strength: float = None,
 )
+
+my_plot.save_fig('openmc_mesh_tally_plot.png')
 ```
 
 Example 4 shows a OpenMC tally plotted with an underlying DAGMC geometry
 ```python
 plot_regular_mesh_tally_with_geometry(
-    tally,
-    dagmc_file_or_trimesh_object,
+    tally=my_tally,
+    dagmc_file_or_trimesh_object='dagmc.h5m',
     std_dev_or_tally_value="tally_value",
-    filename: Optional[str] = None,
-    scale=None,  # LogNorm(),
-    vmin=None,
-    label="",
     x_label="X [cm]",
     y_label="Y [cm]",
-    plane_origin: List[float] = None,
-    plane_normal: List[float] = [0, 0, 1],
-    rotate_mesh: float = 0,
-    rotate_geometry: float = 0,
-    required_units=None,
-    source_strength: float = None,
 )
 ```
 

examples/create_statepoint_file_with_meshes_openmc.py

@@ -1,5 +1,4 @@
 # This minimal example makes a 3D volume and exports the shape to a stp file
-# A surrounding volume called a graveyard is needed for neutronics simulations
 
 import openmc
 import openmc_dagmc_wrapper as odw

examples/create_statepoint_file_with_meshes_openmc_dagmc.py

@@ -5,6 +5,7 @@
 import openmc_dagmc_wrapper as odw
 import openmc_plasma_source as ops
 from stl_to_h5m import stl_to_h5m
+from dagmc_bounding_box import DagmcBoundingBox
 
 # code used to create example.stl
 # import paramak
@@ -24,6 +25,8 @@
     h5m_filename="dagmc.h5m",
 )
 
+my_corners = DagmcBoundingBox("dagmc.h5m").corners()
+
 # makes use of the previously created neutronics geometry (h5m file) and assigns
 # actual materials to the material tags. Sets simulation intensity and specifies
 # the neutronics results to record (know as tallies).
@@ -40,42 +43,42 @@
     tally_type="neutron_effective_dose",
     plane="xy",
     mesh_resolution=(10, 5),
-    bounding_box="dagmc.h5m",
+    bounding_box=my_corners,
 )
 tally2 = odw.MeshTally2D(
     tally_type="neutron_effective_dose",
     plane="yz",
     mesh_resolution=(10, 5),
-    bounding_box="dagmc.h5m",
+    bounding_box=my_corners,
 )
 tally3 = odw.MeshTally2D(
     tally_type="neutron_effective_dose",
     plane="xz",
     mesh_resolution=(10, 5),
-    bounding_box="dagmc.h5m",
+    bounding_box=my_corners,
 )
 tally4 = odw.MeshTally2D(
     tally_type="neutron_effective_dose",
     plane="xy",
     mesh_resolution=(10, 10),
-    bounding_box="dagmc.h5m",
+    bounding_box=my_corners,
 )
 tally5 = odw.MeshTally2D(
     tally_type="neutron_effective_dose",
     plane="yz",
     mesh_resolution=(10, 5),
-    bounding_box="dagmc.h5m",
+    bounding_box=my_corners,
 )
 tally6 = odw.MeshTally2D(
     tally_type="neutron_effective_dose",
     plane="xz",
     mesh_resolution=(10, 5),
-    bounding_box="dagmc.h5m",
+    bounding_box=my_corners,
 )
 
 # tally2 = odw.MeshTally3D(
 #     mesh_resolution=(100, 100, 100),
-#     bounding_box="dagmc.h5m",
+#     bounding_box=my_corners,
 #     tally_type="neutron_effective_dose",
 # )
 

pyproject.toml

@@ -0,0 +1,10 @@
+[build-system]
+requires = [
+    "setuptools >= 45",
+    "wheel",
+    "setuptools_scm[toml] >= 6.2",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "regular_mesh_plotter/_version.py"

regular_mesh_plotter/__init__.py

@@ -1,3 +1,16 @@
+try:
+    from importlib.metadata import version, PackageNotFoundError
+except (ModuleNotFoundError, ImportError):
+    from importlib_metadata import version, PackageNotFoundError
+try:
+    __version__ = version("regular_mesh_plotter")
+except PackageNotFoundError:
+    from setuptools_scm import get_version
+
+    __version__ = get_version(root="..", relative_to=__file__)
+
+__all__ = ["__version__"]
+
 from .core import plot_regular_mesh_values
 from .core import plot_regular_mesh_values_with_geometry
 

regular_mesh_plotter/core.py

@@ -42,10 +42,17 @@ def plot_regular_mesh_values(
         rot = transforms.Affine2D().rotate_deg_around(x_center, y_center, rotate_plot)
 
         image_map = plt.imshow(
-            values, norm=scale, vmin=vmin, extent=extent, transform=rot + base
+            values,
+            norm=scale,
+            vmin=vmin,
+            extent=extent,
+            transform=rot + base,
+            origin="lower",
         )
     else:
-        image_map = plt.imshow(values, norm=scale, vmin=vmin, extent=extent)
+        image_map = plt.imshow(
+            values, norm=scale, vmin=vmin, extent=extent, origin="lower"
+        )
 
     plt.xlabel(x_label)
     plt.ylabel(y_label)

setup.cfg

@@ -0,0 +1,48 @@
+[metadata]
+name = regular_mesh_plotter
+author = The Fusion Energy Development Team
+author_email = mail@jshimwell.com
+description = A Python package for creating publication quality plots of regular mesh tallies with the underlying geometry
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/fusion-energy/regular_mesh_plotter
+license = MIT
+license_file = LICENSE.txt
+classifiers =
+    Natural Language :: English
+    Topic :: Scientific/Engineering
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+project_urls =
+    Source = https://github.com/fusion-energy/regular_mesh_plotter
+    Tracker = https://github.com/fusion-energy/regular_mesh_plotter/issues
+
+[options]
+packages = find:
+python_requires= >=3.6
+install_requires=
+    numpy >= 1.21.1
+    matplotlib >= 3.4.2
+    trimesh
+    shapely
+    scipy
+    pandas
+    dagmc_geometry_slice_plotter
+    openmc_tally_unit_converter
+    setuptools_scm
+
+[options.extras_require]
+tests = 
+    pytest >= 5.4.3
+    pytest-cov>=2.12.1
+    openmc-dagmc-wrapper
+    openmc_plasma_source
+    stl_to_h5m
+
+[flake8]
+per-file-ignores = __init__.py:F401

setup.py

@@ -1,45 +1,4 @@
 import setuptools
 
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
-setuptools.setup(
-    name="regular_mesh_plotter",
-    version="develop",
-    author="The Regular Mesh Plotter Development Team",
-    author_email="mail@jshimwell.com",
-    description="A Python package for creating publication quality plots of regular mesh tallies with the underlying geometry",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/fusion-energy/regular_mesh_plotter",
-    packages=setuptools.find_packages(),
-    classifiers=[
-        "Natural Language :: English",
-        "Topic :: Scientific/Engineering",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: OS Independent",
-    ],
-    python_requires=">=3.6",
-    package_data={
-        "regular_mesh_plotter": [
-            # "requirements.txt",
-            "README.md",
-            "LICENSE",
-        ]
-    },
-    install_requires=[
-        "numpy>=1.21.1",
-        "matplotlib>=3.4.2",
-        "trimesh",
-        "shapely",
-        "scipy",
-        "pandas",
-        "dagmc_geometry_slice_plotter",
-        "openmc_tally_unit_converter",
-    ],
-)
+if __name__ == "__main__":
+    setuptools.setup()

tests/create_statepoint_file_for_testing_using_dagmc.py

@@ -1,5 +1,4 @@
 # This minimal example makes a 3D volume and exports the shape to a stp file
-# A surrounding volume called a graveyard is needed for neutronics simulations
 
 import openmc
 import openmc_dagmc_wrapper as odw
@@ -12,15 +11,15 @@
     distance=180,
 )
 
-my_shape.export_stl("example.stl")
+my_shape.export_stl("tests/example.stl")
 
 # This script converts the CAD stl files generated into h5m files that can be
 # used in DAGMC enabled codes. h5m files created in this way are imprinted,
 # merged, faceted and ready for use in OpenMC. One of the key aspects of this
 # is the assignment of materials to the volumes present in the CAD files.
 
 stl_to_h5m(
-    files_with_tags=[("example.stl", "mat1")],
+    files_with_tags=[("tests/example.stl", "mat1")],
     h5m_filename="dagmc.h5m",
 )