Merge pull request #2 from fusion-energy/adding_tests

added first test and CI

.github/workflows/black.yml

@@ -0,0 +1,32 @@
+name: black
+
+on:
+  push:
+    paths:
+      - '**.py'
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        ref: ${{ github.head_ref }}
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.x
+    - name: Install black
+      run: |
+        python -m pip install --upgrade pip
+        pip install black
+    - name: Run black
+      run: |
+        black .
+    - uses: stefanzweifel/git-auto-commit-action@v4
+      with:
+        commit_message: "[skip ci] Apply formatting changes"

.github/workflows/ci_with_install.yml

@@ -0,0 +1,51 @@
+# This CI will launch a Docker image that contains all the dependencies required
+# within that image the pytest test suite is run 
+
+name: CI with install
+
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+    paths-ignore:
+      - 'docs/**'
+      - '.gitignore'
+      - '*.md'
+      - 'CITATION.cff'
+      - 'LICENSE.txt'
+      - 'readthedocs.yml'
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    container:
+      # image: continuumio/miniconda3:4.10.3
+      image: openmc/openmc:latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # - name: install dependencies
+      #   run: |
+      #     conda install -c conda-forge mamba
+      #     mamba install -c conda-forge openmc
+
+      - name: install package
+        run: |
+          pip install --upgrade pip
+          pip install .
+          python -c "import cylindrical_mesh_plotter"
+
+      - name: install packages for tests
+        run: |
+          pip install .[tests]
+
+      - name: Run test_utils
+        run: |
+          pytest tests
+
+      - name: Run examples
+        run: |
+          cd examples
+          python plot_rz_slices.py

.github/workflows/python-publish.yml

@@ -0,0 +1,40 @@
+# This yml file will trigger a Github Actions event that builds and upload the
+# Python package to PiPy. This makes use of Twine and is triggered when a push
+# to the main branch occures. For more information see:
+# https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+# and for details on the Autobump version section see:
+# https://github.com/grst/python-ci-versioneer
+
+name: Upload Python Package
+
+on:
+  # allows us to run workflows manually
+  workflow_dispatch:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel build twine
+
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: |
+        python -m build
+        twine check dist/*
+        twine upload dist/*

examples/simple_plot.py → examples/plot_rz_slices.py

@@ -9,22 +9,22 @@
 import openmc_cylindrical_mesh_plotter  # adds slice_of_data method to CylindricalMesh
 
 mesh = openmc.CylindricalMesh()
-mesh.phi_grid = np.linspace(0.,2*pi,10)
-mesh.r_grid = np.linspace(0,10,4)
-mesh.z_grid = np.linspace(0,5,5)
+mesh.phi_grid = np.linspace(0.0, 2 * pi, 10)
+mesh.r_grid = np.linspace(0, 10, 4)
+mesh.z_grid = np.linspace(0, 5, 5)
 
-tally = openmc.Tally(name='my_tally')
+tally = openmc.Tally(name="my_tally")
 mesh_filter = openmc.MeshFilter(mesh)
 tally.filters.append(mesh_filter)
 tally.scores.append("flux")
 tallies = openmc.Tallies([tally])
 
-outer_surface = openmc.Sphere(r=100, boundary_type='vacuum')
-cell = openmc.Cell(region = -outer_surface)
+outer_surface = openmc.Sphere(r=100, boundary_type="vacuum")
+cell = openmc.Cell(region=-outer_surface)
 
 material = openmc.Material()
-material.add_nuclide('Fe56', 1)
-material.set_density('g/cm3', 0.1)
+material.add_nuclide("Fe56", 1)
+material.set_density("g/cm3", 0.1)
 my_materials = openmc.Materials([material])
 
 universe = openmc.Universe(cells=[cell])
@@ -37,17 +37,16 @@
 # the distribution of source z values is just a single value
 z_values = openmc.stats.Discrete([2.5], [1])
 # the distribution of source azimuthal angles values is a uniform distribution between 0 and 2 Pi
-angle = openmc.stats.Uniform(a=0., b=2* 3.14159265359)
+angle = openmc.stats.Uniform(a=0.0, b=2 * 3.14159265359)
 # this makes the ring source using the three distributions and a radius
 # could do a point source instead with my_source.space = openmc.stats.Point((5,5., 5))
 my_source.space = openmc.stats.CylindricalIndependent(
-    r=radius, phi=angle,
-    z=z_values, origin=(0.0, 0.0, 0.0))
+    r=radius, phi=angle, z=z_values, origin=(0.0, 0.0, 0.0)
+)
 # sets the direction to isotropic
 my_source.angle = openmc.stats.Isotropic()
 
 
-
 my_settings = openmc.Settings()
 # my_settings.inactive = 0
 my_settings.run_mode = "fixed source"
@@ -60,19 +59,16 @@
 
 statepoint = openmc.StatePoint(sp_filename)
 
-my_tally_result = statepoint.get_tally(name='my_tally')
+my_tally_result = statepoint.get_tally(name="my_tally")
 
 mesh.write_data_to_vtk(
-    filename="my_tally_result.vtk",
-    datasets={"mean": my_tally_result.mean}
+    filename="my_tally_result.vtk", datasets={"mean": my_tally_result.mean}
 )
 
 
-for slice_index in range(len(mesh.phi_grid)-1):
+for slice_index in range(len(mesh.phi_grid) - 1):
     data = mesh.slice_of_data(
-        dataset=my_tally_result.mean,
-        slice_index=slice_index,
-        volume_normalization=True
+        dataset=my_tally_result.mean, slice_index=slice_index, volume_normalization=True
     )
     extent = mesh.get_mpl_plot_extent()
     x_label, y_label = mesh.get_axis_labels()

pyproject.toml

@@ -1,10 +1,41 @@
 [build-system]
-requires = [
-    "setuptools >= 45",
-    "wheel",
-    "setuptools_scm[toml] >= 6.2",
-]
+requires = ["setuptools >= 65.4.0", "setuptools_scm[toml]>=7.0.5"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "cylindrical_mesh_plotter"
+authors = [
+  { name="Jonathan Shimwell", email="[email protected]" },
+]
+license = {file = "LICENSE.txt"}
+description = "A Python package for creating publication quality plots of cylindrical mesh tallies"
+readme = "README.md"
+requires-python = ">=3.8"
+keywords = ["cylindrical", "mesh", "openmc", "tally", "plot", "slice"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "numpy>=1.21.1",
+    "matplotlib>=3.4.2",
+]
+dynamic = ["version"]
+
+
 [tool.setuptools_scm]
-write_to = "src/openmc_cylindrical_mesh_plotter/_version.py"
+write_to = "src/cylindrical_mesh_plotter/_version.py"
+
+
+[project.optional-dependencies]
+tests = [
+    "pytest",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/fusion-energy/cylindrical_mesh_plotter"
+"Bug Tracker" = "https://github.com/fusion-energy/cylindrical_mesh_plotter/issues"
+
+[tool.setuptools]
+package-dir = {"" = "src"}

src/openmc_cylindrical_mesh_plotter/__init__.py

@@ -1 +1 @@
-from .core import *
+from .core import *

src/openmc_cylindrical_mesh_plotter/core.py

@@ -10,15 +10,14 @@ def slice_of_data(
     slice_index=0,
     volume_normalization: bool = True,
 ):
-
     if volume_normalization:
         dataset = dataset.flatten() / self.volumes.T.reshape(-1, 3).flatten()
     else:
         dataset = dataset.flatten()
 
     data_slice = dataset.T.reshape(-1, 3)
 
-    data_slice = data_slice[slice_index::self.dimension[1]]
+    data_slice = data_slice[slice_index :: self.dimension[1]]
 
     return np.flip(data_slice, axis=0)
 

tests/test_slice_of_data.py

@@ -0,0 +1,72 @@
+import openmc
+import numpy as np
+from math import pi
+import matplotlib.pyplot as plt
+import openmc_cylindrical_mesh_plotter  # adds slice_of_data method to CylindricalMesh
+
+
+def test_slice_of_data():
+    mesh = openmc.CylindricalMesh()
+    mesh.phi_grid = np.linspace(0.0, 2 * pi, 10)
+    mesh.r_grid = np.linspace(0, 10, 4)
+    mesh.z_grid = np.linspace(0, 5, 5)
+
+    tally = openmc.Tally(name="my_tally")
+    mesh_filter = openmc.MeshFilter(mesh)
+    tally.filters.append(mesh_filter)
+    tally.scores.append("flux")
+    tallies = openmc.Tallies([tally])
+
+    outer_surface = openmc.Sphere(r=100, boundary_type="vacuum")
+    cell = openmc.Cell(region=-outer_surface)
+
+    material = openmc.Material()
+    material.add_nuclide("Fe56", 1)
+    material.set_density("g/cm3", 0.1)
+    my_materials = openmc.Materials([material])
+
+    universe = openmc.Universe(cells=[cell])
+    my_geometry = openmc.Geometry(universe)
+
+    my_source = openmc.Source()
+
+    # the distribution of radius is just a single value
+    radius = openmc.stats.Discrete([5], [1])
+    # the distribution of source z values is just a single value
+    z_values = openmc.stats.Discrete([2.5], [1])
+    # the distribution of source azimuthal angles values is a uniform distribution between 0 and 2 Pi
+    angle = openmc.stats.Uniform(a=0.0, b=2 * 3.14159265359)
+    # this makes the ring source using the three distributions and a radius
+    # could do a point source instead with my_source.space = openmc.stats.Point((5,5., 5))
+    my_source.space = openmc.stats.CylindricalIndependent(
+        r=radius, phi=angle, z=z_values, origin=(0.0, 0.0, 0.0)
+    )
+    # sets the direction to isotropic
+    my_source.angle = openmc.stats.Isotropic()
+
+    my_settings = openmc.Settings()
+    # my_settings.inactive = 0
+    my_settings.run_mode = "fixed source"
+    my_settings.batches = 10
+    my_settings.particles = 100000
+    my_settings.source = my_source
+
+    model = openmc.model.Model(my_geometry, my_materials, my_settings, tallies)
+    sp_filename = model.run()
+
+    statepoint = openmc.StatePoint(sp_filename)
+
+    my_tally_result = statepoint.get_tally(name="my_tally")
+
+    for slice_index in range(len(mesh.phi_grid) - 1):
+        data = mesh.slice_of_data(
+            dataset=my_tally_result.mean,
+            slice_index=slice_index,
+            volume_normalization=True,
+        )
+        extent = mesh.get_mpl_plot_extent()
+        x_label, y_label = mesh.get_axis_labels()
+        plt.xlabel(x_label)
+        plt.ylabel(y_label)
+        plt.imshow(data, extent=extent)
+        assert data.shape == (4, 3)