Merge pull request #14 from fusion-energy/adding_flake8_linting

added auto lint comments to pushes

.github/workflows/ci_with_install.yml

@@ -1,47 +1,50 @@
 
-# TODO this needs completing, the docker image would currently need a couple of
-# versions of openmc as the current 0.13-dev doesn't create an initial_source.h5
-# while the older versions don't write the required xml tag.
-# <write_initial_source>true</write_initial_source>
-# note to self come back to this once the current version of openmc writes out
-# the initial_source.h5
-
-
-
-# # 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: ghcr.io/fusion-energy/paramak:dependencies
-#     steps:
-#       - name: Checkout repository
-#         uses: actions/checkout@v2
-
-#       - name: install package
-#         run: |
-#           python setup.py install
-
-#       - name: Run test_utils
-#         run: |
-#           pytest tests/test_utils.py -v --cov=openmc_source_plotter --cov-append --cov-report term --cov-report xml
-
-#       - name: Upload to codecov
-#         uses: codecov/codecov-action@v2
+# 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: openmc/openmc:develop
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: install package
+        run: |
+          pip install .
+          python -c "import openmc_source_plotter"
+
+      - name: Run examples
+        run: |
+          python examples/example_get_particle_data.py
+          python examples/example_plot_source_direction.py
+          python examples/example_plot_source_energy.py
+          python examples/example_plot_source_position.py
+          python examples/example_plot_two_source_energies.py
+          pip install openmc_plasma_source
+          python examples/example_plot_plasma_source_position.py
+
+      - name: Run test_utils
+        run: |
+          pip install .[tests]
+          pytest tests -v --cov=openmc_source_plotter --cov-append --cov-report term --cov-report xml
+
+      - name: Upload to codecov
+        uses: codecov/codecov-action@v2

.github/workflows/lint.yaml

@@ -0,0 +1,27 @@
+name: Python Flake8 Lint
+
+on:
+  # Trigger the workflow pull requests to any branch
+  pull_request:
+
+jobs:
+  run-linters:
+    name: lint
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out Git repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Python dependencies
+        run: pip install flake8
+
+      - name: Run linters
+        uses: wearerequired/lint-action@v2
+        with:
+          flake8: true

.gitignore

@@ -131,3 +131,6 @@ dmypy.json
 # openmc files
 *.h5
 *.xml
+
+# version file
+openmc_source_plotter/_version.py

openmc_source_plotter/core.py

@@ -11,7 +11,9 @@
 import plotly.graph_objects as go
 
 
-def sample_initial_particles(source: openmc.source, n_samples=1000, prn_seed=None):
+def sample_initial_particles(
+    source: openmc.source, n_samples: int = 1000, prn_seed: int = None
+):
 
     settings = openmc.Settings()
     settings.particles = 1
@@ -28,10 +30,6 @@ def sample_initial_particles(source: openmc.source, n_samples=1000, prn_seed=Non
 
     geometry.export_to_xml()
 
-    # # model = openmc.Model()
-    # model.geometry = geometry
-    # model.materials = geometry
-
     openmc.lib.init()
     particles = openmc.lib.sample_external_source(
         n_samples=n_samples, prn_seed=prn_seed
@@ -44,13 +42,17 @@ def plot_source_energy(
     source: Union[openmc.Source, List[openmc.Source]],
     n_samples: int = 2000,
     prn_seed: int = 1,
+    energy_bins: Union[str, np.array] = "auto",
 ):
     """makes a plot of the initial creation postions of an OpenMC source(s)
 
     Args:
         source: The openmc.Source object or list of openmc.Source objects to plot.
-        n_smaples: The number of source samples to obtain.
+        n_samples: The number of source samples to obtain.
         prn_seed: The pseudorandom number seed
+        energy_bins: Defaults to 'auto' which uses inbuilt auto binning in Numpy
+            bins can also be manually set by passing in a numpy array of bin
+            edges.
     """
 
     figure = go.Figure()
@@ -60,10 +62,12 @@ def plot_source_energy(
 
     for single_source in source:
 
-        e_values = single_source.energy.sample(n_samples=n_samples, prn_seed=prn_seed)
+        data = sample_initial_particles(single_source, n_samples, prn_seed)
+
+        e_values = [particle.E for particle in data]
 
         # Calculate pdf for source energies
-        probability, bin_edges = np.histogram(e_values, bins="auto", density=True)
+        probability, bin_edges = np.histogram(e_values, bins=energy_bins, density=True)
 
         # Plot source energy histogram
         figure.add_trace(
@@ -94,7 +98,7 @@ def plot_source_position(
 
     Args:
         source: The openmc.Source object or list of openmc.Source objects to plot.
-        n_smaples: The number of source samples to obtain.
+        n_samples: The number of source samples to obtain.
         prn_seed: The pseudorandom number seed
     """
 
@@ -106,7 +110,6 @@ def plot_source_position(
     for single_source in source:
 
         data = sample_initial_particles(single_source, n_samples, prn_seed)
-        print([p.r for p in data])
 
         text = ["Energy = " + str(particle.E) + " eV" for particle in data]
 
@@ -139,7 +142,7 @@ def plot_source_direction(
 
     Args:
         source: The openmc.Source object or list of openmc.Source objects to plot.
-        n_smaples: The number of source samples to obtain.
+        n_samples: The number of source samples to obtain.
         prn_seed: The pseudorandom number seed
     """
     figure = go.Figure()

setup.cfg

@@ -32,5 +32,9 @@ install_requires=
     h5py
     # openmc is also required but can't yet be installed by pip
 
+[options.extras_require]
+tests = 
+    pytest >= 5.4.3
+
 [flake8]
 per-file-ignores = __init__.py:F401

tests/test_core.py

@@ -10,13 +10,6 @@
 class TestUtils(unittest.TestCase):
     def setUp(self):
 
-        self.openmc_exec_dict = {
-            "ci": "/opt/openmc/build/bin/openmc",
-            "laptop": "/home/jshim/miniconda3/envs/openmc_0_11_0/bin/openmc",
-            "desktop": "/home/jshimwell/miniconda3/envs/openmc_0_11_0/bin/openmc",
-        }
-        self.current_computer = "laptop"
-
         # initialises a new source object
         my_source = openmc.Source()
 
@@ -32,17 +25,16 @@ def setUp(self):
         self.my_source = my_source
 
         # makes an initial_source.h5 file with details of the particles
-        self.initial_source_filename = osp.create_initial_particles(
+        self.initial_source_filename = osp.sample_initial_particles(
             source=my_source,
-            number_of_particles=10,
-            openmc_exec=self.openmc_exec_dict[self.current_computer],
+            n_samples=10,
         )
 
     def test_energy_plot(self):
 
         plot = osp.plot_source_energy(
             source=self.my_source,
-            number_of_particles=10000,
+            n_samples=10000,
             energy_bins=np.linspace(0, 20e6, 100),
         )
         assert isinstance(plot, go.Figure)
@@ -51,14 +43,12 @@ def test_position_plot(self):
 
         plot = osp.plot_source_position(
             source=self.my_source,
-            openmc_exec=self.openmc_exec_dict[self.current_computer],
         )
         assert isinstance(plot, go.Figure)
 
     def test_direction_plot(self):
         plot = osp.plot_source_direction(
             source=self.my_source,
-            number_of_particles=100,
-            openmc_exec=self.openmc_exec_dict["laptop"],
+            n_samples=100,
         )
         assert isinstance(plot, go.Figure)