Merge pull request #254 from fusion-energy/develop

General updates from development branch

.circleci/config.yml

@@ -36,16 +36,16 @@ jobs:
       - install
       - run:
           name: run utils tests
-          command: pytest tests/test_utils.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
+          command: pytest tests/tests_units/test_utils.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
       - run:
           name: run shape tests
-          command: pytest tests/test_shape.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
+          command: pytest tests/tests_units/test_shape.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
       - run:
           name: run Reactor tests
-          command: pytest tests/test_reactor.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
+          command: pytest tests/tests_units/test_reactor.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
       - run:
           name: run parametric_shapes tests
-          command: pytest tests/test_parametric_shapes/ -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
+          command: pytest tests/tests_units/test_parametric_shapes/ -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
       - store_test_results:
           path: test-reports
       - store_artifacts:
@@ -64,7 +64,7 @@ jobs:
           name: run parametric_components tests
           command: |
             set -e
-            TEST_FILES=$(circleci tests glob "tests/test_parametric_components/**/*.py" | circleci tests split)
+            TEST_FILES=$(circleci tests glob "tests/tests_units/test_parametric_components/**/*.py" | circleci tests split)
             pytest -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml $TEST_FILES
       - store_test_results:
           path: test-reports
@@ -83,7 +83,7 @@ jobs:
           name: run parametric_reactors tests
           command: |
             set -e
-            TEST_FILES=$(circleci tests glob "tests/test_parametric_reactors/**/*.py" | circleci tests split)
+            TEST_FILES=$(circleci tests glob "tests/tests_units/test_parametric_reactors/**/*.py" | circleci tests split)
             pytest -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml $TEST_FILES
       - store_test_results:
           path: test-reports
@@ -100,7 +100,7 @@ jobs:
       - install
       - run:
           name: run utils tests
-          command: pytest tests_h5m -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
+          command: pytest tests/tests_h5m -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
       - store_test_results:
           path: test-reports
       - store_artifacts:
@@ -116,7 +116,7 @@ jobs:
       - install
       - run:
           name: run utils tests
-          command: pytest tests_show -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
+          command: pytest tests/tests_show -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
       - store_test_results:
           path: test-reports
       - store_artifacts:

.github/workflows/anaconda-publish.yml

@@ -19,11 +19,10 @@ jobs:
             apt install -y libgl1-mesa-glx
             conda install -y anaconda-client conda-build
             conda config --set anaconda_upload no
-            conda install boa -c conda-forge
       - name: Build and publish to conda
         env:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         run: |
-            conda mambabuild conda -c fusion-energy -c cadquery -c conda-forge --config-file conda/conda_build_config.yaml
+            conda build conda -c fusion-energy -c cadquery -c conda-forge --config-file conda/conda_build_config.yaml
             conda convert /opt/conda/conda-bld/linux-64/*.tar.bz2 --platform osx-64 --platform win-64 -o /opt/conda/conda-bld/
             anaconda upload -f /opt/conda/conda-bld/*/*.tar.bz2

.github/workflows/ci_with_docker_build.yml

@@ -17,7 +17,7 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-  
+
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
@@ -26,13 +26,13 @@ jobs:
         run: docker build -t paramak --build-arg cq_version=master .
 
       - name: Run unit tests
-        run: docker run --rm paramak pytest ./tests
+        run: docker run --rm paramak pytest ./tests/tests_units
 
       - name: Test examples
-        run: docker run --rm paramak pytest ./tests_examples
+        run: docker run --rm paramak pytest ./tests/tests_examples
 
       # tests_show require jupyter_cadquery which is not available on conda
       # therefore these tests have been separated out to help with the conda
-      # testing. The tests_h5m tests require CQ master which is tested elsewhere
+      # testing. The tests_h5m tests require CQ master which is tested separately as well
       - name: Test show
-        run: docker run --rm paramak pytest ./tests_show
+        run: docker run --rm paramak pytest ./tests/tests_show

.github/workflows/ci_with_install.yml

@@ -1,5 +1,5 @@
 # This CI will lauch a Docker image that contains all the dependencies required
-# within that image the pytest test suite is run 
+# within that image the pytest test suite is run
 
 name: CI with install
 
@@ -37,9 +37,9 @@ jobs:
 
       - name: Run tests
         run: |
-          pytest tests -v --cov=paramak --cov-append --cov-report term --cov-report xml
-          pytest tests_examples -v --cov=paramak --cov-append --cov-report term --cov-report xml
-          pytest tests_show -v --cov=paramak --cov-append --cov-report term --cov-report xml
+          pytest tests/tests_units -v --cov=paramak --cov-append --cov-report term --cov-report xml
+          pytest tests/tests_examples -v --cov=paramak --cov-append --cov-report term --cov-report xml
+          pytest tests/tests_show -v --cov=paramak --cov-append --cov-report term --cov-report xml
 
       - name: Upload to codecov
         uses: codecov/codecov-action@v2

.github/workflows/ci_with_install_cq_master.yml

@@ -32,13 +32,13 @@ jobs:
 
       - name: Run tests
         run: |
-          pytest tests -v --cov=paramak --cov-append --cov-report term --cov-report xml
-          pytest tests_h5m -v --cov=paramak --cov-append --cov-report term --cov-report xml
+          pytest tests/test_units -v --cov=paramak --cov-append --cov-report term --cov-report xml
+          pytest tests/tests_h5m -v --cov=paramak --cov-append --cov-report term --cov-report xml
 
 # jupyter cadquery doesn't appear to work with the current version of CQ master
 # therefore the show() methods also don't work
-# pytest tests_show -v --cov=paramak --cov-append --cov-report term --cov-report xml
-# pytest tests_examples -v --cov=paramak --cov-append --cov-report term --cov-report xml
+# pytest tests/tests_show -v --cov=paramak --cov-append --cov-report term --cov-report xml
+# pytest tests/tests_examples -v --cov=paramak --cov-append --cov-report term --cov-report xml
 
       - name: Upload to codecov
         uses: codecov/codecov-action@v2

.github/workflows/conda-build-test.yml

@@ -21,9 +21,8 @@ jobs:
             apt install -y libgl1-mesa-glx
             conda install -y anaconda-client conda-build
             conda config --set anaconda_upload no
-            conda install boa -c conda-forge
       - name: Build and test
         env:
           GIT_DESCRIBE_TAG: 0.1
         run: |
-            conda mambabuild conda -c fusion-energy -c cadquery -c conda-forge --config-file conda/conda_build_config.yaml
+            conda build conda -c fusion-energy -c cadquery -c conda-forge --config-file conda/conda_build_config.yaml

.github/workflows/test_demos.yml

@@ -33,4 +33,4 @@ jobs:
 
       - name: Run the notebooks
         run: |
-          pytest tests_examples -v
+          pytest tests/tests_examples -v

Dockerfile

@@ -74,9 +74,6 @@ COPY paramak paramak/
 COPY examples examples/
 
 COPY tests tests/
-COPY tests_h5m tests_h5m/
-COPY tests_show tests_show/
-COPY tests_examples tests_examples/
 
 COPY setup.py setup.py
 COPY setup.cfg setup.cfg

conda/meta.yaml

@@ -24,6 +24,7 @@ requirements:
     - plotly
     - brep_part_finder >=0.4.1 # [not win]
     - brep_to_h5m >=0.3.1 # [not win]
+    - moab * nompi_tempest_*
     # - jupyter-cadquery not available on conda
 
 test:
@@ -32,20 +33,19 @@ test:
     - paramak.parametric_components
     - paramak.parametric_reactors
     - paramak.parametric_shapes
-    - tests
   requires:
     - pytest
     - dagmc_h5m_file_inspector  # [not win]
   source_files:
-    - tests/
+    - tests/tests_units
     - examples/
-    - tests_h5m/  # [not win]
-    # - tests_examples/  # TODO include if cadquery_jupyter gets a conda install
+    - tests/tests_h5m/  # [not win]
+    # - tests/tests_examples/  # TODO include if cadquery_jupyter gets a conda install
   commands:
-    - pytest -v tests_h5m  # [not win]
-    - pytest -v tests
-    # - pytest -v tests_show  # TODO include if cadquery_jupyter gets a conda install
-    # - pytest -v tests_examples  # TODO include if cadquery_jupyter gets a conda install
+    - pytest -v tests/tests_h5m  # [not win]
+    - pytest -v tests/tests_units
+    # - pytest -v tests/tests_show  # TODO include if cadquery_jupyter gets a conda install
+    # - pytest -v tests/tests_examples  # TODO include if cadquery_jupyter gets a conda install
 
 about:
   home: "https://github.com/fusion-energy/paramak"

environment.yml

@@ -15,6 +15,7 @@ dependencies:
   - matplotlib
   - pillow
   - plasmaboundaries
+  - pip
   - pip:
       - sympy
       - sphinx-autodoc-typehints

paramak/parametric_components/blanket_cutter_parallels.py

@@ -1,3 +1,5 @@
+from typing import Iterable, Union
+
 from paramak import ExtrudeStraightShape
 from paramak.utils import cut_solid
 
@@ -28,7 +30,7 @@ def __init__(
         gap_size: float,
         height: float = 2000.0,
         width: float = 2000.0,
-        azimuth_placement_angle=[
+        azimuth_placement_angle: Union[float, Iterable[float]] = [
             0.0,
             36.0,
             72.0,

paramak/parametric_components/blanket_cutters_star.py

@@ -1,4 +1,4 @@
-from typing import List, Union
+from typing import Iterable, Union
 
 from paramak import ExtrudeStraightShape
 
@@ -25,7 +25,7 @@ def __init__(
         distance: float,
         height: float = 2000.0,
         width: float = 2000.0,
-        azimuth_placement_angle: Union[float, List[float]] = [
+        azimuth_placement_angle: Union[float, Iterable[float]] = [
             0.0,
             36.0,
             72.0,

paramak/parametric_components/blanket_fp.py

@@ -1,5 +1,5 @@
 import warnings
-from typing import Optional, Union
+from typing import Optional, Union, Iterable
 
 import mpmath
 import numpy as np
@@ -11,7 +11,9 @@
 
 
 class BlanketFP(RotateMixedShape):
-    """A blanket volume created from plasma parameters.
+    """A blanket volume created from plasma parameters. In might be nessecary
+    to increase the num_points when making long but thin geometry with this
+    component.
 
     Args:
         thickness (float or [float] or callable or [(float), (float)]):
@@ -47,13 +49,13 @@ def __init__(
         start_angle: float,
         stop_angle: float,
         plasma: Optional[Union[paramak.Plasma, paramak.PlasmaBoundaries, paramak.PlasmaFromPoints]] = None,
-        minor_radius: Optional[float] = 150.0,
-        major_radius: Optional[float] = 450.0,
-        triangularity: Optional[float] = 0.55,
-        elongation: Optional[float] = 2.0,
-        vertical_displacement: Optional[float] = 0.0,
-        offset_from_plasma: Union[float, list] = 0.0,
-        num_points: Optional[int] = 50,
+        minor_radius: float = 150.0,
+        major_radius: float = 450.0,
+        triangularity: float = 0.55,
+        elongation: float = 2.0,
+        vertical_displacement: float = 0.0,
+        offset_from_plasma: Union[float, Iterable[float]] = 0.0,
+        num_points: int = 50,
         allow_overlapping_shape=False,
         **kwargs
     ):

paramak/parametric_components/blanket_poloidal_segment.py

@@ -1,5 +1,5 @@
 import warnings
-from typing import Callable, List, Optional, Tuple, Union
+from typing import Callable, Iterable, Optional, Tuple, Union
 
 import numpy as np
 from scipy.optimize import minimize
@@ -29,8 +29,8 @@ class BlanketFPPoloidalSegments(BlanketFP):
 
     def __init__(
         self,
-        segments_angles: Optional[List[float]] = None,
-        num_segments: Optional[int] = 7,
+        segments_angles: Optional[Iterable[float]] = None,
+        num_segments: int = 7,
         length_limits: Optional[Tuple[Union[float, None], Union[float, None]]] = None,
         nb_segments_limits: Optional[Tuple[float, float]] = None,
         segments_gap: Optional[float] = 0.0,
@@ -173,14 +173,14 @@ def create_segment_cutters(self):
             self.segments_cutters = cutting_shape
 
 
-def compute_lengths_from_angles(angles: List[float], distribution: Callable):
+def compute_lengths_from_angles(angles: Iterable[float], distribution: Callable):
     """Computes the length of segments between a set of points on a (x,y)
     distribution.
 
     Args:
-        angles (list): Contains the angles of the points (degree)
-        distribution (callable): function taking an angle as argument and
-            returning (x,y) coordinates.
+        angles: Contains the angles of the points (degrees)
+        distribution: function taking an angle as argument and returning (x,y)
+            coordinates.
 
     Returns:
         list: contains the lengths of the segments.

paramak/parametric_components/center_column_cylinder.py

@@ -1,4 +1,4 @@
-from typing import Optional, Tuple
+from typing import Optional, Tuple, Union
 
 from paramak import RotateStraightShape
 
@@ -40,7 +40,7 @@ def center_height(self):
         return self._center_height
 
     @center_height.setter
-    def center_height(self, value):
+    def center_height(self, value: Union[float, int]):
         if not isinstance(value, (int, float)):
             msg = f"CenterColumnShieldBlock.center_height should be a float or int. Not a {type(value)}"
             raise TypeError(msg)
@@ -52,7 +52,7 @@ def height(self):
         return self._height
 
     @height.setter
-    def height(self, value):
+    def height(self, value: float):
         if value is None:
             raise ValueError("height of the CenterColumnShieldBlock cannot be None")
         self._height = value
@@ -62,7 +62,7 @@ def inner_radius(self):
         return self._inner_radius
 
     @inner_radius.setter
-    def inner_radius(self, value):
+    def inner_radius(self, value: float):
         if hasattr(self, "outer_radius"):
             if value >= self.outer_radius:
                 msg = f"inner_radius ({value}) is larger than outer_radius " "({self.outer_radius})"
@@ -74,7 +74,7 @@ def outer_radius(self):
         return self._outer_radius
 
     @outer_radius.setter
-    def outer_radius(self, value):
+    def outer_radius(self, value: float):
         if hasattr(self, "inner_radius"):
             if value <= self.inner_radius:
                 msg = f"inner_radius ({self.inner_radius}) is larger than " "outer_radius ({value})"

paramak/parametric_components/center_column_flat_top_circular.py

@@ -56,31 +56,31 @@ def arc_height(self):
         return self._arc_height
 
     @arc_height.setter
-    def arc_height(self, arc_height):
+    def arc_height(self, arc_height: float):
         self._arc_height = arc_height
 
     @property
     def inner_radius(self):
         return self._inner_radius
 
     @inner_radius.setter
-    def inner_radius(self, inner_radius):
+    def inner_radius(self, inner_radius: float):
         self._inner_radius = inner_radius
 
     @property
     def mid_radius(self):
         return self._mid_radius
 
     @mid_radius.setter
-    def mid_radius(self, mid_radius):
+    def mid_radius(self, mid_radius: float):
         self._mid_radius = mid_radius
 
     @property
     def outer_radius(self):
         return self._outer_radius
 
     @outer_radius.setter
-    def outer_radius(self, outer_radius):
+    def outer_radius(self, outer_radius: float):
         self._outer_radius = outer_radius
 
     def find_points(self):