using pytest command instead of bash

.circleci/config.yml

@@ -25,11 +25,6 @@ jobs:
           command: 
             pytest tests/test_shape.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
 
-      - run:
-          name: run h5m export (pymoab) tests
-          command: 
-            pytest tests/test_h5m_export.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
-
       - run:
           name: run Reactor tests
           command: 

.github/workflows/ci_with_install.yml

@@ -23,6 +23,29 @@ jobs:
       - name: install package
         run: |
           python setup.py install
-      - name: run tests
+
+      - name: Run test_utils
+        run: |
+          pytest tests/test_utils.py -v --cov=paramak --cov-append --cov-report term --cov-report xml
+
+      - name: Run test_shape
+        run: |
+          pytest tests/test_shape.py -v --cov=paramak --cov-append --cov-report term --cov-report xml
+
+      - name: Run test_reactor
+        run: |
+          pytest tests/test_reactor.py -v --cov=paramak --cov-append --cov-report term --cov-report xml
+
+      - name: Run test_parametric_shapes
+        run: |
+          pytest tests/test_parametric_shapes/ -v --cov=paramak --cov-append --cov-report term --cov-report xml
+
+      - name: Run test_parametric_components
+        run: |
+          pytest tests/test_parametric_components/ -v --cov=paramak --cov-append --cov-report term --cov-report xml
+
+      - name: Run test_parametric_reactors
         run: |
-          bash run_tests.sh
+          pytest tests/test_parametric_reactors/ -v --cov=paramak --cov-append --cov-report term --cov-report xml
+      - name: Upload to codecov
+        uses: codecov/codecov-action@v2

Dockerfile

@@ -35,9 +35,6 @@ ARG cq_version=2.1
 
 
 ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 \
-    PATH=/opt/openmc/bin:/opt/NJOY2016/build:$PATH \
-    LD_LIBRARY_PATH=/opt/openmc/lib:$LD_LIBRARY_PATH \
-    CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx \
     DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get --allow-releaseinfo-change update
@@ -56,40 +53,6 @@ RUN echo installing CadQuery version $cq_version && \
     pip install jupyter-cadquery==2.2.0 && \
     conda clean -afy
 
-# Download Cubit
-RUN wget -O coreform-cubit-2021.5.deb https://f002.backblazeb2.com/file/cubit-downloads/Coreform-Cubit/Releases/Linux/Coreform-Cubit-2021.5%2B15962_5043ef39-Lin64.deb
-
-# install Cubit dependencies
-RUN apt-get install -y libx11-6
-RUN apt-get install -y libxt6
-RUN apt-get install -y libgl1
-RUN apt-get install -y libglu1-mesa
-RUN apt-get install -y libgl1-mesa-glx
-RUN apt-get install -y libxcb-icccm4
-RUN apt-get install -y libxcb-image0
-RUN apt-get install -y libxcb-keysyms1
-RUN apt-get install -y libxcb-render-util0
-RUN apt-get install -y libxkbcommon-x11-0
-RUN apt-get install -y libxcb-randr0
-RUN apt-get install -y libxcb-xinerama0
-
-# Install cubit
-RUN dpkg -i coreform-cubit-2021.5.deb
-
-# installs svalinn plugin for cubit
-RUN wget https://github.com/svalinn/Cubit-plugin/releases/download/0.2.1/svalinn-plugin_debian-10.10_cubit_2021.5.tgz
-RUN tar -xzvf svalinn-plugin_debian-10.10_cubit_2021.5.tgz -C /opt/Coreform-Cubit-2021.5
-
-# writes a non commercial license file
-RUN mkdir -p /root/.config/Coreform/licenses
-RUN printf 'Fri May 28 2021' >> /root/.config/Coreform/licenses/cubit-learn.lic
-
-# helps to identify Cubit related errrors
-ENV CUBIT_VERBOSE=5
-
-# dagmc is needed as it includes the make_watertight command and moab
-RUN conda install -c conda-forge dagmc && \
-    conda clean -afy
 
 COPY requirements.txt requirements.txt
 RUN pip install -r requirements.txt

conda_build.sh

@@ -11,13 +11,13 @@ rm -rf /tmp/conda-build
 
 
 # VERSION=$(echo $GITHUB_REF | sed 's#.*/v##')
-VERSION=0.3.2
+VERSION=0.4.1
 PLACEHOLDER='version="develop"'
 VERSION_FILE='setup.py'
 # Grep checks that the placeholder is in the file. If grep doesn't find
 # the placeholder then it exits with exit code 1 and github actions fails.
 grep "$PLACEHOLDER" "$VERSION_FILE"
-sed -i "s/$PLACEHOLDER/version=\"${VERSION}\"/g" "$VERSION_FILE"
+sed -i "s@$PLACEHOLDER@version=\"${VERSION}\"@g" "$VERSION_FILE"
 
 conda-build conda/ -c cadquery -c conda-forge --croot /tmp/conda-build 
 
@@ -37,4 +37,4 @@ conda-build conda/ -c cadquery -c conda-forge --croot /tmp/conda-build
 
 anaconda upload -f /tmp/conda-build/*/*.tar.bz2
 
-sed -i "s/version=\"${VERSION}\"/$PLACEHOLDER/g" "$VERSION_FILE"
+sed -i "s@version=\"${VERSION}\"@$PLACEHOLDER@g" "$VERSION_FILE"

environment.yml

@@ -12,13 +12,10 @@ dependencies:
   - numpy
   - matplotlib
   - pillow
-  - moab=5.3.0
-  - remove_dagmc_tags
   - pip:
     - sympy
     - plasmaboundaries
     - sphinx-autodoc-typehints
     - sphinxcadquery
     - defusedxml
     - jupyter-cadquery
-    - cad_to_h5m

paramak/__init__.py

@@ -1,6 +1,5 @@
 from .shape import Shape
 from .reactor import Reactor
-from .utils import define_moab_core_and_tags, add_stl_to_moab_core, export_vtk
 from .utils import rotate, extend, distance_between_two_points, diff_between_angles
 from .utils import EdgeLengthSelector, FaceAreaSelector
 

paramak/parametric_reactors/ball_reactor.py

@@ -94,8 +94,6 @@ def __init__(
 
         super().__init__([])
 
-        self.method = 'cubit'
-
         self.inner_bore_radial_thickness = inner_bore_radial_thickness
         self.inboard_tf_leg_radial_thickness = inboard_tf_leg_radial_thickness
         self.center_column_shield_radial_thickness = \

paramak/parametric_reactors/center_column_study_reactor.py

@@ -63,8 +63,6 @@ def __init__(
 
         super().__init__([])
 
-        self.method = 'cubit'
-
         self.inner_bore_radial_thickness = inner_bore_radial_thickness
         self.inboard_tf_leg_radial_thickness = inboard_tf_leg_radial_thickness
         self.center_column_shield_radial_thickness_mid = \

paramak/parametric_reactors/eu_demo_2015_reactor.py

@@ -24,8 +24,6 @@ def __init__(
 
         super().__init__([])
 
-        self.method = 'cubit'
-
         self.rotation_angle = rotation_angle
         self.number_of_tf_coils = number_of_tf_coils
 

paramak/parametric_reactors/submersion_reactor.py

@@ -86,8 +86,6 @@ def __init__(
 
         super().__init__([])
 
-        self.method = 'cubit'
-
         self.inner_bore_radial_thickness = inner_bore_radial_thickness
         self.inboard_tf_leg_radial_thickness = inboard_tf_leg_radial_thickness
         self.center_column_shield_radial_thickness = (