Merge branch 'develop' of github.com:fusion-energy/paramak into develop

.circleci/config.yml

@@ -23,12 +23,12 @@ jobs:
       - 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
+            pytest tests/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
+            pytest tests/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

.github/workflows/ci_with_install.yml

@@ -26,4 +26,3 @@ jobs:
       - name: run tests
         run: |
           bash run_tests.sh
-          curl -s https://codecov.io/bash

conda/meta.yaml

@@ -1,9 +1,9 @@
 {% set name = "paramak" %}
-{% set version = "0.2.3" %}
+{% set data = load_setup_py_data() %}
 
 package:
   name: "{{ name|lower }}"
-  version: "{{ version }}"
+  version: {{ data.get('version') }}
 
 source:
   path: ..
@@ -14,7 +14,7 @@ build:
 
 requirements:
   build:
-    - python 3.8
+    - python {{ python }}
     - setuptools
   run:
     - cadquery
@@ -27,10 +27,12 @@ requirements:
     - python
     - scipy
     - sympy
-    - remove_dagmc_tags
     - nbformat
     - nbconvert
-    # - jupyter-cadquery
+    - ipywidgets
+    - remove_dagmc_tags
+    - moab
+    # - jupyter-cadquery not avaialbe on conda
 
 test:
   imports:
@@ -46,16 +48,25 @@ test:
     - tests/
     - examples/
   commands:
-    - pytest -v
+    - pytest -v tests/test_example_components.py
+    - pytest -v tests/test_example_reactors.py
+    - pytest -v tests/test_example_shapes.py
+    - pytest -v tests/test_parametric_components
+    - pytest -v tests/test_parametric_reactors
+    - pytest -v tests/test_parametric_shapes
+    - pytest -v tests/test_reactor.py
+    - pytest -v tests/test_shape.py
+    - pytest -v tests/test_utils.py
+
 
 about:
-  home: "https://github.com/ukaea/paramak"
+  home: "https://github.com/fusion-energy/paramak"
   license: MIT
   license_family: MIT
   license_file: LICENSE.txt
   summary: "Create 3D fusion reactor CAD models based on input parameters"
   doc_url: https://paramak.readthedocs.io/
-  dev_url: https://github.com/ukaea/paramak
+  dev_url: https://github.com/fusion-energy/paramak
   summary: Paramak - parameter driven fusion reactor model creation
 
 extra:

conda_build.sh

@@ -1,38 +1,40 @@
 
 #assumes anaconda-client and conda-build have been installed
-# conda install anaconda-client
-# conda install conda-build
+# conda install -y anaconda-client
+# conda install -y conda-build
 # anaconda login
 
-pkg='paramak'
-array=( 3.6 3.7 3.8 )
 
+rm -rf /tmp/conda-build
 mkdir -p /tmp/conda-build
 rm -rf /tmp/conda-build
 
-for i in "${array[@]}"
-do
-	conda-build conda/ -c cadquery -c conda-forge --croot /tmp/conda-build --python $i 
-	# conda build conda/meta.yaml -c cadquery -c conda-forge --croot /tmp/cbld
-done
-
-
-# # convert package to other platforms
-platforms=( osx-64 linux-32 linux-64 win-32 win-64 )
-platforms=( linux-64 )
-find /tmp/conda-build/linux-64/ -name *.tar.bz2 | while read file
-do
-    echo $file
-    #conda convert --platform all $file  -o $HOME/conda-bld/
-    for platform in "${platforms[@]}"
-    do
-       conda convert --platform $platform $file  -o /tmp/conda-build/
-    done
-done
-
-
-find /tmp/conda-build/ -name *.tar.bz2 | while read file
-do
-    echo $file
-    anaconda upload $file
-done
+
+# VERSION=$(echo $GITHUB_REF | sed 's#.*/v##')
+VERSION=0.3.2
+PLACEHOLDER='version="develop"'
+VERSION_FILE='setup.py'
+# Grep checks that the placeholder is in the file. If grep doesn't find
+# the placeholder then it exits with exit code 1 and github actions fails.
+grep "$PLACEHOLDER" "$VERSION_FILE"
+sed -i "s/$PLACEHOLDER/version=\"${VERSION}\"/g" "$VERSION_FILE"
+
+conda-build conda/ -c cadquery -c conda-forge --croot /tmp/conda-build 
+
+# converting using all includes quite a few oxs and linux versions (arm arch etc)
+# conda convert /tmp/conda-build/linux-64/*.tar.bz2 --platform all  -o /tmp/conda-build
+
+# option for converting package to specified platforms
+# platforms=( osx-64 linux-32 linux-64 win-32 win-64 )
+# find /tmp/conda-build/linux-64/ -name *.tar.bz2 | while read file
+# do
+#     echo $file
+#     for platform in "${platforms[@]}"
+#     do
+#        conda convert --platform $platform $file  -o /tmp/conda-build/
+#     done
+# done
+
+anaconda upload -f /tmp/conda-build/*/*.tar.bz2
+
+sed -i "s/version=\"${VERSION}\"/$PLACEHOLDER/g" "$VERSION_FILE"

conda_build_config.yaml

@@ -1,4 +1,6 @@
 python:
     - 3.8
+    - 3.7
+    - 3.6
 cadquery:
     - 2.1

docs/source/conf.py

@@ -35,7 +35,7 @@
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #
-needs_sphinx = '3.5.4'
+needs_sphinx = '4.1.2'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -188,3 +188,5 @@
 
 
 # -- Extension configuration -------------------------------------------------
+
+html_favicon = 'favicon.ico'

docs/source/paramak.install.rst

@@ -6,76 +6,80 @@ Installation
 Prerequisites
 -------------
 
-To use the paramak tool you will need Python 3 installed using Anaconda or
-Miniconda
+To use the paramak tool you will need Python 3 installed using Miniconda or
+Anaconda
 
-* `Anaconda <https://www.anaconda.com/>`_
-* `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_
 
-Once you have Anaconda or MiniConda installed then CadQuery can be installed
-into a new enviroment. A more detailed description of installing Cadquery 2 can
-be found here:
-
-* `Cadquery 2 installation <https://cadquery.readthedocs.io/en/latest/installation.html>`_
+* `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_
+* `Anaconda <https://www.anaconda.com/>`_
 
+Once you have Anaconda or MiniConda installed then create a new enviroment
+(Python 3.6, 3.7 or 3.8 are supported).
 
-First create a new enviroment.
 
-.. code-block:: python
+.. code-block:: bash
 
    conda create --name paramak_env python=3.8
 
 
 Then activate the new enviroment.
 
-.. code-block:: python
+.. code-block:: bash
 
    conda activate paramak_env
 
 
-Then install CadQuery.
+Then install the Paramak.
 
-.. code-block:: python
+.. code-block:: bash
 
-   conda install -c conda-forge -c cadquery cadquery=2.1
+   conda install -c fusion-energy -c cadquery -c conda-forge paramak
 
-Now you are ready to install the Paramak
+Now you should be ready to import paramak from your new python enviroment.
 
+Optional neutronics install
+---------------------------
 
-System Installation
--------------------
+You can also install optional dependencies that add neutronics capabilities to
+the paramak. This will install neutronics_material_maker, OpenMC and DAGMC.
+`More details <https://paramak-neutronics.readthedocs.io>`_
 
-The quickest way to install the Paramak is to use pip. In the terminal type...
+Developer Installation
+----------------------
 
-.. code-block:: bash
+If you want to contribute to the paramak or then you might want to install the 
+package using setup tools.
 
-   pip install paramak
+Download and install MiniConda, create a new python enviroment and activate the
+enviroment as covered in the installation procedure above.
 
-Alternatively you can download the repository using the `download link <https://github.com/fusion-energy/paramak/archive/develop.zip>`_ or clone the repository using:
+Then install CadQuery.
 
 .. code-block:: bash
 
-   git clone https://github.com/fusion-energy/paramak.git
+   conda install -c conda-forge -c cadquery cadquery=2.1
 
-Navigate to the paramak repository and within the terminal install the paramak
-package and the dependencies using pip3.
+
+Then install moab.
 
 .. code-block:: bash
 
-   cd paramak
-   pip install .
+   conda install -c conda-forge moab
+
 
-Alternatively you can install the paramak with the following command.
+Then clone the repository
 
 .. code-block:: bash
 
-   python setup.py install
+   git clone https://github.com/fusion-energy/paramak.git
 
-You can also install optional dependencies that add some neutronics
-capabilities to the paramak. This will install neutronics_material_maker and
-parametric_plasma_source. In addition to this you would need DAGMC, OpenMC,
-MOAB and Trelis / Cubit.
-`More details <https://paramak-neutronics.readthedocs.io>`_
+Navigate to the paramak repository and within the terminal install the paramak
+package and the dependencies using pip with e -e (developer option).
+
+.. code-block:: bash
+
+   cd paramak
+   pip install -e .
 
 
 Docker Image Installation

environment.yml

@@ -1,8 +1,8 @@
 name: docs-environment
 
 channels:
-  - cadquery
   - conda-forge
+  - cadquery
 
 dependencies:
   - cadquery=2.1
@@ -12,12 +12,12 @@ dependencies:
   - numpy
   - matplotlib
   - pillow
-  - moab
+  - moab=5.3.0
+  - remove_dagmc_tags
   - pip:
-    - remove_dagmc_tags
     - sympy
     - plasmaboundaries
     - sphinx-autodoc-typehints
     - sphinxcadquery
     - defusedxml
-
+    - jupyter-cadquery

examples/example_parametric_components/make_varible_offset_firstwall.ipynb

@@ -3,8 +3,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
-   "outputs": [],
    "source": [
     "\n",
     "from matplotlib.pyplot import plasma\n",
@@ -50,18 +48,23 @@
     "        filename=filename,\n",
     "        projectionDir=(5,-5,0),\n",
     "        showHidden=True,\n",
-    "    )\n",
-    "\n",
-    "subprocess.check_call(\n",
-    "    [\"convert\", \"-delay\", \"40\", \"random_offset_*.svg\", \"random_offsets.gif\"])\n"
-   ]
+    "    )\n"
+   ],
+   "outputs": [],
+   "metadata": {}
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "source": [
+    "# The following command requres imagemagick installed to convert the svg files into a gif animation\n",
+    "# further details https://imagemagick.org/index.php\n",
+    "\n",
+    "# subprocess.check_call(\n",
+    "#     [\"convert\", \"-delay\", \"40\", \"random_offset_*.svg\", \"random_offsets.gif\"])\n"
+   ],
    "outputs": [],
-   "source": []
+   "metadata": {}
   }
  ],
  "metadata": {
@@ -85,4 +88,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}