Merge pull request #17 from fusion-energy/develop

updated install and optional coolprops for python3.9 support

.circleci/config.yml

@@ -9,21 +9,22 @@ version: 2.1
 jobs:
   build:
     docker:
-      - image: openmc/openmc:develop
+      - image: continuumio/miniconda3:4.9.2
 
     working_directory: ~/repo
 
     steps:
       - checkout
       - run:
           name: install
-          command:
-            pip install .
+          command: |
+            conda install -c conda-forge openmc==0.13.0
+            pip install .[density,tests]
  
       # run tests!
       - run:
           name: run tests
-          command: 
+          command:
             pytest tests -v --cov=neutronics_material_maker --cov-report term --cov-report html:htmlcov --cov-report xml --junitxml=test-reports/junit.xml
       - store_test_results:
           path: test-reports
@@ -32,6 +33,7 @@ jobs:
           path: test-reports
       - run:
           name: install curl
-          command:
+          command: |
+            apt-get --allow-releaseinfo-change update
             apt-get update && apt-get -y install curl
       - run: curl -s https://codecov.io/bash | bash

.github/workflows/python-publish.yml

@@ -25,27 +25,16 @@ jobs:
       with:
         python-version: '3.x'
 
-    - name: Autobump version
-      run: |
-        # from refs/tags/v1.2.3 get 1.2.3
-        VERSION=$(echo $GITHUB_REF | sed 's#.*/v##')
-        PLACEHOLDER='version="develop"'
-        VERSION_FILE='setup.py'
-        # Grep checks that the placeholder is in the file. If grep doesn't find
-        # the placeholder then it exits with exit code 1 and github actions fails.
-        grep "$PLACEHOLDER" "$VERSION_FILE"
-        sed -i "s@$PLACEHOLDER@version=\"${VERSION}\"@g" "$VERSION_FILE"
-      shell: bash
-
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install setuptools wheel build twine
 
     - name: Build and publish
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
+        twine check dist/*
         twine upload dist/*

.gitignore

@@ -1,52 +1,132 @@
-# Compiled python modules.
-**.pyc
-
-.eggs/
-
-# Setuptools distribution folder.
-/dist/
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-# Python egg metadata, regenerated from source files by setuptools.
-/*.egg-info
+# C extensions
+*.so
 
-*.pyo
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
 
-__pycache__/
+# Translations
+*.mo
+*.pot
 
-.idea/
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
 
-.gitignore
+# Flask stuff:
+instance/
+.webassets-cache
 
-.ipynb_checkpoints/
+# Scrapy stuff:
+.scrapy
 
-.pytest_cache/
+# Sphinx documentation
+docs/_build/
 
-*.py[cod]
+# PyBuilder
+target/
 
-build/
+# Jupyter Notebook
+.ipynb_checkpoints
 
-neutronics_material_maker.egg-info/
+# IPython
+profile_default/
+ipython_config.py
 
-.ipynb_checkpoints/
+# pyenv
+.python-version
 
-dist_pac.sh
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
 
-setup.cfg
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
 
-twine_upload.sh
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
 
-upload.sh
+# SageMath parsed files
+*.sage.py
 
-setup.py___jb_old___
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
 
-setup.py___jb_tmp___
+# Spyder project settings
+.spyderproject
+.spyproject
 
-.coverage
+# Rope project settings
+.ropeproject
 
-refs/
+# mkdocs documentation
+/site
 
-new_materials/
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
 
-.vscode/
+# Pyre type checker
+.pyre/
 
-.tox/
+# file containing version number
+_version.py

Dockerfile

@@ -1,35 +1,19 @@
 # build with the following command
 # sudo docker build -t neutronics_material_maker .
 
-FROM ubuntu:18.04
+FROM continuumio/miniconda3:4.9.2
 
-# Updating Ubuntu packages
-RUN apt-get update && yes|apt-get upgrade
 
-# Adding wget and bzip2
-RUN apt-get install -y wget bzip2
-
-# Anaconda installing
-RUN wget https://repo.continuum.io/archive/Anaconda3-2020.02-Linux-x86_64.sh
-
-RUN bash Anaconda3-2020.02-Linux-x86_64.sh -b
-
-RUN rm Anaconda3-2020.02-Linux-x86_64.sh
-
-# Set path to conda
-ENV PATH /root/anaconda3/bin:$PATH
-
-# install openmc from conda involves less sets compared to compiling it from source
+# install openmc from conda
 RUN conda install -c conda-forge openmc
 
-
-# install endf nuclear data
-
-# clone the openmc nuclear data repository
 RUN apt-get update
 RUN apt-get install -y git
+
+# clone the openmc nuclear data repository
 RUN git clone https://github.com/openmc-dev/data.git
 
+# install endf nuclear data
 # run script that converts ACE data to hdf5 data
 RUN python data/convert_nndc71.py --cleanup
 

README.md

@@ -26,24 +26,36 @@ temperature and pressure.
 
 ## Installation
 
+### Conda
+
 To use the code you will need to have OpenMC installed
 [OpenMC](https://docs.openmc.org/en/latest/quickinstall.html).
 
 The recommended method is to install from
 [Conda Forge](https://conda-forge.org) which also installs all the dependencies
 including OpenMC.
 
-```
+```bash
+conda create --name new_env python=3.8
+conda activate new_env
 conda install neutronics_material_maker -c conda-forge
 ```
+### Pip
+Alternatively the code can be easily installed using pip. This method doesn't
+currently include OpenMC so that will have to be installed separately using
+Conda or compiled.
 
-Alternatively the code can be easily installed using pip (which doesn't
-currently include OpenMC)
-
-```
+```bash
 pip install neutronics_material_maker
 ```
 
+To include the optional capability of calculating the density of coolants
+additional packages are needed (CoolProp). A slightly modified pip install
+is required in this case.
+```bash
+pip install "neutronics_material_maker[density]"
+```
+
 ## Features
 
 Materials for using in neutronics codes have two main aspects; a list of

build.sh

@@ -0,0 +1,2 @@
+python3 -m pip install --upgrade build
+python3 -m build

docs/source/conf.py

@@ -37,10 +37,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    "sphinx.ext.autodoc",
-    "sphinx.ext.coverage",
-    "sphinx.ext.napoleon"]
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.coverage", "sphinx.ext.napoleon"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]

docs/source/install.rst

@@ -48,7 +48,7 @@ environment.
 Install (conda + pip)
 ---------------------
 
-Create a new environment (Python 3.6, 3.7 or 3.8 are supported).
+Create a new environment (Python 3.6, 3.7, 3.8, 3.9 are supported).
 
 .. code-block:: bash
 
@@ -76,3 +76,11 @@ Then pip install the package.
 
 Now you should be ready to import neutronics-material-maker from your new python
 environment.
+
+To include the optional capability of calculating the density of coolants
+additional packages are needed (CoolProp). A slightly modified pip install
+is required in this case.
+
+.. code-block:: bash
+
+   pip install "neutronics_material_maker[density]"

neutronics_material_maker/__init__.py

@@ -1,3 +1,16 @@
+try:
+    from importlib.metadata import version, PackageNotFoundError
+except (ModuleNotFoundError, ImportError):
+    from importlib_metadata import version, PackageNotFoundError
+try:
+    __version__ = version("neutronics_material_maker")
+except PackageNotFoundError:
+    from setuptools_scm import get_version
+
+    __version__ = get_version(root="..", relative_to=__file__)
+
+__all__ = ["__version__"]
+
 from .utils import make_fispact_material
 from .utils import make_serpent_material
 from .utils import make_mcnp_material