minke 2.0.0a1__tar.gz

minke-2.0.0a1/.coveragerc

@@ -0,0 +1,9 @@
+[run]
+source = minke
+omit =
+    */python?.?/*
+    */lib-python/?.?/*.py
+    */lib_pypy/_*.py
+    */site-packages/ordereddict.py
+    */site-packages/nose/*
+    */unittest2/*

minke-2.0.0a1/.editorconfig

@@ -0,0 +1,21 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

minke-2.0.0a1/.github/workflows/pypi.yml

@@ -0,0 +1,58 @@
+# This is a basic workflow to help you get started with Actions
+
+name: CI
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the master branch
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+    - uses: actions/checkout@v2
+      
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+        
+    - name: Build wheel
+      run: |
+        pip install -r requirements.txt
+        pip install wheel
+        python setup.py bdist_wheel 
+        
+    - name: pypi-publish
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@v1.3.1
+      with:
+        password: ${{ secrets.pypitoken }}
+
+    - name: Build HTML Docs
+      run: |
+        pip install sphinx
+        pip install kentigern
+        pip install -r requirements.txt
+        pip install -r requirements_dev.txt
+        pip install .
+        cd docs
+        make html
+        
+    - name: SCP Deploy HTML Docs
+      uses: horochx/deploy-via-scp@v1.0.1
+      with:
+        local: docs/_build/html/*
+        remote: /home/danwilliams/code.daniel-williams.co.uk/minke
+        host: ${{ secrets.sshhost }}
+        user: ${{ secrets.sshuser }}
+        key: ${{ secrets.sshkey }}

minke-2.0.0a1/.gitignore

@@ -0,0 +1,62 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Emacs
+*~

minke-2.0.0a1/.gitlab-ci.yml

@@ -0,0 +1,115 @@
+#image: lpmn/minke:latest
+image: python
+stages:
+  - test
+  - build
+  - deploy
+
+# test-python27:
+#   stage: test
+#   script:
+#     - export PYTHONPATH="/usr/local/lib64/python2.7/site-packages"
+#     - echo "pandas" > requirements.txt
+#     - pip install -r requirements.txt
+#     - pip install coverage
+#     - python setup.py install
+#     - coverage run setup.py test
+#     - coverage report -m
+#     #- coverage html	
+#     #- mv htmlcov public/coverage
+#   coverage: '/TOTAL.+ ([0-9]{1,3}%)/'
+#   artifacts:
+#     expire_in: 3h
+#     paths:
+#       - testout
+#       - public
+
+test-python-36:
+  stage: test
+  image: python:3.6
+  script:
+    - pip install -r requirements.txt
+    - pip install coverage
+    - python setup.py install
+    - coverage run setup.py test
+    - coverage report -m
+  allow_failure: true
+
+test-python-37:
+  stage: test
+  image: python:3.7
+  script:
+    - pip install -r requirements.txt
+    - pip install coverage
+    - python setup.py install
+    - coverage run setup.py test
+    - coverage report -m
+  allow_failure: true
+
+pages:
+  stage: build
+  script:
+  - pip install -r requirements.txt
+  - pip install .
+  - pip install sphinx numpydoc  kentigern # sphinxcontrib-versioning
+  - pip install -r requirements_dev.txt
+  - make docs
+  - mv docs/_build/html/ public/
+  artifacts:
+    paths:
+    - public
+  only:
+  - master
+
+
+# # Build receipe for standalone wheels on Linux
+# wheel-27:
+#   image: python:2.7
+#   stage: build
+#   script:
+#     - pip install wheel
+#     # Build wheel
+#     - python setup.py bdist_wheel --universal
+#   dependencies: []
+#   artifacts:
+#     expire_in: 3h
+#     paths:
+#       - dist
+
+wheel-36:
+  image: python:3.6
+  stage: build
+  script:
+    - pip install wheel
+    # Build wheel
+    - python setup.py bdist_wheel --universal
+  dependencies: []
+  artifacts:
+    expire_in: 3h
+    paths:
+      - dist
+
+wheel-37:
+  image: python:3.7
+  stage: build
+  script:
+    - pip install wheel
+    # Build wheel
+    - python setup.py bdist_wheel --universal
+  dependencies: []
+  artifacts:
+    expire_in: 3h
+    paths:
+      - dist
+
+deploy:wheel:
+  stage: deploy
+  script:
+    - pip install twine
+    - twine upload dist/*
+  only:
+    #- master@daniel-williams/minke
+    - tags
+  # except:
+  #   - pushes
+  #   - web

minke-2.0.0a1/.travis/run_tests.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# enable strict test flags
+if [ "$STRICT" = true ]; then
+    _strict="-x --strict"
+else
+    _strict=""
+fi
+
+coverage run --source=minke -m py.test -v ${_strict} tests/

minke-2.0.0a1/.travis/setup_environment.sh

@@ -0,0 +1,112 @@
+#! /bin/bash
+STARTLOC=$(pwd)
+LIBFRAME_VER=v8r26
+LALBRANCH=minke
+mkdir .local
+# CHECK IF WE'RE INSTALLING INTO A VIRTUALENV
+if [ -n "$VIRTUAL_ENV" ]; then 
+    LOCATION=$VIRTUAL_ENV
+    #pip install numpy scipy
+else 
+    LOCATION=.local; 
+fi
+
+
+
+# DEFINE THE DIRECTORIES 
+LALSUITE_PREFIX=${LOCATION}   # install directory: change as appropriate
+LIBFRAME_PREFIX=${LOCATION}
+METAIO_PREFIX=${LOCATION}
+
+
+if [[ $1 = 'GRID' ]]; then
+    echo $GRID
+    echo "Installing on the LIGO Data Grid".
+  LALSUITE_SRCDIR=/usr1/${USER}/repositories; # uncomment for LDG
+elif [[ $1 = 'UWM' ]]; then
+  LALSUITE_SRCDIR=/people/${USER}/repositories; # uncomment for Nemo, UWM
+else
+  LALSUITE_SRCDIR=${HOME}/repositories;
+fi
+
+# MAKE ALL OF THE REQUIRED DIRECTORIES
+mkdir -p ${LALSUITE_SRCDIR}
+mkdir -p ${LALSUITE_PREFIX}
+mkdir -p ${LIBFRAME_PREFIX}
+
+#
+# LIBFRAME
+#
+
+# FETCH LIBFRAME
+cd ${LALSUITE_SRCDIR}
+wget http://lappweb.in2p3.fr/virgo/FrameL/$LIBFRAME_VER.tar.gz  # For the 2015-05-17 release
+tar -xf $LIBFRAME_VER.tar.gz
+cd $LIBFRAME_VER
+
+# CONFIG BUILD INSTALL LIBFRAME
+autoreconf --install
+./configure --prefix=${LIBFRAME_PREFIX} --enable-swig-python
+make                                   # (build results are stored on the src directory)
+make install 
+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${LIBFRAME_PREFIX} # to update the libraries paths
+export PKG_CONFIG_PATH=${PKG_CONFIG_PATH}:${LIBFRAME_PREFIX}/lib/pkgconfig
+
+#
+# MetaIO
+#
+
+# Clone the git repo
+cd ${LALSUITE_SRCDIR}
+git clone git://versions.ligo.org/metaio.git
+
+# Configure make and install
+cd metaio
+
+yes "\n" | ./00boot
+yes "\n" | ./configure --enable-silent-rules --prefix=${METAIO_PREFIX} --enable-swig-python
+make -j 2 --silent || make --silent
+make install --silent
+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${METAIO_PREFIX}/lib
+
+#
+# LALSUITE
+#
+
+# Clone the repo
+cd ${LALSUITE_SRCDIR}
+git clone git://versions.ligo.org/lalsuite.git # replace as appropriate
+
+# Configure make and install
+cd ${LALSUITE_SRCDIR}/lalsuite
+
+# Checkout a specific branch of lalsuite if required
+if [ -n "$LALBRANCH" ]; then 
+    git checkout $LALBRANCH;
+fi
+
+
+./00boot
+./configure --prefix=${LALSUITE_PREFIX} --enable-swig-python
+make -j
+make install
+
+# Now ready the environment (this line needs to be run every time a shell session is started, so add it to the ~/.bashrc file
+source ${LALSUITE_PREFIX}/etc/lalsuiterc
+
+#
+# PyLAL
+#
+cd ${LALSUITE_SRCDIR}/lalsuite/pylal
+rm -rf build
+python setup.py install --prefix=${LALSUITE_PREFIX}
+
+#
+# Glue
+#
+cd ${LALSUITE_SRCDIR}/lalsuite/glue
+rm -rf build
+python setup.py install --prefix=${LALSUITE_PREFIX}
+source ${LALSUITE_PREFIX}/etc/glue-user-env.sh
+
+cd ${STARTLOC}

minke-2.0.0a1/.travis.yml

@@ -0,0 +1,85 @@
+language: python
+sudo: required
+
+addons:
+  apt:
+    packages:
+      # generic packages
+      - gcc
+      - gfortran
+      - libblas-dev
+      - liblapack-dev
+      # lal dependencies
+      - pkg-config
+      - zlib1g-dev
+      - libgsl0-dev
+      - swig
+      - bc
+      - fftw-dev
+      # nds2 dependencies
+      - libsasl2-2
+      # misc python dependencies
+      - libhdf5-serial-dev
+      
+virtualenv:
+  system_site_packages: true
+
+matrix:
+  include:
+    - python: 2.7
+      env: STRICT=false
+    - python: 3.5
+      env: STRICT=false
+    - python: 2.7
+      env: STRICT=true PRE="--pre"
+  allow_failures:
+    - python: 2.7
+      env: STRICT=true PRE="--pre"
+    - python: 3.5
+      env: STRICT=false
+  fast_finish: true
+
+before_install:
+  - sudo add-apt-repository ppa:dns/gnu -y
+  - sudo apt-get update -q
+  - sudo apt-get install --only-upgrade autoconf
+  # update pip
+  - pip install -q ${PRE} --upgrade pip
+  # build and install numpy first
+  - pip install -q ${PRE} "numpy>=1.9.1"
+  # build src packages
+  - source .travis/setup_environment.sh
+  # install cython to speed up scipy build
+  - travis_retry pip install -q ${PRE} --install-option="--no-cython-compile" Cython
+  # install testing dependencies
+  - pip install  ${PRE} -r requirements_dev.txt 
+install:
+  - pip install ${PRE} -r requirements.txt
+  - python setup.py build
+
+script:
+  - coverage run setup.py test
+  # - . .travis/run-tests.sh
+  - pip install .
+
+after_success:
+  - coveralls
+
+cache:
+  apt: true
+  pip: true
+  ccache: true
+  directories:
+    # cache src builds
+    - ${VIRTUAL_ENV}/bin
+    - ${VIRTUAL_ENV}/lib
+    - ${VIRTUAL_ENV}/opt
+    - ${VIRTUAL_ENV}/etc
+
+notifications:
+  webhooks:
+    urls:
+      - https://chat.ligo.org/hooks/wknq4kn5c38yurauidajqt8bse
+    on_success: always#[always|never|change] # default: always
+    on_failure: always#[always|never|change] # default: always
+    on_start: always#[always|never|change] # default: never

minke-2.0.0a1/AUTHORS.rst

@@ -0,0 +1,13 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Daniel Williams <d.williams.2@research.gla.ac.uk>
+
+Contributors
+------------
+
+None yet. Why not be the first?

minke-2.0.0a1/CONTRIBUTING.rst

@@ -0,0 +1,117 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+If you're a member of the LSC and have access to the Gitlab system at
+https://git.ligo.org please submit bug reports at
+https://git.ligo.org/daniel-williams/minke/issues. Non-LSC members are
+welcome and encouraged to submit reports on our public Github
+repository at https://github.com/transientlunatic/minke/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "feature"
+is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+Minke could always use more documentation, whether as part of the
+official Minke docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/transientlunatic/minke/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `minke` for local development.
+
+1. Fork the `minke` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/minke.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv minke
+    $ cd minke/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
+
+    $ flake8 minke tests
+    $ python setup.py test
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 2.6, 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check
+   https://travis-ci.org/transientlunatic/minke/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+    $ python -m unittest tests.test_minke

minke-2.0.0a1/HISTORY.rst

@@ -0,0 +1,62 @@
+=======
+History
+=======
+
+1.1.9 (2021-05-04)
+------------------
+
+* Corrects behaviour of numerical relativity waveforms in geometric units by incorporating the extraction radius.
+
+1.1.6
+-----
+* Provisional Python 3.6 and 3.7 support.
+
+1.1.5
+-----
+* Addition of provisional support for NR hyperbolic waveforms
+* Removal of glue.segments dependency
+
+1.1.4
+-----
+* Bug fix in frame creation for supernovae
+
+1.1.3
+-----
+* Minor fixes to the documentation of the code.
+
+1.1.2
+-----
+* Minor bug-fixes to improve Hardware injection support
+
+1.1.1 (2018-03-27)
+------------------
+* Made a change to the package meta data to allow upload to PYPI.
+
+1.1.0 (2018-03-27)
+------------------
+"Luce Bay"
+
+* Added full support for hardware injection production
+* Added Yakunin Supernova waveform family
+* Added Ringdow waveform support
+* Added support for all lscsoft table formats
+* Added support for editing xml files
+* Added support for String Cusp waveforms
+
+1.0.1 (2017-01-23)
+------------------
+* Added provisional support for hardware injection production
+
+1.0.0 (2016-09-14)
+------------------
+The Anniversary Update.
+
+* ER10 and O2 Readiness
+* Fully capable of producing supernova injections
+* Fully capable of producing lalsimulation-burst waveforms
+* Extensible interface for parameter distributions
+
+0.1.0 (2016-3-14)
+------------------
+
+* First release on PyPI.

minke-2.0.0a1/LICENSE

@@ -0,0 +1,14 @@
+Copyright (c) 2016, Daniel Williams
+All rights reserved.
+
+Permission to use, copy, modify, and/or distribute this software for any
+purpose with or without fee is hereby granted, provided that the above
+copyright notice and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

minke-2.0.0a1/MANIFEST.in

@@ -0,0 +1,11 @@
+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat