Pyadjoint v0.2.0

.gitignore

@@ -1,14 +1,167 @@
-*.egg-info
-*.pyc
-*/__pycache__
-/doc/index.rst
-/doc/example_dataset.rst
-/doc/adjoint_sources/
-/doc/_build/*
-/doc/index_files/*
-/doc/example_dataset_files/*
-*.ipynb_checkpoints*
-dist/*
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+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
-htmlcov
+.coverage.*
 .cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Misc.
+pyadjoint/tests/**png
+pyadjoint/tests/baseline_images/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# 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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Mac OS
+.DS_Store
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/

.travis-update-gh-pages.sh

@@ -9,12 +9,12 @@ if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then
   git config --global user.name "Travis"
 
   # Using token clone gh-pages branch. Pipe to /dev/null to avoid printing the decrypted key.
-  git clone --quiet --branch=gh-pages https://${GH_TOKEN}@github.com/krischer/pyadjoint  gh-pages > /dev/null
+  git clone --quiet --branch=gh-pages https://${GH_TOKEN}@github.com/adjtomo/pyadjoint  gh-pages > /dev/null
 
   # Go there, and overwrite everything with the freshly built contents.
   cd gh-pages
   rm -rf *
-  cp -Rf $TRAVIS_BUILD_DIR/doc/_build/html/* .
+  cp -Rf $TRAVIS_BUILD_DIR/docs/_build/html/* .
 
   # add, commit and push files
   git add -f .

.travis.yml

@@ -37,7 +37,7 @@ install:
 
 script:
   - coverage run --source=src/pyadjoint -m pyadjoint.tests
-  - if [[ $TRAVIS_PYTHON_VERSION == '3.5' ]]; then cd $TRAVIS_BUILD_DIR/doc; make html ; fi
+  - if [[ $TRAVIS_PYTHON_VERSION == '3.5' ]]; then cd $TRAVIS_BUILD_DIR/docs; make html ; fi
 
 after_success:
   - cd $TRAVIS_BUILD_DIR; coveralls

CHANGELOG.md

@@ -1,2 +1,81 @@
-Changelog
----------
+# Change Log
+## v0.1.0
+### Package structure
+- Renamed 'pyadjoint/doc/' -> 'pyadjoint/docs'
+- Renamed 'pyadjoint/src/' -> 'pydjoint/pyadjoint'
+- Removed 'setup.py' in favor of new 'pyproject.toml'
+- Updated setup URLs for dev team and website
+- Reorganized main dir structure to include a utils/ directory which now 
+  houses `dpss` and `utils`. Utils script split into multiple files for 
+  increased organization.
+- Revamped documentation, removed the old notebook and source-code bundled 
+  documentation, moved all docs-related info out of source code and into the 
+  upper-level docs/ directory.
+- New documentation pages for each of the double difference misfit functions, and exponentiated phase
+- New 'furo' theme for documentation
+
+### Bug fixes
+- Plotting: changed `ylim` of figure to max of waveform and not whole plot 
+  because windows were plotted much larger than waveforms
+
+### New features
+- Double difference capabilities added. 
+  - These are placed directly into the respective adjoint sources rather than 
+  	separately (as in Princenton/Mines version) to cut down on redundant code
+  - Controlled with string flag ``choice``=='double_difference'. Requires 
+    additional  waveforms and windows (``observed_dd``, ``synthetic_dd``, 
+    ``windows_dd``)
+  - Main caculate function will return two adjoint sources if 
+    ``double_difference`` is set True
+- Waveform misfit has four choices which include: ``waveform``, ``convolution``, ``waveform_dd`` and ``convolution_dd`` 
+- New Misfit Functions:
+    - Exponentiated phase
+    - Convolved waveform difference
+    - Waveform double difference
+    - Convolved waveform double difference
+    - Multitaper double difference
+- Config class: 
+	- Introduces individual Configs for each misfit function (as in Princeton v)
+	- New `get_config` function which provides single entry point to grab 
+	  Config objects by name
+
+### Code architecture
+- New ``main.py`` script which now holds all the main processing scripts for
+  discovering, calculating and plotting adjoint sources
+- Changed `window` -> `windows` for list of tuples carrying window information
+- Moved plotting functions out of individual adjoint sources and into the
+  main call function
+- All adjoint sources baselined with test data against Princeton/Mines version
+  of code
+- Removed plot capability for User to provide their own Figure object
+- Removed boolean return flag for adjoint source and measurements because these
+  are calculated regardless so might as well return them. May re-introduce if requested.
+- Config now carries information on `adjsrc_type`, removed this from the main
+  calculate_adjoint_source function, as it was redundant to have it in multiple places.
+
+### Class/Function specific
+- AdjointSource class:
+	- New `window` attribute which holds information about input windows used 
+	  to build the adjoint source, and their individual misfit values
+	- Print statement now deals with `window attribute`
+	- Write function cleaned up to include both SPECFEM and ASDF write functions
+- Waveform Misfit adjoint source: 
+	- Edited calculation of Simpsons rule integration to match Princeton ver.
+	  Now has a factor of 1/2 introduced so misfit is 1/2 original value.
+	- Baselined with test data against Priceton/Mines version of code
+- Cross-correlation Traveltime Misfit:
+	- Moves bulk of utility/calculation functions to ``pyadjoint.utils.cctm`` 
+      so that MTM can use them allowing for less redundant code
+- Multitaper Misfit:
+	- Overhauled function into a class to avoid the excessive parameter passing 
+	  between functions, removed unncessary parameter renaming in-function
+	- Renamed many of the internal variables and functions for clarity
+	- Removed redundant CCTM misfit definitions, instead switched to import of
+	  functions from CCTM utility
+	- Moved 'frequency_limit' function into 'mtm' utils and cleaned up. Removed
+	  unncessary functions which were passing too many variables, and included
+	  doc string. Changed some internal parameter names to match the Config
+	- Bugfix frequency limit search was not returning a `search` parameter flag
+	  which is meant to stop the search (from Princeton version)
+
+

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2015, Lion Krischer
+Copyright (c) 2022, adjTomo Dev Team
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -1,8 +1,11 @@
-Pyadjoint
-=========
+# Pyadjoint
 
-PyAdjoint is a Python tool for calculating a variety of adjoint sources for the full waveform inversion problem.  
-
-[Documentation](http://adjtomo.github.io/pyadjoint/) contains details on installation, usage and API.
 
+### Misfit measurement and adjoint source generation
 
+- Pyadjoint is a small misfit measurement package that calculates misfit and adjoint sources on time series
+- [Documentation](https://adjtomo.github.io/pyadjoint) for Pyadjoint can be found on GitHub
+- Can be used standlone, but is also wrapped in [Pyatoa](https://github.com/adjtomo/pyatoa) (alongside 
+  [Pyflex](https://github.com/adjtomo/pyflex))
+- Pyadjoint is part of the [adjTomo ecosystem](https://github.com/adjtomo) of tools for 
+  adjoint tomography and full waveform inversion