Clean history

.gitignore

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+# OS Stuff
+Thumbs.db
+.DS_Store
+.idea
+
+# Mosaic stuff
+mosaic-workspace
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+*.pyc
+*.json
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+.token
+
+# 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/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+_site
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# Example outputs
+*.h5
+!examples/stride/anastasio2D/data/*.h5
+examples/*/*.png
+
+# Legacy code
+legacy/

.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks:
+    - id: flake8

MANIFEST.in

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+include setup.py
+include README.md
+include MANIFEST.in
+include environment.yml
+include requirements.txt
+include requirements-optional.txt

README.md

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+
+
+# Stride - A (somewhat) general optimisation framework for medical ultrasound imaging
+
+## Quickstart
+
+The recommended way to install Stride is through Anaconda's package manager (version >=4.9), which can be downloaded
+in [Anaconda](https://www.continuum.io/downloads) or [Miniconda](https://conda.io/miniconda.html).
+A Python version above 3.7 is recommended to run Stride.
+
+To install Stride, follow these steps:
+
+```sh
+git clone [email protected]:trustimaging/stride.git
+cd stride
+conda env create -f environment.yml
+conda activate stride
+pip install -e .
+```
+
+## Running the examples
+
+To perform a forward run on the alpha2D example:
+
+```sh
+cd examples/stride/alpha2D
+mrun python foward.py
+```
+
+You can control the number of workers and threads per worker by running:
+
+```sh
+mrun -nw 2 -nth 5 python foward.py
+```
+
+You can configure the devito solvers using environment variables. For example, to run the same code on a GPU with OpenACC you can:
+
+```sh
+export DEVITO_COMPILER=pgcc
+export DEVITO_LANGUAGE=openacc
+export DEVITO_PLATFORM=nvidiaX
+mrun -nw 1 -nth 5 python foward.py
+```
+
+Once you've run alpha2D forward, you can run the corresponding inverse problem by doing:
+
+```sh
+mrun python inverse.py
+```
+
+
+## Documentation
+
+You can build and access the documentation by running:
+
+```sh
+cd docs
+make html
+```
+
+and opening the generated ``_build/index.html`` in your browser.