chore: publication

.gitignore

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+# 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
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# 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/
+
+# 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/

Dockerfile

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+FROM ubuntu:20.04
+
+RUN apt-get update &&\
+    apt-get install -y wget &&\
+    apt-get install -y openbabel &&\
+    apt-get -y install software-properties-common &&\
+    apt-get -y install python3-pip
+
+WORKDIR /funnel
+COPY . .
+
+RUN python3 -m pip install -r requirements.txt
+
+EXPOSE 80
+WORKDIR /funnel/app
+CMD python3 -m uvicorn main:app --host 0.0.0.0 --port=80
+
+
+
+
+

LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2023, Technical University of Denmark
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

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+# Web application - Hierarchical generative and regressive machine learning for next generation materials screening
+
+This repository contains the source code for web-application for the paper:
+
+> Ortega, Raul & Benediktsson, Bardi & Sechi, Renata & Jørgensen, Peter & Bhowmik, Arghya. (2023). ["Materials Funnel 2.0 - Data-driven hierarchical search for exploration of vast chemical spaces"](https://chemrxiv.org/engage/chemrxiv/article-details/65130f76ade1178b2429cd68). 10.26434/chemrxiv-2023-s8t6s-v2. 
+
+For the source code of the method implementation https://github.com/raulorteg/hts_funnel
+
+![](figures/website_homepage.png)
+
+## About
+------------------------------
+This is a web-application built to serve as an easier way to interact to the method proposed in _["Materials Funnel 2.0 - Data-driven hierarchical search for exploration of vast chemical spaces"](https://chemrxiv.org/engage/chemrxiv/article-details/65130f76ade1178b2429cd68)_ as a web-application.
+
+* For the source code of the method implementation: https://github.com/raulorteg/hts_funnel
+
+## Installation 
+------------------------------
+1. Clone the repository: ```git clone https://github.com/raulorteg/hts_funnel-app```
+2. Create the python virtual environment (I use python 3.9.14): ```virtualenv --py=python3.9 hts_funnel_app```
+3. Activate virtualenv  ```source hts_funnel_app/bin/activate```
+4. Install requirements ```python -m pip install -r requirements.txt``` Note: Your system might need a different torch installation (https://pytorch.org/get-started/locally/)
+
+## Requirements
+------------------------------
+
+see the ```requirements.txt``` file
+
+
+## Usage
+------------------------------
+
+From `/app` launch the web-application by running the command:
+
+```bash
+python -m uvicorn main:app --reload
+```
+
+Then open `http://127.0.0.1:8000` on the browser to see the web-application.
+
+## Docker
+------------------------------
+
+Build the Docker image
+```bash
+sudo docker build . --tag="funnelapp:latest"
+```
+
+Run the docker image
+```bash
+sudo docker run --rm -it -p 80:80/tcp funnelapp:latest
+```
+
+Then open `http://0.0.0.0:80` on the browser to see the web-application.
+
+## Code formatting
+Use isort 5.10.1 and black 22.10.0:
+```bash
+python -m pip install isort==5.10.1 black==22.10.0 
+```
+
+Sort the imports:
+```bash
+python -m isort <file_or_directory>
+```
+
+
+To format:
+```bash
+python -m black <file_or_directory>
+```