pbjcosmo 1.5.0__tar.gz

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  1. pbjcosmo-1.5.0/LICENSE +21 -0
  2. pbjcosmo-1.5.0/PKG-INFO +153 -0
  3. pbjcosmo-1.5.0/README.md +116 -0
  4. pbjcosmo-1.5.0/pbjcosmo/PBJ.py +961 -0
  5. pbjcosmo-1.5.0/pbjcosmo/__init__.py +5 -0
  6. pbjcosmo-1.5.0/pbjcosmo/binning.py +1015 -0
  7. pbjcosmo-1.5.0/pbjcosmo/config_default/priors.yaml +104 -0
  8. pbjcosmo-1.5.0/pbjcosmo/config_default/priors_cosmo.yaml +104 -0
  9. pbjcosmo-1.5.0/pbjcosmo/fptplus.py +475 -0
  10. pbjcosmo-1.5.0/pbjcosmo/likelihood.py +2548 -0
  11. pbjcosmo-1.5.0/pbjcosmo/templates.py +339 -0
  12. pbjcosmo-1.5.0/pbjcosmo/theory/effective_3D_c0.50_dk1.00_n64_leftopen_opentri-true.txt +24432 -0
  13. pbjcosmo-1.5.0/pbjcosmo/theory/effective_3D_c1.00_dk1.00_n64_leftopen_opentri-true.txt +25424 -0
  14. pbjcosmo-1.5.0/pbjcosmo/theory/effective_3D_c1.50_dk1.00_n63_rightopen_opentri-true.txt +24305 -0
  15. pbjcosmo-1.5.0/pbjcosmo/theory.py +2938 -0
  16. pbjcosmo-1.5.0/pbjcosmo/tools/__init__.py +0 -0
  17. pbjcosmo-1.5.0/pbjcosmo/tools/bispectrum_functions.py +664 -0
  18. pbjcosmo-1.5.0/pbjcosmo/tools/cosmology.py +449 -0
  19. pbjcosmo-1.5.0/pbjcosmo/tools/data_handler.py +339 -0
  20. pbjcosmo-1.5.0/pbjcosmo/tools/param_handler.py +346 -0
  21. pbjcosmo-1.5.0/pbjcosmo/tools/post_process.py +387 -0
  22. pbjcosmo-1.5.0/pbjcosmo/tools/prior_handler.py +166 -0
  23. pbjcosmo-1.5.0/pyproject.toml +49 -0
pbjcosmo-1.5.0/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2024 Chiara Moretti
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
pbjcosmo-1.5.0/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: pbjcosmo
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+ Version: 1.5.0
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+ Summary: Joint analysis of galaxy power spectrum and bispectrum
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+ License: MIT
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+ License-File: LICENSE
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+ Author: Chiara Moretti
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+ Author-email: chiara.moretti1989@gmail.com
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+ Requires-Python: >=3.9,<3.13
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3.9
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Programming Language :: Python :: 3.12
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+ Provides-Extra: dev
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+ Provides-Extra: likelihood
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+ Provides-Extra: theory
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+ Requires-Dist: MGrowth (>=0.1,<0.2) ; extra == "theory"
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+ Requires-Dist: PyYAML (>=6.0.1,<7.0.0)
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+ Requires-Dist: baccoemu (==2.2.1) ; extra == "theory"
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+ Requires-Dist: camb (>=1.5.4,<2.0.0)
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+ Requires-Dist: emcee (>=3.1.4,<4.0.0) ; extra == "likelihood"
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+ Requires-Dist: fast-pt (>=3.1.1,<4.0.0)
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+ Requires-Dist: getdist (>=1.4.7,<2.0.0) ; extra == "likelihood"
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+ Requires-Dist: mkdocs-material (>=9.6.12,<10.0.0) ; extra == "dev"
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+ Requires-Dist: mkdocstrings[python] (>=0.29.1,<0.30.0) ; extra == "dev"
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+ Requires-Dist: nautilus-sampler (>=1.0.2,<2.0.0) ; extra == "likelihood"
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+ Requires-Dist: pandas (>=2.2.1,<3.0.0)
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+ Requires-Dist: pocomc (>=1.0.2,<2.0.0) ; extra == "likelihood"
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+ Requires-Dist: pytest (>=8.4.1,<9.0.0) ; extra == "dev"
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+ Requires-Dist: pytest-cov (>=6.2.1,<7.0.0) ; extra == "dev"
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+ Requires-Dist: tqdm (>=4.65.0,<5.0.0) ; extra == "likelihood"
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+ Requires-Dist: ultranest (>=4.3.2,<5.0.0) ; extra == "likelihood"
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+ Description-Content-Type: text/markdown
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+
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+ # πŸͺ PBJ: Power spectrum & Bispectrum Joint analysis
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+ <!-- [![Pipeline](https://img.shields.io/gitlab/pipeline/chiaramorett/pbj/main?logo=gitlab&label=CI)](https://gitlab.com/chiaramoretti/pbj/pipelines)
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+ [![Release](https://img.shields.io/gitlab/v/release/chiaramoretti/pbj?logo=gitlab)](https://gitlab.com/chiaramoretti/pbj/-/releases)-->
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+
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+ [![Release](https://img.shields.io/badge/version-v1.5.0-forestgreen?logo=gitlab)](https://gitlab.com/your-project/-/tags) <!--
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+ --> [![Documentation](https://img.shields.io/badge/docs-mkdocs-blue?logo=markdown)](https://chiaramoretti.gitlab.io/pbj/) <!--
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+ --> [![Contributors](https://img.shields.io/badge/contributors-19-purple?logo=gitlab)](https://chiaramoretti.gitlab.io/pbj/#contributors-) <!--
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+ --> [![Coverage](https://img.shields.io/badge/coverage-33%-orange?logo=gitlab)](https://gitlab.com/chiaramoretti/pbj/-/pipelines)
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+
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+
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+ **`pbj`** is a Python package for the joint analysis of the galaxy
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+ power spectrum and bispectrum from spectroscopic galaxy clustering.
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+
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+ *Authors*: Chiara Moretti, Andrea Oddo
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+
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+ **Full documentation [here](https://chiaramoretti.gitlab.io/pbj/)**
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+
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+ ## Installation and quickstart πŸš€
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+
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+ See the [Installation
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+ Guide](https://chiaramoretti.gitlab.io/pbj/install) for full
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+ instructions on how to install, and the [Inference
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+ quickstart](https://chiaramoretti.gitlab.io/pbj/inference_quickstart/)
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+ for a brief introduction on how to run chains. More detailed examples
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+ coming soon!
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+
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+ ## Citing πŸ“š
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+
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+ If you use `pbj` in your work, please use the DOI
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+ [10.5281/zenodo.20048910](10.5281/zenodo.20048910) and cite the
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+ following paper:
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+
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+ - [Moretti, C. et
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+ al., JCAP12(2023)025](https://iopscience.iop.org/article/10.1088/1475-7516/2023/12/025),
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+ *Modified gravity and massive neutrinos: constraints from the full
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+ shape analysis of BOSS galaxies and forecasts for Stage IV surveys*
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+
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+ For the original implementation and modelling for the real space bispectrum:
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+
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+ - [Oddo et al.,
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+ 2020](https://ui.adsabs.harvard.edu/abs/2020JCAP...03..056O/abstract)
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+
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+ For the real space power spectrum and bispectrum:
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+
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+ - [Oddo et al.,
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+ 2021](https://ui.adsabs.harvard.edu/abs/2021JCAP...11..038O/abstract)
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+
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+ For the redshift space bispectrum:
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+
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+ - [Rizzo et al.,
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+ 2022](https://ui.adsabs.harvard.edu/abs/2022arXiv220413628R/abstract
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+ )
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+
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+ The code has been validated and used to analyse both simulated and
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+ real data already in a number of papers, a full list can be found in
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+ [this ADS
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+ library](https://ui.adsabs.harvard.edu/public-libraries/xQaO7O9EQ3uyqNileyLpLw)
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+
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+
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+ ## Contributing & Contact 🀝
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+
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+ Feel free to open an issue or a fork and then a pull request!
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+ For questions, reach out to [Chiara Moretti](mailto:chiara.moretti1989@gmail.com).
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+
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+ ## Contributors ✨
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+
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+ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
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+
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+ <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
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+ <!-- prettier-ignore-start -->
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+ <!-- markdownlint-disable -->
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+ <table>
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+ <tbody>
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+ <tr>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/chiaramoretti"><img src="https://gitlab.com/uploads/-/system/user/avatar/5682313/avatar.png?s=100" width="100px;" alt="Chiara Moretti"/><br /><sub><b>Chiara Moretti</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Documentation">πŸ“–</a> <a href="#example-chiaramoretti" title="Examples">πŸ’‘</a> <a href="#ideas-chiaramoretti" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#infra-chiaramoretti" title="Infrastructure (Hosting, Build-Tools, etc)">πŸš‡</a> <a href="#maintenance-chiaramoretti" title="Maintenance">🚧</a> <a href="#mentoring-chiaramoretti" title="Mentoring">πŸ§‘β€πŸ«</a> <a href="#platform-chiaramoretti" title="Packaging/porting to new platform">πŸ“¦</a> <a href="#projectManagement-chiaramoretti" title="Project Management">πŸ“†</a> <a href="#promotion-chiaramoretti" title="Promotion">πŸ“£</a> <a href="#research-chiaramoretti" title="Research">πŸ”¬</a> <a href="https://gitlab.com/Chiara Moretti/pbj/merge_requests?scope=all&state=all&approver_usernames[]=chiaramoretti" title="Reviewed Pull Requests">πŸ‘€</a> <a href="#talk-chiaramoretti" title="Talks">πŸ“’</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/ceoliveri"><img src="https://gitlab.com/uploads/-/system/user/avatar/22042797/avatar.png?s=100" width="100px;" alt="Cecilia Oliveri"/><br /><sub><b>Cecilia Oliveri</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-ceoliveri" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-ceoliveri" title="Promotion">πŸ“£</a> <a href="#research-ceoliveri" title="Research">πŸ”¬</a> <a href="#talk-ceoliveri" title="Talks">πŸ“’</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=ceoliveri" title="Bug reports">πŸ›</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/esarpa"><img src="https://secure.gravatar.com/avatar/190ccd9d88fdf6327008a86a6173ad7243def2898c9c24c21ffd641897f5950a?s=80&d=identicon?s=100" width="100px;" alt="Elena Sarpa"/><br /><sub><b>Elena Sarpa</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-esarpa" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-esarpa" title="Promotion">πŸ“£</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/esefusat"><img src="https://secure.gravatar.com/avatar/741dd8b559710c92545f90095c3e4829a616366658ce616a7422b8e341b624ed?s=80&d=identicon?s=100" width="100px;" alt="Emiliano Sefusatti"/><br /><sub><b>Emiliano Sefusatti</b></sub></a><br /><a href="#ideas-esefusat" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-esefusat" title="Promotion">πŸ“£</a> <a href="#talk-esefusat" title="Talks">πŸ“’</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/emilio.bellini"><img src="https://secure.gravatar.com/avatar/8804e25cfbd9aebfd279c1ceee12d8edb5497c0ab129adbb5f79919c3dca4709?s=80&d=identicon?s=100" width="100px;" alt="Emilio Bellini"/><br /><sub><b>Emilio Bellini</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-emilio.bellini" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-emilio.bellini" title="Promotion">πŸ“£</a> <a href="#research-emilio.bellini" title="Research">πŸ”¬</a> <a href="#talk-emilio.bellini" title="Talks">πŸ“’</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=emilio.bellini" title="Bug reports">πŸ›</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/fverd"><img src="https://secure.gravatar.com/avatar/b74a6987e8e2d58c9d691050189f5164ece896a1f956a703c66c4838ede68024?s=80&d=identicon?s=100" width="100px;" alt="Francesco Verdiani"/><br /><sub><b>Francesco Verdiani</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-fverd" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-fverd" title="Promotion">πŸ“£</a> <a href="#research-fverd" title="Research">πŸ”¬</a> <a href="#talk-fverd" title="Talks">πŸ“’</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/federico.montano"><img src="https://secure.gravatar.com/avatar/14776bad0325cfdc5bd36722f9296bf22cea6e4731a8cd2a9dfd14cd46c7d875?s=80&d=identicon?s=100" width="100px;" alt="Federico Montano"/><br /><sub><b>Federico Montano</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-federico.montano" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#research-federico.montano" title="Research">πŸ”¬</a></td>
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+ </tr>
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+ <tr>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/federico.rizzo"><img src="https://secure.gravatar.com/avatar/14d5b035cd7a67d3aee2a36b77d9a75d351cfcb809e2935e82813edc3a1096d6?s=80&d=identicon?s=100" width="100px;" alt="Federico Rizzo"/><br /><sub><b>Federico Rizzo</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#promotion-federico.rizzo" title="Promotion">πŸ“£</a> <a href="#research-federico.rizzo" title="Research">πŸ”¬</a> <a href="#data-federico.rizzo" title="Data">πŸ”£</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/GiosueGambardella1998"><img src="https://secure.gravatar.com/avatar/430db604f62dfcc585e1ecb5bc1e14b656cb83a938e6b2bb0201534b33eb630c?s=80&d=identicon?s=100" width="100px;" alt="GiosuΓ¨ Gambardella"/><br /><sub><b>GiosuΓ¨ Gambardella</b></sub></a><br /><a href="#promotion-GiosueGambardella1998" title="Promotion">πŸ“£</a> <a href="#research-GiosueGambardella1998" title="Research">πŸ”¬</a> <a href="#talk-GiosueGambardella1998" title="Talks">πŸ“’</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/jacoposalvalaggio"><img src="https://gitlab.com/uploads/-/system/user/avatar/10623230/avatar.png?s=100" width="100px;" alt="Jacopo Salvalaggio"/><br /><sub><b>Jacopo Salvalaggio</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=jacoposalvalaggio" title="Bug reports">πŸ›</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/kpardede96"><img src="https://secure.gravatar.com/avatar/d75c82a35157e745fd56898314e01919bd8ee5eca676b63173fedf5f1ae0ddf3?s=80&d=identicon?s=100" width="100px;" alt="Kevin Pardede"/><br /><sub><b>Kevin Pardede</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-kpardede96" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-kpardede96" title="Promotion">πŸ“£</a> <a href="#research-kpardede96" title="Research">πŸ”¬</a> <a href="#talk-kpardede96" title="Talks">πŸ“’</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/MariaTsedrik"><img src="https://secure.gravatar.com/avatar/562b3d91f195b526cf5f5469e2c14299fadc5cb921b9c62a57d634c46293119e?s=80&d=identicon?s=100" width="100px;" alt="Maria Tsedrik"/><br /><sub><b>Maria Tsedrik</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-MariaTsedrik" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#mentoring-MariaTsedrik" title="Mentoring">πŸ§‘β€πŸ«</a> <a href="#promotion-MariaTsedrik" title="Promotion">πŸ“£</a> <a href="#research-MariaTsedrik" title="Research">πŸ”¬</a> <a href="#talk-MariaTsedrik" title="Talks">πŸ“’</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=MariaTsedrik" title="Bug reports">πŸ›</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/Yousryyy"><img src="https://secure.gravatar.com/avatar/dccaa6cd7c59457196b164ec4d8ca03913dbcede343ccb41873bba1994198adf?s=80&d=identicon?s=100" width="100px;" alt="Mohamed Elkhashab"/><br /><sub><b>Mohamed Elkhashab</b></sub></a><br /><a href="#ideas-Yousryyy" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-Yousryyy" title="Promotion">πŸ“£</a> <a href="#research-Yousryyy" title="Research">πŸ”¬</a> <a href="#talk-Yousryyy" title="Talks">πŸ“’</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/pcarrilho"><img src="https://secure.gravatar.com/avatar/74eb286948240a5d6849bf609248eb0f38ae9df76ab23b178929f8042bb5249a?s=80&d=identicon?s=100" width="100px;" alt="Pedro Carrilho"/><br /><sub><b>Pedro Carrilho</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-pcarrilho" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-pcarrilho" title="Promotion">πŸ“£</a> <a href="#research-pcarrilho" title="Research">πŸ”¬</a> <a href="#talk-pcarrilho" title="Talks">πŸ“’</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=pcarrilho" title="Bug reports">πŸ›</a></td>
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+ </tr>
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+ <tr>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/sujeong-lee"><img src="https://secure.gravatar.com/avatar/502ccd6e96ebc2b8d625b627f1c150bb186279a031e7fdb54be7936016f32658?s=80&d=identicon?s=100" width="100px;" alt="Sujeong Lee"/><br /><sub><b>Sujeong Lee</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-sujeong-lee" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-sujeong-lee" title="Promotion">πŸ“£</a> <a href="#research-sujeong-lee" title="Research">πŸ”¬</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=sujeong-lee" title="Bug reports">πŸ›</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/matildebs"><img src="https://secure.gravatar.com/avatar/76e01baf26278aa27b97eab2bd250cbed58d786eac879b372b7cb8f708d4a0b9?s=80&d=identicon?s=100" width="100px;" alt="matildebs"/><br /><sub><b>matildebs</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-matildebs" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-matildebs" title="Promotion">πŸ“£</a> <a href="#research-matildebs" title="Research">πŸ”¬</a> <a href="#talk-matildebs" title="Talks">πŸ“’</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=matildebs" title="Bug reports">πŸ›</a></td>
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+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/ztchenustc"><img src="https://secure.gravatar.com/avatar/f7a4e34ddee1a5b45ab8d13dcb04fee77c6b520a1320fc3d09de7c40e02cdc31?s=80&d=identicon?s=100" width="100px;" alt="Zhaoting Chen"/><br /><sub><b>Zhaoting Chen</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Documentation">πŸ“–</a> <a href="#research-ztchenustc" title="Research">πŸ”¬</a></td>
132
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/Asser_Elhegawy"><img src="https://gitlab.com/uploads/-/system/user/avatar/31076008/avatar.png?s=100" width="100px;" alt="Asser Elhegawy"/><br /><sub><b>Asser Elhegawy</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=Asser_Elhegawy" title="Bug reports">πŸ›</a></td>
133
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/nebblub"><img src="https://secure.gravatar.com/avatar/5bf6784c13b20208d30248fb733e68a5cfba061cebfd9267ff21faca34a2fe3b?s=80&d=identicon?s=100" width="100px;" alt="nebblu"/><br /><sub><b>nebblu</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Documentation">πŸ“–</a> <a href="#research-nebblub" title="Research">πŸ”¬</a></td>
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+ </tr>
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+ </tbody>
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+ <tfoot>
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+ <tr>
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+ <td align="center" size="13px" colspan="7">
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+ <img src="https://raw.githubusercontent.com/all-contributors/all-contributors-cli/1b8533af435da9854653492b1327a23a4dbd0a10/assets/logo-small.svg">
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+ <a href="https://all-contributors.js.org/docs/en/bot/usage">Add your contributions</a>
141
+ </img>
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+ </td>
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+ </tr>
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+ </tfoot>
145
+ </table>
146
+
147
+ <!-- markdownlint-restore -->
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+ <!-- prettier-ignore-end -->
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+
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+ <!-- ALL-CONTRIBUTORS-LIST:END -->
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+
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+ This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
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+
pbjcosmo-1.5.0/README.md ADDED
@@ -0,0 +1,116 @@
1
+ # πŸͺ PBJ: Power spectrum & Bispectrum Joint analysis
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+ <!-- [![Pipeline](https://img.shields.io/gitlab/pipeline/chiaramorett/pbj/main?logo=gitlab&label=CI)](https://gitlab.com/chiaramoretti/pbj/pipelines)
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+ [![Release](https://img.shields.io/gitlab/v/release/chiaramoretti/pbj?logo=gitlab)](https://gitlab.com/chiaramoretti/pbj/-/releases)-->
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+
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+ [![Release](https://img.shields.io/badge/version-v1.5.0-forestgreen?logo=gitlab)](https://gitlab.com/your-project/-/tags) <!--
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+ --> [![Documentation](https://img.shields.io/badge/docs-mkdocs-blue?logo=markdown)](https://chiaramoretti.gitlab.io/pbj/) <!--
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+ --> [![Contributors](https://img.shields.io/badge/contributors-19-purple?logo=gitlab)](https://chiaramoretti.gitlab.io/pbj/#contributors-) <!--
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+ --> [![Coverage](https://img.shields.io/badge/coverage-33%-orange?logo=gitlab)](https://gitlab.com/chiaramoretti/pbj/-/pipelines)
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+
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+
11
+ **`pbj`** is a Python package for the joint analysis of the galaxy
12
+ power spectrum and bispectrum from spectroscopic galaxy clustering.
13
+
14
+ *Authors*: Chiara Moretti, Andrea Oddo
15
+
16
+ **Full documentation [here](https://chiaramoretti.gitlab.io/pbj/)**
17
+
18
+ ## Installation and quickstart πŸš€
19
+
20
+ See the [Installation
21
+ Guide](https://chiaramoretti.gitlab.io/pbj/install) for full
22
+ instructions on how to install, and the [Inference
23
+ quickstart](https://chiaramoretti.gitlab.io/pbj/inference_quickstart/)
24
+ for a brief introduction on how to run chains. More detailed examples
25
+ coming soon!
26
+
27
+ ## Citing πŸ“š
28
+
29
+ If you use `pbj` in your work, please use the DOI
30
+ [10.5281/zenodo.20048910](10.5281/zenodo.20048910) and cite the
31
+ following paper:
32
+
33
+ - [Moretti, C. et
34
+ al., JCAP12(2023)025](https://iopscience.iop.org/article/10.1088/1475-7516/2023/12/025),
35
+ *Modified gravity and massive neutrinos: constraints from the full
36
+ shape analysis of BOSS galaxies and forecasts for Stage IV surveys*
37
+
38
+ For the original implementation and modelling for the real space bispectrum:
39
+
40
+ - [Oddo et al.,
41
+ 2020](https://ui.adsabs.harvard.edu/abs/2020JCAP...03..056O/abstract)
42
+
43
+ For the real space power spectrum and bispectrum:
44
+
45
+ - [Oddo et al.,
46
+ 2021](https://ui.adsabs.harvard.edu/abs/2021JCAP...11..038O/abstract)
47
+
48
+ For the redshift space bispectrum:
49
+
50
+ - [Rizzo et al.,
51
+ 2022](https://ui.adsabs.harvard.edu/abs/2022arXiv220413628R/abstract
52
+ )
53
+
54
+ The code has been validated and used to analyse both simulated and
55
+ real data already in a number of papers, a full list can be found in
56
+ [this ADS
57
+ library](https://ui.adsabs.harvard.edu/public-libraries/xQaO7O9EQ3uyqNileyLpLw)
58
+
59
+
60
+ ## Contributing & Contact 🀝
61
+
62
+ Feel free to open an issue or a fork and then a pull request!
63
+ For questions, reach out to [Chiara Moretti](mailto:chiara.moretti1989@gmail.com).
64
+
65
+ ## Contributors ✨
66
+
67
+ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
68
+
69
+ <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
70
+ <!-- prettier-ignore-start -->
71
+ <!-- markdownlint-disable -->
72
+ <table>
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+ <tbody>
74
+ <tr>
75
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/chiaramoretti"><img src="https://gitlab.com/uploads/-/system/user/avatar/5682313/avatar.png?s=100" width="100px;" alt="Chiara Moretti"/><br /><sub><b>Chiara Moretti</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Documentation">πŸ“–</a> <a href="#example-chiaramoretti" title="Examples">πŸ’‘</a> <a href="#ideas-chiaramoretti" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#infra-chiaramoretti" title="Infrastructure (Hosting, Build-Tools, etc)">πŸš‡</a> <a href="#maintenance-chiaramoretti" title="Maintenance">🚧</a> <a href="#mentoring-chiaramoretti" title="Mentoring">πŸ§‘β€πŸ«</a> <a href="#platform-chiaramoretti" title="Packaging/porting to new platform">πŸ“¦</a> <a href="#projectManagement-chiaramoretti" title="Project Management">πŸ“†</a> <a href="#promotion-chiaramoretti" title="Promotion">πŸ“£</a> <a href="#research-chiaramoretti" title="Research">πŸ”¬</a> <a href="https://gitlab.com/Chiara Moretti/pbj/merge_requests?scope=all&state=all&approver_usernames[]=chiaramoretti" title="Reviewed Pull Requests">πŸ‘€</a> <a href="#talk-chiaramoretti" title="Talks">πŸ“’</a></td>
76
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/ceoliveri"><img src="https://gitlab.com/uploads/-/system/user/avatar/22042797/avatar.png?s=100" width="100px;" alt="Cecilia Oliveri"/><br /><sub><b>Cecilia Oliveri</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-ceoliveri" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-ceoliveri" title="Promotion">πŸ“£</a> <a href="#research-ceoliveri" title="Research">πŸ”¬</a> <a href="#talk-ceoliveri" title="Talks">πŸ“’</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=ceoliveri" title="Bug reports">πŸ›</a></td>
77
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/esarpa"><img src="https://secure.gravatar.com/avatar/190ccd9d88fdf6327008a86a6173ad7243def2898c9c24c21ffd641897f5950a?s=80&d=identicon?s=100" width="100px;" alt="Elena Sarpa"/><br /><sub><b>Elena Sarpa</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-esarpa" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-esarpa" title="Promotion">πŸ“£</a></td>
78
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/esefusat"><img src="https://secure.gravatar.com/avatar/741dd8b559710c92545f90095c3e4829a616366658ce616a7422b8e341b624ed?s=80&d=identicon?s=100" width="100px;" alt="Emiliano Sefusatti"/><br /><sub><b>Emiliano Sefusatti</b></sub></a><br /><a href="#ideas-esefusat" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-esefusat" title="Promotion">πŸ“£</a> <a href="#talk-esefusat" title="Talks">πŸ“’</a></td>
79
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/emilio.bellini"><img src="https://secure.gravatar.com/avatar/8804e25cfbd9aebfd279c1ceee12d8edb5497c0ab129adbb5f79919c3dca4709?s=80&d=identicon?s=100" width="100px;" alt="Emilio Bellini"/><br /><sub><b>Emilio Bellini</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-emilio.bellini" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-emilio.bellini" title="Promotion">πŸ“£</a> <a href="#research-emilio.bellini" title="Research">πŸ”¬</a> <a href="#talk-emilio.bellini" title="Talks">πŸ“’</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=emilio.bellini" title="Bug reports">πŸ›</a></td>
80
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/fverd"><img src="https://secure.gravatar.com/avatar/b74a6987e8e2d58c9d691050189f5164ece896a1f956a703c66c4838ede68024?s=80&d=identicon?s=100" width="100px;" alt="Francesco Verdiani"/><br /><sub><b>Francesco Verdiani</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-fverd" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-fverd" title="Promotion">πŸ“£</a> <a href="#research-fverd" title="Research">πŸ”¬</a> <a href="#talk-fverd" title="Talks">πŸ“’</a></td>
81
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/federico.montano"><img src="https://secure.gravatar.com/avatar/14776bad0325cfdc5bd36722f9296bf22cea6e4731a8cd2a9dfd14cd46c7d875?s=80&d=identicon?s=100" width="100px;" alt="Federico Montano"/><br /><sub><b>Federico Montano</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-federico.montano" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#research-federico.montano" title="Research">πŸ”¬</a></td>
82
+ </tr>
83
+ <tr>
84
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/federico.rizzo"><img src="https://secure.gravatar.com/avatar/14d5b035cd7a67d3aee2a36b77d9a75d351cfcb809e2935e82813edc3a1096d6?s=80&d=identicon?s=100" width="100px;" alt="Federico Rizzo"/><br /><sub><b>Federico Rizzo</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#promotion-federico.rizzo" title="Promotion">πŸ“£</a> <a href="#research-federico.rizzo" title="Research">πŸ”¬</a> <a href="#data-federico.rizzo" title="Data">πŸ”£</a></td>
85
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/GiosueGambardella1998"><img src="https://secure.gravatar.com/avatar/430db604f62dfcc585e1ecb5bc1e14b656cb83a938e6b2bb0201534b33eb630c?s=80&d=identicon?s=100" width="100px;" alt="GiosuΓ¨ Gambardella"/><br /><sub><b>GiosuΓ¨ Gambardella</b></sub></a><br /><a href="#promotion-GiosueGambardella1998" title="Promotion">πŸ“£</a> <a href="#research-GiosueGambardella1998" title="Research">πŸ”¬</a> <a href="#talk-GiosueGambardella1998" title="Talks">πŸ“’</a></td>
86
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/jacoposalvalaggio"><img src="https://gitlab.com/uploads/-/system/user/avatar/10623230/avatar.png?s=100" width="100px;" alt="Jacopo Salvalaggio"/><br /><sub><b>Jacopo Salvalaggio</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=jacoposalvalaggio" title="Bug reports">πŸ›</a></td>
87
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/kpardede96"><img src="https://secure.gravatar.com/avatar/d75c82a35157e745fd56898314e01919bd8ee5eca676b63173fedf5f1ae0ddf3?s=80&d=identicon?s=100" width="100px;" alt="Kevin Pardede"/><br /><sub><b>Kevin Pardede</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-kpardede96" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-kpardede96" title="Promotion">πŸ“£</a> <a href="#research-kpardede96" title="Research">πŸ”¬</a> <a href="#talk-kpardede96" title="Talks">πŸ“’</a></td>
88
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/MariaTsedrik"><img src="https://secure.gravatar.com/avatar/562b3d91f195b526cf5f5469e2c14299fadc5cb921b9c62a57d634c46293119e?s=80&d=identicon?s=100" width="100px;" alt="Maria Tsedrik"/><br /><sub><b>Maria Tsedrik</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-MariaTsedrik" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#mentoring-MariaTsedrik" title="Mentoring">πŸ§‘β€πŸ«</a> <a href="#promotion-MariaTsedrik" title="Promotion">πŸ“£</a> <a href="#research-MariaTsedrik" title="Research">πŸ”¬</a> <a href="#talk-MariaTsedrik" title="Talks">πŸ“’</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=MariaTsedrik" title="Bug reports">πŸ›</a></td>
89
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/Yousryyy"><img src="https://secure.gravatar.com/avatar/dccaa6cd7c59457196b164ec4d8ca03913dbcede343ccb41873bba1994198adf?s=80&d=identicon?s=100" width="100px;" alt="Mohamed Elkhashab"/><br /><sub><b>Mohamed Elkhashab</b></sub></a><br /><a href="#ideas-Yousryyy" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-Yousryyy" title="Promotion">πŸ“£</a> <a href="#research-Yousryyy" title="Research">πŸ”¬</a> <a href="#talk-Yousryyy" title="Talks">πŸ“’</a></td>
90
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/pcarrilho"><img src="https://secure.gravatar.com/avatar/74eb286948240a5d6849bf609248eb0f38ae9df76ab23b178929f8042bb5249a?s=80&d=identicon?s=100" width="100px;" alt="Pedro Carrilho"/><br /><sub><b>Pedro Carrilho</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-pcarrilho" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-pcarrilho" title="Promotion">πŸ“£</a> <a href="#research-pcarrilho" title="Research">πŸ”¬</a> <a href="#talk-pcarrilho" title="Talks">πŸ“’</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=pcarrilho" title="Bug reports">πŸ›</a></td>
91
+ </tr>
92
+ <tr>
93
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/sujeong-lee"><img src="https://secure.gravatar.com/avatar/502ccd6e96ebc2b8d625b627f1c150bb186279a031e7fdb54be7936016f32658?s=80&d=identicon?s=100" width="100px;" alt="Sujeong Lee"/><br /><sub><b>Sujeong Lee</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-sujeong-lee" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-sujeong-lee" title="Promotion">πŸ“£</a> <a href="#research-sujeong-lee" title="Research">πŸ”¬</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=sujeong-lee" title="Bug reports">πŸ›</a></td>
94
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/matildebs"><img src="https://secure.gravatar.com/avatar/76e01baf26278aa27b97eab2bd250cbed58d786eac879b372b7cb8f708d4a0b9?s=80&d=identicon?s=100" width="100px;" alt="matildebs"/><br /><sub><b>matildebs</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="#ideas-matildebs" title="Ideas, Planning, & Feedback">πŸ€”</a> <a href="#promotion-matildebs" title="Promotion">πŸ“£</a> <a href="#research-matildebs" title="Research">πŸ”¬</a> <a href="#talk-matildebs" title="Talks">πŸ“’</a> <a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=matildebs" title="Bug reports">πŸ›</a></td>
95
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/ztchenustc"><img src="https://secure.gravatar.com/avatar/f7a4e34ddee1a5b45ab8d13dcb04fee77c6b520a1320fc3d09de7c40e02cdc31?s=80&d=identicon?s=100" width="100px;" alt="Zhaoting Chen"/><br /><sub><b>Zhaoting Chen</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Documentation">πŸ“–</a> <a href="#research-ztchenustc" title="Research">πŸ”¬</a></td>
96
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/Asser_Elhegawy"><img src="https://gitlab.com/uploads/-/system/user/avatar/31076008/avatar.png?s=100" width="100px;" alt="Asser Elhegawy"/><br /><sub><b>Asser Elhegawy</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/issues?author_username=Asser_Elhegawy" title="Bug reports">πŸ›</a></td>
97
+ <td align="center" valign="top" width="14.28%"><a href="https://gitlab.com/nebblub"><img src="https://secure.gravatar.com/avatar/5bf6784c13b20208d30248fb733e68a5cfba061cebfd9267ff21faca34a2fe3b?s=80&d=identicon?s=100" width="100px;" alt="nebblu"/><br /><sub><b>nebblu</b></sub></a><br /><a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Code">πŸ’»</a> <a href="https://gitlab.com/Chiara Moretti/pbj/commits/master" title="Documentation">πŸ“–</a> <a href="#research-nebblub" title="Research">πŸ”¬</a></td>
98
+ </tr>
99
+ </tbody>
100
+ <tfoot>
101
+ <tr>
102
+ <td align="center" size="13px" colspan="7">
103
+ <img src="https://raw.githubusercontent.com/all-contributors/all-contributors-cli/1b8533af435da9854653492b1327a23a4dbd0a10/assets/logo-small.svg">
104
+ <a href="https://all-contributors.js.org/docs/en/bot/usage">Add your contributions</a>
105
+ </img>
106
+ </td>
107
+ </tr>
108
+ </tfoot>
109
+ </table>
110
+
111
+ <!-- markdownlint-restore -->
112
+ <!-- prettier-ignore-end -->
113
+
114
+ <!-- ALL-CONTRIBUTORS-LIST:END -->
115
+
116
+ This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!