Merge branch 'dev' of github.com:TeamCOMPAS/COMPAS into lambda_enhancements

Author: themikelau

.github/workflows/compas-compile-ci.yml

@@ -0,0 +1,16 @@
+name: COMPAS compile test
+
+on: [pull_request]
+
+jobs:
+  compas:
+    name: Build COMPAS
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install dependencies 
+        run: sudo apt install g++ libboost-all-dev libgsl-dev libhdf5-serial-dev 
+
+      - name: Build Compas
+        run: cd src && make -j $(nproc) -f Makefile

.github/workflows/latex-compile-ci.yml

@@ -0,0 +1,68 @@
+name: LaTeX compile test
+
+# Test Latex compiles on pull_requests
+# Public documentation on push to dev
+
+on:
+  pull_request:
+  push: 
+      branches: [dev] 
+
+jobs:
+  latex:
+    name: Build LaTeX documentation
+    runs-on: ubuntu-18.04
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install dependencies 
+        run: sudo apt install texlive-base
+        
+      # Need to do pdflatex, bibtex, pdflatex, pdflatex
+      - name: pdflatex main
+        uses: dante-ev/latex-action@latest
+        with:
+          working_directory: docs/COMPAS_LaTeX
+          root_file: main.tex
+          compiler: pdflatex
+          args: -interaction=nonstopmode -shell-escape
+
+      - name: bibtex main
+        uses: dante-ev/latex-action@latest
+        with:
+          working_directory: docs/COMPAS_LaTeX
+          root_file: main.aux
+          compiler: bibtex 
+          args: 
+
+      - name: pdflatex main
+        uses: dante-ev/latex-action@latest
+        with:
+          working_directory: docs/COMPAS_LaTeX
+          root_file: main.tex
+          compiler: pdflatex
+          args: -interaction=nonstopmode -shell-escape
+          
+      - name: pdflatex main
+        uses: dante-ev/latex-action@latest
+        with:
+          working_directory: docs/COMPAS_LaTeX
+          root_file: main.tex
+          compiler: pdflatex
+          args: -interaction=nonstopmode -shell-escape
+
+
+      # If push to dev, publish the documentation
+      - name: publish documentation 
+        if: github.event_name == 'push' 
+        run: |
+          git checkout --orphan Documentation
+          PDF_FILE=COMPAS_Documentation.pdf
+          mv docs/COMPAS_LaTeX/main.pdf $PDF_FILE
+          git rm -rf .
+          git add -f $PDF_FILE
+          git config user.name "Team COMPAS"
+          git config user.email "<>"
+          git commit -m "Documentation update"
+          git push -f --set-upstream origin Documentation

.gitignore

@@ -21,17 +21,24 @@ Thumbs.db
 __pycache__/
 COMPAS_Output*/
 output*/
-.github/
 COMPAS
 *.log
 *.aux
 *.toc
 *.bbl
 *.blg
+*.pdf
+*.eps
+*.png
 *.synctex
 *.synctex(busy)
 *.synctex.gz
 *.synctex.gz(busy)
 
+# docs html
+*_build
+
+*.vscode
+
 Makefile-reinhold
 .gitignore

CODE_OF_CONDUCT.md

@@ -0,0 +1,39 @@
+# COMPAS Code of Conduct
+
+Dear colleagues:
+
+I want to take this opportunity to remind all of us (myself included) 
+how important it is to maintain the highest standards of respectful and tolerant 
+behavior in our professional interactions.  
+
+We are fortunate that Team COMPAS is a diverse group, and we want to benefit 
+from that diversity and make sure that everyone in the team feels comfortable and welcome. 
+
+There are numerous codes of conduct describing what is considered appropriate 
+professional behaviour;  since many of us are based in Australia and connected to OzGrav, 
+let me point to these two in particular:
+
+ASA code of conduct: <https://asa.astronomy.org.au/wp-content/uploads/2020/09/ASA_Code_of_Conduct.pdf>
+
+OzGrav code of conduct: <https://www.ozgrav.org/code-of-conduct.html>
+
+Fundamentally, all of these codes are focused on one thing: 
+maintaining a professional environment where everyone is treated with respect. 
+
+
+If you notice that this is not happening, and are comfortable with doing so, please speak up or let me know offline*.  We (myself included) should aim to be held accountable to each other, respect being challenged for our behavior, and remain willing to get advice on how we as individuals can help create a welcoming community where we can all thrive. Making mistakes is how we learn, both as individuals and as a community. I and others will be very grateful if you let us know about any suggestions and will endeavor to learn from them.  
+
+But there may be situations where this can be very uncomfortable.  
+With that in mind, I’ve asked Prof. Elena Maria Rossi from Leiden University in the 
+Netherlands to act as the COMPAS Ombudsperson, and Elena kindly agreed to do so.  
+In addition to being a brilliant astrophysicist, 
+Elena has a wealth of experience in championing equality and inclusivity; 
+for example, she is the founder and chair of the LISA consortium Diversity and Inclusion committee.  
+If you are experiencing any issues in interactions with COMPAS colleagues and would 
+like to discuss them confidentially with someone who is outside of any local structures, 
+please contact Elena, her contact details can be found at <https://www.universiteitleiden.nl/en/staffmembers/elena-rossi#tab-1> 
+
+Best wishes,
+Ilya 
+
+* see <https://ilyamandel.github.io/> for my contact information

Dockerfile

@@ -4,6 +4,7 @@ WORKDIR /app/COMPAS
 
 RUN apt-get update && apt-get install -y \
     g++ \
+    libhdf5-serial-dev \
     libboost-all-dev \
     libgsl-dev \
     python3 \

README.md

@@ -4,27 +4,50 @@
 
 # Compact Object Mergers: Population Astrophysics & Statistics
 
+[![Documentation](https://img.shields.io/badge/Documentation-latest-orange.svg?style=flat)](https://github.com/TeamCOMPAS/COMPAS/blob/Documentation/COMPAS_Documentation.pdf)
+
 [//]: ## (Outline features)
 COMPAS is a publicly available rapid binary population synthesis code (https://compas.science/) that is designed so that evolution prescriptions and model parameters are easily 
 adjustable.  COMPAS draws properties for a binary star system from a set of initial distributions, and evolves it from zero-age main sequence to the end of its life as two compact 
 remnants.  It has been used for inference from observations of gravitational-wave mergers, Galactic neutron stars, X-ray binaries, and luminous red novae.
 
 ## Documentation
-[Getting started](./docs/getting_started.md)  
-[Specifications](./docs/COMPAS_Doc.pdf)  
-[Post-processing](./postProcessing/README.txt)  
-[Running COMPAS inside a Docker container](./docs/docker.md)  
+https://compas.science/docs
 
 ## Contact
 Please email your queries to compas-user@googlegroups.com. You are also welcome to join the [COMPAS User Google Group](https://groups.google.com/forum/#!members/compas-user) to engage in discussions with COMPAS users and developers.
 
 ## Acknowledgements
-If you use this code or parts of this code for results presented in a scientific publication, we would greatly appreciate if you send us your paper reference and make your input settings and output data publicly available by uploading it to the [COMPAS Zenodo community](https://zenodo.org/communities/compas/). Please also kindly include citations to the two following papers:
+If you use this code or parts of this code for results presented in a scientific publication, we would greatly appreciate if you send us your paper reference and make your input settings and output data publicly available by uploading it to the [COMPAS Zenodo community](https://zenodo.org/communities/compas/). Please also kindly include citations to our COMPAS methods paper https://ui.adsabs.harvard.edu/abs/2021arXiv210910352T/abstract. As the public COMPAS code is a product of work by the entire COMPAS collaboration over many years, we kindly request that, in recognition of this team effort, the paper is cited as “Team COMPAS: J. Riley et al.”. An example bibtex code is:
+
+
+@ARTICLE{COMPAS:2021methodsPaper,
+       author = {{\noopsort{Team COMPAS}}{Team COMPAS: J. Riley} and  {Riley}, Jeff and {Agrawal}, Poojan and {Barrett}, Jim W. and {Boyett}, Kristan N.~K. and {Broekgaarden}, Floor S. and {Chattopadhyay}, Debatri and {Gaebel}, Sebastian M. and {Gittins}, Fabian and {Hirai}, Ryosuke and {Howitt}, George and {Justham}, Stephen and {Khandelwal}, Lokesh and {Kummer}, Floris and {Lau}, Mike Y.~M. and {Mandel}, Ilya and {de Mink}, Selma E. and {Neijssel}, Coenraad and {Riley}, Tim and {van Son}, Lieke and {Stevenson}, Simon and {Vigna-Gomez}, Alejandro and {Vinciguerra}, Serena and {Wagg}, Tom and {Willcox}, Reinhold},
+        title = "{Rapid stellar and binary population synthesis with COMPAS}",
+      journal = {arXiv e-prints},
+     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Solar and Stellar Astrophysics},
+         year = 2021,
+        month = sep,
+          eid = {arXiv:2109.10352},
+        pages = {arXiv:2109.10352},
+archivePrefix = {arXiv},
+       eprint = {2109.10352},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2021arXiv210910352T},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+Note that the preferred acknowledgement relies on \noopsort; to make it work, you'll have to include the following line at the start of your bibtex file:
+@PREAMBLE{ {\providecommand{\noopsort}[1]{}} }
+
+
+
+In addition, we suggest to kindly include the two following papers:
 
 1. Stevenson S., Vigna-Gómez A., Mandel I., Barrett J. W., Neijssel C. J., Perkins D., de Mink S. E., 2017, [Nature Communications, 8, 14906](https://ui.adsabs.harvard.edu/abs/2017NatCo...814906S/abstract)
 2. Vigna-Gómez A., Neijssel C. J., Stevenson S., Barrett J. W., Belczynski K., Justham S., de Mink S., Müller B., Podsiadlowski Ph., Renzo M., Szécsi D., Mandel I., 2018, [MNRAS, 481, 4009](https://ui.adsabs.harvard.edu/abs/2018MNRAS.481.4009V/abstract)
 
-We anticipate releasing a more detailed and comprehensive methods paper in the future. We also greatly appreciate an acknowledgement of the form: 
+We also greatly appreciate an acknowledgement of the form: 
 
 >_Simulations in this paper made use of the COMPAS rapid binary population synthesis code (version X.X.X), which is freely available at http://github.com/TeamCOMPAS/COMPAS_.
 
@@ -52,3 +75,9 @@ Furthermore,
 
 ## License
 [MIT](https://choosealicense.com/licenses/mit/)
+
+
+
+### Highlighted papers that have made use of COMPAS are listed at https://compas.science/science.html ; see https://ui.adsabs.harvard.edu/public-libraries/gzRk1qpbRUy4cP2GydR36Q for a full ADS library
+
+