(compasUtils) merge with dev

.dictionary.txt

@@ -0,0 +1,17 @@
+parms
+hist
+tHeI
+thei
+Hist
+vie
+mye
+NWO
+nd
+lamda
+bject
+accreting
+accrete
+accreted
+YHe
+yhe
+

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

@@ -1,16 +1,75 @@
 name: COMPAS compile test
 
-on: [pull_request]
+on:
+  workflow_dispatch: # allow manual triggering of this workflow
+  pull_request: # run workflow when PRs made to dev (if following files changed)
+    branches:
+      - dev
+    paths: ['src/**', "compas_python_utils/**", "py_tests/**", ".github/workflows/**"]
+  push: # always run workflow on push to the following branch
+    branches:
+      - dev
 
 jobs:
   compas:
     name: Build COMPAS
-    runs-on: ubuntu-18.04
+    runs-on: ${{ matrix.os}}
+    container: ${{matrix.container}}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-20.04]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip' # caching pip dependencies
 
-      - name: Install dependencies 
-        run: sudo apt install g++ libboost-all-dev libgsl-dev libhdf5-serial-dev 
+      - name: Install dependencies on ubuntu
+        if: startsWith(matrix.os, 'ubuntu-20')
+        run: |
+          cd misc/cicd-scripts
+          chmod 755 linux-dependencies
+          ./linux-dependencies
 
       - name: Build Compas
-        run: cd src && make -j $(nproc) -f Makefile
+        run: |
+          cd src && make -j $(nproc) -f Makefile
+          ./COMPAS -v
+
+      - name: Run example COMPAS job
+        run: |
+          pip install --upgrade pip
+          pip install -e .[dev]
+          export COMPAS_ROOT_DIR=${GITHUB_WORKSPACE}
+          cd ${GITHUB_WORKSPACE}/misc/examples/methods_paper_plots/detailed_evolution
+          chmod 755 run.sh
+          cat run.sh
+          ./run.sh
+
+      - name: Run pytests
+        # Run tests and collect coverage data
+        run: |
+          cd ${GITHUB_WORKSPACE}
+          export COMPAS_ROOT_DIR=${GITHUB_WORKSPACE}
+          jupyter-kernelspec list
+          pytest --cov=compas_python_utils/ py_tests/ -m 'not webtest'
+          pytest --cov=compas_python_utils/ --cov-append py_tests/ -m webtest 
+          coverage html
+          coverage-badge -o coverage_badge.svg -f
+
+      - name: Archive code coverage results
+        uses: actions/upload-artifact@v3
+        with:
+          name: code-coverage
+          path: |
+            htmlcov/
+            coverage_badge.svg
+
+      - name: Archive COMPAS run data
+        uses: actions/upload-artifact@v3
+        with:
+          name: COMPAS-run-artifacts
+          path: |
+            py_tests/test_artifacts

.github/workflows/dockerhub-ci.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   release:
     name: Build Docker image and push to DockerHub
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v2
 

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

@@ -5,8 +5,11 @@ name: LaTeX compile test
 
 on:
   pull_request:
+    paths: ['main/**'] # only changes to src/ trigger this workflow
   push: 
-      branches: [dev] 
+      branches: [dev]
+      paths: ['main/**']
+
 
 jobs:
   latex:

.github/workflows/precommit-checks.yml

@@ -0,0 +1,14 @@
+name: precommit checks
+
+on:
+  push:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+      with:
+        python-version: 3.8
+    - uses: pre-commit/action@v3.0.0

.gitignore

@@ -7,7 +7,9 @@
 ehthumbs.db
 Thumbs.db
 
+
 # Compiled source
+*.egg-info/
 *.com
 *.class
 *.dll
@@ -21,6 +23,9 @@ Thumbs.db
 __pycache__/
 COMPAS_Output*/
 output*/
+*.coverage
+test_artifacts/
+
 COMPAS
 *.log
 *.aux
@@ -37,8 +42,7 @@ COMPAS
 
 # docs html
 *_build
-
 *.vscode
 
-Makefile-reinhold
-.gitignore
+/utils/examples/*.ipynb
+/utils/examples/*.h5

.pre-commit-config.yaml

@@ -0,0 +1,8 @@
+default_language_version:
+    python: python3
+repos:
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+    -   id: codespell # Spellchecker
+        args: [--ignore-words=.dictionary.txt, --skip, '*.eps,*.svg,*.ipynb,./misc/*,paper.md,./online-docs/index.rst']

.readthedocs.yaml

@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the online-docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: online-docs/conf.py
+
+# Build only html documentation (specificall, don't build PDF!)
+formats: []
+
+# Set the version of Python and other tools you might need
+python:
+  install:
+    - requirements: requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

Dockerfile

@@ -13,6 +13,7 @@ RUN apt-get update && apt-get install -y \
 
 # RUN pip install numpy awscli
 RUN pip3 install numpy
+RUN pip3 install pyyaml
 
 # Copy only the source required to compile COMPAS
 COPY src/ src/

README.md

@@ -1,11 +1,9 @@
 [//]: ## (grip -b README.md)
 
-![COMPASlogo](docs/media/COMPASlogo.png)
+![COMPASlogo](utils/COMPAS-logo/fullCompasLogo.png)
 
 # 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 
@@ -20,26 +18,33 @@ Please email your queries to compas-user@googlegroups.com. You are also welcome
 ## 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 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},
+@ARTICLE{2022ApJS..258...34R,
+       author = {{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-G{\'o}mez}, Alejandro and {Vinciguerra}, Serena and {Wagg}, Tom and {Willcox}, Reinhold and {Team Compas}},
+        title = "{Rapid Stellar and Binary Population Synthesis with COMPAS}",
+      journal = {\apjs},
+     keywords = {1622, 154, 1108, 162, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Solar and Stellar Astrophysics},
+         year = 2022,
+        month = feb,
+       volume = {258},
+       number = {2},
+          eid = {34},
+        pages = {34},
+          doi = {10.3847/1538-4365/ac416c},
 archivePrefix = {arXiv},
        eprint = {2109.10352},
  primaryClass = {astro-ph.IM},
-       adsurl = {https://ui.adsabs.harvard.edu/abs/2021arXiv210910352T},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2022ApJS..258...34R},
       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:
+
+Note that the preferred acknowledgement relies on \noopsort and cites the paper as TEAM COMPAS; Riley et al.; to make it work, you'll have to include the following line at the start of your bibtex file:
 @PREAMBLE{ {\providecommand{\noopsort}[1]{}} }
 
+and change the author line in the bib entry to:
+
+author = {{\noopsort{Team COMPAS}}{Team COMPAS: Riley, J.} 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}
+
 
 
 In addition, we suggest to kindly include the two following papers:

compas_python_utils/__init__.py

@@ -0,0 +1,11 @@
+
+__all__ = []
+
+__author__ = "Team COMPAS"
+__email__ = "compas email"
+__uri__ = "https://github.com/TeamCOMPAS/COMPAS"
+__license__ = "MIT"
+__description__ = "COMPAS"
+__copyright__ = "Copyright 2022 COMPAS developers"
+__contributors__ = "https://github.com/TeamCOMPAS/COMPAS/graphs/contributors"
+__version__ = "0.0.1"