nmma 0.2.0__tar.gz → 0.2.2__tar.gz

{nmma-0.2.0 → nmma-0.2.2}/.github/workflows/build-deploy-container.yml

@@ -42,7 +42,7 @@ jobs:
 
       - name: Build and push
         id: build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: ./api/Dockerfile

nmma-0.2.2/.github/workflows/continous_integration.yml

@@ -0,0 +1,154 @@
+name: Unit Test nmma
+
+on:
+  push:
+    branches: [main]
+    paths-ignore:
+      - "doc/**"
+  pull_request:
+    branches: [main]
+    paths-ignore:
+      - "doc/**"
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout branch being tested
+        uses: actions/checkout@v4
+
+      - name: Set up Python with Conda ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: ${{ matrix.os == 'macos-latest' && 'arm64' || 'x86_64' }}
+          miniforge-version: latest
+          use-mamba: true
+          mamba-version: "*"
+          activate-environment: nmma_env
+
+      - name: Restore SVD models from cache
+        uses: actions/cache@v4
+        with:
+          path: svdmodels
+          key: svdmodels-${{ hashFiles('**/LICENSE') }}
+          restore-keys: svdmodels-
+          save-always: true
+
+      - name: Get pip cache dir
+        id: pip-cache
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          echo "::set-output name=dir::$(pip cache dir)"
+
+      - name: pip cache
+        uses: actions/cache@v4
+        with:
+          path: ${{ steps.pip-cache.outputs.dir }}
+          key: ${{ runner.os }}-pip-2-${{ hashFiles('**/pyproject.toml', '**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-2-
+          save-always: true
+
+      - name: Update Homebrew
+        if: matrix.os == 'macos-latest'
+        run: |
+          brew update --preinstall
+
+      - name: Configure Homebrew cache
+        if: matrix.os == 'macos-latest'
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/Library/Caches/Homebrew/openmpi--*
+            ~/Library/Caches/Homebrew/downloads/*--openmpi-*
+            ~/Library/Caches/Homebrew/hdf5--*
+            ~/Library/Caches/Homebrew/downloads/*--hdf5-*
+            ~/Library/Caches/Homebrew/gcc--*
+            ~/Library/Caches/Homebrew/downloads/*--gcc-*
+            ~/Library/Caches/Homebrew/openblas--*
+            ~/Library/Caches/Homebrew/downloads/*--openblas-*
+            ~/Library/Caches/Homebrew/lapack--*
+            ~/Library/Caches/Homebrew/downloads/*--lapack-*
+            ~/Library/Caches/Homebrew/basictex--*
+            ~/Library/Caches/Homebrew/downloads/*--basictex-*
+            ~/Library/Caches/Homebrew/cmake--*
+            ~/Library/Caches/Homebrew/downloads/*--cmake-*
+
+          key: brew-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: brew-
+          save-always: true
+
+      - name: Install Homebrew dependencies
+        if: matrix.os == 'macos-latest'
+        run: |
+          env HOMEBREW_NO_AUTO_UPDATE=1 brew install openmpi hdf5 gcc openblas lapack basictex cmake
+          eval "$(/usr/libexec/path_helper)"
+          sudo tlmgr update --self
+          sudo tlmgr install collection-latex
+          sudo tlmgr install collection-fontsrecommended
+          sudo tlmgr install dvipng
+          sudo tlmgr install cm-super
+          sudo tlmgr install type1cm
+      - name: Install Linux Dependencies
+        if: matrix.os == 'ubuntu-latest'
+        uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: openmpi-bin libopenmpi-dev gfortran build-essential libblas3 libblas-dev liblapack3 liblapack-dev libatlas-base-dev texlive texlive-latex-extra texlive-fonts-recommended dvipng cm-super
+          execute_install_scripts: true
+
+      - name: Install dependencies (macOS)
+        if: matrix.os == 'macos-latest'
+        run: |
+          conda install -c conda-forge pyfftw c-compiler ligo-segments python-ligo-lw
+          echo "FC=$(which gfortran-14)" >> $GITHUB_ENV
+          echo "CC=$(which gcc)" >> $GITHUB_ENV
+          echo "CXX=$(which g++)" >> $GITHUB_ENV
+
+      - name: Install dependencies (Ubuntu)
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y texlive texlive-latex-extra texlive-fonts-recommended dvipng cm-super python3-mpi4py
+          
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade git+https://github.com/bitranox/wrapt_timeout_decorator.git
+          python -m pip install pytest pytest-cov flake8 pytest-aiohttp sqlparse freezegun PyJWT joblib coveralls
+          python -m pip install -r  ml_requirements.txt -r grb_requirements.txt -r tf_requirements.txt -r sklearn_requirements.txt
+          python -m pip install .
+          git clone https://github.com/JohannesBuchner/MultiNest && cd MultiNest/build && rm -rf * && cmake .. && make && cd ../..
+          pwd
+
+      - name: Export Libraries
+        run: |
+          echo "LD_LIBRARY_PATH=$HOME/work/nmma/nmma/MultiNest/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+          echo "DYLD_LIBRARY_PATH=$HOME/work/nmma/nmma/MultiNest/lib:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude docs
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude docs,versioneer.py,nmma/_version.py,nmma/tests,nmma/*/__init__.py
+
+      - name: Test with pytest
+        run: |
+          python -m coverage run --source nmma -m pytest nmma/tests/*.py
+
+      - name: Run Coveralls
+        if: ${{ success() }}
+        run: |
+          coveralls --service=github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

nmma-0.2.2/.github/workflows/dependency-installation.yml

@@ -0,0 +1,85 @@
+name: Check NMMA dependencies installation
+on:
+  push:
+    branches: [main]
+    paths: ["*_requirements.txt", "pyproject.toml"]
+  pull_request:
+    branches: [main]
+    paths: ["*_requirements.txt", "pyproject.toml"]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout branch being tested
+        uses: actions/checkout@v4
+
+      - name: Set up Python with Conda ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: ${{ matrix.os == 'macos-latest' && 'arm64' || 'x86_64' }}
+          miniforge-version: latest
+          use-mamba: true
+          mamba-version: "*"
+          activate-environment: nmma_env
+
+      - name: Install linux packages
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y openmpi-bin libopenmpi-dev
+
+      - name: Install Homebrew packages
+        if: matrix.os == 'macos-latest'
+        run: |
+          brew install openmpi hdf5
+          conda install ligo-segments python-ligo-lw
+
+      - name: Install NMMA (base)
+        run: |
+          python -m pip install nmma
+
+      - name: Verify base NMMA installation
+        run: |
+          python -c "import nmma; print(f'NMMA version: {nmma.__version__}')"
+
+      - name: Install and verify NMMA [grb]
+        run: |
+          python -m pip install 'nmma[grb]'
+          python -c "import nmma, afterglowpy; print(f'Successfully imported {nmma.__name__}, {afterglowpy.__name__}')"
+
+      - name: Install and verify NMMA [production]
+        run: |
+          python -m pip install 'nmma[production]'
+          python -c "import nmma, parallel_bilby, nestcheck, mpi4py; print(f'Successfully imported {nmma.__name__}, {parallel_bilby.__name__}, {nestcheck.__name__}, {mpi4py.__name__}')"
+
+      - name: Install and verify NMMA [neuralnet]
+        run: |
+          python -m pip install 'nmma[neuralnet]'
+          python -c "import nmma, torch, nflows, torchvision; print(f'Successfully imported {nmma.__name__}, {torch.__name__}, {nflows.__name__}, {torchvision.__name__}')"
+
+      - name: Install and verify NMMA [tf]
+        run: |
+          python -m pip install 'nmma[tf]'
+          python -c "import nmma, tensorflow; print(f'Successfully imported {nmma.__name__}, {tensorflow.__name__}')"
+
+      - name: Install and verify NMMA [sklearn]
+        run: |
+          python -m pip install 'nmma[sklearn]'
+          python -c "import nmma, sklearn; print(f'Successfully imported {nmma.__name__}, {sklearn.__name__}')"
+
+      - name: Install and verify NMMA [sampler]
+        run: |
+          python -m pip install 'nmma[sampler]'
+          python -c "import nmma, ultranest; print(f'Successfully imported {nmma.__name__}, {ultranest.__name__}')"

{nmma-0.2.0 → nmma-0.2.2}/.github/workflows/deploy-github-pages.yml

@@ -39,6 +39,8 @@ jobs:
         python -m pip install .[doc]
 
     - name: Make dependencies
+      env:
+        SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.SPHINX_GITHUB_CHANGELOG_TOKEN }}
       run: |
         cd doc && make html; cd ../
         touch doc/_build/html/.nojekyll
@@ -51,3 +53,4 @@ jobs:
         build_dir: doc/_build/html/
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.SPHINX_GITHUB_CHANGELOG_TOKEN }}

nmma-0.2.2/.github/workflows/rst-linter.yml

@@ -0,0 +1,22 @@
+name: Lint rst
+
+on:
+    push:
+        paths: ['**/**.rst']
+    pull_request:
+        paths: ['**/**.rst']
+
+jobs:
+    doctor-rst:
+        name: DOCtor-RST
+        runs-on: ubuntu-latest
+        steps:
+            - name: "Checkout code"
+              uses: actions/checkout@v4
+
+            - name: DOCtor-RST
+              uses: docker://oskarstark/doctor-rst
+              with:
+                  args: --short --error-format=github
+              env:
+                  DOCS_DIR: 'doc/'

{nmma-0.2.0 → nmma-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nmma
-Version: 0.2.0
+Version: 0.2.2
 Summary: A nuclear physics multi-messenger Bayesian inference library
 Author-email: "Peter Tsun Ho Pang, Michael Coughlin, Tim Dietrich, Ingo Tews" <nuclear_multimessenger_astronomy@googlegroups.com>
 License: GPLv3
@@ -12,6 +12,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: End Users/Desktop
 Classifier: Intended Audience :: Developers
@@ -23,7 +24,7 @@ Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
 Classifier: Operating System :: MacOS
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Requires-Python: <3.12,>=3.9
+Requires-Python: <3.13,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: future
@@ -34,16 +35,13 @@ Requires-Dist: numpy>=1.9
 Requires-Dist: matplotlib<3.8,>=2.0
 Requires-Dist: scipy>=1.10
 Requires-Dist: pandas<2.0,>=1.3.4
-Requires-Dist: astropy>=4.3.1
-Requires-Dist: scikit-learn<1.2,>=1.0.2
+Requires-Dist: astropy>=5.3.4
 Requires-Dist: pymultinest
 Requires-Dist: sncosmo
 Requires-Dist: dust_extinction
 Requires-Dist: arviz
 Requires-Dist: p_tqdm
-Requires-Dist: ultranest
 Requires-Dist: tornado
-Requires-Dist: tensorflow
 Requires-Dist: notebook
 Requires-Dist: ligo.skymap
 Requires-Dist: healpy
@@ -60,6 +58,7 @@ Requires-Dist: linkify; extra == "doc"
 Requires-Dist: myst-parser; extra == "doc"
 Requires-Dist: sphinx-book-theme; extra == "doc"
 Requires-Dist: sphinx_copybutton; extra == "doc"
+Requires-Dist: sphinx-github-changelog; extra == "doc"
 Provides-Extra: grb
 Requires-Dist: afterglowpy>=0.7.3; extra == "grb"
 Requires-Dist: wrapt_timeout_decorator; extra == "grb"
@@ -67,6 +66,16 @@ Provides-Extra: production
 Requires-Dist: parallel_bilby>=2.0.2; extra == "production"
 Requires-Dist: nestcheck; extra == "production"
 Requires-Dist: mpi4py; extra == "production"
+Provides-Extra: neuralnet
+Requires-Dist: torch; extra == "neuralnet"
+Requires-Dist: nflows; extra == "neuralnet"
+Requires-Dist: torchvision; extra == "neuralnet"
+Provides-Extra: sklearn
+Requires-Dist: scikit-learn>=1.0.2; extra == "sklearn"
+Provides-Extra: tf
+Requires-Dist: tensorflow; extra == "tf"
+Provides-Extra: sampler
+Requires-Dist: ultranest; extra == "sampler"
 
 <p align="center">
     <picture>
@@ -84,17 +93,24 @@ Requires-Dist: mpi4py; extra == "production"
 </div>
 
 
+[![GitHub Repo stars](https://img.shields.io/github/stars/nuclear-multimessenger-astronomy/nmma?style=flat)](https://github.com/nuclear-multimessenger-astronomy/nmma/stargazers)
+[![GitHub forks](https://img.shields.io/github/forks/nuclear-multimessenger-astronomy/nmma?style=flat&color=%2365c563)](https://github.com/nuclear-multimessenger-astronomy/nmma/forks)
+[![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/nmma?label=conda%20downloads)](https://anaconda.org/conda-forge/nmma)
+[![PyPI - Downloads](https://img.shields.io/pypi/dm/nmma?label=PyPI%20downloads)](https://badge.fury.io/py/nmma)
 [![Coverage Status](https://coveralls.io/repos/github/nuclear-multimessenger-astronomy/nmma/badge.svg?branch=main)](https://coveralls.io/github/nuclear-multimessenger-astronomy/nmma?branch=main)
 [![CI](https://github.com/nuclear-multimessenger-astronomy/nmma/actions/workflows/continous_integration.yml/badge.svg)](https://github.com/nuclear-multimessenger-astronomy/nmma/actions/workflows/continous_integration.yml)
 [![PyPI version](https://badge.fury.io/py/nmma.svg)](https://badge.fury.io/py/nmma)
 [![Python version](https://img.shields.io/pypi/pyversions/nmma.svg)](https://badge.fury.io/py/nmma)
 
 
+
+
+Citations to the NMMA code: [Citation record](https://inspirehep.net/literature?sort=mostrecent&size=250&page=1&q=refersto%3Arecid%3A2083145&ui-citation-summary=true)
+
 Read our official documentation: [NMMA Documentation](https://nuclear-multimessenger-astronomy.github.io/nmma/)
 
 Check out our contribution guide: [For contributors](https://nuclear-multimessenger-astronomy.github.io/nmma/contributing.html)
 
-
 A tutorial on how to produce simulations of lightcurves is given here [tutorial-lightcurve_simulation.ipynb](https://github.com/nuclear-multimessenger-astronomy/nmma/blob/main/tutorials/tutorial-lightcurve_simulation.ipynb)
 
 
@@ -117,6 +133,18 @@ When utilizing this code for a publication, kindly make a reference to the packa
       url={https://doi.org/10.1038/s41467-023-43932-6}
 }
 ```
+If you are using the systematics error, please also cite the paper [A data-driven approach for modeling the temporal and spectral evolution of kilonova systematic uncertainties](https://arxiv.org/abs/2410.21978). The BibTeX entry for the paper is:
+```bibtex
+@article{Jhawar:2024ezm,
+    author = "Jhawar, Sahil and Wouters, Thibeau and Pang, Peter T. H. and Bulla, Mattia and Coughlin, Michael W. and Dietrich, Tim",
+    title = "{A data-driven approach for modeling the temporal and spectral evolution of kilonova systematic uncertainties}",
+    eprint = "2410.21978",
+    archivePrefix = "arXiv",
+    primaryClass = "astro-ph.HE",
+    month = "10",
+    year = "2024"
+}
+```
 
 ### Acknowledgments
 If you benefited from participating in our community, we ask that you please acknowledge the Nuclear Multi-Messenger Astronomy collaboration, and particular individuals who helped you, in any publications.

{nmma-0.2.0 → nmma-0.2.2}/README.md

@@ -14,17 +14,24 @@
 </div>
 
 
+[![GitHub Repo stars](https://img.shields.io/github/stars/nuclear-multimessenger-astronomy/nmma?style=flat)](https://github.com/nuclear-multimessenger-astronomy/nmma/stargazers)
+[![GitHub forks](https://img.shields.io/github/forks/nuclear-multimessenger-astronomy/nmma?style=flat&color=%2365c563)](https://github.com/nuclear-multimessenger-astronomy/nmma/forks)
+[![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/nmma?label=conda%20downloads)](https://anaconda.org/conda-forge/nmma)
+[![PyPI - Downloads](https://img.shields.io/pypi/dm/nmma?label=PyPI%20downloads)](https://badge.fury.io/py/nmma)
 [![Coverage Status](https://coveralls.io/repos/github/nuclear-multimessenger-astronomy/nmma/badge.svg?branch=main)](https://coveralls.io/github/nuclear-multimessenger-astronomy/nmma?branch=main)
 [![CI](https://github.com/nuclear-multimessenger-astronomy/nmma/actions/workflows/continous_integration.yml/badge.svg)](https://github.com/nuclear-multimessenger-astronomy/nmma/actions/workflows/continous_integration.yml)
 [![PyPI version](https://badge.fury.io/py/nmma.svg)](https://badge.fury.io/py/nmma)
 [![Python version](https://img.shields.io/pypi/pyversions/nmma.svg)](https://badge.fury.io/py/nmma)
 
 
+
+
+Citations to the NMMA code: [Citation record](https://inspirehep.net/literature?sort=mostrecent&size=250&page=1&q=refersto%3Arecid%3A2083145&ui-citation-summary=true)
+
 Read our official documentation: [NMMA Documentation](https://nuclear-multimessenger-astronomy.github.io/nmma/)
 
 Check out our contribution guide: [For contributors](https://nuclear-multimessenger-astronomy.github.io/nmma/contributing.html)
 
-
 A tutorial on how to produce simulations of lightcurves is given here [tutorial-lightcurve_simulation.ipynb](https://github.com/nuclear-multimessenger-astronomy/nmma/blob/main/tutorials/tutorial-lightcurve_simulation.ipynb)
 
 
@@ -47,6 +54,18 @@ When utilizing this code for a publication, kindly make a reference to the packa
       url={https://doi.org/10.1038/s41467-023-43932-6}
 }
 ```
+If you are using the systematics error, please also cite the paper [A data-driven approach for modeling the temporal and spectral evolution of kilonova systematic uncertainties](https://arxiv.org/abs/2410.21978). The BibTeX entry for the paper is:
+```bibtex
+@article{Jhawar:2024ezm,
+    author = "Jhawar, Sahil and Wouters, Thibeau and Pang, Peter T. H. and Bulla, Mattia and Coughlin, Michael W. and Dietrich, Tim",
+    title = "{A data-driven approach for modeling the temporal and spectral evolution of kilonova systematic uncertainties}",
+    eprint = "2410.21978",
+    archivePrefix = "arXiv",
+    primaryClass = "astro-ph.HE",
+    month = "10",
+    year = "2024"
+}
+```
 
 ### Acknowledgments
 If you benefited from participating in our community, we ask that you please acknowledge the Nuclear Multi-Messenger Astronomy collaboration, and particular individuals who helped you, in any publications.

{nmma-0.2.0 → nmma-0.2.2}/api/Dockerfile

@@ -5,12 +5,13 @@ RUN apt update && apt install gcc -y && apt clean
 COPY api/environment.yml .
 COPY requirements.txt .
 
-RUN mamba env create -f environment.yml && conda clean -afy && \
-        find -name '__pycache__' -type d -exec rm -rf '{}' '+' && \
-        rm -rf /opt/conda/envs/nmma/lib/python3.9/site-packages/pip && \
-        rm -rf /opt/conda/envs/nmma/lib/python3.9/i{dlelib, ensurepip} && \
-        rm -rf /opt/conda/envs/nmma/lib{a,t,l,u}san.so && \
-        find -name '*.a' -delete
+RUN mamba env create -f environment.yml
+RUN conda clean -afy
+RUN find -name '__pycache__' -type d -exec rm -rf '{}' '+'
+RUN rm -rf /opt/conda/envs/nmma/lib/python3.9/site-packages/pip
+RUN rm -rf /opt/conda/envs/nmma/lib/python3.9/i{dlelib, ensurepip}
+RUN rm -rf /opt/conda/envs/nmma/lib{a,t,l,u}san.so
+RUN find -name '*.a' -delete
 
 FROM gcr.io/distroless/base-debian10
 

{nmma-0.2.0 → nmma-0.2.2}/api/environment.yml

@@ -6,6 +6,8 @@ channels:
 dependencies:
 - python=3.9.*
 - numpy
+- numcodecs
+- h5py
 - mpi4py
 
 - pip:

nmma-0.2.2/doc/.doctor-rst.yaml

@@ -0,0 +1,5 @@
+rules:
+    blank_line_after_directive: ~
+exclude_rule_for_file:
+    - path: changelog.rst
+      rule_name: blank_line_after_directive

nmma-0.2.2/doc/changelog.rst

@@ -0,0 +1,8 @@
+Changelog
+-----------
+
+
+.. changelog::
+    :github: https://github.com/nuclear-multimessenger-astronomy/nmma/releases/
+    :pypi: https://pypi.org/project/nmma/
+    :changelog-url: https://nuclear-multimessenger-astronomy.github.io/nmma/changelog.html

{nmma-0.2.0 → nmma-0.2.2}/doc/conf.py

@@ -5,7 +5,7 @@ sys.path.insert(0, os.path.abspath(".."))
 
 import nmma
 
-extensions = ["myst_parser", "sphinx_copybutton"]
+extensions = ["myst_parser", "sphinx_copybutton","sphinx_github_changelog"]
 myst_enable_extensions = [
     "amsmath",
     "colon_fence",
@@ -29,6 +29,8 @@ mathjax_config = {
     },
 }
 
+sphinx_github_changelog_token = os.getenv("SPHINX_GITHUB_CHANGELOG_TOKEN")
+
 
 templates_path = ["_templates"]
 

{nmma-0.2.0 → nmma-0.2.2}/doc/fitting.md

@@ -4,6 +4,27 @@ Given a light curve from an optical survey telescope (and potential follow-up),
 
 In many cases, the lightcurve predicted by each set of parameters is **extremely high-dimensional**, given the number of measurements made. Our goal for this example is to to determine the best-fit model parameters for an object based on its observed lightcurve.
 
+### Filters
+Often you will see that lightcurve may contain data from SDSS, for example `sdssr`, `sdssg`, `sdssr`, etc. Since the current SVD models are only trained for `sdssu` filter, it is advised that the following filter names should be changed to that of Pan-STARRS1 in the lightcurve data file.
+
+:::{table}
+:width: 50%
+:align: center
+
+|  SDSS | Pan-STARRS1 |
+|:-----:|:-----------:|
+| sdssg |    ps1__g   |
+| sdssr |    ps1__r   |
+| sdssi |    ps1__i   |
+| sdssz |    ps1__z   |
+:::
+
+And corresponding to this, the filter flag should be `--filter ps1__g,ps1__r,ps__i,ps1__z`
+
+:::{note}
+The same is applicable for LSST filters.
+:::
+
 ### Example fit to simulated data
 
 Following the quick start, we assume that an injection file has been made generated and made available. For example, there are a number of extra parameters available to modify the light curve sampling, including:

{nmma-0.2.0 → nmma-0.2.2}/doc/index.rst

@@ -208,6 +208,7 @@ requirements.txt file which are necessary for NMMA:
    If everything has gone smoothly, all of these above mentioned "pip install something" commands will show that the requirements have already been satisfied. Otherwise, these will cover the dependencies if not covered by ``pip install .``. Also, if running ``pip install .`` shows something on the lines of "cannot cythonize without cython", do:
 
 .. code::
+
    conda install -c anaconda cython==0.29.24
    pip install
 
@@ -409,6 +410,39 @@ and follow the instructions above.
    module load gcc/9.2.0
    module load openmpi/4.1.1
 
+Internetless Clusters
+^^^^^^^^^^^^^^^^^^^^^
+
+Some cluster resources may not have access to the internet or could block some forms of data transfer. This will cause some difficulties with certain packages and will require some fixes to how NMMA interacts with them and changes to how you call some commands in NMMA. This can also affect how you install NMMA on the cluster. Because the cluster is in some way restricted, it may be that the `conda install nmma -c conda-forge` or the `pip install nmma` commands don't work. Thus to install NMMA, you will need to install from the source. To begin, you will want to copy the NMMA repository from your local to the cluster using an `scp` or `rsync` commmand because likely the git commands will fail. Once NMMA is downloaded to the cluster, navigate to the main directory and run
+
+.. code::
+
+   pip install -r requirements.txt
+   pip install .
+
+and check that the installation was successful by running the first check for NMMA given above. After installation, the next most likely difference is how NMMA uses the trained kilonova models during any form of EM analysis. When running any analysis that requires the use of the trained grid of models you will need to add the `--local-only` flag to the analysis command. For example,
+
+.. code::
+
+   lightcurve-analysis \
+        --model LANLTP2 \
+        --svd-path svdmodels/ \
+        --filters ztfg,ztfi,ztfr \
+        --ztf-sampling \
+        --ztf-uncertainties \
+        --ztf-ToO 180 \
+        --local-only \
+        --interpolation-type tensorflow \
+        --outdir outdir/TP2_ztf \
+        --label TP2_ztf \
+        --prior priors/LANL2022.prior \
+        --tmin 0. \
+        --tmax 14 \
+        --dt 0.1 \
+        --error-budget 1 \
+        --nlive 1024 \
+
+
 Matplotlib fonts
 ^^^^^^^^^^^^^^^^
 
@@ -451,13 +485,17 @@ User Guide
    models
    training
    data_inj_obs
+   systematics
    fitting
+   lfi_analysis
    gw_inference
    joint_inference
    GW-EM-resampling
    combined_analysis
    Cluster_Resources
    contributing
+   changelog
+
 
 .. Indices and tables
 .. ==================

{nmma-0.2.0 → nmma-0.2.2}/doc/joint_inference.md

@@ -4,11 +4,11 @@ A joint inference on gravitational-wave and electromagnetic signals requires NMM
 
 In order to run a multi-messenger inference, we need to follow to main steps:
 
-	nmma_generation config.ini
+	nmma-generation config.ini
 
 Perform the analysis or parameter estimation using:
 
-    nmma_analysis --data-dump <name_of_analysis>_data_dump.pickle
+    nmma-analysis --data-dump <name_of_analysis>_data_dump.pickle
 
 First of all, we set up the `config.ini` file and provide all required data and information.
 
@@ -120,13 +120,13 @@ In order to prepare the joint inference, a `config.ini` file is required which s
 
 The joint inference generation can be performed by running:
     
-    nmma_gw_generation config.ini
+    nmma-generation config.ini
 
-This will generate a `GW170817-AT2017gfo-GRB170817A_data_dump.pickle` file under `outdir/data/` which need to be provided for the joint inference function `nmma_analysis`. 
+This will generate a `GW170817-AT2017gfo-GRB170817A_data_dump.pickle` file under `outdir/data/` which need to be provided for the joint inference function `nmma-analysis`. 
 
 **Running the analysis**
 
-As detailed above, running the analysis with the command `nmma_analysis --data-dump outidr/data/GW170817-AT2017gfo-GRB170817A_data_dump.pickle` requires computational resources on a larger cluster. Below we show an example script for job submission called `jointinf.pbs` on a German cluster:
+As detailed above, running the analysis with the command `nmma-analysis --data-dump outidr/data/GW170817-AT2017gfo-GRB170817A_data_dump.pickle` requires computational resources on a larger cluster. Below we show an example script for job submission called `jointinf.pbs` on a German cluster:
 
     #!/bin/bash
     #PBS -N <name of simulation>
@@ -146,6 +146,23 @@ As detailed above, running the analysis with the command `nmma_analysis --data-d
     export MPI_LAUNCH_TIMEOUT=240
     
     cd $PBS_O_WORKDIR
-    mpirun -np 512 omplace -c 0-127:st=4 nmma_analysis --data-dump <absolute path to folder>/outdir/data/GW170817-AT2017gfo-GRB170817A_data_dump.pickle --nlive 1024 --nact 10 --maxmcmc 10000 --sampling-seed 20210213 --no-plot --outdir <absolute path to outdir/result folder>
+    mpirun -np 512 omplace -c 0-127:st=4 nmma-analysis --data-dump <absolute path to folder>/outdir/data/GW170817-AT2017gfo-GRB170817A_data_dump.pickle --nlive 1024 --nact 10 --maxmcmc 10000 --sampling-seed 20210213 --no-plot --outdir <absolute path to outdir/result folder>
 
 Note that settings might differ from cluster to cluster and also the installation of NMMA might be changed (conda vs. python installation). 
+
+
+**Maximum mass constraint from a joint analysis**
+
+From a joint posterior of GW and lightcurve data from a BNS, one can derive an upper limit on the TOV mass, if one assumes that the remnant collapsed to a black hole. The idea is to determine the posterior distribution on the remnant's mass from the posterior distribution of the individual neutron star masses $m_1$, $m_2$ and the ejecta and compare this to the TOV mass of EOSs. 
+
+This can be done via the command 
+    
+    maximum-mass-constraint --outdir <path to folder> --joint-posterior <path to the file with samples from GW+EM analysis>  --prior <path to a bilby prior file> --eos-path-macro <path to macroscopic EOS> --eos-path-micro <path to microscopic EOS> [--use-M-Kepler]
+
+The last flag determines whether the remnant mass is compared against the TOV mass or the maximum mass limit for a rotating NS (Kepler limit). The latter is less conservative. The joint posterior should contain the parameters chirp mass, eta_star, log10_mdisk, log10_mej_dyn as named columns. Here, eta_star is $η* = \ln(0.25-η)$ from the symmetric mass ratio $η$. The macroscopic EOS curves must have the central pressure p0 in MeV/fm³ of each NS mass as last column. 
+
+If --use-M-Kepler is set, the prior file needs to contain two additional fiducial paramters for the quasi-universal relations: 
+
+    ratio_R = Gaussian(name = "R", mu = 1.255, sigma = 0.024)
+    delta = Uniform(name="delta", minimum = -0.0125, maximum = 0.0125)
+