nmma 0.1.3__tar.gz → 0.2.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {nmma-0.1.3 → nmma-0.2.1}/.gitattributes +2 -1
- {nmma-0.1.3 → nmma-0.2.1}/.github/workflows/build-deploy-container.yml +37 -35
- nmma-0.2.1/.github/workflows/continous_integration.yml +153 -0
- nmma-0.2.1/.github/workflows/dependency-installation.yml +85 -0
- {nmma-0.1.3 → nmma-0.2.1}/.github/workflows/deploy-github-pages.yml +4 -2
- nmma-0.2.1/.github/workflows/rst-linter.yml +22 -0
- nmma-0.2.1/CITATION.cff +54 -0
- nmma-0.2.1/Dockerfile +58 -0
- nmma-0.2.1/PKG-INFO +148 -0
- nmma-0.2.1/README.md +69 -0
- {nmma-0.1.3 → nmma-0.2.1}/api/Dockerfile +7 -6
- {nmma-0.1.3 → nmma-0.2.1}/api/environment.yml +2 -0
- nmma-0.2.1/assets/a3d3.png +0 -0
- nmma-0.2.1/assets/erc.png +0 -0
- nmma-0.2.1/assets/nsf.png +0 -0
- nmma-0.2.1/doc/.doctor-rst.yaml +5 -0
- nmma-0.2.1/doc/changelog.rst +8 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/conf.py +3 -1
- {nmma-0.1.3 → nmma-0.2.1}/doc/contributing.md +2 -1
- {nmma-0.1.3 → nmma-0.2.1}/doc/data_inj_obs.md +9 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/fitting.md +21 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/gw_inference.md +2 -2
- {nmma-0.1.3 → nmma-0.2.1}/doc/index.rst +52 -20
- {nmma-0.1.3 → nmma-0.2.1}/doc/joint_inference.md +23 -6
- nmma-0.2.1/doc/lfi_analysis.md +38 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/models.md +2 -2
- nmma-0.2.1/doc/observing-scenarios-light-curves.md +73 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/training.md +12 -1
- {nmma-0.1.3 → nmma-0.2.1}/doc_requirements.txt +2 -1
- nmma-0.2.1/example_files/lbol/ztf23bqun/23bqun_bbdata.csv +12 -0
- nmma-0.2.1/example_files/lbol/ztf23bqun/Arnett_modified.priors +4 -0
- nmma-0.2.1/example_files/lbol/ztf23bqun/lbol_test_corner.png +0 -0
- nmma-0.2.1/example_files/lbol/ztf23bqun/lbol_test_lightcurves.png +0 -0
- nmma-0.2.1/example_files/lbol/ztf23bqun/run.sh +17 -0
- nmma-0.2.1/example_files/sim_events/bns_O4_injections.dat +2001 -0
- nmma-0.2.1/ml_requirements.txt +3 -0
- nmma-0.2.1/nmma/__init__.py +1 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/analysis.py +631 -72
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/analysis_condor.py +2 -2
- nmma-0.2.1/nmma/em/analysis_lbol.py +421 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/create_injection_condor.py +1 -1
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/create_lightcurves.py +20 -11
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/create_lightcurves_condor.py +4 -2
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/create_svdmodel.py +2 -2
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/detect_lightcurves.py +28 -18
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/gwem_resampling_utils.py +7 -6
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/injection.py +57 -11
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/io.py +38 -22
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/lightcurve_marginalization.py +15 -8
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/likelihood.py +135 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/manual.py +2 -2
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/model.py +143 -159
- nmma-0.2.1/nmma/em/model_lbol.py +71 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/model_parameters.py +127 -1
- nmma-0.2.1/nmma/em/prior.py +267 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/svdmodel_benchmark.py +113 -46
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/training.py +20 -26
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/utils.py +81 -16
- nmma-0.2.1/nmma/em/utils_lbol.py +72 -0
- nmma-0.2.1/nmma/em/validate_lightcurve.py +103 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/eos/create_injection.py +7 -4
- {nmma-0.1.3 → nmma-0.2.1}/nmma/joint/conversion.py +14 -9
- {nmma-0.1.3 → nmma-0.2.1}/nmma/joint/likelihood.py +114 -40
- nmma-0.2.1/nmma/joint/maximum_mass_constraint.py +130 -0
- nmma-0.2.1/nmma/joint/maximum_mass_constraint_utils.py +192 -0
- nmma-0.2.1/nmma/mlmodel/dataprocessing.py +413 -0
- nmma-0.2.1/nmma/mlmodel/embedding.py +284 -0
- nmma-0.2.1/nmma/mlmodel/frozen-flow-weights.pth +0 -0
- nmma-0.2.1/nmma/mlmodel/inference.py +55 -0
- nmma-0.2.1/nmma/mlmodel/normalizingflows.py +132 -0
- nmma-0.2.1/nmma/mlmodel/resnet.py +468 -0
- nmma-0.2.1/nmma/mlmodel/similarity_embedding_weights.pth +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/pbilby/analysis/likelihood.py +16 -25
- {nmma-0.1.3 → nmma-0.2.1}/nmma/pbilby/generation.py +24 -25
- {nmma-0.1.3 → nmma-0.2.1}/nmma/pbilby/parser/shared.py +17 -8
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/analysis.py +32 -11
- nmma-0.2.1/nmma/tests/analysis_lbol.py +55 -0
- nmma-0.2.1/nmma/tests/data/Bu2019nsbh/ztfr.joblib +0 -0
- nmma-0.2.1/nmma/tests/data/Bu2019nsbh.joblib +0 -0
- nmma-0.2.1/nmma/tests/data/Bu2019nsbh_tf/ztfr.h5 +0 -0
- nmma-0.2.1/nmma/tests/data/GW+KN+GRB_posterior +7508 -0
- nmma-0.2.1/nmma/tests/data/Ka2017_injection.json +28 -0
- nmma-0.2.1/nmma/tests/data/ZTF23aaxeacr_partial.csv +6 -0
- nmma-0.2.1/nmma/tests/data/eos_macro/1.dat +85 -0
- nmma-0.2.1/nmma/tests/data/eos_macro/10.dat +80 -0
- nmma-0.2.1/nmma/tests/data/eos_macro/2.dat +80 -0
- nmma-0.2.1/nmma/tests/data/eos_macro/3.dat +83 -0
- nmma-0.2.1/nmma/tests/data/eos_macro/4.dat +86 -0
- nmma-0.2.1/nmma/tests/data/eos_macro/5.dat +88 -0
- nmma-0.2.1/nmma/tests/data/eos_macro/6.dat +82 -0
- nmma-0.2.1/nmma/tests/data/eos_macro/7.dat +86 -0
- nmma-0.2.1/nmma/tests/data/eos_macro/8.dat +77 -0
- nmma-0.2.1/nmma/tests/data/eos_macro/9.dat +82 -0
- nmma-0.2.1/nmma/tests/data/eos_micro/1.dat +225 -0
- nmma-0.2.1/nmma/tests/data/eos_micro/10.dat +225 -0
- nmma-0.2.1/nmma/tests/data/eos_micro/2.dat +225 -0
- nmma-0.2.1/nmma/tests/data/eos_micro/3.dat +225 -0
- nmma-0.2.1/nmma/tests/data/eos_micro/4.dat +225 -0
- nmma-0.2.1/nmma/tests/data/eos_micro/5.dat +225 -0
- nmma-0.2.1/nmma/tests/data/eos_micro/6.dat +225 -0
- nmma-0.2.1/nmma/tests/data/eos_micro/7.dat +225 -0
- nmma-0.2.1/nmma/tests/data/eos_micro/8.dat +225 -0
- nmma-0.2.1/nmma/tests/data/eos_micro/9.dat +225 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/injections.py +29 -0
- nmma-0.2.1/nmma/tests/maximum_mass.py +31 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/models.py +2 -13
- nmma-0.2.1/nmma/tests/tools.py +50 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/training.py +17 -1
- {nmma-0.1.3 → nmma-0.2.1}/nmma/utils/gitlab.py +33 -16
- {nmma-0.1.3 → nmma-0.2.1}/nmma/utils/models.py +40 -22
- {nmma-0.1.3 → nmma-0.2.1}/nmma/utils/models_tools.py +4 -6
- nmma-0.2.1/nmma.egg-info/PKG-INFO +148 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma.egg-info/SOURCES.txt +69 -1
- {nmma-0.1.3 → nmma-0.2.1}/nmma.egg-info/entry_points.txt +6 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma.egg-info/requires.txt +19 -5
- nmma-0.2.1/nmma.egg-info/top_level.txt +2 -0
- nmma-0.2.1/priors/Bu2023Ye.prior +9 -0
- nmma-0.2.1/priors/Piro2021.prior +5 -0
- nmma-0.2.1/priors/maximum_mass_resampling.prior +4 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/sncosmo-generic.prior +1 -1
- {nmma-0.1.3 → nmma-0.2.1}/pyproject.toml +25 -16
- {nmma-0.1.3 → nmma-0.2.1}/requirements.txt +3 -4
- nmma-0.2.1/sampler_requirements.txt +1 -0
- nmma-0.2.1/sklearn_requirements.txt +1 -0
- nmma-0.2.1/slurm.sub +19 -0
- nmma-0.2.1/tf_requirements.txt +1 -0
- nmma-0.2.1/tools/__init__.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/tools/analysis_slurm.py +1 -1
- nmma-0.2.1/tools/convert_skyportal_lcs.py +57 -0
- {nmma-0.1.3 → nmma-0.2.1}/tools/corner_plot.py +122 -73
- {nmma-0.1.3 → nmma-0.2.1}/tools/make_lcs.py +9 -3
- {nmma-0.1.3 → nmma-0.2.1}/tools/make_lcs_LANL.py +8 -2
- {nmma-0.1.3 → nmma-0.2.1}/tools/make_lcs_hdf5.py +8 -2
- {nmma-0.1.3 → nmma-0.2.1}/tools/make_lcs_kasen.py +8 -2
- nmma-0.2.1/tools/plot_svdmodel_benchmarks.py +91 -0
- {nmma-0.1.3 → nmma-0.2.1}/tools/resample_grid.py +8 -2
- nmma-0.2.1/tools/tf_training_calls.sh +52 -0
- nmma-0.1.3/.github/workflows/continous_integration.yml +0 -131
- nmma-0.1.3/PKG-INFO +0 -98
- nmma-0.1.3/README.md +0 -34
- nmma-0.1.3/nmma/__init__.py +0 -1
- nmma-0.1.3/nmma/em/prior.py +0 -121
- nmma-0.1.3/nmma/tests/tools.py +0 -24
- nmma-0.1.3/nmma/utils/zenodo.py +0 -249
- nmma-0.1.3/nmma.egg-info/PKG-INFO +0 -98
- nmma-0.1.3/nmma.egg-info/top_level.txt +0 -1
- nmma-0.1.3/priors/Piro2021.prior +0 -5
- {nmma-0.1.3 → nmma-0.2.1}/.flake8 +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/.github/ISSUE_TEMPLATE/bug_report.md +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/.github/ISSUE_TEMPLATE/feature_request.md +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/.github/workflows/delete-branch-cache.yml +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/.github/workflows/publish-to-anaconda.yml +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/.github/workflows/publish-to-pypi.yml +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/.gitignore +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/.pep8speaks.yml +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/.pre-commit-config.yaml +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/LICENSE +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/MANIFEST.in +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/api/app.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/api/log.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/Cluster_Resources.md +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/GW-EM-resampling.md +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/Makefile +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/_static/.nmma-docs.css.un~ +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/_static/favicon-light.png +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/_static/light-logo.svg +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/_static/nmma-docs.css +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/_static/nmma-docs.css~ +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/combined_analysis.md +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/gwemopt_light_curves_detection.md +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/images/Corner_narrow_Bulla.png +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/images/ZTF21abjvfbc_corner.png +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/images/ZTF21abjvfbc_lightcurves.png +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/images/ZTF_corner.png +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/images/ZTF_lightcurves.png +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/images/corner_samples.png +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/images/dark-logo.svg +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/images/injection_corner.png +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/images/injection_lightcurves.png +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/images/light-logo.svg +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/images/training_lightcurves.png +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/doc/quick-start-guide.rst +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/docker-compose.yml +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/NICER/J0030_3spot_RM.txt +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/NICER/NICER+XMM_J0740_RM.txt +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/NICER/NICER_x_XMM_J0740_XPSI_STU_NSX_FIH_radius_mass.txt +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF20abwysqy.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abdequz.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abdhqle.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abdpqpq.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abinaiu.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abisoui.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abitmou.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abivhns.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abjpkvy.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abjrhzz.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abjrmes.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abjtdua.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF21abjvfbc.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/candidate_data/ZTF23aaxeacr.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/eos/ALF2.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/lightcurves/AT2017gfo.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/lightcurves/AT2017gfo_GRB170817A_reduced.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/lightcurves/AT2017gfo_reduced.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/lightcurves/GRB211211A.txt +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/prior/GW170817_AT2017gfo.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/prior/GW170817_AT2017gfo_GRB170817A.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/prior/ZTF_Bu2019lm.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/sim_events/injections.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/tools/gwem_resampling/GRB211211A_NSBH_posterior_samples.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/tools/gwem_resampling/GRB211211A_posterior_samples.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/tools/gwem_resampling/GWsamples.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/tools/gwem_resampling/GWsamples_NSBH.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/tools/gwem_resampling/gwsamples_generation.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/tools/gwem_resampling/posterior_probability.txt +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/yaml/doc_example.yaml +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/example_files/zenodo/gw_posteriors.txt +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/grb_requirements.txt +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/__pycache__/__init__.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/__init__.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/__pycache__/__init__.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/__pycache__/likelihood.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/__pycache__/model.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/__pycache__/utils.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/combine_EOS.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/create_injection_slurm.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/create_lightcurves_slurm.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/ZTF_revisit_kde_i.joblib +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/ZTF_revisit_kde_public.joblib +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/ZTF_sampling_public.pkl +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/ZTF_uncer_params.pkl +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/__init__.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/__pycache__/__init__.cpython-38.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/lims_ToO_180_g.joblib +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/lims_ToO_180_r.joblib +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/lims_ToO_300_g.joblib +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/lims_ToO_300_r.joblib +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/lims_i.joblib +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/lims_public_g.joblib +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/lims_public_r.joblib +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/sampling_ToO_180.pkl +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/data/sampling_ToO_300.pkl +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/gwem_Hubble_estimate.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/gwem_resampling.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/gwem_resampling_condor.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/gwsamples_creation.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/em/injection_summary.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/eos/__init__.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/eos/__pycache__/__init__.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/eos/__pycache__/eos.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/eos/__pycache__/tov.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/eos/__pycache__/utils.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/eos/eos.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/eos/tov.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/eos/utils.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/gw/likelihood.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/joint/__init__.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/joint/__pycache__/__init__.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/joint/__pycache__/constraints.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/joint/__pycache__/conversion.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/joint/__pycache__/likelihood.cpython-37.pyc +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/joint/constraints.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/pbilby/analysis/__init__.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/pbilby/analysis/analysis_run.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/pbilby/analysis/main.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/pbilby/parser/__init__.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/pbilby/parser/analysis.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/pbilby/parser/generation.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/__init__.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/Bu2019lm_injection.json +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/Me2017_injection.json +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/TrPi2018_pinned_parameters.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.001_mejwind0.010_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.001_mejwind0.030_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.001_mejwind0.050_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.001_mejwind0.070_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.001_mejwind0.090_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.001_mejwind0.110_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.001_mejwind0.130_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.005_mejwind0.010_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.005_mejwind0.030_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.005_mejwind0.050_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.005_mejwind0.070_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.005_mejwind0.090_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.005_mejwind0.110_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.005_mejwind0.130_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.010_mejwind0.010_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.010_mejwind0.030_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.010_mejwind0.050_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.010_mejwind0.070_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.010_mejwind0.090_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.010_mejwind0.110_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.010_mejwind0.130_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.020_mejwind0.010_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.020_mejwind0.030_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.020_mejwind0.050_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.020_mejwind0.070_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.020_mejwind0.090_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.020_mejwind0.110_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/bulla/nsns_nph1.0e+06_mejdyn0.020_mejwind0.130_phi45_45.6.dat +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/tests/data/lowmass_collapsar_updated.h5 +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma/utils/__init__.py +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/nmma.egg-info/dependency_links.txt +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/AnBa2022.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/AnBa2022_sparse.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/Bu2019lm.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/Bu2019lm_TrPi2018GRB211211A.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/Bu2019nsbh.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/Bu2019nsbh_TrPi2018_GRB211211A.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/Bu2022Ye.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/GWBNS.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/GWNSBH.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/Ka2017.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/LANL2022.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/Me2017.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/Sr2023.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/TrPi2018.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/TrPi2018_onaxis.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/ZTF_lgrb.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/ZTF_sgrb.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/injec_alspin.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/salt2.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/priors/sncosmo-generic_TrPi2018.prior +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/production_requirements.txt +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/setup.cfg +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/tutorials/README.md +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/tutorials/tutorial-KN-models-training.ipynb +0 -0
- {nmma-0.1.3 → nmma-0.2.1}/tutorials/tutorial-lightcurve_simulation.ipynb +0 -0
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${{ runner.os }}-pip-2-
|
|
61
|
+
save-always: true
|
|
62
|
+
|
|
63
|
+
- name: Update Homebrew
|
|
64
|
+
if: matrix.os == 'macos-latest'
|
|
65
|
+
run: |
|
|
66
|
+
brew update --preinstall
|
|
67
|
+
|
|
68
|
+
- name: Configure Homebrew cache
|
|
69
|
+
if: matrix.os == 'macos-latest'
|
|
70
|
+
uses: actions/cache@v4
|
|
71
|
+
with:
|
|
72
|
+
path: |
|
|
73
|
+
~/Library/Caches/Homebrew/openmpi--*
|
|
74
|
+
~/Library/Caches/Homebrew/downloads/*--openmpi-*
|
|
75
|
+
~/Library/Caches/Homebrew/hdf5--*
|
|
76
|
+
~/Library/Caches/Homebrew/downloads/*--hdf5-*
|
|
77
|
+
~/Library/Caches/Homebrew/gcc--*
|
|
78
|
+
~/Library/Caches/Homebrew/downloads/*--gcc-*
|
|
79
|
+
~/Library/Caches/Homebrew/openblas--*
|
|
80
|
+
~/Library/Caches/Homebrew/downloads/*--openblas-*
|
|
81
|
+
~/Library/Caches/Homebrew/lapack--*
|
|
82
|
+
~/Library/Caches/Homebrew/downloads/*--lapack-*
|
|
83
|
+
~/Library/Caches/Homebrew/basictex--*
|
|
84
|
+
~/Library/Caches/Homebrew/downloads/*--basictex-*
|
|
85
|
+
~/Library/Caches/Homebrew/cmake--*
|
|
86
|
+
~/Library/Caches/Homebrew/downloads/*--cmake-*
|
|
87
|
+
|
|
88
|
+
key: brew-${{ hashFiles('**/pyproject.toml') }}
|
|
89
|
+
restore-keys: brew-
|
|
90
|
+
save-always: true
|
|
91
|
+
|
|
92
|
+
- name: Install Homebrew dependencies
|
|
93
|
+
if: matrix.os == 'macos-latest'
|
|
94
|
+
run: |
|
|
95
|
+
env HOMEBREW_NO_AUTO_UPDATE=1 brew install openmpi hdf5 gcc openblas lapack basictex cmake
|
|
96
|
+
eval "$(/usr/libexec/path_helper)"
|
|
97
|
+
sudo tlmgr update --self
|
|
98
|
+
sudo tlmgr install collection-latex
|
|
99
|
+
sudo tlmgr install collection-fontsrecommended
|
|
100
|
+
sudo tlmgr install dvipng
|
|
101
|
+
sudo tlmgr install cm-super
|
|
102
|
+
sudo tlmgr install type1cm
|
|
103
|
+
- name: Install Linux Dependencies
|
|
104
|
+
if: matrix.os == 'ubuntu-latest'
|
|
105
|
+
uses: awalsh128/cache-apt-pkgs-action@latest
|
|
106
|
+
with:
|
|
107
|
+
packages: openmpi-bin libopenmpi-dev gfortran build-essential libblas3 libblas-dev liblapack3 liblapack-dev libatlas-base-dev texlive texlive-latex-extra texlive-fonts-recommended dvipng cm-super
|
|
108
|
+
execute_install_scripts: true
|
|
109
|
+
|
|
110
|
+
- name: Install dependencies (macOS)
|
|
111
|
+
if: matrix.os == 'macos-latest'
|
|
112
|
+
run: |
|
|
113
|
+
conda install -c conda-forge pyfftw c-compiler ligo-segments python-ligo-lw
|
|
114
|
+
echo "FC=$(which gfortran-11)" >> $GITHUB_ENV
|
|
115
|
+
echo "CC=$(which gcc)" >> $GITHUB_ENV
|
|
116
|
+
echo "CXX=$(which g++)" >> $GITHUB_ENV
|
|
117
|
+
|
|
118
|
+
- name: Install dependencies (Ubuntu)
|
|
119
|
+
if: matrix.os == 'ubuntu-latest'
|
|
120
|
+
run: |
|
|
121
|
+
sudo apt-get update
|
|
122
|
+
sudo apt-get install -y texlive texlive-latex-extra texlive-fonts-recommended dvipng cm-super
|
|
123
|
+
- name: Install Python dependencies
|
|
124
|
+
run: |
|
|
125
|
+
python -m pip install --upgrade git+https://github.com/bitranox/wrapt_timeout_decorator.git
|
|
126
|
+
python -m pip install pytest pytest-cov flake8 pytest-aiohttp sqlparse freezegun PyJWT joblib coveralls
|
|
127
|
+
python -m pip install -r ml_requirements.txt -r grb_requirements.txt -r tf_requirements.txt -r sklearn_requirements.txt
|
|
128
|
+
python -m pip install .
|
|
129
|
+
git clone https://github.com/JohannesBuchner/MultiNest && cd MultiNest/build && rm -rf * && cmake .. && make && cd ../..
|
|
130
|
+
pwd
|
|
131
|
+
|
|
132
|
+
- name: Export Libraries
|
|
133
|
+
run: |
|
|
134
|
+
echo "LD_LIBRARY_PATH=$HOME/work/nmma/nmma/MultiNest/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
|
|
135
|
+
echo "DYLD_LIBRARY_PATH=$HOME/work/nmma/nmma/MultiNest/lib:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
|
|
136
|
+
|
|
137
|
+
- name: Lint with flake8
|
|
138
|
+
run: |
|
|
139
|
+
# stop the build if there are Python syntax errors or undefined names
|
|
140
|
+
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude docs
|
|
141
|
+
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
|
|
142
|
+
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude docs,versioneer.py,nmma/_version.py,nmma/tests,nmma/*/__init__.py
|
|
143
|
+
|
|
144
|
+
- name: Test with pytest
|
|
145
|
+
run: |
|
|
146
|
+
python -m coverage run --source nmma -m pytest nmma/tests/*.py
|
|
147
|
+
|
|
148
|
+
- name: Run Coveralls
|
|
149
|
+
if: ${{ success() }}
|
|
150
|
+
run: |
|
|
151
|
+
coveralls --service=github
|
|
152
|
+
env:
|
|
153
|
+
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
|
|
@@ -0,0 +1,85 @@
|
|
|
1
|
+
name: Check NMMA dependencies installation
|
|
2
|
+
on:
|
|
3
|
+
push:
|
|
4
|
+
branches: [main]
|
|
5
|
+
paths: ["*_requirements.txt", "pyproject.toml"]
|
|
6
|
+
pull_request:
|
|
7
|
+
branches: [main]
|
|
8
|
+
paths: ["*_requirements.txt", "pyproject.toml"]
|
|
9
|
+
workflow_dispatch:
|
|
10
|
+
|
|
11
|
+
jobs:
|
|
12
|
+
build:
|
|
13
|
+
runs-on: ${{ matrix.os }}
|
|
14
|
+
defaults:
|
|
15
|
+
run:
|
|
16
|
+
shell: bash -el {0}
|
|
17
|
+
strategy:
|
|
18
|
+
fail-fast: false
|
|
19
|
+
matrix:
|
|
20
|
+
os: ["ubuntu-latest", "macos-latest"]
|
|
21
|
+
python-version: ["3.9", "3.10", "3.11", "3.12"]
|
|
22
|
+
|
|
23
|
+
steps:
|
|
24
|
+
- name: Checkout branch being tested
|
|
25
|
+
uses: actions/checkout@v4
|
|
26
|
+
|
|
27
|
+
- name: Set up Python with Conda ${{ matrix.python-version }}
|
|
28
|
+
uses: conda-incubator/setup-miniconda@v3
|
|
29
|
+
with:
|
|
30
|
+
python-version: ${{ matrix.python-version }}
|
|
31
|
+
architecture: ${{ matrix.os == 'macos-latest' && 'arm64' || 'x86_64' }}
|
|
32
|
+
miniforge-version: latest
|
|
33
|
+
use-mamba: true
|
|
34
|
+
mamba-version: "*"
|
|
35
|
+
activate-environment: nmma_env
|
|
36
|
+
|
|
37
|
+
- name: Install linux packages
|
|
38
|
+
if: matrix.os == 'ubuntu-latest'
|
|
39
|
+
run: |
|
|
40
|
+
sudo apt-get update
|
|
41
|
+
sudo apt-get install -y openmpi-bin libopenmpi-dev
|
|
42
|
+
|
|
43
|
+
- name: Install Homebrew packages
|
|
44
|
+
if: matrix.os == 'macos-latest'
|
|
45
|
+
run: |
|
|
46
|
+
brew install openmpi hdf5
|
|
47
|
+
conda install ligo-segments python-ligo-lw
|
|
48
|
+
|
|
49
|
+
- name: Install NMMA (base)
|
|
50
|
+
run: |
|
|
51
|
+
python -m pip install 'nmma @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
|
|
52
|
+
|
|
53
|
+
- name: Verify base NMMA installation
|
|
54
|
+
run: |
|
|
55
|
+
python -c "import nmma; print(f'NMMA version: {nmma.__version__}')"
|
|
56
|
+
|
|
57
|
+
- name: Install and verify NMMA [grb]
|
|
58
|
+
run: |
|
|
59
|
+
python -m pip install 'nmma[grb] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
|
|
60
|
+
python -c "import nmma, afterglowpy; print(f'Successfully imported {nmma.__name__}, {afterglowpy.__name__}')"
|
|
61
|
+
|
|
62
|
+
- name: Install and verify NMMA [production]
|
|
63
|
+
run: |
|
|
64
|
+
python -m pip install 'nmma[production] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
|
|
65
|
+
python -c "import nmma, parallel_bilby, nestcheck, mpi4py; print(f'Successfully imported {nmma.__name__}, {parallel_bilby.__name__}, {nestcheck.__name__}, {mpi4py.__name__}')"
|
|
66
|
+
|
|
67
|
+
- name: Install and verify NMMA [neuralnet]
|
|
68
|
+
run: |
|
|
69
|
+
python -m pip install 'nmma[neuralnet] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
|
|
70
|
+
python -c "import nmma, torch, nflows, torchvision; print(f'Successfully imported {nmma.__name__}, {torch.__name__}, {nflows.__name__}, {torchvision.__name__}')"
|
|
71
|
+
|
|
72
|
+
- name: Install and verify NMMA [tf]
|
|
73
|
+
run: |
|
|
74
|
+
python -m pip install 'nmma[tf] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
|
|
75
|
+
python -c "import nmma, tensorflow; print(f'Successfully imported {nmma.__name__}, {tensorflow.__name__}')"
|
|
76
|
+
|
|
77
|
+
- name: Install and verify NMMA [sklearn]
|
|
78
|
+
run: |
|
|
79
|
+
python -m pip install 'nmma[sklearn] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
|
|
80
|
+
python -c "import nmma, sklearn; print(f'Successfully imported {nmma.__name__}, {sklearn.__name__}')"
|
|
81
|
+
|
|
82
|
+
- name: Install and verify NMMA [sampler]
|
|
83
|
+
run: |
|
|
84
|
+
python -m pip install 'nmma[sampler] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
|
|
85
|
+
python -c "import nmma, ultranest; print(f'Successfully imported {nmma.__name__}, {ultranest.__name__}')"
|
|
@@ -6,7 +6,6 @@ on:
|
|
|
6
6
|
|
|
7
7
|
jobs:
|
|
8
8
|
build:
|
|
9
|
-
|
|
10
9
|
runs-on: ubuntu-latest
|
|
11
10
|
strategy:
|
|
12
11
|
fail-fast: false
|
|
@@ -40,15 +39,18 @@ jobs:
|
|
|
40
39
|
python -m pip install .[doc]
|
|
41
40
|
|
|
42
41
|
- name: Make dependencies
|
|
42
|
+
env:
|
|
43
|
+
SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.SPHINX_GITHUB_CHANGELOG_TOKEN }}
|
|
43
44
|
run: |
|
|
44
45
|
cd doc && make html; cd ../
|
|
45
46
|
touch doc/_build/html/.nojekyll
|
|
46
47
|
|
|
47
48
|
- name: Deploy to GitHub Pages
|
|
48
|
-
if: success()
|
|
49
|
+
if: success() && github.repository_owner == 'nuclear-multimessenger-astronomy'
|
|
49
50
|
uses: crazy-max/ghaction-github-pages@v2
|
|
50
51
|
with:
|
|
51
52
|
target_branch: gh-pages
|
|
52
53
|
build_dir: doc/_build/html/
|
|
53
54
|
env:
|
|
54
55
|
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
|
|
56
|
+
SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.SPHINX_GITHUB_CHANGELOG_TOKEN }}
|
|
@@ -0,0 +1,22 @@
|
|
|
1
|
+
name: Lint rst
|
|
2
|
+
|
|
3
|
+
on:
|
|
4
|
+
push:
|
|
5
|
+
paths: ['**/**.rst']
|
|
6
|
+
pull_request:
|
|
7
|
+
paths: ['**/**.rst']
|
|
8
|
+
|
|
9
|
+
jobs:
|
|
10
|
+
doctor-rst:
|
|
11
|
+
name: DOCtor-RST
|
|
12
|
+
runs-on: ubuntu-latest
|
|
13
|
+
steps:
|
|
14
|
+
- name: "Checkout code"
|
|
15
|
+
uses: actions/checkout@v4
|
|
16
|
+
|
|
17
|
+
- name: DOCtor-RST
|
|
18
|
+
uses: docker://oskarstark/doctor-rst
|
|
19
|
+
with:
|
|
20
|
+
args: --short --error-format=github
|
|
21
|
+
env:
|
|
22
|
+
DOCS_DIR: 'doc/'
|
nmma-0.2.1/CITATION.cff
ADDED
|
@@ -0,0 +1,54 @@
|
|
|
1
|
+
cff-version: 1.2.0
|
|
2
|
+
title: "NMMA"
|
|
3
|
+
abstract: "An updated nuclear-physics and multi-messenger astrophysics framework for binary neutron star mergers"
|
|
4
|
+
message: "If you use this code, please cite this repository along with the paper"
|
|
5
|
+
repository-code: "https://github.com/nuclear-multimessenger-astronomy/nmma"
|
|
6
|
+
url: "https://gitlab.com/Theodlz/nmma-models"
|
|
7
|
+
license: "GPL-3.0"
|
|
8
|
+
authors:
|
|
9
|
+
- given-names: "Peter"
|
|
10
|
+
name-particle: "T. H."
|
|
11
|
+
family-names: "Pang"
|
|
12
|
+
- given-names: "Tim"
|
|
13
|
+
family-names: "Dietrich"
|
|
14
|
+
- given-names: "Michael"
|
|
15
|
+
family-names: "Coughlin"
|
|
16
|
+
name-particle: "W."
|
|
17
|
+
- given-names: "Mattia"
|
|
18
|
+
family-names: "Bulla"
|
|
19
|
+
- given-names: "Ingo"
|
|
20
|
+
family-names: "Tews"
|
|
21
|
+
- given-names: "Mouza"
|
|
22
|
+
family-names: "Almualla"
|
|
23
|
+
- given-names: "Tyler"
|
|
24
|
+
family-names: "Barna"
|
|
25
|
+
- given-names: "Weizmann"
|
|
26
|
+
family-names: "Kiendrebeogo"
|
|
27
|
+
- given-names: "Nina"
|
|
28
|
+
family-names: "Kunert"
|
|
29
|
+
- given-names: "Gargi"
|
|
30
|
+
family-names: "Mansingh"
|
|
31
|
+
- given-names: "Brandon"
|
|
32
|
+
family-names: "Reed"
|
|
33
|
+
- given-names: "Niharika"
|
|
34
|
+
family-names: "Sravan"
|
|
35
|
+
- given-names: "Andrew"
|
|
36
|
+
family-names: "Toivonen"
|
|
37
|
+
- given-names: "Sarah"
|
|
38
|
+
family-names: "Antier"
|
|
39
|
+
- given-names: "Robert"
|
|
40
|
+
family-names: "VandenBerg"
|
|
41
|
+
name-particle: "O."
|
|
42
|
+
- given-names: "Jack"
|
|
43
|
+
family-names: "Heinzel"
|
|
44
|
+
- given-names: "Vsevolod"
|
|
45
|
+
family-names: "Nedora"
|
|
46
|
+
- given-names: "Pouyan"
|
|
47
|
+
family-names: "Salehi"
|
|
48
|
+
- given-names: "Ritwik"
|
|
49
|
+
family-names: "Sharma"
|
|
50
|
+
- given-names: "Rahul"
|
|
51
|
+
family-names: "Somasundaram"
|
|
52
|
+
- given-names: "Chris"
|
|
53
|
+
name-particle: "Van Den"
|
|
54
|
+
family-names: "Broeck"
|
nmma-0.2.1/Dockerfile
ADDED
|
@@ -0,0 +1,58 @@
|
|
|
1
|
+
# Use official Ubuntu 22.04 image as base
|
|
2
|
+
FROM ubuntu:22.04
|
|
3
|
+
|
|
4
|
+
# Update the repository for package indexes
|
|
5
|
+
RUN apt-get update
|
|
6
|
+
|
|
7
|
+
# Install dependencies
|
|
8
|
+
RUN apt-get install -y \
|
|
9
|
+
python3 \
|
|
10
|
+
git \
|
|
11
|
+
python3-pip \
|
|
12
|
+
&& apt-get clean \
|
|
13
|
+
&& rm -rf /var/lib/apt/lists/*
|
|
14
|
+
|
|
15
|
+
# Set work directory
|
|
16
|
+
WORKDIR /work
|
|
17
|
+
|
|
18
|
+
# Clone the Git repository
|
|
19
|
+
RUN git clone https://github.com/nuclear-multimessenger-astronomy/nmma/
|
|
20
|
+
|
|
21
|
+
# Set the working directory to the cloned repository
|
|
22
|
+
WORKDIR /work/nmma
|
|
23
|
+
|
|
24
|
+
RUN apt-get update
|
|
25
|
+
RUN apt-get install -y libopenmpi-dev openmpi-bin openmpi-doc
|
|
26
|
+
RUN apt install -y python3-mpi4py
|
|
27
|
+
#install dependencies
|
|
28
|
+
RUN pip3 install numpy
|
|
29
|
+
RUN pip3 install -r /work/nmma/doc_requirements.txt -r /work/nmma/grb_requirements.txt -r /work/nmma/production_requirements.txt -r /work/nmma/requirements.txt
|
|
30
|
+
|
|
31
|
+
# Clone and build Multinest
|
|
32
|
+
RUN git clone https://github.com/JohannesBuchner/MultiNest
|
|
33
|
+
|
|
34
|
+
WORKDIR /work/nmma/MultiNest
|
|
35
|
+
|
|
36
|
+
RUN apt-get install -y \
|
|
37
|
+
cmake \
|
|
38
|
+
liblapacke-dev \
|
|
39
|
+
liblapack-dev \
|
|
40
|
+
libblas-dev
|
|
41
|
+
|
|
42
|
+
RUN cd build && cmake .. && make
|
|
43
|
+
|
|
44
|
+
# Set environment variable
|
|
45
|
+
ENV LD_LIBRARY_PATH=/work/nmma/MultiNest/lib:$LD_LIBRARY_PATH
|
|
46
|
+
|
|
47
|
+
# Clone and install PyMultiNest
|
|
48
|
+
RUN git clone https://github.com/JohannesBuchner/PyMultiNest/ /work/nmma/PyMultiNest
|
|
49
|
+
WORKDIR /work/nmma/PyMultiNest
|
|
50
|
+
RUN python3 setup.py install --user
|
|
51
|
+
|
|
52
|
+
# Add the executable path to the enviromental variable PATH
|
|
53
|
+
ENV PATH=$PATH:$HOME/.local/bin/
|
|
54
|
+
|
|
55
|
+
RUN pip3 install nmma
|
|
56
|
+
RUN pip3 install --upgrade Flask Jinja2
|
|
57
|
+
|
|
58
|
+
CMD ["bash"]
|
nmma-0.2.1/PKG-INFO
ADDED
|
@@ -0,0 +1,148 @@
|
|
|
1
|
+
Metadata-Version: 2.1
|
|
2
|
+
Name: nmma
|
|
3
|
+
Version: 0.2.1
|
|
4
|
+
Summary: A nuclear physics multi-messenger Bayesian inference library
|
|
5
|
+
Author-email: "Peter Tsun Ho Pang, Michael Coughlin, Tim Dietrich, Ingo Tews" <nuclear_multimessenger_astronomy@googlegroups.com>
|
|
6
|
+
License: GPLv3
|
|
7
|
+
Project-URL: Homepage, https://github.com/nuclear-multimessenger-astronomy/nmma
|
|
8
|
+
Project-URL: Documentation, https://nuclear-multimessenger-astronomy.github.io/nmma/
|
|
9
|
+
Project-URL: Download, https://pypi.org/project/nmma/#files
|
|
10
|
+
Project-URL: Tracker, https://github.com/nuclear-multimessenger-astronomy/nmma/issues
|
|
11
|
+
Classifier: Programming Language :: Python :: 3
|
|
12
|
+
Classifier: Programming Language :: Python :: 3.9
|
|
13
|
+
Classifier: Programming Language :: Python :: 3.10
|
|
14
|
+
Classifier: Programming Language :: Python :: 3.11
|
|
15
|
+
Classifier: Programming Language :: Python :: 3.12
|
|
16
|
+
Classifier: Intended Audience :: Science/Research
|
|
17
|
+
Classifier: Intended Audience :: End Users/Desktop
|
|
18
|
+
Classifier: Intended Audience :: Developers
|
|
19
|
+
Classifier: Natural Language :: English
|
|
20
|
+
Classifier: Topic :: Scientific/Engineering
|
|
21
|
+
Classifier: Topic :: Scientific/Engineering :: Astronomy
|
|
22
|
+
Classifier: Topic :: Scientific/Engineering :: Physics
|
|
23
|
+
Classifier: Operating System :: POSIX
|
|
24
|
+
Classifier: Operating System :: Unix
|
|
25
|
+
Classifier: Operating System :: MacOS
|
|
26
|
+
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
|
|
27
|
+
Requires-Python: <3.13,>=3.9
|
|
28
|
+
Description-Content-Type: text/markdown
|
|
29
|
+
License-File: LICENSE
|
|
30
|
+
Requires-Dist: future
|
|
31
|
+
Requires-Dist: bilby>=2.1.1
|
|
32
|
+
Requires-Dist: bilby_pipe>=1.1.0
|
|
33
|
+
Requires-Dist: colorcet
|
|
34
|
+
Requires-Dist: numpy>=1.9
|
|
35
|
+
Requires-Dist: matplotlib<3.8,>=2.0
|
|
36
|
+
Requires-Dist: scipy>=1.10
|
|
37
|
+
Requires-Dist: pandas<2.0,>=1.3.4
|
|
38
|
+
Requires-Dist: astropy>=4.3.1
|
|
39
|
+
Requires-Dist: pymultinest
|
|
40
|
+
Requires-Dist: sncosmo
|
|
41
|
+
Requires-Dist: dust_extinction
|
|
42
|
+
Requires-Dist: arviz
|
|
43
|
+
Requires-Dist: p_tqdm
|
|
44
|
+
Requires-Dist: tornado
|
|
45
|
+
Requires-Dist: notebook
|
|
46
|
+
Requires-Dist: ligo.skymap
|
|
47
|
+
Requires-Dist: healpy
|
|
48
|
+
Provides-Extra: doc
|
|
49
|
+
Requires-Dist: sphinx>=5.0; extra == "doc"
|
|
50
|
+
Requires-Dist: sphinx_math_dollar; extra == "doc"
|
|
51
|
+
Requires-Dist: recommonmark; extra == "doc"
|
|
52
|
+
Requires-Dist: numpydoc; extra == "doc"
|
|
53
|
+
Requires-Dist: sphinx-rtd-theme; extra == "doc"
|
|
54
|
+
Requires-Dist: notedown; extra == "doc"
|
|
55
|
+
Requires-Dist: jsx-lexer; extra == "doc"
|
|
56
|
+
Requires-Dist: linkify-it-py; extra == "doc"
|
|
57
|
+
Requires-Dist: linkify; extra == "doc"
|
|
58
|
+
Requires-Dist: myst-parser; extra == "doc"
|
|
59
|
+
Requires-Dist: sphinx-book-theme; extra == "doc"
|
|
60
|
+
Requires-Dist: sphinx_copybutton; extra == "doc"
|
|
61
|
+
Requires-Dist: sphinx-github-changelog; extra == "doc"
|
|
62
|
+
Provides-Extra: grb
|
|
63
|
+
Requires-Dist: afterglowpy>=0.7.3; extra == "grb"
|
|
64
|
+
Requires-Dist: wrapt_timeout_decorator; extra == "grb"
|
|
65
|
+
Provides-Extra: production
|
|
66
|
+
Requires-Dist: parallel_bilby>=2.0.2; extra == "production"
|
|
67
|
+
Requires-Dist: nestcheck; extra == "production"
|
|
68
|
+
Requires-Dist: mpi4py; extra == "production"
|
|
69
|
+
Provides-Extra: neuralnet
|
|
70
|
+
Requires-Dist: torch; extra == "neuralnet"
|
|
71
|
+
Requires-Dist: nflows; extra == "neuralnet"
|
|
72
|
+
Requires-Dist: torchvision; extra == "neuralnet"
|
|
73
|
+
Provides-Extra: sklearn
|
|
74
|
+
Requires-Dist: scikit-learn>=1.0.2; extra == "sklearn"
|
|
75
|
+
Provides-Extra: tf
|
|
76
|
+
Requires-Dist: tensorflow; extra == "tf"
|
|
77
|
+
Provides-Extra: sampler
|
|
78
|
+
Requires-Dist: ultranest; extra == "sampler"
|
|
79
|
+
|
|
80
|
+
<p align="center">
|
|
81
|
+
<picture>
|
|
82
|
+
<source media="(prefers-color-scheme: dark)" width="600px" height="300px" srcset="https://github.com/nuclear-multimessenger-astronomy/nmma/blob/main/doc/images/dark-logo.svg">
|
|
83
|
+
<source media="(prefers-color-scheme: light)" width="600px" height="300px" srcset="https://github.com/nuclear-multimessenger-astronomy/nmma/blob/main/doc/images/light-logo.svg">
|
|
84
|
+
<img alt="NMMA">
|
|
85
|
+
</picture>
|
|
86
|
+
</p>
|
|
87
|
+
|
|
88
|
+
|
|
89
|
+
<div align="center">
|
|
90
|
+
<h1>NMMA</h1>
|
|
91
|
+
<h2>a pythonic library for probing nuclear physics and cosmology with multimessenger analysis</h2>
|
|
92
|
+
<br/><br/>
|
|
93
|
+
</div>
|
|
94
|
+
|
|
95
|
+
|
|
96
|
+
[](https://github.com/nuclear-multimessenger-astronomy/nmma/stargazers)
|
|
97
|
+
[](https://github.com/nuclear-multimessenger-astronomy/nmma/forks)
|
|
98
|
+
[](https://anaconda.org/conda-forge/nmma)
|
|
99
|
+
[](https://badge.fury.io/py/nmma)
|
|
100
|
+
[](https://coveralls.io/github/nuclear-multimessenger-astronomy/nmma?branch=main)
|
|
101
|
+
[](https://github.com/nuclear-multimessenger-astronomy/nmma/actions/workflows/continous_integration.yml)
|
|
102
|
+
[](https://badge.fury.io/py/nmma)
|
|
103
|
+
[](https://badge.fury.io/py/nmma)
|
|
104
|
+
|
|
105
|
+
|
|
106
|
+
|
|
107
|
+
|
|
108
|
+
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)
|
|
109
|
+
|
|
110
|
+
Read our official documentation: [NMMA Documentation](https://nuclear-multimessenger-astronomy.github.io/nmma/)
|
|
111
|
+
|
|
112
|
+
Check out our contribution guide: [For contributors](https://nuclear-multimessenger-astronomy.github.io/nmma/contributing.html)
|
|
113
|
+
|
|
114
|
+
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)
|
|
115
|
+
|
|
116
|
+
|
|
117
|
+
### Citing NMMA
|
|
118
|
+
|
|
119
|
+
When utilizing this code for a publication, kindly make a reference to the package by its name, NMMA, and a citation to the companion paper [An updated nuclear-physics and multi-messenger astrophysics framework for binary neutron star mergers](https://www.nature.com/articles/s41467-023-43932-6). The BibTeX entry for the paper is:
|
|
120
|
+
```bibtex
|
|
121
|
+
@article{Pang:2022rzc,
|
|
122
|
+
title={An updated nuclear-physics and multi-messenger astrophysics framework for binary neutron star mergers},
|
|
123
|
+
author={Peter T. H. Pang and Tim Dietrich and Michael W. Coughlin and Mattia Bulla and Ingo Tews and Mouza Almualla and Tyler Barna and Weizmann Kiendrebeogo and Nina Kunert and Gargi Mansingh and Brandon Reed and Niharika Sravan and Andrew Toivonen and Sarah Antier and Robert O. VandenBerg and Jack Heinzel and Vsevolod Nedora and Pouyan Salehi and Ritwik Sharma and Rahul Somasundaram and Chris Van Den Broeck},
|
|
124
|
+
journal={Nature Communications},
|
|
125
|
+
year={2023},
|
|
126
|
+
month={Dec},
|
|
127
|
+
day={20},
|
|
128
|
+
volume={14},
|
|
129
|
+
number={1},
|
|
130
|
+
pages={8352},
|
|
131
|
+
issn={2041-1723},
|
|
132
|
+
doi={10.1038/s41467-023-43932-6},
|
|
133
|
+
url={https://doi.org/10.1038/s41467-023-43932-6}
|
|
134
|
+
}
|
|
135
|
+
```
|
|
136
|
+
|
|
137
|
+
### Acknowledgments
|
|
138
|
+
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.
|
|
139
|
+
Please use the following text for this acknowledgment:
|
|
140
|
+
> We acknowledge the Nuclear Multi-Messenger Astronomy collective as an open community of multi-domain experts and collaborators. This community and \<names of individuals\>, in particular, were important for the development of this project.
|
|
141
|
+
|
|
142
|
+
### Funding
|
|
143
|
+
We gratefully acknowledge previous and current support from the U.S. National Science Foundation (NSF) Harnessing the Data Revolution (HDR) Institute for <a href="https://a3d3.ai">Accelerating AI Algorithms for Data Driven Discovery (A3D3)</a> under Cooperative Agreement No. <a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=2117997">PHY-2117997</a> and the European Research Council (ERC) under the European Union's Starting Grant (Grant No. <a href="https://doi.org/10.3030/101076369">101076369</a>).
|
|
144
|
+
|
|
145
|
+
<p align="center">
|
|
146
|
+
<img src="https://github.com/nuclear-multimessenger-astronomy/nmma/blob/main/assets/a3d3.png" alt="A3D3" width="200"/>
|
|
147
|
+
<img src="https://github.com/nuclear-multimessenger-astronomy/nmma/blob/main/assets/nsf.png" alt="NSF" width="200"/>
|
|
148
|
+
<img src="https://github.com/nuclear-multimessenger-astronomy/nmma/blob/main/assets/erc.png" alt="ERC" width="200"/>
|