Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Incorporating the Gammapy wrapper in agnpy #119

Merged
merged 81 commits into from
Aug 10, 2022
Merged

Incorporating the Gammapy wrapper in agnpy #119

merged 81 commits into from
Aug 10, 2022

Commits on Apr 26, 2022

  1. added first instance of Gammapy wrapper for agnpy

    @cosimoNigro
    cosimoNigro committed Apr 26, 2022
    Configuration menu
    Copy the full SHA
    d0b5864 View commit details
    Browse the repository at this point in the history

Commits on Apr 27, 2022

  1. added also EC model

    @cosimoNigro
    cosimoNigro committed Apr 27, 2022
    Configuration menu
    Copy the full SHA
    5785b32 View commit details
    Browse the repository at this point in the history

Commits on May 5, 2022

  1. started working on Quentin suggestions

    @cosimoNigro
    cosimoNigro committed May 5, 2022
    Configuration menu
    Copy the full SHA
    a146a9a View commit details
    Browse the repository at this point in the history

  2. added Gammapy installation to test configuration

    @cosimoNigro
    cosimoNigro committed May 5, 2022
    Configuration menu
    Copy the full SHA
    170ed5a View commit details
    Browse the repository at this point in the history

Commits on May 9, 2022

  1. properly added separation of parameters and setting of ranges and scales

    @cosimoNigro
    cosimoNigro committed May 9, 2022
    Configuration menu
    Copy the full SHA
    7008f75 View commit details
    Browse the repository at this point in the history

Commits on May 10, 2022

  1. re-ordered the Gammapy wrapper, set parameters and scaling for all th… 

    …e model parameters
    @cosimoNigro
    cosimoNigro committed May 10, 2022
    Configuration menu
    Copy the full SHA
    90cf385 View commit details
    Browse the repository at this point in the history

  2. added some tests, quite some discrepancy between agnpy and the Gammap… 

    …y wrapper
    @cosimoNigro
    cosimoNigro committed May 10, 2022
    Configuration menu
    Copy the full SHA
    5f3402d View commit details
    Browse the repository at this point in the history

  3. added norm as the last of the parameters, will explain in the docs no… 

    …t to touch it
    @cosimoNigro
    cosimoNigro committed May 10, 2022
    Configuration menu
    Copy the full SHA
    e226518 View commit details
    Browse the repository at this point in the history

  4. fix failing test in PR #119

    @cosimoNigro
    cosimoNigro committed May 10, 2022
    Configuration menu
    Copy the full SHA
    6ada321 View commit details
    Browse the repository at this point in the history

  5. install dev version of Gammapy in the test workflow

    @cosimoNigro
    cosimoNigro committed May 10, 2022
    Configuration menu
    Copy the full SHA
    73bf2a2 View commit details
    Browse the repository at this point in the history

Commits on May 11, 2022

  1. inverted order of installation Gammapy / agnpy to check if the astrop… 

    …y version issue in the tests persists
    @cosimoNigro
    cosimoNigro committed May 11, 2022
    Configuration menu
    Copy the full SHA
    4956918 View commit details
    Browse the repository at this point in the history

Commits on May 20, 2022

  1. removed python 3.7 from the tests

    @cosimoNigro
    cosimoNigro committed May 20, 2022
    Configuration menu
    Copy the full SHA
    dda1618 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'gammapy_model' of github.com:cosimoNigro/agnpy into gam… 

    …mapy_model
    @cosimoNigro
    cosimoNigro committed May 20, 2022
    Configuration menu
    Copy the full SHA
    1d3bab2 View commit details
    Browse the repository at this point in the history

Commits on May 31, 2022

  1. added a cleverer parameter separation, modified the ExternalComptonSp… 

    …ectralModel class initialisation
    @cosimoNigro
    cosimoNigro committed May 31, 2022
    Configuration menu
    Copy the full SHA
    5427032 View commit details
    Browse the repository at this point in the history

  2. added tests for the new ExternalComptonSpectralModel class

    @cosimoNigro
    cosimoNigro committed May 31, 2022
    Configuration menu
    Copy the full SHA
    f41d5db View commit details
    Browse the repository at this point in the history

  3. increased minimum required python version to 3.8, for compatibility w… 

    …ith Gammapy
    @cosimoNigro
    cosimoNigro committed May 31, 2022
    Configuration menu
    Copy the full SHA
    60b69a9 View commit details
    Browse the repository at this point in the history

  4. modified workflow config

    @cosimoNigro
    cosimoNigro committed May 31, 2022
    Configuration menu
    Copy the full SHA
    5de674a View commit details
    Browse the repository at this point in the history

Commits on Jun 3, 2022

  1. added tests for EC on different targets

    @cosimoNigro
    cosimoNigro committed Jun 3, 2022
    Configuration menu
    Copy the full SHA
    c13fca7 View commit details
    Browse the repository at this point in the history

  2. updated Mrk421 2011 data with proper provenance

    @cosimoNigro
    cosimoNigro committed Jun 3, 2022
    Configuration menu
    Copy the full SHA
    99ee722 View commit details
    Browse the repository at this point in the history

  3. re-generate Mrk421 and PKS1510-089 SED data

    @cosimoNigro
    cosimoNigro committed Jun 3, 2022
    Configuration menu
    Copy the full SHA
    5e01dee View commit details
    Browse the repository at this point in the history

  4. improved Gammapy wrapper tests with numerical check

    @cosimoNigro
    cosimoNigro committed Jun 3, 2022
    Configuration menu
    Copy the full SHA
    7b18716 View commit details
    Browse the repository at this point in the history

Commits on Jun 4, 2022

  1. solved failing test by reducing the comparison range for Synch and SS… 

    …C computed with agnpy and Gammapy
    @cosimoNigro
    cosimoNigro committed Jun 4, 2022
    Configuration menu
    Copy the full SHA
    0a1c8f6 View commit details
    Browse the repository at this point in the history

Commits on Jun 20, 2022

  1. produced standardised MWL SED data

    @cosimoNigro
    cosimoNigro committed Jun 20, 2022
    Configuration menu
    Copy the full SHA
    75af26b View commit details
    Browse the repository at this point in the history

  2. started to update the SSC notebook

    @cosimoNigro
    cosimoNigro committed Jun 20, 2022
    Configuration menu
    Copy the full SHA
    fc6342a View commit details
    Browse the repository at this point in the history

  3. added small script to check the speed of the fit with Gammapy

    @cosimoNigro
    cosimoNigro committed Jun 20, 2022
    Configuration menu
    Copy the full SHA
    e1764cf View commit details
    Browse the repository at this point in the history

Commits on Jul 9, 2022

  1. added t_var among the parameters and function to add systematics to f… 

    …lux points errors
    @cosimoNigro
    cosimoNigro committed Jul 9, 2022
    Configuration menu
    Copy the full SHA
    8d564e7 View commit details
    Browse the repository at this point in the history

Commits on Jul 11, 2022

  1. corrected EC model not to use agnpy.targets for initialisation

    @cosimoNigro
    cosimoNigro committed Jul 11, 2022
    Configuration menu
    Copy the full SHA
    512a359 View commit details
    Browse the repository at this point in the history

  2. updated EC and SSC tutorials to new Gammapy version and added tutoria… 

    …l using MCMC
    @cosimoNigro
    cosimoNigro committed Jul 11, 2022
    Configuration menu
    Copy the full SHA
    aa2c88f View commit details
    Browse the repository at this point in the history

  3. removed experiments/check_gammapy_fit.py

    @cosimoNigro
    cosimoNigro committed Jul 11, 2022
    Configuration menu
    Copy the full SHA
    8d2583f View commit details
    Browse the repository at this point in the history

Commits on Jul 12, 2022

  1. try to improve the fit

    @cosimoNigro
    cosimoNigro committed Jul 12, 2022
    Configuration menu
    Copy the full SHA
    5c445d1 View commit details
    Browse the repository at this point in the history

Commits on Jul 15, 2022

  1. updated tests, something off in the thermal components of the EC scen… 

    …ario, to be investigated
    @cosimoNigro
    cosimoNigro committed Jul 15, 2022
    Configuration menu
    Copy the full SHA
    a01c8a9 View commit details
    Browse the repository at this point in the history

  2. updated notebook

    @cosimoNigro
    cosimoNigro committed Jul 15, 2022
    Configuration menu
    Copy the full SHA
    12b840b View commit details
    Browse the repository at this point in the history

Commits on Jul 16, 2022

  1. modified Gammapy wrapper to use log10

    @cosimoNigro
    cosimoNigro committed Jul 16, 2022
    Configuration menu
    Copy the full SHA
    3b40038 View commit details
    Browse the repository at this point in the history

  2. re-run notebooks, EC fit still not converging

    @cosimoNigro
    cosimoNigro committed Jul 16, 2022
    Configuration menu
    Copy the full SHA
    06f8101 View commit details
    Browse the repository at this point in the history

Commits on Jul 18, 2022

  1. updated the notebooks, notebook with Gammapy fit definitive [ci skip]

    @cosimoNigro
    cosimoNigro committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    056b259 View commit details
    Browse the repository at this point in the history

  2. imporved description of Mrk421 notebooks both for simple fitting and … 

    …MCMC [ci skip]
    @cosimoNigro
    cosimoNigro committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    fbf1e04 View commit details
    Browse the repository at this point in the history

  3. final version od the SSC Gammapy fit tutorial

    @cosimoNigro
    cosimoNigro committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    42f9e1b View commit details
    Browse the repository at this point in the history

Commits on Jul 19, 2022

  1. finsihed and polished MCMC tutorial

    @cosimoNigro
    cosimoNigro committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    bc09504 View commit details
    Browse the repository at this point in the history

  2. discrepancy left in the EC computation

    @cosimoNigro
    cosimoNigro committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    1d369f3 View commit details
    Browse the repository at this point in the history

Commits on Jul 22, 2022

  1. corrected improper multiplication of frequency in BB spectrum computa… 

    …tion
    @cosimoNigro
    cosimoNigro committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    1f9f407 View commit details
    Browse the repository at this point in the history

  2. finally got matching EC models for agnpy and Gammapy wrappers

    @cosimoNigro
    cosimoNigro committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    82968a0 View commit details
    Browse the repository at this point in the history

  3. re-run notebooks, EC fit of PKS1510-089 failing, to be checked

    @cosimoNigro
    cosimoNigro committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    552cd39 View commit details
    Browse the repository at this point in the history

  4. fix failing test

    @cosimoNigro
    cosimoNigro committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    a56e8fb View commit details
    Browse the repository at this point in the history

Commits on Jul 26, 2022

  1. minor fix in nuFnu expression of DT BB radiation

    @cosimoNigro
    cosimoNigro committed Jul 26, 2022
    Configuration menu
    Copy the full SHA
    d9ff1ca View commit details
    Browse the repository at this point in the history

  2. increased the Lorenz factor grid in the wrapper tests

    @cosimoNigro
    cosimoNigro committed Jul 26, 2022
    Configuration menu
    Copy the full SHA
    b322308 View commit details
    Browse the repository at this point in the history

  3. added SSA option in EC wrapper model

    @cosimoNigro
    cosimoNigro committed Jul 26, 2022
    Configuration menu
    Copy the full SHA
    d7a9a87 View commit details
    Browse the repository at this point in the history

Commits on Jul 27, 2022

  1. corrected normalisation of BB spectra

    @cosimoNigro
    cosimoNigro committed Jul 27, 2022
    Configuration menu
    Copy the full SHA
    a843494 View commit details
    Browse the repository at this point in the history

Commits on Jul 28, 2022

  1. change the boundary of log10_k_e

    @cosimoNigro
    cosimoNigro committed Jul 28, 2022
    Configuration menu
    Copy the full SHA
    167d734 View commit details
    Browse the repository at this point in the history

  2. started to modify the docs to better include the new notebooks [ci skip]

    @cosimoNigro
    cosimoNigro committed Jul 28, 2022
    Configuration menu
    Copy the full SHA
    6251a7f View commit details
    Browse the repository at this point in the history

Commits on Jul 29, 2022

  1. corrected small error in the emission region params for EC [ci skip]

    @cosimoNigro
    cosimoNigro committed Jul 29, 2022
    Configuration menu
    Copy the full SHA
    e048c2e View commit details
    Browse the repository at this point in the history

  2. re-formatted notebook, gammapy fit of PKS1510-089 still not convergin… 

    …g [ci skip]
    @cosimoNigro
    cosimoNigro committed Jul 29, 2022
    Configuration menu
    Copy the full SHA
    e9b1dda View commit details
    Browse the repository at this point in the history

Commits on Aug 1, 2022

  1. started refactoring of class for fitting, removed wrapper sub-module

    @cosimoNigro
    cosimoNigro committed Aug 1, 2022
    Configuration menu
    Copy the full SHA
    c702462 View commit details
    Browse the repository at this point in the history

  2. refactoring of the sub-module for fitting, added core class handling … 

    …model parameters
    @cosimoNigro
    cosimoNigro committed Aug 1, 2022
    Configuration menu
    Copy the full SHA
    7727b06 View commit details
    Browse the repository at this point in the history

  3. redefined gammapy wrapper to use the parameters defined in agnpy/fit/… 

    …core.py
    @cosimoNigro
    cosimoNigro committed Aug 1, 2022
    Configuration menu
    Copy the full SHA
    6c03ff5 View commit details
    Browse the repository at this point in the history

  4. added sherpa wrapper using functions and parameters in core, evaluati… 

    …on missing
    @cosimoNigro
    cosimoNigro committed Aug 1, 2022
    Configuration menu
    Copy the full SHA
    cbfd01b View commit details
    Browse the repository at this point in the history

  5. added fit/models to handle the gammapy or sherpa backends

    @cosimoNigro
    cosimoNigro committed Aug 1, 2022
    Configuration menu
    Copy the full SHA
    a48a623 View commit details
    Browse the repository at this point in the history

  6. changed submodule name from wrapper to fit in agnpy/__init__.py

    @cosimoNigro
    cosimoNigro committed Aug 1, 2022
    Configuration menu
    Copy the full SHA
    706f0ad View commit details
    Browse the repository at this point in the history

  7. make the wrapper work for the SSC scenario

    @cosimoNigro
    cosimoNigro committed Aug 1, 2022
    Configuration menu
    Copy the full SHA
    1957d85 View commit details
    Browse the repository at this point in the history

Commits on Aug 2, 2022

  1. improved general parameters handling for Gammapy wrapper, completed E… 

    …C integration in the new scheme
    @cosimoNigro
    cosimoNigro committed Aug 2, 2022
    Configuration menu
    Copy the full SHA
    d67538f View commit details
    Browse the repository at this point in the history

  2. minor bug in functions to sort disk parameters fixed

    @cosimoNigro
    cosimoNigro committed Aug 2, 2022
    Configuration menu
    Copy the full SHA
    6670956 View commit details
    Browse the repository at this point in the history

Commits on Aug 3, 2022

  1. small fixes in EC parameters

    @cosimoNigro
    cosimoNigro committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    903a3a7 View commit details
    Browse the repository at this point in the history

  2. added sherpa wrappers for SSC and EC scenarios

    @cosimoNigro
    cosimoNigro committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    c179345 View commit details
    Browse the repository at this point in the history

  3. set the L_disk as a log-scaled parameters, to allow adjustment during… 

    … fit
    @cosimoNigro
    cosimoNigro committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    fe8fd63 View commit details
    Browse the repository at this point in the history

  4. fixed tests for gammapy wrapper

    @cosimoNigro
    cosimoNigro committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    22a3a25 View commit details
    Browse the repository at this point in the history

  5. added option to raise an error in case of unavailable backend

    @cosimoNigro
    cosimoNigro committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    c624147 View commit details
    Browse the repository at this point in the history

  6. added functionalities, to sherpa and Gammapy wrappers, to initialise … 

    …model parameters using agnpy.emission_region and agnpy.targets objects
    @cosimoNigro
    cosimoNigro committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    869983e View commit details
    Browse the repository at this point in the history

  7. all tests for agnpy and sherpa wrappers passing, missing tests on fit… 

    …ting
    @cosimoNigro
    cosimoNigro committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    d677b4c View commit details
    Browse the repository at this point in the history

  8. added pip install sherpa to github CI workflow

    @cosimoNigro
    cosimoNigro committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    b2e49e5 View commit details
    Browse the repository at this point in the history

  9. removing incomplete function accidentally left incomplete in agnpy/te… 

    …sts/test_fit.py
    @cosimoNigro
    cosimoNigro committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    6f3b026 View commit details
    Browse the repository at this point in the history

Commits on Aug 4, 2022

  1. added separated test sub-module to perform the Mrk421 and PKS1501-089… 

    … with the two wrappers and check their outcome [ci skip]
    @cosimoNigro
    cosimoNigro committed Aug 4, 2022
    Configuration menu
    Copy the full SHA
    ea10a75 View commit details
    Browse the repository at this point in the history

Commits on Aug 5, 2022

  1. added functions to directly load flux points through sherpa and gammapy

    @cosimoNigro
    cosimoNigro committed Aug 5, 2022
    Configuration menu
    Copy the full SHA
    0d728f4 View commit details
    Browse the repository at this point in the history

  2. moved function to add systematics to gammapy FluxPoints to agnpy.fit.… 

    …utils
    @cosimoNigro
    cosimoNigro committed Aug 5, 2022
    Configuration menu
    Copy the full SHA
    5108af9 View commit details
    Browse the repository at this point in the history

  3. made also the sherpa wrapper use energy as dependent variable (was us… 

    …ing frequency before)
    @cosimoNigro
    cosimoNigro committed Aug 5, 2022
    Configuration menu
    Copy the full SHA
    b8dd4e8 View commit details
    Browse the repository at this point in the history

  4. added utilities to compute flux points to the tests

    @cosimoNigro
    cosimoNigro committed Aug 5, 2022
    Configuration menu
    Copy the full SHA
    9bafdce View commit details
    Browse the repository at this point in the history

  5. modified the two SSC fit tutorials to use the new wrappers

    @cosimoNigro
    cosimoNigro committed Aug 5, 2022
    Configuration menu
    Copy the full SHA
    7b9289a View commit details
    Browse the repository at this point in the history

Commits on Aug 10, 2022

  1. tried to fix the normalisation of the DT and disk black bodies. Adopt… 

    …ed analytical result for DT, and a numerical integration on a large grid for the disk.
    @cosimoNigro
    cosimoNigro committed Aug 10, 2022
    Configuration menu
    Copy the full SHA
    5228546 View commit details
    Browse the repository at this point in the history

  2. finally got the same results with sherpa and gammapy for the fit of P… 

    …KS1510-089
    @cosimoNigro
    cosimoNigro committed Aug 10, 2022
    Configuration menu
    Copy the full SHA
    f107995 View commit details
    Browse the repository at this point in the history

  3. re-run all the notebooks

    @cosimoNigro
    cosimoNigro committed Aug 10, 2022
    Configuration menu
    Copy the full SHA
    5bf39b2 View commit details
    Browse the repository at this point in the history

  4. adapted the docs to include the new notebook tutorials

    @cosimoNigro
    cosimoNigro committed Aug 10, 2022
    Configuration menu
    Copy the full SHA
    61638be View commit details
    Browse the repository at this point in the history

  5. added the final version of the page of the docs gathering all the fit… 

    …ting examples
    @cosimoNigro
    cosimoNigro committed Aug 10, 2022
    Configuration menu
    Copy the full SHA
    98dbda4 View commit details
    Browse the repository at this point in the history

  6. changed agnpy.fit.utils to agnpy.utils.data, to avoid import conflicts

    @cosimoNigro
    cosimoNigro committed Aug 10, 2022
    Configuration menu
    Copy the full SHA
    d9e3a79 View commit details
    Browse the repository at this point in the history