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Separating the cluster theory and models from Firecrown into an independent module. #345

Merged
merged 83 commits into from
Dec 11, 2023
Merged

Separating the cluster theory and models from Firecrown into an independent module. #345

merged 83 commits into from
Dec 11, 2023

Commits on Oct 4, 2023

  1. Temp commit

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Commits on Oct 5, 2023

  1. Midstage of refactor. 

    Removed old cluster number count classes

Added new Kernel base class, with MassObservable and Redshift subclasses

Added some simple implementations of Kernel

Added Kernel Factories

Still WIP.
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  2. Another round of commits. 

    Stuck with the issue that the models in modelling tools also needs to know about the data (bounds for kernels)
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Commits on Oct 9, 2023

  1. flake8 is angry

    @mattkwiecien
    mattkwiecien committed Oct 9, 2023
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  2. Removing factories in favor of explicit references.

    @mattkwiecien
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Commits on Oct 10, 2023

  1. Added some true mass and true redshift kernels 

    Committing all work and going to start tests to check workflow.
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  2. Added some beginning unit tests and fixed issues involving code.

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Commits on Oct 12, 2023

  1. Cosmosis running. Number counts seem correct. 

    Need to rethink how we include analytic solutions

Currently this is working but not how I want it
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  2. Changing up the approach to have the cluster module compute by z, m o… 

    …bserved bins.
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    mattkwiecien committed Oct 12, 2023
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Commits on Oct 13, 2023

  1. Changes to use numcosmo integration instead.

    @mattkwiecien
    mattkwiecien committed Oct 13, 2023
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  2. Moving files around to directories that make more sense. 

    This is going to show up as a delete and add in git.
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  3. Tried to tidy up the complicated integral bounds method.

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    mattkwiecien committed Oct 13, 2023
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  4. Small changes to support the mean mass calculation. 

    Noticed a bug? in the previous code with limits for integration.
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Commits on Oct 16, 2023

  1. Updated numcosmo integration to pass in vectors 

    Updated rest of the abundance code to do vector operations

Implemented a cache for HMF for now since it doesn't accept a vector of scale factors.
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Commits on Oct 17, 2023

  1. Refactored the integration limits and integrator out of the cluster a… 

    …bundance.
    @mattkwiecien
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  2. Switching to Bocquet16 for speed improvements 

    Small fixes.
    @mattkwiecien
    mattkwiecien committed Oct 17, 2023
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  3. Adding tests for cluster kernels.

    @mattkwiecien
    mattkwiecien committed Oct 17, 2023
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  4. Added unit tests for abundance and abundance data classes.

    @mattkwiecien
    mattkwiecien committed Oct 17, 2023
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Commits on Oct 18, 2023

  1. mv __init__ to murata

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    m-aguena committed Oct 18, 2023
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  2. rm leftover code

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    m-aguena committed Oct 18, 2023
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  3. update example

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    m-aguena committed Oct 18, 2023
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  4. rename Murata classes

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    m-aguena committed Oct 18, 2023
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  5. Fixing a small bug in the new Murata class 

    Adding unit tests for the new Murata classes
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    mattkwiecien committed Oct 18, 2023
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Commits on Oct 19, 2023

  1. Deferring the handling of building arguments, and how to read those a… 

    …rguments, to each integrator
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  2. Fixing unit tests for new args reader changes

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    mattkwiecien committed Oct 19, 2023
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  3. Added covering unit tests for the integrator classes

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  4. Added test for unbinned Murata

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    mattkwiecien committed Oct 19, 2023
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  5. Increased test coverage to 100% for all cluster classes

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    mattkwiecien committed Oct 19, 2023
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Commits on Oct 20, 2023

  1. Improving method names, adding typing.

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    mattkwiecien committed Oct 20, 2023
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Commits on Oct 23, 2023

  1. Fixing other unit tests by making params optional to modeling tools u… 

    …pdate.
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    mattkwiecien committed Oct 23, 2023
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  2. Mypy type fixes.

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    mattkwiecien committed Oct 23, 2023
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Commits on Oct 25, 2023

  1. Fixed all mypy complaints.

    @mattkwiecien
    mattkwiecien committed Oct 25, 2023
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Commits on Oct 31, 2023

  1. Finished refactoring to use an integrand wrapper in each integrator.

    @mattkwiecien
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  2. type checking fixes

    @mattkwiecien
    mattkwiecien committed Oct 31, 2023
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  3. Removing ArgReader references, updating tests.

    @mattkwiecien
    mattkwiecien committed Oct 31, 2023
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Commits on Nov 2, 2023

  1. Implemented scipy integrator! Success!

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  2. Added test coverage for scipy 

    All cluster modules at 100% test coverage.
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  3. Fixing all mypy strict errors except generic type npt.NDarray (no way… 

    … around this)

Updating mass proxy tests.
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  4. Testing the binned cluster count statistic.

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  5. Single commit for removing mypy linting the tests, not sure if we wan… 

    …t to keep this?
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  6. Merge branch 'master' into clusters-stubs

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  7. Some needed changes after merging with master. 

    Have not modified the cluster code to use new Updatable ModelingTools yet.
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  8. Forgot to run flake8!

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Commits on Nov 7, 2023

  1. Introducing a mock integrator for testing number counts.

    @mattkwiecien
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  2. Fixing pylint errors. 

    Extracting some methods.
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  3. Pylint changes to integrators.

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  4. Fixing remaining pylint issues, except docstrings.

    @mattkwiecien
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  5. Filling in doc strings.

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  6. Finishing docstrings for cluster module.

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  7. Docstrings for tests.

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  8. Extract method refactoring based on pylint suggestion.

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Commits on Nov 10, 2023

  1. Moving cluster sacc data fixture into conftest.py

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  2. Replacing mock class using built-in unittest.mock.

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  3. Replaced mock kernel with unittest mock in cluster abundance.

    @mattkwiecien
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  4. Removing mock kernel in favor of unittest.mock for integrators.

    @mattkwiecien
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  5. Unifying tests for numcosmo and scipy.

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  6. Replace variable with inline call.

    @mattkwiecien
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  7. Fixing error in cluster kernel tests.

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  8. Updating unit test to capture error found on CI.

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  9. Fixed test and extracted a method to replace some confusing conditona… 

    …l logic.
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  10. Adding docstrings to my new public methods.

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Commits on Nov 14, 2023

  1. Merge branch 'master' into clusters-stubs

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Commits on Nov 28, 2023

  1. Moving sky area from a constructor parameter to an argument to the cl… 

    …uster abundance

Adding some tests to capture some edge cases exposed when moving sky_area.
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  2. Unfortunately there's no easy way to get the mock to enforce number o… 

    …f arguments on methods in tests.
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  3. Making cluster abundance updatable. 

    Adjusting tests

Adding some mypy type checking here and there
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  4. Adding a new ClusterProperty flag

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Commits on Nov 29, 2023

  1. Updating the comparison script for numcosmo integration methods. 

    Allowing a user to pass in an integration method into the num cosmo integrator.
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Commits on Dec 1, 2023

  1. Adding new NDimensionalBin class and SaccBin implementation. 

    Updating the cluster abundance data to return SaccBins instead of confusing built in types

Adding tests, and updating sacc file to reflect proper structure

Fixing mypy/pylint complaints.
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  2. Merge branch 'master' into clusters-stubs

    @mattkwiecien
    mattkwiecien committed Dec 1, 2023
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  3. Forgot to update tests for ClusterAbundance

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  4. Python 3.9, 3.10 tests are failing on build server, while 3.11 passin… 

    …g locally. Switching 3.11 syntax for older syntax.

Updating cluster abundance tests to be more better.
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Commits on Dec 3, 2023

  1. Improving tests.

    @mattkwiecien
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  2. Updating code to latest numcosmo version.

    @mattkwiecien
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  3. Missed places to upgrade numcosmo references.

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Commits on Dec 4, 2023

  1. Changes to binning.py

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  2. Changes to test marking. 

    Updating verifying bin dimensions on the statistic.
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  3. Removing numcosmo name from integrator tests.

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Commits on Dec 5, 2023

  1. Removing dimension from abundance data tests. 

    Moving shared attributes to base class integrator

Adding proper normalization to gaussian
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Commits on Dec 6, 2023

  1. Forgot to fix imports.

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  2. Making pylint happy with parenthesis

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  3. Fixing pylint CI errors.

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Commits on Dec 7, 2023

  1. Adding a unit test to check normalization of MurataUnbinned 

    Some PR review changes

Adding more tests for the binning module.
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Commits on Dec 11, 2023

  1. Pylint import order error.

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