Merge in updates from master (#174)

* pyccl optional (#153) * pyccl optional * oops * Add simple halo model (#150) * remove depracated likelihood.theory calls * codestyle * sphinx compatability update * sphinx compatability update 2204 * add build tools * move rtd python ver * rtd try different pyver * rtd try different order * conda on rtd * update rtd mock import * add rtd theme * add rtd theme correctly * add rtd theme in setup.cfg * Testing yaml instead of yml. * added docs conda env * add full requirements in docs * pin tensorflow dep * started basic halo model * started basic pyhm implementation and tests * pkmm computation with z loop * remove empty functions * test against precomputed value * codestyle and fix test * add missing default files * added docs * line length * remove refernce to bias model in docs * improve docs --------- Co-authored-by: Hidde Jense <[email protected]> * Deprecations update (#155) * pyccl optional * oops * remove pkg_resources * str path * pudate latest * fix * py311 * py311 * py311 * typo * Update docs/soliket-docs.yml * Update soliket-tests.yml --------- Co-authored-by: Ian Harrison <[email protected]> * Pycharm tidies (#161) * pyccl optional * oops * remove pkg_resources * str path * added new warnings, fails * pudate latest * changes for new reqs * fix * py311 * py311 * py311 * update halomodel codestyle * Mist tidy * typo * brackets --------- Co-authored-by: Ian Harrison <[email protected]> * Run tests only on PR open, review requests (#159) * run tests only on PR open, review requests * added some extra instructions in docs * reorder on setting * line break * reset what is written in docs * Add more flake8 requirements (#157) * added new warnings, fails * changes for new reqs * update halomodel codestyle * whitespace warnings * added zstar to crosscorrelation (#165) * Implementation of the lensing power spectrum computation with CCL (#166) * Implementing the lensing power spectrum computation with CCL. Added a flag to choose whether to use CAMB or CCL to compute this power spectrum. * Adding test to check CCL and CAMB agree to predict the CMB lensing power spectrum --------- Co-authored-by: Raphaël Kou <[email protected]> * solving bug in mflike (#170) * Fix readme (#173) * stricter indentation * Update README.rst * Dev check ell range mflike (#171) * change to lmax requirements * removing comments in modified files * solving style issues * solving issues in test mflike * solving codestyle issues * switched from hard-coded to l_bpws-depndt multipole * fixed codestyle --------- Co-authored-by: Martina Gerbino <[email protected]> Co-authored-by: Ian Harrison <[email protected]> * Resolving packages path with cobaya tools (#169) * Fix extra letter in calibration params * Use cobaya tools to resolve packages path * flake * Revert "flake" This reverts commit 526acde. * Update yaml files with correct paramnames and paths For the `test_multi.py`, I switched from `MFLike` to `TestMFLike`, coherently with `test_mflike.py` * Update paths in test_multi * Enable multi and mflike in test_runs * bug fix * Avoid overwrite global packages_path * flake * Change pathfinding to data with packages path * Revert to request forcing rootdir * Point to `tox.ini` directory --------- Co-authored-by: mgerbino <[email protected]> Co-authored-by: Ian Harrison <[email protected]> --------- Co-authored-by: Antony Lewis <[email protected]> Co-authored-by: Hidde Jense <[email protected]> Co-authored-by: raphkou <[email protected]> Co-authored-by: Raphaël Kou <[email protected]> Co-authored-by: Serena Giardiello <[email protected]> Co-authored-by: mgerbino <[email protected]> Co-authored-by: Martina Gerbino <[email protected]> Co-authored-by: Giacomo Galloni <[email protected]>
simonsobs · Jun 7, 2024 · 2f9139a · 2f9139a
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diff --git a/.github/workflows/codestyle.yml b/.github/workflows/codestyle.yml
@@ -10,11 +10,11 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
-      - name: Install Conda w/ Python 3.10
+      - name: Install Conda w/ Python 3.11
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-activate-base: false
-          python-version: '3.10'
+          python-version: '3.11'
           channels: conda-forge
       - name: Install Dependencies
         shell: bash -el {0}
@@ -23,4 +23,4 @@ jobs:
       - name: Check Code Style
         shell: bash -el {0}
         run: |
-          tox -e codestyle
+          tox -e codestyle
diff --git a/.github/workflows/compatibility.yml b/.github/workflows/compatibility.yml
@@ -9,8 +9,8 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.10']
-        toxenv: [py310-test-all-latest]
+        python-version: ['3.11']
+        toxenv: [py311-test-all-latest]
         # release: [main, latest] # there are no releases yet so this would break
         release: [main]
     steps:
@@ -33,4 +33,4 @@ jobs:
       - name: Run Tests
         shell: bash -el {0}
         run: |
-          tox -e ${{ matrix.toxenv }} ${{ matrix.toxargs }} -- ${{ matrix.toxposargs }}
+          tox -e ${{ matrix.toxenv }} ${{ matrix.toxargs }} -- ${{ matrix.toxposargs }}
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -1,6 +1,10 @@
 name: Testing
 
-on: [push, pull_request]
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
 
 jobs:
   test:
@@ -13,8 +17,8 @@ jobs:
 
           - name: latest supported versions
             os: ubuntu-latest
-            python-version: '3.10'
-            toxenv: py310-test-all-latest-cov
+            python-version: '3.11'
+            toxenv: py311-test-all-latest-cov
 
           - name: oldest supported versions
             os: ubuntu-latest
@@ -23,8 +27,8 @@ jobs:
 
           - name: macOS 11
             os: macos-11
-            python-version: '3.10'
-            toxenv: py310-test-latest
+            python-version: '3.11'
+            toxenv: py311-test-latest
 
     steps:
       - name: Checkout repository

diff --git a/README.rst b/README.rst
@@ -1,26 +1,26 @@
-=======
+====================================
 SOLikeT: SO Likelihoods and Theories
-=======
+====================================
 
-.. image:: https://github.com/simonsobs/soliket/workflows/Testing/badge.svg
+|workflow-badge| |coverage-badge| |docs-badge|
+
+.. |workflow-badge| image:: https://github.com/simonsobs/soliket/workflows/Testing/badge.svg
    :target: https://github.com/simonsobs/SOLikeT/actions?query=workflow%3ATesting
-   :alt: Testing Status
-
-.. image:: https://codecov.io/gh/simonsobs/SOLikeT/branch/master/graph/badge.svg?token=ND945EQDWR 
+   :alt: Testing Status   
+.. |coverage-badge| image:: https://codecov.io/gh/simonsobs/SOLikeT/branch/master/graph/badge.svg?token=ND945EQDWR 
    :target: https://codecov.io/gh/simonsobs/SOLikeT
    :alt: Test Coverage
-
-.. image:: https://readthedocs.org/projects/soliket/badge/?version=latest
+.. |docs-badge| image:: https://readthedocs.org/projects/soliket/badge/?version=latest
    :target: https://soliket.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
 
 SOLikeT is a centralized package for likelihood and theory implementations for the `Simons Observatory <https://simonsobservatory.org/>`_.
 For more extensive details please see our main documentation pages at: `http://soliket.readthedocs.io/ <http://soliket.readthedocs.io/>`_.
 
 .. image:: docs/images/Sky_UCSD2b.jpg
-   :target: https://simonsobservatory.org/
-   :alt: Simons Observatory Logo
-   :width: 200
+  :target: https://simonsobservatory.org/
+  :alt: Simons Observatory Logo
+  :width: 200
 
 Installation
 ============

diff --git a/docs/conf.py b/docs/conf.py
@@ -13,7 +13,7 @@
 for module in MOCK_MODULES:
     sys.modules[module] = mock.Mock()
 
-import soliket
+import soliket # noqa F401
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

diff --git a/docs/index.rst b/docs/index.rst
@@ -35,6 +35,7 @@ The pages here describe how to install and run SOLikeT, and document the functio
    bandpass
    foreground
    bias
+   halo_model
 
 .. toctree::
    :caption: Likelihood codes

diff --git a/docs/soliket-docs.yml b/docs/soliket-docs.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python>=3.8,<3.11
+  - python>=3.8,<3.12
   - pip
   - pytest-cov
   - compilers

diff --git a/requirements.txt b/requirements.txt
@@ -17,3 +17,4 @@ pyccl
 sacc
 fgspectra>=1.1.0
 syslibrary
+pyhalomodel
diff --git a/setup.cfg b/setup.cfg
@@ -21,26 +21,27 @@ install_requires =
     camb
     getdist
     cobaya
-    pyccl
     sacc
     fgspectra>=1.1.0
-    syslibrary
+    syslibrary>=0.2.0
+    pyhalomodel
 
 [options.package_data]
-soliket = *.yaml,*.bibtex,clusters/data/*,clusters/data/selFn_equD56/*,lensing/data/*.txt,lensing/data/*.fits,mflike/*.yaml,tests/*.yaml,data/xcorr_simulated/*.txt,data/CosmoPower/CP_paper/CMB/*.pkl,tests/data/test_bandpass/*,cross_correlation/*.yaml,tests/data/*.fits
+soliket = *.yaml,*.bibtex,clusters/data/*,clusters/data/selFn_equD56/*,lensing/data/*.txt,lensing/data/*.fits,mflike/*.yaml,tests/*.yaml,data/xcorr_simulated/*.txt,data/CosmoPower/CP_paper/CMB/*.pkl,tests/data/test_bandpass/*,cross_correlation/*.yaml,tests/data/*.fits,halo_model/*.yaml
 testpaths = "soliket"
 text_file_format = rst
 
 [options.extras_require]
-all = 
+all =
     cosmopower
+    pyccl
 docs =
     sphinx
     sphinx_rtd_theme
 
 [flake8]
-select = E713,E704,E703,E714,E741,E10,E11,E20,E22,E23,E25,E27,E301,E302,E304,E9,
-		 F405,F406,F5,F6,F7,F8,E501
+select = E713,E704,E703,E714,E741,E10,E11,E20,E22,E23,E25,E262,E27,E301,E302,E304,E9,
+         F405,F406,F5,F6,F7,F8,E501,W191,F401,W1,W292,W293,W3
 max-line-length = 90
 exclude = .tox,build,cobaya_packages,test,.eggs
 

diff --git a/setup.py b/setup.py
@@ -5,7 +5,6 @@
 # other information are set in the setup.cfg file.
 
 import os
-import sys
 
 from setuptools import setup
 

diff --git a/soliket-tests.yml b/soliket-tests.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python>=3.8,<3.11
+  - python>=3.8,<3.12
   - pip
   - pytest-cov
   - compilers

diff --git a/soliket/__init__.py b/soliket/__init__.py
@@ -3,12 +3,12 @@
 # from .studentst import StudentstLikelihood  # noqa: F401
 from .ps import PSLikelihood, BinnedPSLikelihood  # noqa: F401
 from .mflike import MFLike  # noqa: F401
-from .mflike import TheoryForge_MFLike
+from .mflike import TheoryForge_MFLike # noqa F401
 from .cross_correlation import CrossCorrelationLikelihood, GalaxyKappaLikelihood, ShearKappaLikelihood  # noqa: F401, E501
 from .xcorr import XcorrLikelihood  # noqa: F401
-from .foreground import Foreground
-from .bandpass import BandPass
-from .cosmopower import CosmoPower, CosmoPowerDerived
+from .foreground import Foreground # noqa F401
+from .bandpass import BandPass # noqa F401
+from .cosmopower import CosmoPower, CosmoPowerDerived  # noqa F401
 from .ccl import CCL  # noqa: F401
 
 try: