Merge pull request #1 from dhuppenkothen/GPTool_fixes

Fixes for GP Modeling code

.github/workflows/ci_test.yml

@@ -25,6 +25,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+          repository: ${{github.event.pull_request.head.repo.full_name}}
 
       # Found this solution at
       # https://monadical.com/posts/filters-github-actions.html#Case-2-Pull-request
@@ -45,8 +48,9 @@ jobs:
   ci-tests:
     needs: check_commit
     if: ${{ needs.check_commit.outputs.match != 'true' }}
-    name: ${{ matrix.os }}, ${{ matrix.tox_env }}
+    # name: ${{ matrix.os }}, ${{ matrix.tox_env }}
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
     strategy:
       fail-fast: false
       matrix:
@@ -55,45 +59,71 @@ jobs:
           # we select only a few, in order to conserve resources. If you add
           # an additional environment, please include a comment to indicate
           # why it is useful.
-          - os: ubuntu-latest
+          - name: Black test
+            os: ubuntu-latest
             python: '3.10'
             tox_env: 'black'
+            experimental: false
+
           # Basic tests on the oldest & newest supported versions of Python,
           # recording coverage data for the latter.
-          - os: ubuntu-latest
+          - name: Py3.8 with old Astropy version
+            os: ubuntu-latest
             python: '3.8'
-            tox_env: 'py38-test'
-          - os: ubuntu-latest
+            tox_env: 'py38-test-astropy4-cov'
+            experimental: false
+
+          - name: Linux, Py3.10 with coverage
+            os: ubuntu-latest
             python: '3.10'
             tox_env: 'py310-test-cov'
+            experimental: false
 
           # Basic tests on alternative operating systems.
-          - os: windows-latest
-            python: '3.10'
-            tox_env: 'py310-test'
-          - os: macos-latest
-            python: '3.10'
-            tox_env: 'py310-test'
+          - name: Windows, Py3.11 with coverage
+            os: windows-latest
+            python: '3.11'
+            tox_env: 'py311-test-cov'
+            experimental: false
+
+          - name: Mac OS, Py3.11
+            os: macos-latest
+            python: '3.11'
+            tox_env: 'py311-test'
+            experimental: false
 
           # Test with all optional dependencies installed.
-          - os: ubuntu-latest
-            python: '3.10'
-            tox_env: 'py310-test-alldeps-cov'
+          - name: Linux, Py3.11 all dependencies and coverage
+            os: ubuntu-latest
+            python: '3.11'
+            tox_env: 'py311-test-alldeps-cov'
             use_remote_data: true
+            experimental: false
 
-          # Test with the various supported releases of Astropy.
-          - os: ubuntu-latest
-            python: '3.8'
-            tox_env: 'py38-test-astropy4-cov'
+          # Development version of dependencies
+          - name: Linux, Py3.11 with dev versions of dependencies
+            os: ubuntu-latest
+            python: '3.11'
+            tox_env: 'py311-test-devdeps'
+            experimental: false
 
-          - os: ubuntu-latest
-            python: '3.10'
-            tox_env: 'py310-test-astropy5'
+          # Test with all optional dependencies installed.
+          - name: Slow tests on Linux, Py3.11, all deps and coverage
+            os: ubuntu-latest
+            python: '3.11'
+            tox_env: 'py311-test-alldeps-cov'
+            use_remote_data: true
+            experimental: false
+            slow: true
 
-          # Development version of dependencies
-          - os: ubuntu-latest
-            python: '3.10'
-            tox_env: 'py310-test-devdeps'
+          # Test with all optional dependencies installed.
+          - name: Slow tests on Linux, Py3.11, basic deps and coverage
+            os: ubuntu-latest
+            python: '3.11'
+            tox_env: 'py311-test-cov'
+            use_remote_data: true
+            experimental: false
+            slow: true
 
     steps:
     - name: Check out repository
@@ -119,14 +149,19 @@ jobs:
         python -c "import pip; print(f'pip {pip.__version__}')"
         python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
         python -c "import tox; print(f'tox {tox.__version__}')"
-    - name: Run tests
-      if: "! matrix.use_remote_data"
-      run: tox -e ${{ matrix.tox_env }}
-    - name: Run tests with remote data
-      if: "matrix.use_remote_data"
+    - name: Run quick tests
+      if: "(! matrix.use_remote_data) && (! matrix.slow)"
+      run: tox -e ${{ matrix.tox_env }} --
+    - name: Run quick tests with remote data
+      if: "matrix.use_remote_data && (! matrix.slow)"
       run: |
         pip install pytest-remotedata
         tox -e ${{ matrix.tox_env }} -- --remote-data=any
+    - name: Run slow tests with remote data
+      if: "matrix.use_remote_data && matrix.slow"
+      run: |
+        pip install pytest-remotedata
+        tox -e ${{ matrix.tox_env }} -- --remote-data=any -m slow --run-slow
     - name: Upload coverage to codecov
       if: "endsWith(matrix.tox_env, '-cov')"
       uses: codecov/codecov-action@v3

docs/changes/737.feature.rst

@@ -0,0 +1,2 @@
+- Implemented the Lomb Scargle Fourier Transform (fast and slow versions)
+- Using which wrote the corresponding :class:`LombScargleCrossspectrum` and :class:`LombScarglePowerspectrum`

docs/changes/739.feature.rst

@@ -2,7 +2,7 @@ This is a JAX implementation of the GP tool by `Hubener et al <https://arxiv.org
 for QPO detection and parameter analysis.
 
 This feature makes use of tinygp library for Gaussian Processes implementation, and jaxns for nested sampling,
-and is kept in the stingray.modeling.gpmodelling module.
+and is kept in the stingray.modeling.gpmodeling module.
 
 Main features of the module are:
 

docs/changes/753.bugfix.rst

@@ -0,0 +1 @@
+Update tstart and tseg when using Lightcurve.truncate()

docs/changes/755.breaking.rst

@@ -0,0 +1 @@
+Remove legacy interface and obsolete large data machinery.

docs/changes/756.bugfix.rst

@@ -0,0 +1 @@
+Changed list comprehension to generator expression to reduce memory usage.

docs/changes/757.trivial.rst

@@ -0,0 +1 @@
+Speedup creation of events in ``EventList.from_lc``

docs/changes/760.bugfix.rst

@@ -0,0 +1,2 @@
++ Fix a bug with segment sizes not exact multiples of dt when dealing with light curves
++ Fix a bug when light curve segments contain complex values

docs/core.rst

@@ -1,9 +1,9 @@
 Core Stingray Functionality
 ***************************
 
-Here we show how many of the core Stingray classes and methods 
-work in practice. We start with basic data constructs for 
-event data and light curve data, and then show how to produce 
+Here we show how many of the core Stingray classes and methods
+work in practice. We start with basic data constructs for
+event data and light curve data, and then show how to produce
 various Fourier products from these data sets.
 
 Working with Event Data
@@ -85,3 +85,20 @@ Multi-taper Periodogram
    :maxdepth: 2
 
    notebooks/Multitaper/multitaper_example.ipynb
+
+
+Lomb Scargle Crossspectrum
+--------------------------
+.. toctree::
+   :maxdepth: 2
+
+   notebooks/LombScargle/LombScargleCrossspectrum_tutorial.ipynb
+
+
+Lomb Scargle Powerspectrum
+--------------------------
+
+.. toctree::
+   :maxdepth: 2
+
+   notebooks/LombScargle/LombScarglePowerspectrum_tutorial.ipynb

docs/dataexplo.rst

@@ -26,3 +26,15 @@ black hole binary using NICER data.
    :maxdepth: 2
 
    notebooks/Spectral Timing/Spectral Timing Exploration.ipynb
+
+
+Studying very slow variability with the Lomb-Scargle periodogram
+================================================================
+
+In this Tutorial, we will show an example of how to use the Lomb-Scargle
+periodogram and cross spectrum to study very slow variability in a light curve.
+
+.. toctree::
+   :maxdepth: 2
+
+   notebooks/LombScargle/Very slow variability with Lomb-Scargle methods.ipynb

docs/index.rst

@@ -21,26 +21,35 @@ Features
 Current Capabilities
 --------------------
 
-Currently implemented functionality in this library comprises:
+1. Data handling and simulation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 * loading event lists from fits files of a few missions (RXTE/PCA, NuSTAR/FPM, XMM-Newton/EPIC, NICER/XTI)
 * constructing light curves from event data, various operations on light curves (e.g. addition, subtraction, joining, and truncation)
+* simulating a light curve with a given power spectrum
+* simulating a light curve from another light curve and a 1-d (time) or 2-d (time-energy) impulse response
+* simulating an event list from a given light curve _and_ with a given energy spectrum
 * Good Time Interval operations
-* power spectra in Leahy, rms normalization, absolute rms and no normalization
-* averaged power spectra
-* dynamical power spectra
+
+2. Fourier methods
+~~~~~~~~~~~~~~~~~~
+* power spectra and cross spectra in Leahy, rms normalization, absolute rms and no normalization
+* averaged power spectra and cross spectra
+* dynamical power spectra and cross spectra
 * maximum likelihood fitting of periodograms/parametric models
 * (averaged) cross spectra
 * coherence, time lags
-* cross correlation functions
-* RMS spectra and lags (time vs energy, time vs frequency); *needs testing*
+* Variability-Energy spectra, like covariance spectra and lags *needs testing*
 * covariance spectra; *needs testing*
 * bispectra; *needs testing*
 * (Bayesian) quasi-periodic oscillation searches
-* simulating a light curve with a given power spectrum
-* simulating a light curve from another light curve and a 1-d (time) or 2-d (time-energy) impulse response
-* simulating an event list from a given light curve _and_ with a given energy spectrum
+* Lomb-Scargle periodograms and cross spectra
+
+3. Other time series methods
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 * pulsar searches with Epoch Folding, :math:`Z^2_n` test
+* Gaussian Processes for QPO studies
+* cross correlation functions
 
 Future Plans
 ------------
@@ -104,6 +113,20 @@ To install all required and recommended dependencies in a recent installation, y
 
     $ pip install astropy scipy matplotlib numpy h5py tqdm numba pint-pulsar emcee corner statsmodels pyfftw tbb
 
+For the Gaussian Process modeling in `stingray.modeling.gpmodeling`, you'll need the following extra packages
+
++ jax
++ jaxns
++ tensorflow
++ tensorflow-probability
++ tinygp
++ etils
++ typing_extensions
+
+Most of these are installed via ``pip``, but if you have an Nvidia GPU available, you'll want to take special care 
+following the installation instructions for jax and tensorflow(-probability) in order to enable GPU support and 
+take advantage of those speed-ups. 
+
 For development work, you will need the following extra libraries:
 
 + pytest

setup.cfg

@@ -39,7 +39,6 @@ all =
     pyfftw
     h5py
     pint-pulsar
-    zarr
     numcodecs
     pyyaml
     xarray
@@ -107,6 +106,7 @@ filterwarnings =
     ignore:Large Datasets may not be processed efficiently:UserWarning
     ignore:.*is a deprecated alias for:DeprecationWarning
     ignore:.*HIERARCH card will be created.*:
+    ignore:.*FigureCanvasAgg is non-interactive.*:UserWarning
 
 ;addopts = --disable-warnings
 

stingray/__init__.py

@@ -12,6 +12,7 @@
     from stingray.events import *
     from stingray.lightcurve import *
     from stingray.utils import *
+    from stingray.lombscargle import *
     from stingray.powerspectrum import *
     from stingray.crossspectrum import *
     from stingray.multitaper import *
@@ -22,4 +23,4 @@
     from stingray.stats import *
     from stingray.bispectrum import *
     from stingray.varenergyspectrum import *
-    from stingray.largememory import *
+    from stingray.lombscargle import *