package release

.github/workflows/ci.yml

@@ -14,35 +14,36 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install it
       run: |
         python -m pip install -U pip setuptools wheel
-        python -m pip install -e .[tests]
-    - name: Lint with flake8
+        python -m pip install .[tests] -v
+    - name: Lint with Ruff
+      uses: chartboost/ruff-action@v1
+      with:
+        args: "check"
+      continue-on-error: true
+    - name: Check types with mypy
       run: |
-        pip install flake8 wemake-python-styleguide
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --statistics
+        mypy ./kalman_detector/
+      continue-on-error: true
     - name: Run pytest and Generate coverage report
       run: |
-        pip install pytest pytest-cov
         pytest --cov=./ --cov-report=xml
       continue-on-error: false
     - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
-        token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
         name: codecov-umbrella
         fail_ci_if_error: true
-
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/release.yml

@@ -0,0 +1,30 @@
+name: Upload Python Package to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/kalman_detector
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel
+      - name: Build package
+        run: |
+          python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -1,3 +1,55 @@
+# Created by https://www.toptal.com/developers/gitignore/api/macos,windows,linux,python,visualstudiocode
+# Edit at https://www.toptal.com/developers/gitignore?templates=macos,windows,linux,python,visualstudiocode
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### macOS Patch ###
+# iCloud generated files
+*.icloud
+
+### Python ###
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -20,7 +72,6 @@ parts/
 sdist/
 var/
 wheels/
-pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -50,6 +101,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+cover/
 
 # Translations
 *.mo
@@ -72,6 +124,7 @@ instance/
 docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -82,7 +135,9 @@ profile_default/
 ipython_config.py
 
 # pyenv
-.python-version
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -91,7 +146,22 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.lock
 
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
 
 # Celery stuff
@@ -127,3 +197,75 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+.benchmarks/
+
+# LSP config files
+pyrightconfig.json
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+.ionide
+
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# End of https://www.toptal.com/developers/gitignore/api/macos,windows,linux,python,visualstudiocode

README.md

@@ -5,21 +5,21 @@
 [![License](https://img.shields.io/github/license/pravirkr/kalman_detector)](https://github.com/pravirkr/kalman_detector/blob/main/LICENSE)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-Python Implementation of the Kalman filter detector for detecting smoothly variying signals buried in gaussian noise (like Fast Radio Bursts).
+A Python Implementation of a Kalman filter detector for detecting smoothly variying signals hidden in gaussian noise, such as Fast Radio Bursts (FRBs).
 
-The detection statistic is designed to receive I(f), a sequence of observed "amplitudes" (where f is an arbitrary indexed parameter) and decide between:
+The detection statistic is designed to process `I(f)`, a sequence of observed "amplitudes" (where `f` is an arbitrary indexed parameter), and decide between the following hypotheses:
 
-```
+```markdown
 H0: I(f) = N(f)         Pure gaussian noise
-H1: I(f) = A(f) + N(f)  A(f) is a smooth gaussian process with the smoothness parameter unknown. 
+H1: I(f) = A(f) + N(f)  A(f) is a smooth gaussian process with an unknown smoothness parameter. 
 ```
 
 ## Installation
 
 The quickest way to install the package is to use [pip](https://pip.pypa.io):
 
 ```bash
-pip install -U git+https://github.com/pravirkr/kalman_detector
+pip install -U kalman_detector
 ```
 
 ## Usage
@@ -32,31 +32,44 @@ kalman.prepare_fits(ntrials=10000)
 kalman.get_significance(spectrum)
 ```
 
+### Example
+
+An example script demonstrating how to use the Kalman detector can be found in the [examples](examples/frb_kalman.py) directory.
+
+|           |           |
+| --------- | --------- |
+| ![Kalman demo for FRB171003](examples/frb171003_kalman.png) | ![Kalman demo for FRB171004](examples/frb171004_kalman.png) |
+
 ### Efficiency
 
+An example efficiency plot can be generates using:
+
 ```python
 python -m kalman_detector.efficiency
 ```
 
 ## Citation
-Please cite [Kumar, Zackay & Law (2023)](https://ui.adsabs.harvard.edu/abs/2023arXiv230607914K) if you find this code useful in your research.
+
+Please cite [Kumar, Zackay & Law (2024)](https://ui.adsabs.harvard.edu/abs/2024ApJ...960..128K) if you find this code useful in your research.
 The BibTeX entry for the paper is:
 
 ```bash
-@article{Kumar:2023,
+@ARTICLE{2024ApJ...960..128K,
        author = {{Kumar}, Pravir and {Zackay}, Barak and {Law}, Casey J.},
-        title = "{Detecting Fast Radio Bursts with Spectral Structure using the Continuous Forward Algorithm}",
-      journal = {arXiv e-prints},
-     keywords = {Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics},
-         year = 2023,
-        month = jun,
-          eid = {arXiv:2306.07914},
-        pages = {arXiv:2306.07914},
-          doi = {10.48550/arXiv.2306.07914},
+        title = "{Detecting Fast Radio Bursts with Spectral Structure Using the Continuous Forward Algorithm}",
+      journal = {\apj},
+     keywords = {Radio astronomy, Radio transient sources, Astronomy data analysis, Astrostatistics techniques, Interstellar scintillation, 1338, 2008, 1858, 1886, 855, Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics},
+         year = 2024,
+        month = jan,
+       volume = {960},
+       number = {2},
+          eid = {128},
+        pages = {128},
+          doi = {10.3847/1538-4357/ad0964},
 archivePrefix = {arXiv},
        eprint = {2306.07914},
  primaryClass = {astro-ph.HE},
-       adsurl = {https://ui.adsabs.harvard.edu/abs/2023arXiv230607914K},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2024ApJ...960..128K},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
-```
+```