riptide-ffa 0.2.6__tar.gz → 0.2.7__tar.gz

{riptide_ffa-0.2.6 → riptide_ffa-0.2.7}/.github/workflows/CI.yml

@@ -23,9 +23,17 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           make install
+      - name: Build documentation
+        if: matrix.python-version == '3.12'
+        run: make docs
+      - name: Lint
+        run: make lint
       - name: Test
         run: |
-          make tests
+          make test
+      - name: Check source distribution
+        if: matrix.python-version == '3.12'
+        run: make check-sdist
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v5
         env:

riptide_ffa-0.2.7/.github/workflows/publish.yml

@@ -0,0 +1,36 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          make install
+
+      - name: Test
+        run: make test
+
+      - name: Build source distribution
+        run: python -m build --sdist
+
+      - name: Upload to PyPI
+        env:
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+          TWINE_USERNAME: __token__
+        run: python -m twine upload dist/*.tar.gz

{riptide_ffa-0.2.6 → riptide_ffa-0.2.7}/.readthedocs.yaml

@@ -9,7 +9,10 @@ build:
 
 python:
   install:
-    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
 
 sphinx:
   configuration: docs/source/conf.py

{riptide_ffa-0.2.6 → riptide_ffa-0.2.7}/CHANGELOG.md

@@ -4,16 +4,18 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 0.2.7 - 2026-09-20
+
+Internal refactoring and improvements: Fix documentation, add CI stages to check source distribution build, add linting with `ruff` and make a general code cleanup pass.
+
 ## 0.2.6 - 2026-09-10
 
 This version modernises the project layout and packaging, and fixes issues in candidate plotting and downsampled variance calculations.
 
 ### Fixed
 
-- Candidate plots now normalise each sub-integration independently for better contrast,
-  contributed by Dejiang Yin.
-- Corrected the downsampled variance calculation for factors very close to an integer,
-  thanks to Francesco Coti Zelati for reporting the issue.
+- Candidate plots now normalise each sub-integration independently for better contrast, contributed by Dejiang Yin.
+- Corrected the downsampled variance calculation for factors very close to an integer, thanks to Francesco Coti Zelati for reporting the issue.
 
 
 ## 0.2.5 - 2023-12-23

riptide_ffa-0.2.7/Makefile

@@ -0,0 +1,53 @@
+.DEFAULT_GOAL := help
+PKG = riptide-ffa
+DOCS_SPHINXOPTS = --fail-on-warning --nitpicky --keep-going
+
+check-sdist: ## Build and smoke-test the source distribution in a temporary virtualenv
+	@set -eu; \
+	tmpdir="$$(mktemp -d)"; \
+	on_exit() { \
+		status=$$?; \
+		if [ "$$status" -eq 0 ]; then \
+			printf '\033[1;32m✅ Source distribution smoke test passed\033[0m\n'; \
+		else \
+			printf '\033[1;31m❌ Source distribution smoke test failed\033[0m\n' >&2; \
+		fi; \
+		rm -rf "$$tmpdir"; \
+		exit "$$status"; \
+	}; \
+	trap on_exit EXIT; \
+	python -m build --sdist --outdir "$$tmpdir/dist"; \
+	python -m venv "$$tmpdir/venv"; \
+	"$$tmpdir/venv/bin/python" -m pip install "$$tmpdir"/dist/*.tar.gz; \
+	cd "$$tmpdir"; \
+	"$$tmpdir/venv/bin/python" -c "import riptide; print(riptide.__version__)"; \
+	"$$tmpdir/venv/bin/rffa" --help >/dev/null; \
+	"$$tmpdir/venv/bin/rseek" --help >/dev/null
+
+docs: ## Build clean HTML documentation in docs/build/html
+	$(MAKE) -C docs clean html SPHINXOPTS="$(DOCS_SPHINXOPTS)"
+
+install: ## Install the package in editable mode with dev and docs dependencies
+	pip install -e '.[dev,docs]'
+
+lint: ## Run the linter
+	ruff check src tests
+
+# GLORIOUS hack to autogenerate Makefile help
+# This simply parses the double hashtags that follow each Makefile command
+# https://marmelab.com/blog/2016/02/29/auto-documented-makefile.html
+help: ## Print this help message
+	@echo "Makefile help for ${PKG}"
+	@echo "===================================================================="
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}'
+
+test: ## Run the unit tests and print a coverage report
+	pytest --cov=src/ --cov-report=term-missing
+
+ci: ## Run all checks for continuous integration
+	$(MAKE) docs
+	$(MAKE) lint
+	$(MAKE) test
+	$(MAKE) check-sdist
+
+.PHONY: check-sdist docs install lint help test ci

{riptide_ffa-0.2.6 → riptide_ffa-0.2.7}/PKG-INFO

@@ -1,58 +1,43 @@
 Metadata-Version: 2.4
 Name: riptide-ffa
-Version: 0.2.6
+Version: 0.2.7
 Summary: Pulsar searching with the Fast Folding Algorithm (FFA)
 Author-email: Vincent Morello <vmorello@gmail.com>
 Maintainer-email: Vincent Morello <vmorello@gmail.com>
-License: MIT License
-        
-        Copyright (c) 2017-2021 Vincent Morello
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-        
-Project-URL: homepage, https://github.com/vmorello/riptide
-Project-URL: documentation, https://riptide-ffa.readthedocs.io
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/v-morello/riptide
+Project-URL: Documentation, https://riptide-ffa.readthedocs.io
+Project-URL: Repository, https://github.com/v-morello/riptide
+Project-URL: Issues, https://github.com/v-morello/riptide/issues
 Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: C
-Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: C++
 Classifier: Operating System :: Unix
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Topic :: Scientific/Engineering :: Astronomy
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: astropy
-Requires-Dist: pandas
-Requires-Dist: schema
-Requires-Dist: pyyaml
-Requires-Dist: threadpoolctl
-Requires-Dist: pytest
-Requires-Dist: pytest-cov
-Requires-Dist: matplotlib
-Requires-Dist: numpy
+Requires-Dist: astropy>=5.0
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: numpy>=1.23
+Requires-Dist: pandas>=1.5
+Requires-Dist: pydantic<3,>=2
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: threadpoolctl>=3.1
+Provides-Extra: docs
+Requires-Dist: sphinx<8,>=7.4; python_version < "3.11" and extra == "docs"
+Requires-Dist: sphinx<9,>=8.2; python_version >= "3.11" and extra == "docs"
+Requires-Dist: sphinx-rtd-theme<4,>=3; extra == "docs"
 Provides-Extra: dev
-Requires-Dist: build; extra == "dev"
-Requires-Dist: twine; extra == "dev"
+Requires-Dist: build>=1.0; extra == "dev"
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: ruff>=0.11; extra == "dev"
+Requires-Dist: twine>=4.0; extra == "dev"
 Dynamic: license-file
 
 [![arXiv](http://img.shields.io/badge/astro.ph-2004.03701-B31B1B.svg)](https://arxiv.org/abs/2004.03701)   ![License](https://img.shields.io/badge/License-MIT-green.svg)   ![Python versions](https://img.shields.io/pypi/pyversions/riptide-ffa.svg)  ![CI status](https://github.com/v-morello/riptide/actions/workflows/CI.yml/badge.svg?branch=master)   [![codecov](https://codecov.io/gh/v-morello/riptide/branch/master/graph/badge.svg)](https://codecov.io/gh/v-morello/riptide)
@@ -102,7 +87,7 @@ And then in the base directory of `riptide` run
 make install
 ```
 
-This simply runs ``pip install`` in [editable mode](https://pip.pypa.io/en/latest/reference/pip_install/#editable-installs), which means you can freely edit the code. It also installs any required dependencies with ``pip`` that are not present already. The installer also adds links to two command-line apps in your python environment using [console_scripts entry points](https://python-packaging.readthedocs.io/en/latest/command-line-scripts.html):  
+This runs ``pip install`` in [editable mode](https://pip.pypa.io/en/latest/reference/pip_install/#editable-installs), which means you can freely edit the code. It also installs the development and documentation dependencies. The installer adds links to two command-line apps in your python environment using [console_scripts entry points](https://python-packaging.readthedocs.io/en/latest/command-line-scripts.html):
 
 * `rffa`: The full end-to-end pipeline to search multiple DM trials, see below for details on how to use it.
 * `rseek`: A lightweight app to search a single time series and print significant candidates found, useful for quick data checks.
@@ -117,4 +102,3 @@ And you should see the full help of both applications.
 
 
 
-

{riptide_ffa-0.2.6 → riptide_ffa-0.2.7}/README.md

@@ -45,7 +45,7 @@ And then in the base directory of `riptide` run
 make install
 ```
 
-This simply runs ``pip install`` in [editable mode](https://pip.pypa.io/en/latest/reference/pip_install/#editable-installs), which means you can freely edit the code. It also installs any required dependencies with ``pip`` that are not present already. The installer also adds links to two command-line apps in your python environment using [console_scripts entry points](https://python-packaging.readthedocs.io/en/latest/command-line-scripts.html):  
+This runs ``pip install`` in [editable mode](https://pip.pypa.io/en/latest/reference/pip_install/#editable-installs), which means you can freely edit the code. It also installs the development and documentation dependencies. The installer adds links to two command-line apps in your python environment using [console_scripts entry points](https://python-packaging.readthedocs.io/en/latest/command-line-scripts.html):
 
 * `rffa`: The full end-to-end pipeline to search multiple DM trials, see below for details on how to use it.
 * `rseek`: A lightweight app to search a single time series and print significant candidates found, useful for quick data checks.
@@ -60,4 +60,3 @@ And you should see the full help of both applications.
 
 
 
-

riptide_ffa-0.2.7/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

riptide_ffa-0.2.7/docs/source/conf.py

@@ -0,0 +1,58 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+
+
+# -- Project information -----------------------------------------------------
+
+project = "riptide-ffa"
+copyright = "2021, Vincent Morello"
+author = "Vincent Morello"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+# NOTE: sphinx.ext.autosectionlabel makes it easy to reference other
+# sections in the docs
+# See: https://stackoverflow.com/a/54843636
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx_rtd_theme",
+    "sphinx.ext.autosectionlabel",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+nitpick_ignore = [
+    ("py:class", "ndarray"),
+    ("py:class", "optional"),
+]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+pygments_style = "sphinx"

riptide_ffa-0.2.7/docs/source/docker.rst

@@ -0,0 +1,18 @@
+Docker Image
+============
+
+The riptide `Dockerfile`_ is located in the ``docker`` subdirectory. To build the image, clone the repository and in its base directory type:
+
+.. _`Dockerfile`: https://github.com/v-morello/riptide/blob/master/docker/Dockerfile
+
+.. code-block:: console
+
+    make docker
+
+Which builds an image named ``riptide-ffa``. Both python and ipython are installed within the docker image. To start a container:
+
+.. code-block:: console
+
+    docker run -it --rm riptide-ffa
+
+Feel free to adapt the Dockerfile to your needs. Refer to your favourite docker cheat sheet for further information.

riptide_ffa-0.2.7/docs/source/index.rst

@@ -0,0 +1,52 @@
+riptide: Finding pulsars with the Fast Folding Algorithm (FFA)
+==============================================================
+
+.. image:: http://img.shields.io/badge/astro.ph-2004.03701-B31B1B.svg
+   :target: https://arxiv.org/abs/2004.03701
+   :alt: arXiv
+  
+.. image:: https://github.com/v-morello/riptide/actions/workflows/CI.yml/badge.svg?branch=master
+   :alt: Build status
+  
+.. image:: https://codecov.io/gh/v-morello/riptide/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/v-morello/riptide
+   :alt: Coverage
+
+
+``riptide`` ("sea\ **r**\ ch\ **i**\ ng for **p**\ ulsars in the **ti**\ me **d**\ omain") is a pulsar searching
+package that implements the Fast Folding Algorithm (FFA), the theoretically optimal search method
+for periodic signals. Its interface is entirely in python while the core algorithms are implemented
+in C++. riptide provides:  
+
+* A library of functions and classes to manipulate and search individual dedispersed time series  
+* A pipeline executable to process a set of DM trials and output a list of candidate files, plots and other data products
+
+
+Citation
+--------
+
+If using ``riptide`` contributes to a project that leads to a scientific publication, please cite the article:  
+`Optimal periodicity searching: Revisiting the Fast Folding Algorithm for large scale pulsar surveys`__
+
+__ https://arxiv.org/abs/2004.03701
+
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Contents:
+
+   installation
+   quickstart
+   kernfuncs
+   pipeline
+   docker
+   reference
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+

riptide_ffa-0.2.7/docs/source/installation.rst

@@ -0,0 +1,31 @@
+Installation
+============
+
+The easiest method is to use pip install, which pulls the latest release from PyPI and installs all required dependencies:
+
+.. code-block:: console
+
+   pip install riptide-ffa
+
+
+Alternatively you can clone the repository and run ``make install``
+
+.. code-block:: console
+
+   git clone https://github.com/v-morello/riptide
+   cd riptide/
+   make install
+
+This runs ``pip install`` in `editable mode`_, which means you can freely edit the code.
+It also installs the development and documentation dependencies. You can check that it all works
+by running the test suite in a Python or IPython console:
+
+    >>> import riptide
+    >>> riptide.test()
+
+.. _`editable mode`: https://pip.pypa.io/en/latest/reference/pip_install/#editable-installs
+
+There should also now be two command-line apps in your python environment:
+
+* ``rseek``: A lightweight app to search a single time series and print significant candidates found, useful for quick data checks. See :ref:`The rseek command-line app`.
+* ``rffa``: The full end-to-end pipeline to search multiple DM trials, see :ref:`Using the Pipeline`.

riptide_ffa-0.2.7/docs/source/kernfuncs.rst

@@ -0,0 +1,13 @@
+FFA kernel functions
+====================
+
+The python interface of ``riptide`` exposes some lower-level functions related to calculating the folding transform (interchangeably called FFA transform) of input data at some base integer period.
+There is also a kernel function to calculate S/N. These are:  
+
+* ``ffa2``: FFA transform of a two-dimensional input that represents a pulse stack. The ``m`` lines of the input represent pulses in chronological order, and the ``p`` columns represent the phase dimension  
+* ``ffa1``: FFA transform of a one-dimensional input, that represents a time series. The function simply selects the largest number of entire pulses that fit in the data, reshapes them into a two-dimensional array, and calls ``ffa2()``  
+* ``ffafreq``: Returns the trial folding frequencies corresponding to every line in the output of an FFA transform  
+* ``ffaprd``: Same as ``ffafreq``, but returns trial periods instead
+* ``boxcar_snr``: Compute the S/N ratio of pulse profile(s) by concolving them with a range of boxcar filters with different widths.
+
+See :ref:`API Reference` for further details.