Update docs

.git_archival.txt

@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.github/workflows/pytest.yml

@@ -1,15 +1,20 @@
 name: pytest
 
-# Only build PRs, the master branch, and releases.
+# Only build PRs, the main branch, and releases.
 on:
   pull_request:
   push:
     branches:
-      - master
+      - main
   release:
     types:
       - published
 
+# Cancel any previous run of the test job.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test:
 
@@ -19,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, ]  # macos, windows]  # Only Linux currently.
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.10, 3.11, 3.12, 3.13]
 
     env:
       # Used for coveralls flag
@@ -28,15 +33,9 @@ jobs:
 
     steps:
 
-      # Cancel any previous run of the test job; [pin v0.6.0]
-      - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@ce177499ccf9fd2aded3b0426c97e5434c2e8a73
-        with:
-          access_token: ${{ github.token }}
-
       # Checks-out your repository under $GITHUB_WORKSPACE
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           # Need to fetch more than the last commit so that setuptools_scm can
           # create the correct version string. If the number of commits since
@@ -52,21 +51,21 @@ jobs:
         run: git fetch origin 'refs/tags/*:refs/tags/*'
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements-dev.txt
+          python -m pip install .[all]
 
       - name: Test with pytest
         run: pytest --cov=pyfftlog --flake8
 
       - name: Coveralls
-        # [pin v20201129]
-        uses: AndreMiras/coveralls-python-action@f5fd5c309b39d01599fb92c72d4f7409ea78aec9
+        # [pin @develop@20230609]
+        uses: AndreMiras/coveralls-python-action@65c1672f0b8a201702d86c81b79187df74072505
         with:
           parallel: true
           flag-name: ${{ matrix.python-version }} (${{ matrix.os }})
@@ -77,22 +76,22 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Coveralls Finished
-      # [pin v20201129]
-      uses: AndreMiras/coveralls-python-action@f5fd5c309b39d01599fb92c72d4f7409ea78aec9
+      # [pin @develop@20230609]
+      uses: AndreMiras/coveralls-python-action@65c1672f0b8a201702d86c81b79187df74072505
       with:
         parallel-finished: true
 
   deploy:
     needs: test
     name: Deploy to PyPI
     runs-on: ubuntu-latest
-    # Only from the origin repository, not forks; only master and tags.
-    if: github.repository_owner == 'prisae' && (github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/'))
+    # Only from the origin repository, not forks; only main and tags.
+    if: github.repository_owner == 'emsig' && (github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/'))
 
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           # Need to fetch more than the last commit so that setuptools_scm can
           # create the correct version string. If the number of commits since
@@ -108,37 +107,34 @@ jobs:
         run: git fetch origin 'refs/tags/*:refs/tags/*'
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install wheel
-          pip install -r requirements-dev.txt
+          python -m pip install build setuptools-scm
 
       - name: Build source and wheel distributions
-        if: github.ref == 'refs/heads/master'
+        if: github.ref == 'refs/heads/main'
         run: |
           # Change setuptools-scm local_scheme to "no-local-version" so the
           # local part of the version isn't included, making the version string
           # compatible with Test PyPI.
-          sed --in-place "s/'root'/'local_scheme':'no-local-version','root'/g" setup.py
+          sed --in-place 's/version_file/local_scheme = "no-local-version"\nversion_file/g' pyproject.toml
 
       - name: Build source and wheel distributions
         run: |
           # Build source and wheel packages
-          python setup.py sdist
-          python setup.py bdist_wheel
+          python -m build
           echo ""
           echo "Generated files:"
           ls -lh dist/
 
       - name: Publish to Test PyPI
         if: success()
-        # Hash corresponds to v1.4.1
-        uses: pypa/gh-action-pypi-publish@54b39fb9371c0b3a6f9f14bb8a67394defc7a806
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.TEST_PYPI_PASSWORD }}
@@ -150,8 +146,7 @@ jobs:
       - name: Publish to PyPI
         # Only for releases
         if: success() && github.event_name == 'release'
-        # Hash corresponds to v1.4.1
-        uses: pypa/gh-action-pypi-publish@54b39fb9371c0b3a6f9f14bb8a67394defc7a806
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.PYPI_PASSWORD }}

.gitignore

@@ -4,6 +4,7 @@ __pycache__/
 # Sphinx
 docs/_build/
 docs/examples/
+docs/sg_execution_times.rst
 
 # Pytest and coverage related
 htmlcov

CHANGELOG.rst

@@ -2,6 +2,14 @@ Changelog
 #########
 
 
+v0.2.1 : pyproject.toml
+-----------------------
+
+**2024-10-18**
+
+Maintenance; changed from ``setup.py`` to ``pyproject.toml``.
+
+
 v0.2.0 : First packaged release
 -------------------------------
 

MANIFEST.in

@@ -1,8 +1,6 @@
 prune docs
 prune tests
 prune examples
-exclude requirements.txt
-exclude requirements-dev.txt
-exclude .readthedocs.yml
 exclude .gitignore
-exclude .coveragerc
+exclude .git_archival.txt
+exclude .gitattributes

Makefile

@@ -0,0 +1,48 @@
+help:
+	@echo "Commands:"
+	@echo ""
+	@echo "  install        install in editable mode"
+	@echo "  dev-install    install in editable mode with dev requirements"
+	@echo "  pytest         run the test suite and report coverage"
+	@echo "  flake8         style check with flake8"
+	@echo "  html           build docs (update existing)"
+	@echo "  html-clean     build docs (new, removing any existing)"
+	@echo "  preview        renders docs in Browser"
+	@echo "  linkcheck      check all links in docs"
+	@echo "  clean          clean up all generated files"
+	@echo ""
+
+install:
+	python -m pip install -e .
+
+dev-install:
+	python -m pip install -e .[all]
+
+.ONESHELL:
+pytest:
+	rm -rf .coverage htmlcov/ .pytest_cache/
+	pytest --cov=pyfftlog --mpl
+	coverage html
+
+flake8:
+	flake8 docs/conf.py pyfftlog/ tests/ examples/
+
+html:
+	cd docs && make html
+
+html-clean:
+	cd docs && rm -rf examples/* _build/ && make html
+
+preview:
+	xdg-open docs/_build/html/index.html
+
+linkcheck:
+	cd docs && make linkcheck
+
+clean:
+	python -m pip uninstall pyfftlog -y
+	rm -rf build/ dist/ .eggs/ pyfftlog.egg-info/ pyfftlog/version.py  # build
+	rm -rf */__pycache__/ */*/__pycache__/      # python cache
+	rm -rf .coverage htmlcov/ .pytest_cache/    # tests and coverage
+	rm -rf docs/_build/ docs/examples/*         # docs
+	rm docs/sg_execution_times.rst

README.rst

@@ -1,27 +1,10 @@
-.. image:: https://readthedocs.org/projects/pyfftlog/badge/?version=latest
-   :target: https://pyfftlog.readthedocs.io/en/latest
-   :alt: Documentation Status
-.. image:: https://github.com/prisae/pyfftlog/workflows/pytest/badge.svg?branch=master
-   :target: https://github.com/prisae/pyfftlog/actions
-   :alt: GitHub Actions
-.. image:: https://coveralls.io/repos/github/prisae/pyfftlog/badge.svg?branch=master
-   :target: https://coveralls.io/github/prisae/pyfftlog?branch=master
-   :alt: Coveralls
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3830364.svg
-   :target: https://doi.org/10.5281/zenodo.3830364
-   :alt: Zenodo DOI
-
-
-.. sphinx-inclusion-marker
-
-
 `pyfftlog` - A python version of FFTLog
 =======================================
 
 This is a python version of the logarithmic FFT code *FFTLog* as presented in
 Appendix B of `Hamilton (2000)
-<http://dx.doi.org/10.1046/j.1365-8711.2000.03071.x>`_ and published at
-`casa.colorado.edu/~ajsh/FFTLog <http://casa.colorado.edu/~ajsh/FFTLog>`_.
+<https://dx.doi.org/10.1046/j.1365-8711.2000.03071.x>`_ and published at
+`jila.colorado.edu/~ajsh/FFTLog <https://jila.colorado.edu/~ajsh/FFTLog>`_.
 
 A simple `f2py`-wrapper (`fftlog`) can be found on `github.com/prisae/fftlog
 <https://github.com/prisae/fftlog>`_.  Tests have shown that `fftlog` is a bit
@@ -62,8 +45,8 @@ Hankel transform.
 The FFTLog algorithm was originally proposed by `Talman (1978)
 <http://dx.doi.org/10.1016/0021-9991(78)90107-9>`_.
 
-*For the full documentation, see* `casa.colorado.edu/~ajsh/FFTLog
-<http://casa.colorado.edu/~ajsh/FFTLog>`_.
+*For the full documentation, see* `jila.colorado.edu/~ajsh/FFTLog
+<https://jila.colorado.edu/~ajsh/FFTLog>`_.
 
 
 Installation
@@ -92,7 +75,7 @@ All releases have a Zenodo-DOI, which can be found on `10.5281/zenodo.3830364
 <https://doi.org/10.5281/zenodo.3830364>`_.
 
 Be kind and give credits by citing `Hamilton (2000)
-<http://dx.doi.org/10.1046/j.1365-8711.2000.03071.x>`_. See the
+<https://dx.doi.org/10.1046/j.1365-8711.2000.03071.x>`_. See the
 `references-section
 <https://pyfftlog.readthedocs.io/en/stable/references.html>`_ in the manual for
 full references.

docs/conf.py

@@ -1,7 +1,6 @@
 import time
 import warnings
 from pyfftlog import __version__
-from sphinx_gallery.sorting import ExplicitOrder, FileNameSortKey
 
 # ==== 1. Extensions  ====
 
@@ -26,16 +25,17 @@
 
 # Sphinx gallery configuration
 sphinx_gallery_conf = {
-    'examples_dirs': '../examples',
-    'gallery_dirs': 'examples',
-    'subsection_order': ExplicitOrder([
-        '../examples/contrib',
-        ]),
+    'examples_dirs': [
+        '../examples',
+        ],
+    'gallery_dirs': [
+        'examples',
+        ],
     'capture_repr': ('_repr_html_', '__repr__'),
     # Patter to search for example files
     "filename_pattern": r"\.py",
     # Sort gallery example by file name instead of number of lines (default)
-    "within_subsection_order": FileNameSortKey,
+    "within_subsection_order": "FileNameSortKey",
     # Remove the settings (e.g., sphinx_gallery_thumbnail_number)
     'remove_config_comments': True,
     # Show memory
@@ -88,7 +88,6 @@
 html_theme = 'sphinx_rtd_theme'
 html_theme_options = {
     'logo_only': True,
-    'display_version': True,
     'prev_next_buttons_location': 'both',
 }
 html_static_path = ['_static']
@@ -109,12 +108,9 @@
 }
 
 htmlhelp_basename = 'pyfftlogdoc'
-
-
-# -- CSS fixes --
-def setup(app):
-    app.add_stylesheet("style.css")
-
+html_css_files = [
+    "style.css",
+]
 
 # ==== 4. Other Document Type Settings ====
 # Options for LaTeX output

docs/index.rst

@@ -7,7 +7,6 @@ pyfftlog
 Version: |version| ~ Date: |today|
 
 .. include:: ../README.rst
-  :start-after: sphinx-inclusion-marker
 
 .. toctree::
    :maxdepth: 2

docs/references.rst

@@ -7,7 +7,7 @@ References
    power spectrum: Monthly Notices of the Royal Astronomical Society, 312,
    pages 257--284; DOI: `10.1046/j.1365-8711.2000.03071.x
    <https://doi.org/10.1046/j.1365-8711.2000.03071.x>`_; Website of FFTLog:
-   `casa.colorado.edu/~ajsh/FFTLog <http://casa.colorado.edu/~ajsh/FFTLog>`_.
+   `jila.colorado.edu/~ajsh/FFTLog <https://jila.colorado.edu/~ajsh/FFTLog>`_.
 .. [Talm78] Talman, J. D., 1978, Numerical Fourier and Bessel transforms in
    logarithmic variables: Journal of Computational Physics, 29, pages 35--48;
    DOI: `10.1016/0021-9991(78)90107-9

examples/contrib/sinetransform.py

@@ -18,7 +18,7 @@
 """
 import pyfftlog
 import numpy as np
-import scipy.integrate
+import scipy as sp
 import matplotlib.pyplot as plt
 
 ###############################################################################
@@ -108,7 +108,7 @@
 Recon_Fun = np.zeros((len(t)))
 for i in range(len(t)):
     Recon_Fun[i] = (np.sqrt(2/np.pi)**-1) * \
-       scipy.integrate.trapz(f, a_f*np.sin(t[i]*f))
+       sp.integrate.trapezoid(f, a_f*np.sin(t[i]*f))
 
 # Plotting the input function and the reconstructed input function and also
 # the distribution of the a(f) vs f.

examples/fftlogtest.py

@@ -4,7 +4,7 @@
 
 This example is a translation of `fftlogtest.f` from the Fortran package
 `FFTLog`, which was presented in Appendix B of [Hami00]_ and published at
-http://casa.colorado.edu/~ajsh/FFTLog. It serves as an example for the python
+https://jila.colorado.edu/~ajsh/FFTLog. It serves as an example for the python
 package `pyfftlog` (which is a Python version of `FFTLog`), in the same manner
 as the original file `fftlogtest.f` serves as an example for Fortran package
 `FFTLog`.