Merge pull request #32 from LabForComputationalVision/pyprojecttoml

Switch all metadata to pyproject.toml

.gitignore

@@ -39,3 +39,6 @@ docs/_build
 docs/api
 
 .idea
+
+# created automatically by setuptools.scm, don't track
+version.py

.readthedocs.yml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "mambaforge-4.10"
+    python: "3.10"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -24,9 +24,9 @@ formats:
   - htmlzip
 
 # Optionally set the version of Python and requirements required to build your docs
-conda:
-  environment: docs/environment.yml
 python:
   install:
     - method: pip
       path: .
+      extra_requirements:
+        - docs

CITATION.cff

@@ -17,9 +17,8 @@ authors:
   given-names: Nikhil
 - family-names: Ward
   given-names: Brian
-orcid: https://orcid.org/0000-0000-0000-0000
 title: "Pyrtools: tools for multi-scale image processing"
-version: v1.0.3
+version: v1.0.4
 date-released: 2023-11-20
 doi: 10.5281/zenodo.10161031
 url: "https://github.com/LabForComputationalVision/pyrtools"

README.md

@@ -6,7 +6,7 @@
 [![Build Status](https://github.com/LabForComputationalVision/pyrtools/workflows/build/badge.svg)](https://github.com/LabForComputationalVision/pyrtools/actions?query=workflow%3Abuild)
 [![Documentation Status](https://readthedocs.org/projects/pyrtools/badge/?version=latest)](https://pyrtools.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/137527035.svg)](https://zenodo.org/doi/10.5281/zenodo.10161031)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/LabForComputationalVision/pyrtools/v1.0.3?filepath=TUTORIALS%2F)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/LabForComputationalVision/pyrtools/v1.0.4?filepath=TUTORIALS%2F)
 [![codecov](https://codecov.io/gh/LabForComputationalVision/pyrtools/branch/main/graph/badge.svg?token=Ei9TYftdYi)](https://codecov.io/gh/LabForComputationalVision/pyrtools)
 
 Briefly, the tools include:
@@ -20,10 +20,11 @@ Briefly, the tools include:
     auto-scaling options, rounding to integer zoom factors to avoid
     resampling artifacts, and useful labeling (dimensions and gray-range).
 
-This is a python 3 port of Eero Simoncelli's matlabPyrTools, but it
-does not attempt to recreate all of the matlab code from
-matlabPyrTools. The goal is to create a Python interface for the C
-code at the heart of matlabPyrTools.
+This is a python 3 port of Eero Simoncelli's
+[matlabPyrTools](https://github.com/LabForComputationalVision/matlabPyrTools),
+but it does not attempt to recreate all of the matlab code from matlabPyrTools.
+The goal is to create a Python interface for the C code at the heart of
+matlabPyrTools.
 
 **NOTE**: If you are only interested in the complex steerable pyramid, we have a
 pytorch implementation in the
@@ -49,19 +50,6 @@ want the changes you make in the directory to be reflected in your
 install) from the root directory of this project. The core of this
 code is the C code, and the pip install will compile it nicely.
 
-## Dependencies
-
-Dependencies are documented in `setup.py`.
-
-IPython is optional. If it's not installed,
-`pyrtools.display_tools.animshow` must be called with `as_html5=False`
-(but since this is for displaying the animated image in a Jupyter /
-IPython notebook, you probably won't need that functionality).
-
-For the C code to compile, we require `gcc` version >= 6, because of
-[this
-issue](https://stackoverflow.com/questions/46504700/gcc-compiler-not-recognizing-fno-plt-option)
-
 # Pyramid resources
 
 If you would like to learn more about pyramids and why they're helpful
@@ -78,23 +66,9 @@ for image processing, here are some resources to get you started:
  - Notes from Eero Simoncelli on [the Steerable
    Pyramid](http://www.cns.nyu.edu/~eero/STEERPYR/)
 
-# Authors
-
-Rob Young and Eero Simoncelli, 7/13
-
-William Broderick, 6/17
-
-William Broderick, Pierre-Étienne Fiquet, Zhuo Wang, Zahra Kadkhodaie,
-Nikhil Parthasarathy, and the Lab for Computational Vision, 4/19
-
 # Usage:
 
-method parameters mimic the matlab function parameters except that there's no
-need to pass pyr or pind, since the pyPyrTools version pyr and pyrSize are
-properties of the class.
-
-- load modules (note that if you installed via pip, you can skip the
-  first two lines):
+- load modules:
 ```
 import pyrtools as pt
 ```
@@ -109,41 +83,29 @@ pyr = pt.pyramids.LaplacianPyramid(img)
 recon_img = pyr.recon_pyr()
 ```
 
-Please see `TUTORIALS/02_pyramids.ipynb` for more examples.  You can
-start this with: `jupyter notebook 02_pyramids.ipynb` if you have iPython
-and Jupyter installed.
+Please see `TUTORIALS/02_pyramids.ipynb` for more examples.
 
-# Testing
+# For developres
 
-All code should be considered a beta release.  By that we mean that it is being
-actively developed and tested.  You can find unit tests in
-`TESTS/unitTests.py` and run them with `python TESTS/unitTests.py`.
+## Testing
 
-If you're using functions or parameters that do not have associated unit
-tests you should test this yourself to make sure the results are correct.
-You could then submit your test code, so that we can build more complete
-unit tests.
+You can find unit tests in `TESTS/unitTests.py` and run them with `python
+TESTS/unitTests.py`.
 
-# Build the documentation
+## Build the documentation
 
 NOTE: If you just want to read the documentation, you do not need to
 do this; documentation is built automatically on
 [readthedocs](https://pyrtools.readthedocs.io/en/latest/).
 
 However, it can be built locally as well. You would do this if you've
 made changes locally to the documentation (or the docstrings) that you
-would like to examine before pushing. The virtual environment required
-to do so is defined in `docs/environment.yml`, so to create that
-environment and build the docs, do the following from the project's
-root directory:
+would like to examine before pushing.
 
 ```
-# install sphinx and required packages to build documentation
-conda env create -f docs/environment.yml
-# activate the environment
-conda activate pyrtools_docs
-# install pyrtools
-pip install -e .
+# create a new virtual environment and then...
+# install pyrtools with sphinx and documentation-related dependencies
+pip install -e .[docs]
 # build documentation
 cd docs/
 make html
@@ -152,10 +114,3 @@ make html
 The index page of the documentation will then be located at
 `docs/_build/html/index.html`, open it in your browser to navigate
 around.
-
-The `pyrtools_docs` environment you're creating contains the package
-`sphinx` and several extensions for it that are required to build the
-documentation. You also need to install `pyrtools` from your local
-version so that `sphinx` can import the library and grab all of the
-docstrings (you're installing the local version so you can see all the
-changes you've made).

docs/index.rst

@@ -10,7 +10,7 @@
 		     :target: https://github.com/LabForComputationalVision/pyrtools/actions?query=workflow%3Abuild
 
 .. |binder| image:: https://mybinder.org/badge_logo.svg
-		    :target: https://mybinder.org/v2/gh/LabForComputationalVision/pyrtools/v1.0.3?filepath=TUTORIALS%2F
+		    :target: https://mybinder.org/v2/gh/LabForComputationalVision/pyrtools/v1.0.4?filepath=TUTORIALS%2F
 
 .. |doi| image:: https://zenodo.org/badge/137527035.svg
   :target: https://zenodo.org/doi/10.5281/zenodo.10161031

docs/installation.rst

@@ -37,4 +37,4 @@ When installing from source on Linux or Mac, we require ``gcc`` version >= 6 in
 order for the C code to compile, because of `this issue
 <https://stackoverflow.com/questions/46504700/gcc-compiler-not-recognizing-fno-plt-option>`_
 
-When installing from source on Windows, Microsoft Visual C++ 14.0 or greater is required, which can be obtained with `Microsoft C++ Build Tools <https://visualstudio.microsoft.com/visual-cpp-build-tools/`_.
+When installing from source on Windows, Microsoft Visual C++ 14.0 or greater is required, which can be obtained with `Microsoft C++ Build Tools <https://visualstudio.microsoft.com/visual-cpp-build-tools/>`_.

docs/quickstart.rst

@@ -11,14 +11,6 @@ In the python interpreter, then call::
 
   import pyrtools as pt
 
-which should run without errors if the install worked correctly. If
-you have an issue with the installation, it will most likely be with
-the compilation of the C code. There is hopefully a warning of this
-when you import the library, but if you get an error message along the
-lines of `lib not defined` when attempting to build a pyramid or call
-the functions `corrDn`, `upConv`, or `pointOp`, this is probably
-what's at fault.
-
 Create pyramid::
 
   pyr = pt.pyramids.LaplacianPyramid(img)
@@ -28,7 +20,7 @@ Reconstruct image from pyramid::
   recon_img = pyr.recon_pyr()
 
 For more details, see the jupyter notebooks included in the
-`TUTORIALS/` directory, static versions of which are linked in the
+``TUTORIALS/`` directory, static versions of which are linked in the
 navigation sidebar. You can play around with a live version of them in
 order to test out the code before downloading on `binder
-<https://mybinder.org/v2/gh/LabForComputationalVision/pyrtools/v1.0.3?filepath=TUTORIALS%2F>`_
+<https://mybinder.org/v2/gh/LabForComputationalVision/pyrtools/v1.0.4?filepath=TUTORIALS%2F>`_

pyproject.toml

@@ -1,3 +1,51 @@
+[project]
+name = "pyrtools"
+dynamic = ["version"]
+authors = [{name="Pyrtools authors"}]
+description = "Python tools for multi-scale image processing, including Laplacian pyramids, Wavelets, and Steerable Pyramids."
+readme = "README.md"
+requires-python = ">=3.7"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Intended Audience :: Science/Research",
+]
+keywords = ['image processing', 'visual information processing', 'computational models']
+
+dependencies = ['numpy>=1.1',
+                'scipy>=0.18',
+                'matplotlib>=1.5',
+                'tqdm>=4.29',
+                'requests>=2.21']
+
+[project.optional-dependencies]
+docs = [
+  'sphinx',
+  'numpydoc',
+  # because of this issue:
+  # https://nbsphinx.readthedocs.io/en/0.6.0/installation.html#Pygments-Lexer-for-Syntax-Highlighting
+  'ipython',
+  'nbsphinx',
+  'nbsphinx_link',
+  'sphinxcontrib-apidoc',
+  # fix sphinx 7 incompatibility issue
+  'sphinx_rtd_theme>=1.3.0rc1'
+]
+
 [build-system]
-requires = ["setuptools", "wheel"]
+requires = ["setuptools", "wheel", "setuptools-scm[toml]"]
 build-backend = "setuptools.build_meta"
+
+[project.urls]
+"Homepage" = "https://github.com/LabForComputationalVision/pyrtools"
+"Documentation" = "https://pyrtools.readthedocs.io/en/latest/"
+"Download" = "https://zenodo.org/records/10403034"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools_scm]
+write_to = "src/pyrtools/version.py"
+version_scheme = 'python-simplified-semver'
+local_scheme = 'no-local-version'

setup.py

@@ -2,15 +2,6 @@
 
 from wheel.bdist_wheel import bdist_wheel
 from setuptools import setup, Extension
-import importlib
-import os
-
-# copied from kymatio's setup.py: https://github.com/kymatio/kymatio/blob/master/setup.py
-pyrtools_version_spec = importlib.util.spec_from_file_location('pyrtools_version',
-                                                               'pyrtools/version.py')
-pyrtools_version_module = importlib.util.module_from_spec(pyrtools_version_spec)
-pyrtools_version_spec.loader.exec_module(pyrtools_version_module)
-VERSION = pyrtools_version_module.version
 
 # Adapted from the cibuildwheel example https://github.com/joerick/python-ctypes-package-sample
 # it marks the wheel as not specific to the Python API version.
@@ -25,33 +16,15 @@ def get_tag(self):
 
 
 setup(
-    name='pyrtools',
-    version=VERSION,
-    long_description=open('README.md', 'r').read(),
-    long_description_content_type='text/markdown',
-    description='Python tools for multi-scale image processing, including Laplacian pyramids, Wavelets, and Steerable Pyramids',
-    license='MIT',
-    url='https://github.com/LabForComputationalVision/pyrtools',
-    author='Eero Simoncelli',
-    author_email='[email protected]',
-    keywords='multi-scale image-processing',
-    packages=['pyrtools', 'pyrtools.pyramids', 'pyrtools.tools', 'pyrtools.pyramids.c'],
-    package_data={'': ['*.h', 'LICENSE']},
-    install_requires=['numpy>=1.1',
-                      'scipy>=0.18',
-                      'matplotlib>=1.5',
-                      'tqdm>=4.29',
-                      'requests>=2.21'],
     ext_modules=[Extension('pyrtools.pyramids.c.wrapConv',
-                           sources=['pyrtools/pyramids/c/py.c',
-                                    'pyrtools/pyramids/c/convolve.c',
-                                    'pyrtools/pyramids/c/edges.c',
-                                    'pyrtools/pyramids/c/wrap.c',
-                                    'pyrtools/pyramids/c/internal_pointOp.c'],
-                           depends=['pyrtools/pyramids/c/meta.h',
-                                    'pyrtools/pyramids/c/convolve.h',
-                                    'pyrtools/pyramids/c/internal_pointOp.h'],
+                           sources=['src/pyrtools/pyramids/c/py.c',
+                                    'src/pyrtools/pyramids/c/convolve.c',
+                                    'src/pyrtools/pyramids/c/edges.c',
+                                    'src/pyrtools/pyramids/c/wrap.c',
+                                    'src/pyrtools/pyramids/c/internal_pointOp.c'],
+                           depends=['src/pyrtools/pyramids/c/meta.h',
+                                    'src/pyrtools/pyramids/c/convolve.h',
+                                    'src/pyrtools/pyramids/c/internal_pointOp.h'],
                            extra_compile_args=['-fPIC', '-shared'])],
     cmdclass={"bdist_wheel": WheelABINone},
-    tests='TESTS',
     )