Replaced setup.cfg and setup.py with pyproject.toml

docs/_build/_modules/waltlabtools/model.html

@@ -72,15 +72,13 @@
 
   <h1>Source code for waltlabtools.model</h1><div class="highlight"><pre>
 <span></span><span class="kn">from</span> <span class="nn">collections.abc</span> <span class="kn">import</span> <span class="n">Callable</span>
-<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Optional</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span>
 
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">from</span> <span class="nn">matplotlib.scale</span> <span class="kn">import</span> <span class="n">ScaleBase</span>
 
 <span class="kn">from</span> <span class="nn">.core</span> <span class="kn">import</span> <span class="n">coerce_array</span>
 
-<span class="n">EPS</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span><span class="o">.</span><span class="n">resolution</span>
-
 
 <div class="viewcode-block" id="Model">
 <a class="viewcode-back" href="../../waltlabtools.html#waltlabtools.model.Model">[docs]</a>

pyproject.toml

@@ -2,9 +2,57 @@
 # Minimum requirements for the build system to execute.
 requires = ["setuptools", "wheel"]
 
+[project]
+name = "waltlabtools"
+dynamic = ["version"]
+dependencies = [
+    "numpy>=1.11",
+    "scipy>=1.7",
+    "pandas>=1.3",
+    "matplotlib>=3.4",
+    "scikit-learn>=1.2",
+]
+requires-python = ">= 3.8"
+authors = [
+    {name = "Tyler Dougan", email = "tyler_dougan@hst.harvard.edu"}
+]
+description = "A collection of tools for biomedical research assay analysis in Python."
+readme = "README.rst"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+]
+
+[project.optional-dependencies]
+jax = ["jax"]
+numba = ["numba"]
+all = [
+    "jax",
+    "numba",
+    "jupyterlab",
+    "numexpr",
+    "bottleneck",
+    "jinja2",
+    "openpyxl"
+]
+
+[project.urls]
+Homepage = "https://github.com/tylerdougan/waltlabtools/"
+Documentation = "https://waltlabtools.readthedocs.io/en/latest/"
+PyPI = "https://pypi.org/project/waltlabtools/"
+"Issue Tracker" = "https://github.com/tylerdougan/waltlabtools/issues"
+Anaconda = "https://anaconda.org/tylerdougan/waltlabtools"
+
+[tool.setuptools.dynamic]
+version = {attr = "waltlabtools.__version__"}
+
 [tool.ruff.lint]
 select = ["E4", "E7", "E9", "F", "I", "UP", "B", "PD", "NPY", "RUF", "S", "A", "C", "ICN", "PIE", "SIM", "PLC", "PLE", "PLR", "PLW", "PERF", "FURB"]
-# "N", "D", "ARG"
 ignore = ["B028", "PLR0913", "RUF012", "C901", "PLR0912", "PLR0915", "PD101"]
 
 [tool.ruff.lint.pydocstyle]

requirements.txt

@@ -1,11 +1,12 @@
 # Required
-python >= 3.8
-scikit-learn
-numpy
-scipy
-matplotlib
-pandas
+python>=3.8
+numpy>=1.11
+scipy>=1.7
+pandas>=1.3
+matplotlib>=3.4
+scikit-learn>=1.2
 
 # Optional
 jax
 numba
+openpyxl

src/waltlabtools.egg-info/PKG-INFO

@@ -0,0 +1,133 @@
+Metadata-Version: 2.1
+Name: waltlabtools
+Version: 1.0.0b1
+Summary: A collection of tools for biomedical research assay analysis in Python.
+Home-page: https://github.com/tylerdougan/waltlabtools
+Download-URL: https://pypi.org/project/waltlabtools/#files
+Author: Tyler Dougan
+Author-email: tyler_dougan@hst.harvard.edu
+License: GNU General Public License v3 (GPLv3)
+Project-URL: Bug Tracker, https://github.com/tylerdougan/waltlabtools/issues
+Project-URL: Documentation, https://waltlabtools.readthedocs.io/README.html
+Project-URL: Conda, https://anaconda.org/tylerdougan/waltlabtools
+Keywords: python,numpy,modeling,curve-fitting,diagnostics,biomedical-data-science,calibration-curve,assay,elisa,concentrations,mosaic
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: matplotlib>=3.3
+Requires-Dist: numpy>=1.16
+Requires-Dist: pandas>=0.25
+Requires-Dist: scipy>=1.3
+Requires-Dist: scikit-learn>=0.21
+
+waltlabtools
+============
+
+.. image:: https://img.shields.io/conda/vn/tylerdougan/waltlabtools?label=Anaconda
+   :target: https://anaconda.org/tylerdougan/waltlabtools
+   :alt: Conda
+.. image:: https://img.shields.io/pypi/v/waltlabtools?label=PyPI
+   :target: https://pypi.org/project/waltlabtools
+   :alt: PyPI
+.. image:: https://img.shields.io/readthedocs/waltlabtools?label=Documentation
+   :target: https://waltlabtools.readthedocs.io/en/latest/
+   :alt: Documentation
+.. image:: https://img.shields.io/github/repo-size/tylerdougan/waltlabtools?label=GitHub
+   :target: https://github.com/tylerdougan/waltlabtools
+   :alt: GitHub
+
+
+A collection of tools for biomedical research assay analysis in Python.
+
+Key Features
+------------
+
+-  Analysis for assays such as
+   `digital ELISA <http://www.ncbi.nlm.nih.gov/pmc/articles/pmc2919230/>`__,
+   including single-molecule array (Simoa) assays
+-  Read instrument-generated files and calculate calibration curves,
+   concentrations, limits of detection, and more
+-  Free and open-source software under the
+   `GNU General Public License v3 <https://www.gnu.org/licenses/gpl-3.0.en.html>`__
+
+Getting Started
+---------------
+
+Installation
+^^^^^^^^^^^^
+
+You can install waltlabtools using
+`Anaconda <https://anaconda.org/tylerdougan/waltlabtools>`__ (recommended) or
+`PyPI <https://pypi.org/project/waltlabtools/>`__. If you're not comfortable
+with the command line, begin by installing
+`Anaconda Navigator <https://www.anaconda.com/products/individual>`__. Then follow
+`these instructions <https://docs.anaconda.com/anaconda/navigator/tutorials/manage-channels/>`__
+to add the channel ``tylerdougan``, and install waltlabtools from this channel.
+
+Alternatively, install waltlabtools from the command line with
+``conda install -c tylerdougan waltlabtools`` (recommended; requires you to
+first install Anaconda or
+`Miniconda <https://docs.conda.io/en/latest/miniconda.html>`__) or
+``pip install waltlabtools`` (requires
+`pip <https://pip.pypa.io/en/stable/getting-started/>`__, which should come
+with Python).
+
+
+Dependencies
+^^^^^^^^^^^^
+
+- waltlabtools requires
+
+  - `numpy <https://numpy.org/doc/stable/index.html>`__ ≥ 1.10
+
+  - `scipy <https://docs.scipy.org/doc/scipy/getting_started.html>`__ ≥ 1.3
+
+- If installing with pip or conda, numpy and scipy will be installed
+  automatically
+
+- Specific modules have additional requirements:
+
+  - `waltlabtools.read <https://waltlabtools.readthedocs.io/en/latest/waltlabtools.read.html>`__
+    (for importing data from Quanterix instruments) requires
+
+    - `pandas <https://pandas.pydata.org>`__ ≥ 0.25
+
+- waltlabtools also plays well with
+
+  - `JAX <https://jax.readthedocs.io/en/latest/index.html>`__
+    for accelerated numerical computing – waltlabtools will use jax.numpy
+    instead of numpy if jax is loaded
+
+  - `JupyterLab <https://jupyterlab.readthedocs.io/en/stable/>`__
+    for interactively writing code
+
+  - `pandas <https://pandas.pydata.org>`__
+    for data import/export and organization
+
+  - `matplotlib <https://matplotlib.org>`__ for plotting
+
+  - `scikit-learn <https://scikit-learn.org/stable/>`__ for data analysis
+
+All of these packages can all be installed using
+`conda <https://docs.conda.io/projects/conda/en/latest/user-guide/install/download.html>`__
+or `pip <https://pypi.org>`__.
+
+
+Usage
+^^^^^
+
+.. code-block:: python
+
+   import waltlabtools as wlt  # waltlabtools main functionality
+
+-----
+
+
+Development of waltlabtools is led by the
+`Walt Lab <https://waltlab.bwh.harvard.edu>`__ for Advanced Diagnostics
+at `Brigham and Women's Hospital <https://www.brighamandwomens.org>`__,
+`Harvard Medical School <https://hms.harvard.edu>`__, and the
+`Wyss Institute for Biologically Inspired Engineering <https://wyss.harvard.edu>`__.

src/waltlabtools.egg-info/SOURCES.txt

@@ -0,0 +1,19 @@
+LICENSE
+README.rst
+pyproject.toml
+setup.cfg
+setup.py
+src/waltlabtools/__init__.py
+src/waltlabtools/_backend.py
+src/waltlabtools/_plot.py
+src/waltlabtools/cal_curve.py
+src/waltlabtools/core.py
+src/waltlabtools/dropna.py
+src/waltlabtools/model.py
+src/waltlabtools/mosaic.py
+src/waltlabtools/read.py
+src/waltlabtools.egg-info/PKG-INFO
+src/waltlabtools.egg-info/SOURCES.txt
+src/waltlabtools.egg-info/dependency_links.txt
+src/waltlabtools.egg-info/requires.txt
+src/waltlabtools.egg-info/top_level.txt

src/waltlabtools.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

src/waltlabtools.egg-info/requires.txt

@@ -0,0 +1,5 @@
+matplotlib>=3.3
+numpy>=1.16
+pandas>=0.25
+scipy>=1.3
+scikit-learn>=0.21

src/waltlabtools.egg-info/top_level.txt

@@ -0,0 +1 @@
+waltlabtools

src/waltlabtools/__init__.py

@@ -3,3 +3,5 @@
 from .core import *
 from .model import *
 from .read import *
+
+__version__ = "v1.0.0b23"