update package (#36)

* update minimum Python to 3.8 * stop document Excel parsing and Rachel-style neutralization * `black` formatting * `black` formatting * `ruff` linting * move examples to notebooks * run tests through GitHub actions * remove Travis testing * add GitHub actions to repo * update version to 0.6.0 * `black` formatting * sanitize `RuntimeWarning` in fitting * fix `nbval` sanitize specs
jbloomlab · Dec 3, 2023 · 34c7325 · 34c7325
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,35 @@
+name: Run tests
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    name: Run tests
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+
+      - name: install python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: install package and dependencies
+        run: pip install -e . && pip install -r test_requirements.txt
+
+      - name: lint code with ruff
+        run: ruff check .
+
+      - name: check code format with black
+        run: black --check .
+
+      - name: test code with `pytest`
+        run: pytest
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,6 @@
 .*
 ~*
+!.github
 !.gitignore
 !.travis.yml
 !.flake8

diff --git a/.travis.yml b/.travis.yml
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -6,6 +6,21 @@ All notable changes to this project will be documented in this file.
 
 The format is based on `Keep a Changelog <https://keepachangelog.com>`_.
 
+0.6.0
+------
+
+Fixed
++++++
+- Code format with ``black``
+- Lint with ``ruff``
+- Test with GitHub Actions rather than Travis
+- Move examples in docs to notebooks so they can be tested with ``nbval`` and added to docs with ``nbsphinx``
+- Update minimum Python to 3.8 and test on 3.11
+
+Removed
++++++++
+- Stop document the "Rachel-style neutralization" and parsing from Excel as these may be deprecated eventually.
+
 0.5.7
 ------
 

diff --git a/README.rst b/README.rst
@@ -1,12 +1,19 @@
 ======================================
 neutcurve
 ======================================
-.. image:: https://travis-ci.org/jbloomlab/neutcurve.svg
-    :target: https://travis-ci.org/jbloomlab/neutcurve.svg
 
 .. image:: https://img.shields.io/pypi/v/neutcurve.svg
         :target: https://pypi.python.org/pypi/neutcurve
 
+.. image:: https://github.com/jbloomlab/neutcurve/actions/workflows/test.yaml/badge.svg
+        :target: https://github.com/jbloomlab/neutcurve/actions/workflows/test.yaml
+
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+        :target: https://github.com/psf/black
+
+.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json
+        :target: https://github.com/astral-sh/ruff
+
 ``neutcurve`` is a Python package written by the `Bloom lab <https://research.fhcrc.org/bloom/en.html>`_ for plotting neutralization curves.
 
 See the `neutcurve documentation <https://jbloomlab.github.io/neutcurve/>`_ for details on how to install and use ``neutcurve``.
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-#
 # neutcurve documentation build configuration file.
 #
 # This file is execfile()d with the current directory set to its
@@ -21,7 +19,7 @@
 import re
 import sys
 
-sys.path.insert(0, '{0}/..'.format(os.path.abspath('.')))
+sys.path.insert(0, "{}/..".format(os.path.abspath(".")))
 
 
 # -- General configuration ------------------------------------------------
@@ -36,52 +34,54 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-        'sphinx.ext.autodoc',
-        'sphinx.ext.doctest',
-        'sphinx.ext.mathjax',
-        'sphinx.ext.githubpages',
-        'sphinx.ext.viewcode',
-        'nb2plots',
-        ]
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.viewcode",
+    "nb2plots",
+    "nbsphinx",
+    "nbsphinx_link",
+]
 
 # avoid cropping of plots included using nbplot
 # directive along lines described here:
 # https://github.com/matplotlib/matplotlib/issues/4563#issuecomment-381366101
-nbplot_rcparams = {'savefig.bbox': 'tight'}
+nbplot_rcparams = {"savefig.bbox": "tight"}
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'neutcurve'
+project = "neutcurve"
 copyright = f"2019--{datetime.datetime.now().year}, Bloom lab"  # noqa: A001
-author = u'the Bloom lab'
+author = "the Bloom lab"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
 # Read in the version from file
-versionfile = os.path.abspath(os.path.join(
-        os.path.dirname(__file__), '../neutcurve/__init__.py'))
+versionfile = os.path.abspath(
+    os.path.join(os.path.dirname(__file__), "../neutcurve/__init__.py")
+)
 with open(versionfile) as f:
     versiontext = f.read()
-versionmatches = re.findall(
-            r'__version__\s+=\s+[\'"]([^\'"]+)[\'"]',
-            versiontext)
+versionmatches = re.findall(r'__version__\s+=\s+[\'"]([^\'"]+)[\'"]', versiontext)
 if len(versionmatches) != 1:
-    raise ValueError(f"found {len(versionmatches)} matches for version "
-                     f"in {versionfile}")
+    raise ValueError(
+        f"found {len(versionmatches)} matches for version " f"in {versionfile}"
+    )
 else:
     versionstring = versionmatches[0]
 # The full version, including alpha/beta/rc tags.
@@ -92,16 +92,21 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'README.rst',
-                    'examples/README.rst']
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "README.rst",
+    "examples/README.rst",
+]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -112,49 +117,48 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
 html_theme_options = {
-        'logo': 'BloomLogo.jpg',
-        'logo_name': 'true',
-        'description': 'Fit and plot neutralization curves',
-        'github_button': 'true',
-        'github_user': 'jbloomlab',
-        'github_repo': 'neutcurve',
-        'github_banner': 'true',
-        'travis_button': 'true',
-        'sidebar_width': '250px',
-        }
+    "logo": "BloomLogo.jpg",
+    "logo_name": "true",
+    "description": "Fit and plot neutralization curves",
+    "github_button": "true",
+    "github_user": "jbloomlab",
+    "github_repo": "neutcurve",
+    "github_banner": "true",
+    "sidebar_width": "250px",
+}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
 #
 # This is required for the alabaster theme
 # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
 html_sidebars = {
-    '**': [
-        'about.html',
-        'navigation.html',
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
-        'donate.html',
+    "**": [
+        "about.html",
+        "navigation.html",
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
+        "donate.html",
     ]
 }
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'neutcurvedoc'
+htmlhelp_basename = "neutcurvedoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -163,15 +167,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -181,19 +182,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'neutcurve.tex', u'neutcurve Documentation',
-     u'the Bloom lab', 'manual'),
+    (master_doc, "neutcurve.tex", "neutcurve Documentation", "the Bloom lab", "manual"),
 ]
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'neutcurve', u'neutcurve Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "neutcurve", "neutcurve Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -202,7 +199,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'neutcurve', u'neutcurve Documentation',
-     author, 'neutcurve', 'Fit and plot neutralization curves',
-     'Miscellaneous'),
-    ]
+    (
+        master_doc,
+        "neutcurve",
+        "neutcurve Documentation",
+        author,
+        "neutcurve",
+        "Fit and plot neutralization curves",
+        "Miscellaneous",
+    ),
+]
diff --git a/docs/curvefits_example.nblink b/docs/curvefits_example.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../notebooks/curvefits_example.ipynb"
+}