Move to modern package management: automatic upload to pypi, ruff, pyproject.toml...

Author: jdehning

.github/workflows/release.yaml

@@ -0,0 +1,20 @@
+name: Publish to PyPI.org
+on:
+  release:
+    types: [published]
+jobs:
+  pypi:
+    name: upload release to PyPI
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      # IMPORTANT: this permission is mandatory for Trusted Publishing
+      id-token: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - run: python3 -m pip install --upgrade build && python3 -m build
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/ruff.yaml

@@ -0,0 +1,19 @@
+name: Ruff
+on: [ push, pull_request ]
+jobs:
+  ruff-check:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set Python Version
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.13"
+
+    - name: Python Ruff Lint and Format
+      uses: adityabhangle658/[email protected]
+
+
+

docs/conf.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 # Configuration file for the Sphinx documentation builder.
 #
 # This file does only contain a selection of the most common options. For a
@@ -13,21 +11,25 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
-import sys
 import re
-sys.path.insert(0, os.path.abspath('../'))
+import sys
+
+sys.path.insert(0, os.path.abspath("../"))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'Mr. Estimator'
-copyright = '2018, Paul Spitzner, Jonas Dehning, Annika Hagemann, Jens Wilting, Viola Priesemann'
-author = 'Paul Spitzner, Jonas Dehning, Annika Hagemann, Jens Wilting, Viola Priesemann'
+project = "Mr. Estimator"
+copyright = (
+    "2018, Paul Spitzner, Jonas Dehning, Annika Hagemann, "
+    "Jens Wilting, Viola Priesemann"
+)
+author = "Paul Spitzner, Jonas Dehning, Annika Hagemann, Jens Wilting, Viola Priesemann"
 
 verstr = "unknown"
 try:
-    verstrline = open('../mrestimator/_version.py', "rt").read()
-except EnvironmentError:
+    verstrline = open("../mrestimator/_version.py").read()
+except OSError:
     pass
 else:
     VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
@@ -36,7 +38,7 @@
         verstr = mo.group(1)
     else:
         raise RuntimeError("unable to find version in mrestimator/_version.py")
-print('sphinx found version: {}'.format(verstr))
+print(f"sphinx found version: {verstr}")
 # The short X.Y version
 version = verstr
 # The full version, including alpha/beta/rc tags
@@ -53,40 +55,34 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.napoleon',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
     # 'numpydoc',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.viewcode',
-    'm2r',
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "m2r",
     # 'sphinx_autorun'
 ]
 
 
 # Mock imports
-autodoc_mock_imports = [
-    'numpy',
-    'matplotlib',
-    'matplotlib.pyplot',
-    'scipy',
-    'neo'
-]
+autodoc_mock_imports = ["numpy", "matplotlib", "matplotlib.pyplot", "scipy", "neo"]
 
 # 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", ".md"]
 # source_suffix = '.rst'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -98,10 +94,10 @@
 # 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 = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 
 # Napoleon settings
@@ -113,8 +109,8 @@
 # napoleon_use_admonition_for_examples = False
 # napoleon_use_admonition_for_notes = False
 # napoleon_use_admonition_for_references = False
-napoleon_use_ivar = True # True enables links for attribute types
-napoleon_use_param = True # True enables links for parameter types
+napoleon_use_ivar = True  # True enables links for attribute types
+napoleon_use_param = True  # True enables links for parameter types
 napoleon_use_rtype = False
 
 # -- Options for HTML output -------------------------------------------------
@@ -124,23 +120,23 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # 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 = {
-    'collapse_navigation': False,
-    'display_version': False,
-    'navigation_depth': 4,
-    'sticky_navigation': True,
+    "collapse_navigation": False,
+    "display_version": False,
+    "navigation_depth": 4,
+    "sticky_navigation": True,
 }
 
 # 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.
@@ -153,14 +149,14 @@
 # html_sidebars = {}
 
 # icons
-html_favicon = 'media/favicon.ico'
-html_logo = 'media/logo.png'
+html_favicon = "media/favicon.ico"
+html_logo = "media/logo.png"
 
 
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'mredoc'
+htmlhelp_basename = "mredoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -169,15 +165,12 @@
     # 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',
@@ -187,19 +180,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'mre.tex', 'mre Documentation',
-     'Paul Spitzner', 'manual'),
+    (master_doc, "mre.tex", "mre Documentation", "Paul Spitzner", "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, 'mre', 'mre Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "mre", "mre Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -208,19 +197,26 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'mre', 'mre Documentation',
-     author, 'mre', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "mre",
+        "mre Documentation",
+        author,
+        "mre",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 
 # -- Extension configuration -------------------------------------------------
 
-intersphinx_mapping = {'python': ('http://docs.python.org/3', None),
-                       'numpy': ('http://docs.scipy.org/doc/numpy', None),
-                       'scipy': ('http://docs.scipy.org/doc/scipy/reference', None),
-                       'matplotlib': ('http://matplotlib.sourceforge.net', None)
-                       }
+intersphinx_mapping = {
+    "python": ("http://docs.python.org/3", None),
+    "numpy": ("http://docs.scipy.org/doc/numpy", None),
+    "scipy": ("http://docs.scipy.org/doc/scipy/reference", None),
+    "matplotlib": ("http://matplotlib.sourceforge.net", None),
+}
 
 # -- Options for todo extension ----------------------------------------------
 

examples/basic_usage.ipynb

@@ -48,10 +48,10 @@
     }
    ],
    "source": [
-    "#imports the toolbox\n",
+    "# imports the toolbox\n",
     "import mrestimator as mre\n",
     "\n",
-    "#ensures that the plots are embedded in the notebook\n",
+    "# ensures that the plots are embedded in the notebook\n",
     "%matplotlib inline "
    ]
   },
@@ -79,7 +79,9 @@
     }
    ],
    "source": [
-    "data = mre.simulate_branching(m=0.98, a=1000,subp=0.05, length=20000, numtrials=10, seed=43771)"
+    "data = mre.simulate_branching(\n",
+    "    m=0.98, a=1000, subp=0.05, length=20000, numtrials=10, seed=43771\n",
+    ")"
    ]
   },
   {
@@ -144,7 +146,14 @@
     }
    ],
    "source": [
-    "result = mre.full_analysis(data, kmax=500, coefficientmethod='trialseparated', dt=1, dtunit=' bp steps', fitfuncs=['e', 'eo'])"
+    "result = mre.full_analysis(\n",
+    "    data,\n",
+    "    kmax=500,\n",
+    "    coefficientmethod=\"trialseparated\",\n",
+    "    dt=1,\n",
+    "    dtunit=\" bp steps\",\n",
+    "    fitfuncs=[\"e\", \"eo\"],\n",
+    ")"
    ]
   }
  ],

examples/getting_started/create_example_data.py

@@ -1,35 +1,32 @@
 import os
+
 import numpy as np
-import matplotlib.pyplot as plt
+
 import mrestimator as mre
 
 # set  working directory to use relative paths
 os.chdir(os.path.dirname(__file__))
 try:
-    os.mkdir('./data')
+    os.mkdir("./data")
 except FileExistsError:
     pass
 
 h = np.ones(10000)
-h[int(len(h)/3):int(len(h)/3+10)] += 100
-h*=2
+h[int(len(h) / 3) : int(len(h) / 3 + 10)] += 100
+h *= 2
 foo = mre.simulate_branching(m=0.995, h=h, numtrials=10, seed=314)
 sub = mre.simulate_subsampling(foo, prob=0.1, seed=271)
 
 h = np.vstack((np.arange(0, len(h)), h))
 
 hdr = "two column file containing a time index and the time series of the drive\n"
 hdr += "one timestep per row\n\n"
-np.savetxt('./data/drive.tsv', h.T, fmt='%5d', header=hdr)
+np.savetxt("./data/drive.tsv", h.T, fmt="%5d", header=hdr)
 hdr = "original trials with full activity\n"
 hdr += "one trial in each column, increasing timesteps in each row\n\n"
-np.savetxt('./data/full.tsv', foo.T, fmt='%5d', header=hdr)
+np.savetxt("./data/full.tsv", foo.T, fmt="%5d", header=hdr)
 for idx, ts in enumerate(sub):
-    hdr = ''
-    hdr += 'subsampled trials in indivual files with one column each\n'
-    hdr += 'this is trial {:02d}\n\n'.format(idx)
-    np.savetxt('./data/sub_{:02d}.tsv'.format(idx), ts, fmt='%5d', header=hdr)
-
-
-
-
+    hdr = ""
+    hdr += "subsampled trials in indivual files with one column each\n"
+    hdr += f"this is trial {idx:02d}\n\n"
+    np.savetxt(f"./data/sub_{idx:02d}.tsv", ts, fmt="%5d", header=hdr)