added flake with 100 size

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 100

.gitignore

@@ -1,2 +1,3 @@
 .idea/
 /.venv
+dist

.pre-commit-config.yaml

@@ -6,14 +6,27 @@ repos:
       - id: end-of-file-fixer
       - id: check-yaml
 
-#  - repo: https://github.com/pycqa/flake8
-#    rev: 6.0.0
-#    hooks:
-#      - id: flake8
-#        args: [ '--max-line-length=70' ]
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        args: [ '--max-line-length=100' ]
+
 
   - repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:
       - id: black
         args: [--line-length=70]
+
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.4
+    hooks:
+      - id: docformatter
+        args: [--in-place, --recursive, --blank, --force-wrap, --wrap-summaries=100,--wrap-descriptions=100]
+
+  - repo: https://github.com/pre-commit/mirrors-autopep8
+    rev: v1.5.7
+    hooks:
+      - id: autopep8
+        args: [--in-place, --aggressive, --aggressive, --recursive, --max-line-length=100]

docs/examples/aif/plot_aif_parker.py

@@ -1,9 +1,8 @@
-"""
-======================================
-The Parker AIF - a play with variables
-======================================
+"""======================================
+
+The Parker AIF - a play with variables ======================================  Simulating a Parker
+AIF with different settings.
 
-Simulating a Parker AIF with different settings.
 """
 
 import matplotlib.pyplot as plt
@@ -17,7 +16,8 @@
 # %%
 # Generate synthetic AIF with default settings and plot the result.
 
-# Define time points in units of seconds - in this case we use a time resolution of 0.5 sec and a total duration of 6 minutes.
+# Define time points in units of seconds - in this case we use a time
+# resolution of 0.5 sec and a total duration of 6 minutes.
 t = np.arange(0, 6 * 60, 0.5)
 
 # Create an AIF with default settings
@@ -31,7 +31,8 @@
 plt.show()
 
 # %%
-# The bolus arrival time (BAT) defaults to 0s. What happens if we change it? Let's try, by changing it in steps of 30s:
+# The bolus arrival time (BAT) defaults to 0s. What happens if we
+# change it? Let's try, by changing it in steps of 30s:
 
 ca = osipi.aif_parker(t, BAT=0)
 plt.plot(t, ca, "b-", label="BAT = 0s")

docs/examples/aif/plot_dummy.py

@@ -17,7 +17,8 @@
 # %%
 # Generate synthetic AIF with default settings and plot the result.
 
-# Define time points in units of seconds - in this case we use a time resolution of 0.5 sec and a total duration of 6 minutes.
+# Define time points in units of seconds - in this case we use a time
+# resolution of 0.5 sec and a total duration of 6 minutes.
 t = np.arange(0, 6 * 60, 0.5)
 
 # Create an AIF with default settings
@@ -31,7 +32,8 @@
 plt.show()
 
 # %%
-# The bolus arrival time (BAT) defaults to 30s. What happens if we change it? Let's try, by changing it in steps of 30s:
+# The bolus arrival time (BAT) defaults to 30s. What happens if we
+# change it? Let's try, by changing it in steps of 30s:
 
 ca = osipi.aif_parker(t, BAT=0)
 plt.plot(t, ca, "b-", label="BAT = 0s")

docs/examples/tissue/plot_extended_tofts.py

@@ -17,14 +17,16 @@
 # %%
 # Generate Parker AIF with default settings.
 
-# Define time points in units of seconds - in this case we use a time resolution of 1 sec and a total duration of 6 minutes.
+# Define time points in units of seconds - in this case we use a time
+# resolution of 1 sec and a total duration of 6 minutes.
 t = np.arange(0, 6 * 60, 1)
 
 # Create an AIF with default settings
 ca = osipi.aif_parker(t)
 
 # %%
-# Plot the tissue concentrations for an extracellular volume fraction of 0.2 and 3 different plasma volumes of 0.05, 0.2 and 0.6
+# Plot the tissue concentrations for an extracellular volume fraction
+# of 0.2 and 3 different plasma volumes of 0.05, 0.2 and 0.6
 Ktrans = 0.2  # in units of 1/min
 ve = 0.2  # volume fraction between 0 and 1
 vp = [0.05, 0.2, 0.6]  # volume fraction between 0 and 1
@@ -40,7 +42,8 @@
 plt.show()
 
 # %%
-# Comparing different discretization methods for an extracellular volume fraction of 0.2, Ktrans of 0.2 /min and vp of 0.05
+# Comparing different discretization methods for an extracellular
+# volume fraction of 0.2, Ktrans of 0.2 /min and vp of 0.05
 ct = osipi.extended_tofts(
     t, ca, Ktrans, ve, vp[0]
 )  # Defaults to Convolution

docs/examples/tissue/plot_tofts.py

@@ -17,14 +17,17 @@
 # %%
 # Generate Parker AIF with default settings.
 
-# Define time points in units of seconds - in this case we use a time resolution of 1 sec and a total duration of 6 minutes.
+# Define time points in units of seconds - in this case we use a time
+# resolution of 1 sec and a total duration of 6 minutes.
 t = np.arange(0, 6 * 60, 1)
 
 # Create an AIF with default settings
 ca = osipi.aif_parker(t)
 
 # %%
-# Plot the tissue concentrations for an extracellular volume fraction of 0.2 and 3 different transfer rate constants of 0.05, 0.2 and 0.6 /min
+# Plot the tissue concentrations for an extracellular volume fraction
+# of 0.2 and 3 different transfer rate constants of 0.05, 0.2 and 0.6
+# /min
 Ktrans = [0.05, 0.2, 0.6]  # in units of 1/min
 ve = 0.2  # volume fraction between 0 and 1
 ct = osipi.tofts(t, ca, Ktrans=Ktrans[0], ve=ve)
@@ -39,7 +42,8 @@
 plt.show()
 
 # %%
-# Comparing different discretization methods for an extracellular volume fraction of 0.2 and Ktrans of 0.2 /min
+# Comparing different discretization methods for an extracellular
+# volume fraction of 0.2 and Ktrans of 0.2 /min
 ct = osipi.tofts(
     t, ca, Ktrans=Ktrans[1], ve=ve
 )  # Defaults to Convolution

docs/source/conf.py

@@ -5,7 +5,7 @@
 
 import os
 
-# -- Project information -----------------------------------------------------
+# -- Project information ---------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 import sys
 
@@ -14,24 +14,28 @@
 author = "OSIPI"
 release = "0.1.1"
 
-# -- Path setup --------------------------------------------------------------
+# -- Path setup ------------------------------------------------------
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here
+# documentation root, use os.path.abspath to make it absolute, like
+# shown here
 
 sys.path.insert(0, os.path.abspath("../../src"))
 
-# -- General configuration ---------------------------------------------------
+# -- General configuration -------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 # Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones
 extensions = [
     "sphinx.ext.napoleon",  # parsing of NumPy and Google style docstrings
     "sphinx.ext.autodoc",  # sphinx autodocumentation generation
-    "sphinx.ext.autosummary",  # generates function/method/attribute summary lists
+    # generates function/method/attribute summary lists
+    "sphinx.ext.autosummary",
     "sphinx.ext.viewcode",  # viewing source code
-    # generate links to the documentation of objects in external projects
+    # generate links to the documentation of objects in external
+    # projects
     "sphinx.ext.intersphinx",
     "autodocsumm",
     "myst_parser",  # parser for markdown language
@@ -61,19 +65,23 @@
     "download_all_examples": False,
 }
 
-# This way a link to other methods, classes, or modules can be made with back ticks so that you don't have to use qualifiers like :class:, :func:, :meth: and the likes
+# This way a link to other methods, classes, or modules can be made
+# with back ticks so that you don't have to use qualifiers like
+# :class:, :func:, :meth: and the likes
 default_role = "obj"
 
-# Add any paths that contain templates here, relative to this directory
+# Add any paths that contain templates here, relative to this
+# directory
 templates_path = ["_templates"]
 
 # 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 = []
 
-# -- Extension configuration -------------------------------------------------
-# Map intersphinx to pre-exisiting documentation from other projects used in this project
+# -- Extension configuration -----------------------------------------
+# Map intersphinx to pre-exisiting documentation from other projects
+# used in this project
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
@@ -86,16 +94,19 @@
 
 autosummary_generate = True  # enable autosummary extension
 
-# Tell sphinx-autodoc-typehints to generate stub parameter annotations including types, even if the parameters aren't explicitly documented.
+# Tell sphinx-autodoc-typehints to generate stub parameter annotations
+# including types, even if the parameters aren't explicitly
+# documented.
 always_document_param_types = True
 
 # Remove auto-generated API docs from sidebars.
 remove_from_toctrees = ["_autosummary/*"]
 
-# -- Options for HTML output -------------------------------------------------
+# -- Options for HTML output -----------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-# The theme to use for HTML and HTML Help pages.  See the documentation for a list of builtin themes
+# The theme to use for HTML and HTML Help pages.  See the
+# documentation for a list of builtin themes
 html_theme = "pydata_sphinx_theme"
 
 html_theme_options = {
@@ -111,7 +122,10 @@
     "doc_path": "docs/source",
 }
 
-# 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"
+# 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"]
 
 # The suffix(es) of source filenames.

docs/source/generated/examples/aif/plot_aif_parker.py

@@ -1,9 +1,8 @@
-"""
-======================================
-The Parker AIF - a play with variables
-======================================
+"""======================================
+
+The Parker AIF - a play with variables ======================================  Simulating a Parker
+AIF with different settings.
 
-Simulating a Parker AIF with different settings.
 """
 
 import matplotlib.pyplot as plt
@@ -17,7 +16,8 @@
 # %%
 # Generate synthetic AIF with default settings and plot the result.
 
-# Define time points in units of seconds - in this case we use a time resolution of 0.5 sec and a total duration of 6 minutes.
+# Define time points in units of seconds - in this case we use a time
+# resolution of 0.5 sec and a total duration of 6 minutes.
 t = np.arange(0, 6 * 60, 0.5)
 
 # Create an AIF with default settings
@@ -31,7 +31,8 @@
 plt.show()
 
 # %%
-# The bolus arrival time (BAT) defaults to 0s. What happens if we change it? Let's try, by changing it in steps of 30s:
+# The bolus arrival time (BAT) defaults to 0s. What happens if we
+# change it? Let's try, by changing it in steps of 30s:
 
 ca = osipi.aif_parker(t, BAT=0)
 plt.plot(t, ca, "b-", label="BAT = 0s")

docs/source/generated/examples/aif/plot_dummy.py

@@ -17,7 +17,8 @@
 # %%
 # Generate synthetic AIF with default settings and plot the result.
 
-# Define time points in units of seconds - in this case we use a time resolution of 0.5 sec and a total duration of 6 minutes.
+# Define time points in units of seconds - in this case we use a time
+# resolution of 0.5 sec and a total duration of 6 minutes.
 t = np.arange(0, 6 * 60, 0.5)
 
 # Create an AIF with default settings
@@ -31,7 +32,8 @@
 plt.show()
 
 # %%
-# The bolus arrival time (BAT) defaults to 30s. What happens if we change it? Let's try, by changing it in steps of 30s:
+# The bolus arrival time (BAT) defaults to 30s. What happens if we
+# change it? Let's try, by changing it in steps of 30s:
 
 ca = osipi.aif_parker(t, BAT=0)
 plt.plot(t, ca, "b-", label="BAT = 0s")

docs/source/generated/examples/tissue/plot_extended_tofts.py

@@ -17,14 +17,16 @@
 # %%
 # Generate Parker AIF with default settings.
 
-# Define time points in units of seconds - in this case we use a time resolution of 1 sec and a total duration of 6 minutes.
+# Define time points in units of seconds - in this case we use a time
+# resolution of 1 sec and a total duration of 6 minutes.
 t = np.arange(0, 6 * 60, 1)
 
 # Create an AIF with default settings
 ca = osipi.aif_parker(t)
 
 # %%
-# Plot the tissue concentrations for an extracellular volume fraction of 0.2 and 3 different plasma volumes of 0.05, 0.2 and 0.6
+# Plot the tissue concentrations for an extracellular volume fraction
+# of 0.2 and 3 different plasma volumes of 0.05, 0.2 and 0.6
 Ktrans = 0.2  # in units of 1/min
 ve = 0.2  # volume fraction between 0 and 1
 vp = [0.05, 0.2, 0.6]  # volume fraction between 0 and 1
@@ -40,7 +42,8 @@
 plt.show()
 
 # %%
-# Comparing different discretization methods for an extracellular volume fraction of 0.2, Ktrans of 0.2 /min and vp of 0.05
+# Comparing different discretization methods for an extracellular
+# volume fraction of 0.2, Ktrans of 0.2 /min and vp of 0.05
 ct = osipi.extended_tofts(
     t, ca, Ktrans, ve, vp[0]
 )  # Defaults to Convolution

docs/source/generated/examples/tissue/plot_tofts.py

@@ -17,14 +17,17 @@
 # %%
 # Generate Parker AIF with default settings.
 
-# Define time points in units of seconds - in this case we use a time resolution of 1 sec and a total duration of 6 minutes.
+# Define time points in units of seconds - in this case we use a time
+# resolution of 1 sec and a total duration of 6 minutes.
 t = np.arange(0, 6 * 60, 1)
 
 # Create an AIF with default settings
 ca = osipi.aif_parker(t)
 
 # %%
-# Plot the tissue concentrations for an extracellular volume fraction of 0.2 and 3 different transfer rate constants of 0.05, 0.2 and 0.6 /min
+# Plot the tissue concentrations for an extracellular volume fraction
+# of 0.2 and 3 different transfer rate constants of 0.05, 0.2 and 0.6
+# /min
 Ktrans = [0.05, 0.2, 0.6]  # in units of 1/min
 ve = 0.2  # volume fraction between 0 and 1
 ct = osipi.tofts(t, ca, Ktrans=Ktrans[0], ve=ve)
@@ -39,7 +42,8 @@
 plt.show()
 
 # %%
-# Comparing different discretization methods for an extracellular volume fraction of 0.2 and Ktrans of 0.2 /min
+# Comparing different discretization methods for an extracellular
+# volume fraction of 0.2 and Ktrans of 0.2 /min
 ct = osipi.tofts(
     t, ca, Ktrans=Ktrans[1], ve=ve
 )  # Defaults to Convolution