Merge pull request #84 from phobson/update-readme

update example figure for readme

Author: phobson

.coveragerc

@@ -2,7 +2,6 @@
 [run]
 source = probscale
 branch = True
-include = probscale/*.py
 omit =
     probscale/tests/*
 

.github/workflows/black.yml

@@ -1,13 +1,10 @@
-name: black
+name: Lint with Black
 
-on: [pull_request]
+on: [push, pull_request]
 
 jobs:
-  black:
+  lint:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - name: Black Code Formatter
-      uses: lgeiger/[email protected]
-      with:
-        args: ". --check --exclude=docs/*"
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable

.github/workflows/check-test-coverage.yml

@@ -1,4 +1,4 @@
-name: Coverage via codecov
+name: Coverage (with doctests)
 on:
   push:
     branches: [ master ]
@@ -19,9 +19,9 @@ jobs:
         python -m pip install --upgrade pip
         pip install pytest pytest-cov pytest-mpl coverage docopt
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install scipy
+        pip install scipy seaborn
         export MPL_IMGCOMP_TOLERANCE=20
-        coverage run --source probscale check_probscale.py --doctest-modules --mpl --cov-report=xml
+        coverage run -m pytest --mpl --doctest-glob="probscale/*.py" --cov-report=xml
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
       with:

.github/workflows/python-runtests-all.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Image comparison tests
+name: Run units test (w/ img comps)
 
 on:
   push:
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
         matrix:
-          python-version: ["3.8", "3.9", "3.10", "3.11"]
+          python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2
@@ -31,4 +31,4 @@ jobs:
     - name: Test with pytest
       run: |
         export MPL_IMGCOMP_TOLERANCE=20
-        python check_probscale.py --mpl --doctest-modules
+        python -m pytest --mpl

CONTRIBUTING.rst

@@ -79,7 +79,7 @@ Ready to contribute? Here's how to set up `probscale` for local development.
 
 5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
 
-    $ python check_probscale.py --mpl --pep8 --cov
+    $ python -m pytest --mpl --pep8 --cov
 
 6. Commit your changes and push your branch to GitHub::
 
@@ -115,35 +115,6 @@ To run a subset of tests::
 $ py.test tests.test_probscale
 
 
-Configuring Sublime Text 3 to run the tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-In Sublime, got to Tools -> Build System -> New Build System.
-Then add the following configuration and save as "probscale.sublime-build"::
-
-    {
-        "working_dir": "<path to the git repository>",
-        "cmd": "<full path of the python executable> check_probscale.py --verbose <other pytest options>",
-    }
-
-
-Configuring Atom to run the tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-In Atom, install the build_ package, create a new file called ".atom-build.yml" in the
-top level of the project directory, and add the following contents::
-
-    cmd: "<full path of the python executable>"
-    name: "probscale"
-    args:
-      - check_probscale.py
-      - --verbose
-      - <other pytest options ...>
-    cwd: <path to the git repository>
-    sh: false
-    keymap: ctrl-b
-    atomCommandName: namespace:testprobscale
-
 After this, hitting ctrl+b in either text editor will run the test suite.
 
 .. _build: https://atom.io/packages/build

README.md

@@ -2,11 +2,9 @@
 
 Real probability scales for matplotlib
 
-![Code Style](https://github.com/matplotlib/mpl-probscale/workflows/black/badge.svg)
 ![Coverage](https://github.com/matplotlib/mpl-probscale/workflows/Coverage%20via%20codecov/badge.svg)
 ![Linter](https://github.com/matplotlib/mpl-probscale/workflows/Lint%20with%20flake8/badge.svg)
-![Basic Tests](https://github.com/matplotlib/mpl-probscale/workflows/Basic%20unit%20tests/badge.svg)
-![Image Comparisons](https://github.com/matplotlib/mpl-probscale/workflows/Image%20comparison%20tests/badge.svg)
+![Tests](https://github.com/matplotlib/mpl-probscale/workflows/Image%20comparison%20tests/badge.svg)
 
 [Sphinx Docs](http://matplotlib.org/mpl-probscale/)
 
@@ -30,38 +28,20 @@ cd mpl-probscale
 pip install -e .
 ```
 
-### Additional Depedencies
-
-This library depends on **pytest** framework.
-The current release version does not have it listed as a hard dependency, however.
-So for now you will need to install ``pytest`` yourself to use mpl-probscale:
-
-`pip install pytest`
-
-or
-
-`conda install pytest --channel=conda-forge`
-
-In the next release, this depedency will be made optional.
-
 ## Quick start
 
 Simply importing `probscale` lets you use probability scales in your matplotlib figures:
 
 ```python
 import matplotlib.pyplot as plt
 import probscale
-import seaborn
-clear_bkgd = {'axes.facecolor':'none', 'figure.facecolor':'none'}
-seaborn.set(style='ticks', context='notebook', rc=clear_bkgd)
 
 fig, ax = plt.subplots(figsize=(8, 4))
 ax.set_ylim(1e-2, 1e2)
 ax.set_yscale('log')
 
 ax.set_xlim(0.5, 99.5)
 ax.set_xscale('prob')
-seaborn.despine(fig=fig)
 ```
 
 ![Alt text](docs/img/example.png "Example axes")

check_probscale.py

@@ -0,0 +1,38 @@
+# %%
+from pathlib import Path
+
+from matplotlib import pyplot
+from scipy import stats
+import probscale  # nothing else needed
+
+beta = stats.beta(a=3, b=4)
+weibull = stats.weibull_min(c=5)
+scales = [
+    {"scale": {"value": "linear"}, "label": "Linear (built-in)"},
+    {"scale": {"value": "log", "base": 10}, "label": "Log. Base 10 (built-in)"},
+    {"scale": {"value": "log", "base": 2}, "label": "Log. Base 2 (built-in)"},
+    {"scale": {"value": "logit"}, "label": "Logit (built-in)"},
+    {"scale": {"value": "prob"}, "label": "Standard Normal Probability (this package)"},
+    {
+        "scale": {"value": "prob", "dist": weibull},
+        "label": "Weibull probability scale, c=5 (this package)",
+    },
+    {
+        "scale": {"value": "prob", "dist": beta},
+        "label": "Beta probability scale, α=3 & β=4 (this package)",
+    },
+]
+
+N = len(scales)
+fig, axes = pyplot.subplots(nrows=N, figsize=(9, N - 1), constrained_layout=True)
+for scale, ax in zip(scales, axes.flat):
+    ax.set_xscale(**scale["scale"])
+    ax.text(0.0, 0.1, scale["label"] + " →", transform=ax.transAxes)
+    ax.set_xlim(left=0.5, right=99.5)
+    ax.set_yticks([])
+    ax.spines.left.set_visible(False)
+    ax.spines.right.set_visible(False)
+    ax.spines.top.set_visible(False)
+
+outpath = Path(__file__).parent.joinpath("../img/example.png").resolve()
+fig.savefig(outpath, dpi=300)

docs/examples/example.py

@@ -180,7 +180,6 @@ def block_parser(part, rgxin, rgxout, fmtin, fmtout):
     i = 0
     decorator = None
     while 1:
-
         if i == N:
             # nothing left to parse -- the last line
             break
@@ -215,7 +214,6 @@ def block_parser(part, rgxin, rgxout, fmtin, fmtout):
 
             rest = []
             while i < N:
-
                 # look ahead; if the next line is blank, or a comment, or
                 # an output line, we're done
 
@@ -278,7 +276,6 @@ class EmbeddedSphinxShell(object):
     """An embedded IPython instance to run inside Sphinx"""
 
     def __init__(self, exec_lines=None, state=None):
-
         self.cout = DecodingStringIO("")
 
         if exec_lines is None:
@@ -526,7 +523,6 @@ def process_output(
         TAB = " " * 4
 
         if is_doctest and output is not None:
-
             found = output
             found = found.strip()
             submitted = data.strip()
@@ -693,7 +689,6 @@ def process_pure_python(self, content):
         ct = 0
 
         for lineno, line in enumerate(content):
-
             line_stripped = line.strip()
             if not len(line):
                 output.append(line)
@@ -770,7 +765,6 @@ def custom_doctest(self, decorator, input_lines, found, submitted):
 
 
 class IPythonDirective(Directive):
-
     has_content = True
     required_arguments = 0
     optional_arguments = 4  # python, suppress, verbatim, doctest
@@ -973,7 +967,6 @@ def setup(app):
 
 # Simple smoke test, needs to be converted to a proper automatic test.
 def test():
-
     examples = [
         r"""
 In [9]: pwd

docs/img/example.png

@@ -158,7 +158,6 @@
     def format_template(template, **kw):
         return jinja2.Template(template).render(**kw)
 
-
 except ImportError:
     import jinja
 
@@ -652,7 +651,6 @@ def render_figures(
     close_figs = not context or close_figs
 
     for i, code_piece in enumerate(code_pieces):
-
         if not context or config.plot_apply_rcparams:
             clear_state(config.plot_rcparams, close_figs)
         elif close_figs:

docs/sphinxext/ipython_directive.py

@@ -164,10 +164,8 @@ def __init__(self, filename, target_dir):
         if not op.exists(outfilename) or (
             op.getmtime(outfilename) < op.getmtime(filename)
         ):
-
             self.exec_file()
         else:
-
             print("skipping {0}".format(self.filename))
 
     @property
@@ -226,8 +224,7 @@ def plotfunc(self):
         return ""
 
     def extract_docstring(self):
-        """ Extract a module-level docstring
-        """
+        """Extract a module-level docstring"""
         lines = open(self.filename).readlines()
         start_row = 0
         if lines[0].startswith("#!"):
@@ -332,7 +329,6 @@ def main(app):
 
     # Write individual example files
     for filename in glob.glob(op.join(source_dir, "*.py")):
-
         ex = ExampleGenerator(filename, target_dir)
 
         banner_data.append(

docs/sphinxext/plot_directive.py

@@ -1,14 +0,0 @@
-from pkg_resources import resource_filename
-
-import probscale
-
-
-def test(*args):
-    try:
-        import pytest
-    except ImportError:
-        raise ImportError("`pytest` is required to run the test suite")
-
-    options = [resource_filename("probscale", "tests")]
-    options.extend(list(args))
-    return pytest.main(options)

docs/sphinxext/plot_generator.py

@@ -37,6 +37,7 @@ def search(substr: str, content: str):
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 INSTALL_REQUIRES = ["numpy", "matplotlib"]
 PACKAGE_DATA = {