Auto formatting (#60)

* COVERAGE: Fix some coverage regressions from pylint PR * ISORT: Run isort on source and tests * BLACK: Run black on source and tests * BLACK: Run black on source and tests * FORMATTING: Add tests and verification for autoformatting * FORMATTING: Add black/isort to root to simplify * Add preliminary contributor guide instructions Closes #59
sandialabs · Mar 4, 2023 · 992772b · 992772b
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diff --git a/.github/workflows/regression-tests.yml b/.github/workflows/regression-tests.yml
@@ -27,8 +27,13 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install numpy scipy numpy_groupies pytest-cov coverage coveralls sphinx_rtd_theme flake8
+        python -m pip install numpy scipy numpy_groupies pytest-cov coverage coveralls \
+          sphinx_rtd_theme isort black pylint mypy
         pip install .
+    - name: Check auto-formatters
+      run: |
+        isort --check .
+        black --check .
 #    - name: Lint with flake8
 #      run: |
 #        # stop the build if there are Python syntax errors or undefined names

diff --git a/CONTRIBUTOR_GUIDE.md b/CONTRIBUTOR_GUIDE.md
@@ -0,0 +1,53 @@
+# Python Tensor Toolbox Contributor Guide
+
+## Issues
+If you are looking to get started or want to propose a change please start by checking
+current or filing a new [issue](https://github.com/sandialabs/pyttb/issues).
+
+## Working on PYTTB locally
+1. clone your fork and enter the directory
+    ```
+    git clone git@github.com:<your username>/pyttb.git
+    cd pyttb
+    ```
+    1. setup your desired python environment as appropriate
+
+1. install dependencies
+    ```
+    We use a mix of pyproject.toml, and setup.py currently. We are
+    still iterating on simplifying the setup procedure.
+    ```
+
+1. Checkout a branch and make your changes
+    ```
+    git checkout -b my-new-feature-branch
+    ```
+1. Formatters and linting
+   1. Run autoformatters from root of project (they will change your code)
+       ```commandline
+       isort .
+       black .
+       ```
+   1. Pylint and mypy coverage is work in progress (these only raise errors)
+      ```commandline
+      mypy pyttb/
+      pylint pyttb/file_name.py  //Today only tensor is compliant
+      ```
+
+1. Run tests (at desired fidelity)
+    1. Just doctests (enabled by default)
+        ```commandline
+        pytest
+        ```
+   1. Functional tests
+        ```commandline
+        pytest .
+        ```
+   1. All tests (linting and formatting checks)
+        ```commandline
+        pytest . --packaging
+        ```
+   1. With coverage
+        ```commandline
+        pytest . --cov=pyttb --cov-report=term-missing
+        ```
diff --git a/README.md b/README.md
@@ -15,11 +15,17 @@ for computing low-rank tensor models.
 * `sptensor`: sparse tensors
 * `ktensor`: Kruskal tensors
 * `tenmat`: matricized tensors
+* `ttensor`: Tucker tensors
 
 **Tensor Algorithms:**
 * `cp_als`, `cp_apr`: Canonical Polyadic (CP) decompositions
+* `tucker_als`: Tucker decompostions
 
+# Getting Started
 Check out the [Documentation](https://pyttb.readthedocs.io) to get started.
 
+# Contributing
+Check out our [contributing guide](CONTRIBUTOR_GUIDE.md).
+
 ---
 [![Regression tests](https://github.com/sandialabs/pyttb/actions/workflows/regression-tests.yml/badge.svg)](https://github.com/sandialabs/pyttb/actions/workflows/regression-tests.yml) [![Coverage Status](https://coveralls.io/repos/github/sandialabs/pyttb/badge.svg?branch=main)](https://coveralls.io/github/sandialabs/pyttb?branch=main)
diff --git a/conftest.py b/conftest.py
@@ -2,21 +2,30 @@
 # LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the
 # U.S. Government retains certain rights in this software.
 
+import numpy
+
 # content of conftest.py
 import pytest
-import numpy
+
 import pyttb
+
+
 @pytest.fixture(autouse=True)
 def add_packages(doctest_namespace):
-    doctest_namespace['np'] = numpy
-    doctest_namespace['ttb'] = pyttb
+    doctest_namespace["np"] = numpy
+    doctest_namespace["ttb"] = pyttb
 
 
 def pytest_addoption(parser):
-    parser.addoption('--packaging', action='store_true', dest="packaging",
-                 default=False, help="enable slow packaging tests")
+    parser.addoption(
+        "--packaging",
+        action="store_true",
+        dest="packaging",
+        default=False,
+        help="enable slow packaging tests",
+    )
 
 
 def pytest_configure(config):
     if not config.option.packaging:
-        setattr(config.option, 'markexpr', 'not packaging')
+        setattr(config.option, "markexpr", "not packaging")
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -18,22 +18,23 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../../'))
-sys.path.insert(0, os.path.abspath('../'))
-sys.path.insert(0, os.path.abspath('.'))
+
+sys.path.insert(0, os.path.abspath("../../"))
+sys.path.insert(0, os.path.abspath("../"))
+sys.path.insert(0, os.path.abspath("."))
 
 from pyttb import __version__
 
 # -- Project information -----------------------------------------------------
 
-project = 'pyttb'
-copyright = ''
-author = 'Danny Dunlavy, Nick Johnson'
+project = "pyttb"
+copyright = ""
+author = "Danny Dunlavy, Nick Johnson"
 
 # The short X.Y version
 version = __version__
 # The full version, including alpha/beta/rc tags
-release = ''
+release = ""
 
 
 # -- General configuration ---------------------------------------------------
@@ -46,11 +47,11 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
+    "sphinx.ext.autodoc",
     "sphinx.ext.intersphinx",
-    'sphinx.ext.mathjax',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon'
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
 ]
 
 napoleon_use_param = False
@@ -59,19 +60,19 @@
 intersphinx_mapping = {
     "numpy": ("http://docs.scipy.org/doc/numpy/", "numpy.inv"),
     "python": ("http://docs.python.org/3.6/", "python.inv"),
-    }
+}
 
 # 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"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -86,15 +87,15 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # 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
@@ -121,7 +122,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pyttbdoc'
+htmlhelp_basename = "pyttbdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -130,37 +131,36 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
-    'pointsize': '10pt',
-
+    "pointsize": "10pt",
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
-    'figure_align': 'htbp',
+    "figure_align": "htbp",
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'pyttb.tex', 'pyttb Documentation',
-     'Danny Dunlavy, Nick Johnson', 'manual'),
+    (
+        master_doc,
+        "pyttb.tex",
+        "pyttb Documentation",
+        "Danny Dunlavy, Nick Johnson",
+        "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, 'pyttb', 'pyttb Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pyttb", "pyttb Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -169,13 +169,19 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'pyttb', 'pyttb Documentation',
-     author, 'Danny Dunlavy, Nick Johnson', 'Python Tensor Toolbox',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "pyttb",
+        "pyttb Documentation",
+        author,
+        "Danny Dunlavy, Nick Johnson",
+        "Python Tensor Toolbox",
+        "Miscellaneous",
+    ),
 ]
 
 
 # -- Extension configuration -------------------------------------------------
 # Autodoc settings
 autoclass_content = "class"
-autodoc_member_order = 'bysource'
+autodoc_member_order = "bysource"
diff --git a/pyttb/__init__.py b/pyttb/__init__.py
@@ -2,33 +2,34 @@
 # LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the
 # U.S. Government retains certain rights in this software.
 
-__version__ = '1.3.8'
+__version__ = "1.3.8"
 
+import warnings
+
+from pyttb.cp_als import cp_als
+from pyttb.cp_apr import *
+from pyttb.export_data import export_data
+from pyttb.import_data import import_data
+from pyttb.khatrirao import khatrirao
 from pyttb.ktensor import ktensor
-from pyttb.sptensor import sptensor
-from pyttb.tensor import tensor
+from pyttb.pyttb_utils import *
 from pyttb.sptenmat import sptenmat
+from pyttb.sptensor import sptensor
 from pyttb.sptensor3 import sptensor3
 from pyttb.sumtensor import sumtensor
 from pyttb.symktensor import symktensor
 from pyttb.symtensor import symtensor
 from pyttb.tenmat import tenmat
+from pyttb.tensor import tensor
 from pyttb.ttensor import ttensor
-
-from pyttb.pyttb_utils import *
-from pyttb.khatrirao import khatrirao
-from pyttb.cp_apr import *
-from pyttb.cp_als import cp_als
 from pyttb.tucker_als import tucker_als
 
-from pyttb.import_data import import_data
-from pyttb.export_data import export_data
 
-import warnings
 def ignore_warnings(ignore=True):
     if ignore:
-        warnings.simplefilter('ignore')
+        warnings.simplefilter("ignore")
     else:
-        warnings.simplefilter('default')
+        warnings.simplefilter("default")
+
 
 ignore_warnings(True)