.editorconfig

+# https://editorconfig.org/
+# https://github.com/editorconfig/editorconfig-vim
+# https://github.com/editorconfig/editorconfig-emacs
+
+root = true
+
+[*]
+indent_style = space
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.py]
+indent_size = 4
+
+[*.rst]
+indent_size = 4
+
+[*.cpp]
+indent_size = 2
+
+[*.hpp]
+indent_size = 2
+
+# There may be one in doc/
+[Makefile]
+indent_style = tab
+
+# https://github.com/microsoft/vscode/issues/1679
+[*.md]
+trim_trailing_whitespace = false
\ No newline at end of file

.github/dependabot.yml

+version: 2
+updates:
+    # Set update schedule for GitHub Actions
+    - package-ecosystem: "github-actions"
+      directory: "/"
+      schedule:
+          interval: "weekly"
+
+# vim: sw=4

.github/workflows/autopush.yml

+name: Gitlab mirror
+on:
+    push:
+        branches:
+        - main
+
+jobs:
+    autopush:
+        name: Automatic push to gitlab.tiker.net
+        if: startsWith(github.repository, 'inducer/')
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   run: |
+                curl -L -O https://tiker.net/ci-support-v0
+                . ./ci-support-v0
+                mirror_github_to_gitlab
+
+            env:
+                GITLAB_AUTOPUSH_KEY: ${{ secrets.GITLAB_AUTOPUSH_KEY }}
+
+# vim: sw=4

.github/workflows/ci.yml

+name: CI
+on:
+    push:
+        branches:
+        - main
+    pull_request:
+        paths-ignore:
+        - 'doc/*.rst'
+    schedule:
+        - cron:  '17 3 * * 0'
+
+concurrency:
+    group: ${{ github.head_ref || github.ref_name }}
+    cancel-in-progress: true
+
+jobs:
+    ruff:
+        name: Ruff
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: actions/setup-python@v5
+        -   name: "Main Script"
+            run: |
+                pip install ruff
+                ruff check
+
+    typos:
+        name: Typos
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: crate-ci/typos@master
+
+    validate_cff:
+        name: Validate CITATION.cff
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: actions/setup-python@v5
+            with:
+                python-version: '3.x'
+        -   run: |
+                pip install cffconvert
+                cffconvert -i CITATION.cff --validate
+
+    pylint:
+        name: Pylint
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.x'
+        -   name: "Main Script"
+            run: |
+                EXTRA_INSTALL="numpy pymbolic orderedsets"
+                curl -L -O https://gitlab.tiker.net/inducer/ci-support/raw/main/prepare-and-run-pylint.sh
+                . ./prepare-and-run-pylint.sh "$(basename $GITHUB_REPOSITORY)"
+
+    mypy:
+        name: Mypy
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.x'
+        -   name: "Main Script"
+            run: |
+                EXTRA_INSTALL="numpy siphash24"
+                curl -L -O https://gitlab.tiker.net/inducer/ci-support/raw/main/prepare-and-run-mypy.sh
+                . ./prepare-and-run-mypy.sh python3 mypy
+
+    pytest:
+        name: Pytest on Py${{ matrix.python-version }} ${{ matrix.os }}
+        runs-on: ${{ matrix.os }}
+        strategy:
+            matrix:
+                python-version: ["3.10", "3.12", "3.x", "pypy3.10"]
+                os: [ubuntu-latest, macos-latest]
+        steps:
+        -   uses: actions/checkout@v4
+        -
+            uses: actions/setup-python@v5
+            with:
+                python-version: ${{ matrix.python-version }}
+        -   name: "Main Script"
+            run: |
+                # untested, causes import error with Pytest >= 6.2.0
+                # AK, 2020-12-13
+                rm pytools/mpiwrap.py
+
+                EXTRA_INSTALL="numpy frozendict immutabledict orderedsets constantdict immutables pyrsistent attrs siphash24"
+                curl -L -O https://gitlab.tiker.net/inducer/ci-support/raw/main/build-and-test-py-project.sh
+                . ./build-and-test-py-project.sh
+
+                # Also run with optimizations turned on, since opt_frozen_dataclass
+                # depends on the __debug__ setting.
+                python -O -m pytest pytools/test/test_dataclasses.py
+
+    pytest_nonumpy:
+        name: Pytest without Numpy
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.x'
+        -   name: "Main Script"
+            run: |
+                EXTRA_INSTALL="siphash24"
+                rm pytools/{convergence,spatial_btree,obj_array,mpiwrap}.py
+                curl -L -O https://gitlab.tiker.net/inducer/ci-support/raw/main/build-and-test-py-project.sh
+                . ./build-and-test-py-project.sh
+
+    #examples:
+    #    name: Examples Py3
+    #    runs-on: ubuntu-latest
+    #    steps:
+    #    -   uses: actions/checkout@v4
+    #    -
+    #        uses: actions/setup-python@v5
+    #        with:
+    #            python-version: '3.x'
+    #    -   name: "Main Script"
+    #        run: |
+    #            EXTRA_INSTALL="numpy pymbolic"
+    #            curl -L -O https://tiker.net/ci-support-v0
+    #            . ./ci-support-v0
+    #            build_py_project_in_venv
+    #            run_examples
+
+    downstream_tests:
+        strategy:
+            matrix:
+                downstream_project: [loopy, pytato]
+        name: Tests for downstream project ${{ matrix.downstream_project }}
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   name: "Main Script"
+            env:
+                DOWNSTREAM_PROJECT: ${{ matrix.downstream_project }}
+            run: |
+                curl -L -O https://tiker.net/ci-support-v0
+                . ./ci-support-v0
+                test_downstream "$DOWNSTREAM_PROJECT"
+
+    docs:
+        name: Documentation
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.x'
+        -   name: "Main Script"
+            run: |
+                EXTRA_INSTALL="numpy"
+                curl -L -O https://tiker.net/ci-support-v0
+                . ci-support-v0
+                build_py_project_in_venv
+                build_docs
+
+# vim: sw=4

.gitignore

@@ -13,3 +13,9 @@ distribute*egg
 distribute*tar.gz
 
 .cache
+.mypy_cache
+
+*.dat
+
+.pylintrc.yml
+.run-pylint.py

.gitlab-ci.yml

-Python 2.6:
-  script:
-  - py_version=2.6
-  - export EXTRA_INSTALL="numpy"
-  - curl -L -O -k https://gitlab.tiker.net/inducer/ci-support/raw/master/build-and-test-py-project.sh
-  - ". ./build-and-test-py-project.sh"
-  tags:
-  - python2.6
-  except:
-  - tags
-  artifacts:
-    reports:
-      junit: test/pytest.xml
+Pytest:
+  script: |
+    # untested, causes import error with Pytest >= 6.2.0
+    # AK, 2020-12-13
+    rm pytools/mpiwrap.py
 
-Python 2.7:
-  script:
-  - py_version=2.7
-  - export EXTRA_INSTALL="numpy"
-  - curl -L -O -k https://gitlab.tiker.net/inducer/ci-support/raw/master/build-and-test-py-project.sh
-  - ". ./build-and-test-py-project.sh"
+    export EXTRA_INSTALL="numpy siphash24"
+    curl -L -O https://gitlab.tiker.net/inducer/ci-support/raw/main/build-and-test-py-project.sh
+    . ./build-and-test-py-project.sh
   tags:
-  - python2.7
+  - python3
   except:
   - tags
   artifacts:
     reports:
       junit: test/pytest.xml
 
-Python 3.6:
-  script:
-  - py_version=3.6
-  - export EXTRA_INSTALL="numpy"
-  - curl -L -O -k https://gitlab.tiker.net/inducer/ci-support/raw/master/build-and-test-py-project.sh
-  - ". ./build-and-test-py-project.sh"
+Pytest without Numpy:
+  script: |
+    EXTRA_INSTALL="siphash24"
+    rm pytools/{convergence,spatial_btree,obj_array,mpiwrap}.py
+    curl -L -O https://gitlab.tiker.net/inducer/ci-support/raw/main/build-and-test-py-project.sh
+    . ./build-and-test-py-project.sh
   tags:
-  - python3.6
+  - python3
   except:
   - tags
   artifacts:
     reports:
       junit: test/pytest.xml
 
-Python 3.7:
+# Examples:
+#   script: |
+#     EXTRA_INSTALL="numpy pymbolic"
+#     curl -L -O https://tiker.net/ci-support-v0
+#     . ./ci-support-v0
+#     build_py_project_in_venv
+#     run_examples
+#   tags:
+#   - python3
+#   except:
+#   - tags
+
+Ruff:
   script:
-  - py_version=3.7
-  - export EXTRA_INSTALL="numpy"
-  - curl -L -O -k https://gitlab.tiker.net/inducer/ci-support/raw/master/build-and-test-py-project.sh
-  - ". ./build-and-test-py-project.sh"
+  - pipx install ruff
+  - ruff check
   tags:
-  - python3.7
+  - docker-runner
   except:
   - tags
-  artifacts:
-    reports:
-      junit: test/pytest.xml
 
-Flake8:
+Mypy:
   script:
-  - curl -L -O -k https://gitlab.tiker.net/inducer/ci-support/raw/master/prepare-and-run-flake8.sh
-  - ". ./prepare-and-run-flake8.sh pytools test"
+  - curl -L -O https://gitlab.tiker.net/inducer/ci-support/raw/main/prepare-and-run-mypy.sh
+  - ". ./prepare-and-run-mypy.sh python3 mypy"
   tags:
-  - python3.6
+  - python3
   except:
   - tags
 
 Pylint:
   script:
-  - EXTRA_INSTALL="pymbolic matplotlib mpi4py"
-  - py_version=3.6
-  - curl -L -O -k https://gitlab.tiker.net/inducer/ci-support/raw/master/prepare-and-run-pylint.sh
-  - ". ./prepare-and-run-pylint.sh pytools test/test_*.py"
+  - EXTRA_INSTALL="numpy pymbolic orderedsets siphash24"
+  - py_version=3
+  - curl -L -O https://gitlab.tiker.net/inducer/ci-support/raw/main/prepare-and-run-pylint.sh
+  - . ./prepare-and-run-pylint.sh "$CI_PROJECT_NAME"
   tags:
-  - python3.6
+  - python3
   except:
   - tags
 
 Documentation:
   script:
-  - EXTRA_INSTALL="numpy"
-  - curl -L -O -k https://gitlab.tiker.net/inducer/ci-support/raw/master/build-docs.sh
+  - EXTRA_INSTALL="numpy siphash24"
+  - curl -L -O https://gitlab.tiker.net/inducer/ci-support/raw/main/build-docs.sh
   - ". ./build-docs.sh"
   tags:
-  - python3.5
-  only:
-  - master
+  - python3
+
+Downstream:
+  parallel:
+    matrix:
+    - DOWNSTREAM_PROJECT: [loopy, pytato]
+  tags:
+  - large-node
+  - "docker-runner"
+  script: |
+    curl -L -O https://tiker.net/ci-support-v0
+    . ./ci-support-v0
+    test_downstream "$DOWNSTREAM_PROJECT"
 
+# vim: sw=2

.pylintrc-local.yml

+- arg: ignore
+  val:
+    - mpiwrap.py
+- arg: ignored-modules
+  val:
+  - matplotlib
+  - siphash24

CITATION.cff

+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Kloeckner"
+  given-names: "Andreas"
+  orcid: "https://orcid.org/0000-0003-1228-519X"
+- family-names: "Christensen"
+  given-names: "Nick"
+- family-names: "Wala"
+  given-names: "Matt"
+- family-names: "Fikl"
+  given-names: "Alex"
+- family-names: "Stevens"
+  given-names: "James"
+- family-names: "Diener"
+  given-names: "Matthias"
+- family-names: "Kulkarni"
+  given-names: "Kaushik"
+- family-names: "Witherden"
+  given-names: "Freddie"
+- family-names: "Kempf"
+  given-names: "Dominic"
+- family-names: "Gibson"
+  given-names: "Thomas H."
+- family-names: "Fernando"
+  given-names: "Isuru"
+- family-names: "Yu"
+  given-names: "Yichao"
+- family-names: "Wei"
+  given-names: "Xiaoyu"
+- family-names: "Drix"
+  given-names: "Damien"
+- family-names: "Hoag"
+  given-names: "Ellis"
+- family-names: "Gao"
+  given-names: "Hao"
+- family-names: "Dercksen"
+  given-names: "Koen"
+- family-names: "Kocak"
+  given-names: "Kubilay"
+- family-names: "Ofitserov"
+  given-names: "Nikita"
+
+title: "pytools"
+version: 2022.1.7
+doi: 10.5281/zenodo.6533949
+date-released: 2022-05-04
+url: "https://github.com/inducer/pytools"
+license: MIT

MANIFEST.in

-include LICENSE
-
-include doc/*rst
-include doc/Makefile
-include doc/conf.py

README.rst

+Pytools: Lots of Little Utilities
+=================================
+
+.. image:: https://gitlab.tiker.net/inducer/pytools/badges/main/pipeline.svg
+    :alt: Gitlab Build Status
+    :target: https://gitlab.tiker.net/inducer/pytools/commits/main
+.. image:: https://github.com/inducer/pytools/workflows/CI/badge.svg?branch=main
+    :alt: Github Build Status
+    :target: https://github.com/inducer/pytools/actions?query=branch%3Amain+workflow%3ACI
+.. image:: https://badge.fury.io/py/pytools.png
+    :alt: Python Package Index Release Page
+    :target: https://pypi.org/project/pytools/
+.. image:: https://zenodo.org/badge/1575270.svg
+    :alt: Zenodo DOI for latest release
+    :target: https://zenodo.org/badge/latestdoi/1575270
+
 Pytools is a big bag of things that are "missing" from the Python standard
 library. This is mainly a dependency of my other software packages, and is
 probably of little interest to you unless you use those. If you're curious
@@ -5,14 +21,16 @@ nonetheless, here's what's on offer:
 
 * A ton of small tool functions such as `len_iterable`, `argmin`,
   tuple generation, permutation generation, ASCII table pretty printing,
-  GvR's mokeypatch_xxx() hack, the elusive `flatten`, and much more.
-* Michele Simionato's decorator module
-* A time-series logging module, `pytools.log`.
+  GvR's monkeypatch_xxx() hack, the elusive `flatten`, and much more.
 * Batch job submission, `pytools.batchjob`.
 * A lexer, `pytools.lex`.
+* A persistent key-value store, `pytools.persistent_dict`.
 
 Links:
 
 * `Documentation <https://documen.tician.de/pytools>`_
 
 * `Github <https://github.com/inducer/pytools>`_
+
+* ``pytools.log`` has been spun out into a separate project,
+  `logpyle <https://github.com/illinois-ceesd/logpyle>`__.

doc/Makefile

@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line.
 SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
+SPHINXBUILD   = python $(shell which sphinx-build)
 SPHINXPROJ    = pytools
 SOURCEDIR     = .
 BUILDDIR      = _build
@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file

doc/codegen.rst

+.. automodule:: pytools.codegen

doc/conf.py

-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-#
-# pytools documentation build configuration file, created by
-# sphinx-quickstart on Wed Jun 14 16:28:43 2017.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-# 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.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+from __future__ import annotations
 
+from urllib.request import urlopen
 
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = ['sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.viewcode']
-
-# Add any paths that contain templates here, relative to this directory.
-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'
 
-# The master toctree document.
-master_doc = 'index'
+_conf_url = \
+        "https://raw.githubusercontent.com/inducer/sphinxconfig/main/sphinxconfig.py"
+with urlopen(_conf_url) as _inf:
+    exec(compile(_inf.read(), _conf_url, "exec"), globals())
 
-# General information about the project.
-project = 'pytools'
-copyright = '2017, Andreas Kloeckner'
-author = 'Andreas Kloeckner'
+copyright = "2009-21, Andreas Kloeckner"
+author = "Andreas Kloeckner"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -59,119 +17,33 @@ author = 'Andreas Kloeckner'
 #
 # The short X.Y version.
 ver_dic = {}
-exec(compile(open("../pytools/version.py").read(), "../pytools/version.py", 'exec'), ver_dic)
+exec(compile(open("../pytools/version.py").read(), "../pytools/version.py", "exec"),
+        ver_dic)
 version = ".".join(str(x) for x in ver_dic["VERSION"])
 release = ver_dic["VERSION_TEXT"]
 
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# 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
-
 # 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']
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = False
-
-
-# -- 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 = 'alabaster'
-
-html_theme_options = {
-        "extra_nav_links": {
-            "🚀 Github": "https://github.com/inducer/pytools",
-            "💾 Download Releases": "https://pypi.python.org/pypi/pytools",
-            }
-        }
-
-html_sidebars = {
-    '**': [
-        'about.html',
-        'navigation.html',
-        'relations.html',
-        'searchbox.html',
-    ]
-}
-
-# 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 = {}
-
-# 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']
-
-
-# -- Options for HTMLHelp output ------------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'pytoolsdoc'
-
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-    # 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',
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+intersphinx_mapping = {
+    "loopy": ("https://documen.tician.de/loopy", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "pymbolic": ("https://documen.tician.de/pymbolic", None),
+    "pytest": ("https://docs.pytest.org/en/stable", None),
+    "setuptools": ("https://setuptools.pypa.io/en/latest", None),
+    "python": ("https://docs.python.org/3", None),
+    "platformdirs": ("https://platformdirs.readthedocs.io/en/latest", None),
 }
 
-# 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, 'pytools.tex', 'pytools Documentation',
-     'Andreas Kloeckner', 'manual'),
+nitpicky = True
+nitpick_ignore_regex = [
+    ["py:class", r"typing_extensions\.(.+)"],
+    ["py:class", r"ReadableBuffer"],
 ]
 
-
-# -- 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, 'pytools', 'pytools Documentation',
-     [author], 1)
-]
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-    (master_doc, 'pytools', 'pytools Documentation',
-     author, 'pytools', 'One line description of project.',
-     'Miscellaneous'),
-]
-
-
-
+autodoc_type_aliases = {
+    "GraphT": "pytools.graph.GraphT",
+    "NodeT": "pytools.graph.NodeT",
+}

doc/convergence.rst

+Testing convergence
+-------------------
+
+.. automodule:: pytools.convergence

doc/graph.rst

+.. automodule:: pytools.graph

doc/index.rst

@@ -8,7 +8,14 @@ Welcome to pytools's documentation!
     reference
     obj_array
     persistent_dict
+    convergence
+    graph
+    tag
+    codegen
+    mpi
     misc
+    🚀 Github <https://github.com/inducer/pytools>
+    💾 Download Releases <https://pypi.python.org/pypi/pytools>
 
 Indices and tables
 ==================

doc/misc.rst

@@ -20,7 +20,7 @@ and say::
 User-visible changes
 ====================
 
-Version 2017.4
+Version 2020.4
 --------------
 
 .. note::
@@ -28,6 +28,14 @@ Version 2017.4
     This version is currently under development. You can get snapshots from
     Pytools's `git repository <https://github.com/inducer/pytools>`_
 
+* :mod:`pytools.codegen` was added.
+
+Version 2020.3
+--------------
+
+* Type annotations were added.
+* Python 2 support was dropped.
+
 .. _license:
 
 License

doc/mpi.rst

+.. automodule:: pytools.mpi

doc/reference.rst

 .. automodule:: pytools
+.. automodule:: pytools.datatable
+
+.. automodule:: pytools.graphviz

doc/tag.rst

+.. automodule:: pytools.tag