merge with main

.github/workflows/bleeding-edge.yaml

@@ -0,0 +1,54 @@
+name: CI (bleeding edge)
+# this workflow is heavily inspired from pandas, see
+# https://github.com/pandas-dev/pandas/blob/master/.github/workflows/python-dev.yml
+
+# goals: check stability against
+# - dev version of Python, numpy, and matplotlib
+# - building with future pip default options
+
+on:
+  push:
+    branches:
+      - main
+  schedule:
+    # run this every day at 3 am UTC
+    - cron: '0 3 * * *'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: Python3.10-dev
+    timeout-minutes: 60
+
+    concurrency:
+      group: ${{ github.ref }}-dev
+      cancel-in-progress: true
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python Dev Version
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.10-dev'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install --upgrade setuptools wheel
+        python -m pip install git+https://github.com/numpy/numpy.git
+        python -m pip install git+https://github.com/matplotlib/matplotlib.git
+        python -m pip install cython
+
+    - name: Build yt
+      # --no-build-isolation is used to guarantee that build time dependencies
+      # are not installed by pip as specified from pyproject.toml, hence we get
+      # to use the dev version of numpy at build time.
+      run: |
+        python setup.py build_ext -q -j2
+        python -m pip install -e .[test] --no-build-isolation
+
+    - name: Run Tests
+      run: pytest -vvv

.github/workflows/build-test-pytest.yaml

@@ -1,6 +1,13 @@
 name: Build and Test
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    paths-ignore:
+      - "doc/**"
+      - README.md
 
 defaults:
   run:

.github/workflows/build-test.yaml

@@ -1,6 +1,13 @@
 name: Build and Test
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    paths-ignore:
+      - "doc/**"
+      - README.md
 
 defaults:
   run:

.github/workflows/rules-checks.yaml

@@ -1,3 +1,6 @@
+# FUTURE: this file can be deleted at condition that warnings are treated
+# as errors in all CI jobs covering h5py.
+# In practice, this will only be possible when we're done transitioning to pytest.
 name: Auto review bad practice
 on: [pull_request]
 

.github/workflows/wheels.yaml

@@ -0,0 +1,60 @@
+name: Build CI Wheels
+
+on:
+  push:
+    branches:
+      - main
+      - stable
+    tags:
+      - 'yt-*'
+
+jobs:
+  build_wheels:
+    name: Wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04, windows-latest, macos-latest]
+      fail-fast: false
+
+    steps:
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: 3.9
+
+      - uses: s-weigand/setup-conda@v1
+        if: matrix.os == 'windows-latest'
+        with:
+          update-conda: true
+          conda-channels: conda-forge
+          activate-conda: true
+          python-version: 3.9
+
+      - uses: actions/checkout@v2
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==1.9.0
+
+      - name: Install dependencies and yt
+        shell: bash
+        env:
+          dependencies: "full"
+          LDFLAGS: "-static-libstdc++"
+        run: source ./tests/ci_install.sh
+
+      - name: Build wheels for CPython
+        run: |
+          python -m cibuildwheel --output-dir dist
+        env:
+          CIBW_BUILD: "cp36-* cp37-* cp38-* cp39-*"
+          CIBW_ARCHS_LINUX: "x86_64"
+          CIBW_ARCHS_MACOS: "x86_64"
+          CIBW_ARCHS_WINDOWS: "auto"
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+          CIBW_MANYLINUX_I686_IMAGE: manylinux2014
+          CIBW_ENVIRONMENT: "LDFLAGS='-static-libstdc++'"
+
+      - uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: ./dist/*.whl

.pre-commit-config.yaml

@@ -28,34 +28,38 @@ repos:
     - id: no-commit-to-branch
       args: [--branch, main]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.19.1
+    rev: v2.21.0
     hooks:
     - id: pyupgrade
       args: [--py36-plus]
 -   repo: https://github.com/psf/black
-    rev: 21.5b2
+    rev: 21.6b0
     hooks:
     - id: black
       language_version: python3
 -   repo: https://github.com/PyCQA/isort
-    rev: '5.8.0'
+    rev: '5.9.2'
     hooks:
     - id: isort
-      additional_dependencies: [toml]
+      name: isort (python)
+    - id: isort
+      name: isort (cython)
+      types: [cython]
 -   repo: https://github.com/PyCQA/flake8
     rev: '3.9.2'
     hooks:
     - id: flake8
       additional_dependencies: [
         flake8-bugbear>=20.3.2, # GH PR 2851
-        flake8-logging-format
+        flake8-logging-format,
+        flake8-2020==1.6.0,
       ]
 -   repo: https://github.com/asottile/blacken-docs
     rev: v1.10.0
     hooks:
     -   id: blacken-docs
         additional_dependencies: [black==20.8b1]
 -   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.8.0
+    rev: v1.9.0
     hooks:
     -   id: rst-backticks

CONTRIBUTING.rst

@@ -118,17 +118,11 @@ Feel free to `blog <https://blog.yt-project.org/>`_ about, `tweet
 Long-Term Projects
 ------------------
 
-There are some wild-eyed, out-there ideas that have been bandied about for the
-future directions of yt -- some of them even written into the mission
-statement.  The ultimate goal is to move past simple analysis and visualization
-of data and begin to approach it from the other side, of generating data,
-running solvers.  We also hope to increase its ability to act as an in situ
-analysis code, by presenting a unified protocol.  Other projects include
-interfacing with ParaView and VisIt, creating a web GUI for running
-simulations, creating a run-tracker that follows simulations in progress, a
-federated database for simulation outputs, and so on and so forth.
-
-yt is an ambitious project.  Let's be ambitious together.
+There are some out-there ideas that have been bandied about for the
+future directions of yt -- stuff like fun new types of visualization, remapping
+of coordinates, new ways of accessing data, and even new APIs to make life easier.
+
+yt is an ambitious project.  Let's be ambitious together!
 
 yt Community Code of Conduct
 ----------------------------
@@ -362,7 +356,7 @@ How To Read The Source Code
 
 If you just want to *look* at the source code, you may already have it on your
 computer.  If you build yt using the install script, the source is available at
-``$YT_DEST/src/yt-git``.  See :ref:`source-installation` for more details about
+``$YT_DEST/src/yt-git``.  See :ref:`install-from-source` for more details about
 to obtain the yt source code if you did not build yt using the install
 script.
 
@@ -401,10 +395,9 @@ the following subdirectories:
    classes for data regions, covering grids, time series, and so on.  This
    also includes derived fields and derived quantities.
 
-``gui``
-   This is where all GUI components go.  Typically this will be some small
-   tool used for one or two things, which contains a launching mechanism on
-   the command line.
+``units``
+   This used to be where all the unit-handling code resided, but as of now it's
+   mostly just a thin wrapper around unyt.
 
 ``utilities``
    All broadly useful code that doesn't clearly fit in one of the other
@@ -434,33 +427,7 @@ Building yt
 +++++++++++
 
 If you have made changes to any C or Cython (``.pyx``) modules, you have to
-rebuild yt.  If your changes have exclusively been to Python modules, you will
-not need to re-build, but (see below) you may need to re-install.
-
-Note that you will need a functioning compilation environment to build yt. On
-linux this typically means installing the package that sets up a basic build
-environment (e.g. ``build-essential`` on Debian and Ubuntu). On MacOS this means
-installing the XCode command line tools. On Windows this means installing the
-version of the Microsoft Visual C++ compiler that is appropriate for your
-version of Python. See `the Python wiki
-<https://wiki.python.org/moin/WindowsCompilers>`_ for more details.
-
-If you are running from a clone that is executable in-place (i.e., has been
-installed via the installation script or you have run ``setup.py develop``) you
-can rebuild these modules by executing:
-
-.. code-block:: bash
-
-  $ python setup.py develop
-
-If you have previously "installed" via ``setup.py install`` you have to
-re-install:
-
-.. code-block:: bash
-
-  $ python setup.py install
-
-Only one of these two options is needed.
+rebuild yt before your changes are usable. See :ref:`install-from-source`.
 
 .. _requirements-for-code-submission:
 
@@ -585,7 +552,7 @@ Here's a more detailed flowchart of how to submit changes.
    this at: https://github.com/yt-project/yt/fork.
 #. If you have used the installation script, the source code for yt can be
    found in ``$YT_DEST/src/yt-git``.  Alternatively see
-   :ref:`source-installation` for instructions on how to build yt from the
+   :ref:`install-from-source` for instructions on how to build yt from the
    git repository. (Below, in :ref:`reading-source`, we describe how to
    find items of interest.) If you have already forked the repository then
    you can clone your fork locally::

MANIFEST.in

@@ -1,10 +1,16 @@
 include README* CREDITS COPYING.txt CITATION  setupext.py CONTRIBUTING.rst
 include yt/visualization/mapserver/html/map.js
 include yt/visualization/mapserver/html/map_index.html
+include yt/visualization/mapserver/html/Leaflet.Coordinates-0.1.5.css
+include yt/visualization/mapserver/html/Leaflet.Coordinates-0.1.5.src.js
 include yt/utilities/tests/cosmology_answers.yml
 include yt/utilities/mesh_types.yaml
 exclude scripts/pr_backport.py
-recursive-include yt *.py *.pyx *.pxd *.h *.hpp README* *.txt LICENSE* *.cu
+exclude yt/utilities/lib/cykdtree/c_kdtree.cpp
+prune tests
+prune docker
+prune answer-store
+recursive-include yt *.py *.pyx *.pxi *.pxd *.h *.hpp README* *.txt LICENSE* *.cu
 recursive-include doc *.rst *.txt *.py *.ipynb *.png *.jpg *.css *.html
 recursive-include doc *.h *.c *.sh *.svgz *.pdf *.svg *.pyx
 include doc/README doc/activate doc/activate.csh doc/cheatsheet.tex
@@ -13,5 +19,8 @@ prune doc/source/reference/api/generated
 prune doc/build
 recursive-include yt/visualization/volume_rendering/shaders *.fragmentshader *.vertexshader
 include yt/sample_data_registry.json
+include conftest.py
 prune yt/frontends/_skeleton
 recursive-include yt/frontends/amrvac *.par
+exclude .codecov.yml .coveragerc .git-blame-ignore-revs .gitmodules .hgchurn .mailmap
+exclude .pre-commit-config.yaml clean.sh nose_answer.cfg nose_unit.cfg

README.md

@@ -1,6 +1,7 @@
 # The yt Project
 
-![Supported Python Version](https://img.shields.io/badge/python%20version-≥%203.6-important)
+[![PyPI](https://img.shields.io/pypi/v/yt)](https://pypi.org/project/yt)
+[![Supported Python Versions](https://img.shields.io/pypi/pyversions/yt)](https://pypi.org/project/yt/)
 [![Latest Documentation](https://img.shields.io/badge/docs-latest-brightgreen.svg)](http://yt-project.org/docs/dev/)
 [![Users' Mailing List](https://img.shields.io/badge/Users-List-lightgrey.svg)](https://mail.python.org/archives/list/yt-users@python.org//)
 [![Devel Mailing List](https://img.shields.io/badge/Devel-List-lightgrey.svg)](https://mail.python.org/archives/list/yt-dev@python.org//)
@@ -10,14 +11,15 @@
 
 <!--- Tests and style --->
 ![Build and Test](https://github.com/yt-project/yt/workflows/Build%20and%20Test/badge.svg?branch=main)
+[![CI (bleeding edge)](https://github.com/yt-project/yt/actions/workflows/bleeding-edge.yaml/badge.svg)](https://github.com/yt-project/yt/actions/workflows/bleeding-edge.yaml)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/yt-project/yt/main.svg)](https://results.pre-commit.ci/latest/github/yt-project/yt/main)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
 <!--- [![codecov](https://codecov.io/gh/yt-project/yt/branch/main/graph/badge.svg)](https://codecov.io/gh/yt-project/yt) --->
 
-<a href="http://yt-project.org"><img src="doc/source/_static/yt_logo.png" width="300"></a>
+<a href="http://yt-project.org"><img src="https://raw.githubusercontent.com/yt-project/yt/main/doc/source/_static/yt_logo.png" width="300"></a>
 
-yt is an open-source, permissively-licensed python package for analyzing and
+yt is an open-source, permissively-licensed Python library for analyzing and
 visualizing volumetric data.
 
 yt supports structured, variable-resolution meshes, unstructured meshes, and
@@ -50,54 +52,11 @@ conda install -c conda-forge yt
 or with pip:
 
 ```shell
-pip install yt
+python -m pip install yt
 ```
 
-To get set up with a development version, you want to clone this repository:
-
-```shell
-git clone https://github.com/yt-project/yt yt-git
-cd yt-git
-```
-
-and work within a conda environment:
-
-```shell
-# Create a conda environment named yt-git
-$ conda create -n yt-git python=3.6
-# Activate it
-$ source activate yt-git
-# Make sure you run the latest version of conda
-$ conda update conda
-# Install yt's runtime dependencies
-$ conda install -c conda-forge yt --only-deps
-# Install yt's build dependencies
-$ conda install -c conda-forge cython
-# Make sure you run the latest version of pip
-$ pip install --upgrade pip
-$ pip install -v -e .
-# Output installed packages
-$ conda env export
-```
-
-Alternatively, you can install yt in a
-[virtualenv](https://packaging.python.org/installing/#creating-virtual-environments):
-
-```shell
-# It is conventional to create virtualenvs at ~/.virtualenv/
-$ mkdir -p ~/.virtualenv
-# Assuming your version of Python 3 meets the minimal requirement
-# create a virtualenv named yt-git
-$ python3 -m venv ~/.virtualenv/yt-git
-# Activate it
-$ source ~/.virtualenv/yt-git/bin/activate
-# Make sure you run the latest version of pip
-$ pip install --upgrade pip
-# Assuming you have cd'd into yt-git
-$ pip install -e .
-# Output installed packages
-$ pip freeze
-```
+More information on the various ways to install yt, and in particular to install from source,
+can be found on [the project's website](https://yt-project.org/docs/dev/installing.html).
 
 ## Getting Started