Merge branch 'master' into index_chunksize

.coveragerc

@@ -13,8 +13,6 @@ omit=*.yml
 	 yt/mods.py
 	 yt/utilities/fits_image.py
 	 yt/utilities/lodgeit.py
-	 yt/utilities/lru_cache.py
-	 yt/utilities/poster/*
 	 yt/visualization/_mpl_imports.py
 
 ignore_errors = True

.git-blame-ignore-revs

@@ -0,0 +1,15 @@
+# transition to isort
+7edfcee093cca277307aabdb180e0ffc69768291
+81418e459f16c48d6b7a75d6ef8035dfe9651b39
+
+# transition to black
+ebadee629414aed2c7b6526e22a419205329ec38
+
+# automated trailing whitespace removal
+3ee548b04a41dfbc009921c492fba6a0682651ca
+
+# converting to f-strings
+ad898e8e3954bc348daaa449d5ed73db778785e9
+ef51ad5199692afcf1a8ab491aa115c00c423113
+323ac4ddd4e99d6b951666736d4e9b03b6cfa21e
+f7445f02022293f1b089cd8907000301516354bf

.github/PULL_REQUEST_TEMPLATE.md

@@ -20,9 +20,10 @@ detail.  Why is this change required?  What problem does it solve?-->
 
 <!-- Note that some of these check boxes may not apply to all pull requests -->
 
-- [ ] pass `flake8 yt/`
-- [ ] pass `isort -rc . --check-only`
 - [ ] pass `black --check yt/`
+- [ ] pass `isort . --check --diff`
+- [ ] pass `flake8 yt/`
+- [ ] pass `flynt yt/ --fail-on-change --dry-run -e yt/extern`
 - [ ] New features are documented, with docstrings and narrative docs
 - [ ] Adds a test for any bugs fixed. Adds tests for new features.
 

.github/mergeable.yml

@@ -9,5 +9,5 @@ mergeable:
           message: "WIP pull requests can't be merged."
       - do: label
         must_include:
-          regex: 'bug|enhancement|new feature|docs|infrastructure'
+          regex: 'bug|enhancement|new feature|docs|infrastructure|dead code|refactor'
           message: "Please label this pull request with one of: bug, enhancement, new feature, docs or infrastructure."

.github/workflows/rules-checks.yaml

@@ -0,0 +1,33 @@
+name: Auto review bad practice
+on: [pull_request]
+
+jobs:
+  h5py-bad-practices:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: check-h5py-import
+      # check that we don't alias h5py to h5
+      # reason: discoverability is important since this module's api
+      # is unstable and we want to be able to check for potential future failures
+      id: h5-import
+      run: |
+        grep -r -n "import _h5py as h5" yt | grep -v "import _h5py as h5py" | cat > h5-imports.log
+        if [ -s h5-imports.log ] ; then
+          echo "Please do not import h5py as h5. Here are the faulty lines."
+          cat h5-imports.log
+          exit 1
+        fi
+
+    - name: check-h5py-filemode
+      id: h5-file-mode
+      # check that a mode argument is always present in calls to h5py.File()
+      # reason: the default value is different in older versions 'w' VS newer ones 'r'
+      run: |
+        grep -E -r -n "h5py\.File\([^,]+\)" yt | cat > h5-mode.log
+        if [ -s h5-mode.log ] ; then
+          echo "h5py.File() should never be called without an explicit mode argument."
+          echo "Here are the faulty lines."
+          cat h5-mode.log
+          exit 1
+        fi

.github/workflows/slash-command-dispatch.yml

@@ -0,0 +1,20 @@
+name: Slash Command Dispatch
+on:
+  issue_comment:
+    types: [created]
+jobs:
+  slashCommandDispatch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Slash Command Dispatch
+        uses: peter-evans/slash-command-dispatch@v2
+        with:
+          token: ${{ secrets.PAT }}
+          commands: |
+            help
+            format
+            rebase
+            isort
+            black
+            flynt
+          repository: yt-project/slash-command-processor

.github/workflows/style-checks.yaml

@@ -0,0 +1,79 @@
+name: Style Checks
+on: [pull_request]
+
+jobs:
+  flake8:
+    name: flake8
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Setup Python
+      uses: actions/setup-python@master
+      with:
+        python-version: 3.8
+    - name: install
+      id: install
+      run : pip install -r tests/lint_requirements.txt
+
+    - name: check
+      id: flake8
+      run: |
+        flake8 --version
+        flake8 yt/
+
+  black:
+    name: black
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Setup Python
+      uses: actions/setup-python@master
+      with:
+        python-version: 3.8
+    - name: install
+      id: install
+      run : pip install -r tests/lint_requirements.txt
+
+    - name: check
+      id: black
+      run: |
+        black --version
+        black --check --diff yt/ 
+        
+  isort:
+    name: isort
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Setup Python
+      uses: actions/setup-python@master
+      with:
+        python-version: 3.8
+    - name: install
+      id: install
+      run : pip install -r tests/lint_requirements.txt
+
+    - name: check
+      id: isort
+      run: |
+        isort --version-number
+        isort . --check --diff
+
+  flynt:
+    name: flynt
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Setup Python
+      uses: actions/setup-python@master
+      with:
+        python-version: 3.8
+    - name: install
+      id: install
+      run : pip install -r tests/lint_requirements.txt
+
+    - name: check
+      id: flynt
+      run: |
+        flynt --version
+        flynt yt --fail-on-change --dry-run --exclude yt/extern

.pep8speaks.yml

@@ -75,8 +75,6 @@ pycodestyle:
         - \*/__config__.py
         - yt/visualization/_mpl_imports.py
         - yt/utilities/lodgeit.py
-        - yt/utilities/lru_cache.py
-        - yt/utilities/poster/\*
         - yt/extern/\*
         - yt/mods.py
         - yt/utilities/fits_image.py

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+-   repo: https://github.com/ambv/black
+    rev: 19.10b0
+    hooks:
+    - id: black
+      language_version: python3.7
+-   repo: https://github.com/timothycrosley/isort
+    rev: '5.2.1'  # keep in sync with tests/lint_requirements.txt
+    hooks:
+    -   id: isort
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: '3.8.1'  # keep in sync with tests/lint_requirements.txt
+    hooks:
+    -   id: flake8
+-   repo: https://github.com/ikamensh/flynt
+    rev: '0.52'  # keep in sync with tests/lint_requirements.txt
+    hooks:
+    -   id: flynt

.travis.yml

@@ -19,6 +19,7 @@ addons:
 env:
   global:
     PIP=pip
+    HOMEBREW_NO_AUTO_UPDATE=1
 
 before_install:
   - |
@@ -30,9 +31,8 @@ before_install:
     else
       sudo mkdir -p /usr/local/man
       sudo chown -R "${USER}:admin" /usr/local/man
-      brew update
-      brew install python ccache hdf5 proj geos openmpi netcdf
-      brew uninstall gdal postgis numpy
+      HOMEBREW_NO_AUTO_UPDATE=1 brew install hdf5 proj geos open-mpi netcdf ccache
+      HOMEBREW_NO_AUTO_UPDATE=1 brew uninstall gdal postgis numpy  # WHY?
       export PATH=/usr/local/opt/ccache/libexec:$PATH
     fi
     mkdir -p $HOME/.config/yt
@@ -51,42 +51,26 @@ install:
     $PIP install --upgrade setuptools
     echo "Travis build stage: $TRAVIS_BUILD_STAGE_NAME"
     # install dependencies yt
-    if [[ ${TRAVIS_BUILD_STAGE_NAME} == "lint" ]]; then
-      export TRAVIS_BUILD_STAGE_NAME="Lint"
-    fi
-    if [[ ${TRAVIS_BUILD_STAGE_NAME} != "Lint" ]]; then
-      if [[ $MINIMAL == 1 ]]; then
-        # Ensure numpy and cython are installed so dependencies that need to be built
-        # don't error out
-        # The first numpy to support py3.6 is 1.12, but numpy 1.13 matches 
-        # unyt so we'll match it here. 
-        $PIP install numpy==1.13.3 cython==0.26.1
-        $PIP install -r tests/test_minimal_requirements.txt
-      else
-        # Getting cartopy installed requires getting cython and numpy installed
-        # first; this is potentially going to be fixed with the inclusion of
-        # pyproject.toml in cartopy.
-        # These versions are pinned, so we will need to update/remove them when
-        # the hack is no longer necessary.
-        $PIP install numpy==1.18.1 cython==0.29.6
-        CFLAGS="$CFLAGS -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H" $PIP install -r tests/test_requirements.txt
-      fi
-      $PIP install -e .
+    if [[ $MINIMAL == 1 ]]; then
+      # Ensure numpy and cython are installed so dependencies that need to be built
+      # don't error out
+      # The first numpy to support py3.6 is 1.12, but numpy 1.13 matches 
+      # unyt so we'll match it here. 
+      $PIP install numpy==1.13.3 cython==0.26.1
+      $PIP install -r tests/test_minimal_requirements.txt
     else
-      $PIP install -r tests/lint_requirements.txt
+      # Getting cartopy installed requires getting cython and numpy installed
+      # first; this is potentially going to be fixed with the inclusion of
+      # pyproject.toml in cartopy.
+      # These versions are pinned, so we will need to update/remove them when
+      # the hack is no longer necessary.
+      $PIP install -r tests/test_prerequirements.txt
+      CFLAGS="$CFLAGS -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H" $PIP install -r tests/test_requirements.txt
     fi
+    $PIP install -e .
 
 jobs:
   include:
-    - stage: Lint
-      python: 3.6
-      script: flake8 yt/
-
-    - stage: Lint
-      python: 3.6
-      script: isort --check-only -rc yt/
-      script: black --check yt/
-
     - stage: tests
       name: "Python: 3.6 Minimal Dependency Unit Tests"
       python: 3.6
@@ -116,21 +100,13 @@ jobs:
       name: "MacOS: Unit Tests"
       os: osx
       osx_image: xcode10.1
-      language: generic  # https://github.com/travis-ci/travis-ci/issues/2312
+      language: shell
       env: PIP=pip3
       cache:
-        pip: false
-        directories:
+        - directories:
           - $HOME/Library/Caches/pip
-          # `cache` does not support `env`-like `global` so copy-paste from top
-          - $HOME/.ccache  # https://github.com/travis-ci/travis-ci/issues/5853
       script: nosetests -c nose_unit.cfg
 
 after_success:
-  - |
-    if [[ ${TRAVIS_BUILD_STAGE_NAME} == "lint" ]]; then
-      export TRAVIS_BUILD_STAGE_NAME="Lint"
-    fi
-    if [[ ${TRAVIS_BUILD_STAGE_NAME} != "Lint" ]]; then
-      codecov
-    fi
+  - codecov
+

CONTRIBUTING.rst

@@ -52,10 +52,10 @@ of a repository; in this case the fork will live in the space under your
 username on github, rather than the ``yt-project``. If you have never made a
 fork of a repository on github, or are unfamiliar with this process, here is a
 short article about how to do so:
-https://help.github.com/en/github/getting-started-with-github/fork-a-repo . 
+https://help.github.com/en/github/getting-started-with-github/fork-a-repo .
 The documentation for
 ``yt`` lives in the ``doc`` directory in the root of the yt git
-repository. To make a contribution to the yt documentation you will 
+repository. To make a contribution to the yt documentation you will
 make your changes in your own fork of ``yt``.  When you are done,
 issue a pull request through the website for your new fork, and we can comment
 back and forth and eventually accept your changes. See :ref:`sharing-changes` for
@@ -87,7 +87,7 @@ usually we end up accepting.
 
 For more information, see :ref:`contributing-code`, where we spell out how to
 get up and running with a development environment, how to commit, and how to
-use GitHub. When you're ready to share your changes with the community, refer to 
+use GitHub. When you're ready to share your changes with the community, refer to
 :ref:`sharing-changes` to see how to contribute them back upstream.
 
 Online Presence
@@ -337,12 +337,12 @@ revision specifier will not show more recent changes to the repository. An
 alternative option is to use ``checkout`` on a branch. In yt the ``master``
 branch is our primary development branch, so checking out ``master`` should
 return you to the tip (or most up-to-date revision specifier) on the ``master``
-branch. 
+branch.
 
 .. code-block:: bash
-   
+
    $ git checkout master
-   
+
 Lastly, if you want to use this new downloaded version of your yt repository as
 the *active* version of yt on your computer (i.e. the one which is executed when
 you run yt from the command line or the one that is loaded when you do ``import
@@ -723,8 +723,8 @@ Below are a list of rules for coding style in yt. Some of these rules are
 suggestions are not explicitly enforced, while some are enforced via automated
 testing.
 
-The yt project uses ``flake8`` to report on code correctness (syntax + anti-pattern
-detection), and ``black`` for automated formatting.
+The yt project uses ``flake8`` to report on code correctness (syntax +
+anti-pattern detection), and ``isort``, ``black`` and ``flynt`` for automated formatting.
 
 To check the coding style of your contributions locally you will need to install those
 tools, which can be done for instance with ``pip``:
@@ -738,7 +738,9 @@ Then run the checks from the top level of the repository with
 .. code-block:: bash
 
     $ flake8 yt/
-    $ black --check
+    $ black --check yt/
+    $ isort --check yt/
+    $ flynt --fail-on-change --dry-run -e yt/extern yt/
 
 These will respectively print out any ``flake8`` errors or warnings that your newly added
 code triggers, and a list of files that are currenlty not compliant with ``black``. Note
@@ -781,7 +783,7 @@ If you wish to automate this process you may be interested in using `pre-commit
 
     $ pre-commit install
 
-So that ``black``, ``flake8`` and ``isort`` will run and update your changes every time
+So that ``black``, ``flynt`, ``flake8`` and ``isort`` will run and update your changes every time
 you commit new code. This setup is not required so you have the option of checking for
 code style only in the late stage of a branch when we need to validate it for merging.
 
@@ -822,6 +824,9 @@ Source code style guide
    return value of a function, do not store it in a variable.
  * Add tests for new functionality. When fixing a bug, consider adding a test to
    prevent the bug from recurring.
+ * Use f-strings for string-formatting (https://www.python.org/dev/peps/pep-0498/), except 
+   in logging function where the recommended syntax is
+   ``mylog.info("Something %s", "value")``.
 
 API Style Guide
 ---------------