pre-commit check compliant for github action

.github/workflows/build_workflow.yml

@@ -1,82 +1,76 @@
 name: CI/CD Build Workflow
 
 on:
-    push:
-        branches: [master]
+  push:
+    branches: [master]
 
-    pull_request:
-        branches: [master]
+  pull_request:
+    branches: [master]
 
-    workflow_dispatch:
+  workflow_dispatch:
 
 jobs:
-    check-jobs-to-skip:
-        runs-on: ubuntu-latest
-        outputs:
-            should_skip: ${{ steps.skip_check.outputs.should_skip }}
-        steps:
-            - id: skip_check
-              uses: fkirc/skip-duplicate-actions@master
-              with:
-                  cancel_others: true
-                  paths_ignore: '["**/README.rst", "**/docs/**", "**/ISSUE_TEMPLATE/**", "**/pull_request_template.md", "**/.vscode/**"]'
+  check-jobs-to-skip:
+    runs-on: ubuntu-latest
+    outputs:
+      should_skip: ${{ steps.skip_check.outputs.should_skip }}
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
+        with:
+          cancel_others: true
+          paths_ignore: '["**/README.md", "**/docs/**", "**/ISSUE_TEMPLATE/**", "**/pull_request_template.md", "**/.vscode/**"]'
 
-    pre-commit-hooks:
-        needs: check-jobs-to-skip
-        if: ${{ needs.check-jobs-to-skip.outputs.should_skip != 'true'}} || ${{ github.event_name == 'push' }}
-        runs-on: ubuntu-latest
-        timeout-minutes: 2
-        steps:
-            - name: Checkout Code Repository
-              uses: actions/checkout@v2
+  pre-commit-hooks:
+    needs: check-jobs-to-skip
+    if: ${{ needs.check-jobs-to-skip.outputs.should_skip != 'true'}} || ${{ github.event_name == 'push' }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 2
+    steps:
+      - name: Checkout Code Repository
+        uses: actions/checkout@v2
 
-            - name: Set up Python 3.9
-              uses: actions/setup-python@v2
-              with:
-                  python-version: 3.9
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
 
-            # Run all pre-commit hooks on all the files.
-            # Getting only staged files can be tricky in case a new PR is opened
-            # since the action is run on a branch in detached head state
-            - name: Install and Run Pre-commit
-              uses: pre-commit/action@v2.0.3
+      # Run all pre-commit hooks on all the files.
+      # Getting only staged files can be tricky in case a new PR is opened
+      # since the action is run on a branch in detached head state
+      - name: Install and Run Pre-commit
+        uses: pre-commit/action@v2.0.3
 
-    build:
-        needs: check-jobs-to-skip
-        if: ${{ needs.check-jobs-to-skip.outputs.should_skip != 'true'}} || ${{ github.event_name == 'push' }}
-        runs-on: ubuntu-latest
-        defaults:
-            run:
-                shell: bash -l {0}
-        timeout-minutes: 5
-        steps:
-            - uses: actions/checkout@v2
+  build:
+    needs: check-jobs-to-skip
+    if: ${{ needs.check-jobs-to-skip.outputs.should_skip != 'true'}} || ${{ github.event_name == 'push' }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    timeout-minutes: 5
+    steps:
+      - uses: actions/checkout@v2
 
-            - name: Cache Conda
-              uses: actions/cache@v2
-              env:
-                  # Increase this value to reset cache if conda/dev.yml has not changed in the workflow
-                  CACHE_NUMBER: 0
-              with:
-                  path: ~/conda_pkgs_dir
-                  key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-publish
+      - name: Cache Conda
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if conda/dev.yml has not changed in the workflow
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-publish
 
-            - name: Set up Conda Environment
-              uses: conda-incubator/setup-miniconda@v2
-              with:
-                  activate-environment: "xcdat_dev"
-                  environment-file: conda-env/dev.yml
-                  channel-priority: strict
-                  auto-update-conda: true
-                  # IMPORTANT: This needs to be set for caching to work properly!
-                  use-only-tar-bz2: true
+      - name: Set up Conda Environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: "pcmdi_metrics_dev"
+          environment-file: conda-env/dev.yml
+          channel-priority: strict
+          auto-update-conda: true
+          # IMPORTANT: This needs to be set for caching to work properly!
+          use-only-tar-bz2: true
 
-            - name: Run Tests
-              run: |
-                  pytest
-
-            - name: Upload Coverage Report
-              uses: codecov/codecov-action@v1
-              with:
-                  file: "tests_coverage_reports/coverage.xml"
-                  fail_ci_if_error: true
+      - name: Run Tests
+        run: |
+          pytest

.pre-commit-config.yaml

@@ -1,27 +1,30 @@
-exclude: "docs|node_modules|migrations|.git|.tox"
+exclude: "docs|node_modules|migrations|.git|.tox|sample_setups/(external-setups|jsons)|tests/deprecated"
 default_stages: [commit]
 fail_fast: true
 
 repos:
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v3.4.0
-      hooks:
-          - id: trailing-whitespace
-          - id: end-of-file-fixer
-          - id: check-yaml
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
 
-    # Need to use flake8 GitHub mirror due to CentOS git issue with GitLab
-    # https://github.com/pre-commit/pre-commit/issues/1206
-    - repo: https://github.com/pycqa/flake8
-      rev: 3.9.2
-      hooks:
-          - id: flake8
-            args: ["--config=setup.cfg"]
-            additional_dependencies: [flake8-isort]
-            exclude: ^sample_setups/jsons/
+  - repo: https://github.com/psf/black
+    rev: 21.9b0
+    hooks:
+      - id: black
 
-    - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.910
-      hooks:
-          - id: mypy
-            args: ["--config=setup.cfg"]
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.9.3
+    hooks:
+      - id: isort
+
+  # Need to use flake8 GitHub mirror due to CentOS git issue with GitLab
+  # https://github.com/pre-commit/pre-commit/issues/1206
+  - repo: https://github.com/pycqa/flake8
+    rev: 3.9.2
+    hooks:
+      - id: flake8
+        args: ["--config=setup.cfg"]
+        additional_dependencies: [flake8-isort]

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2021, Lawrence Livermore National Security, LLC 
+Copyright (c) 2021, Lawrence Livermore National Security, LLC
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -1,5 +1,5 @@
 <img src="share/pcmdi/PMPLogo_1359x1146px_300dpi.png" width="15%" height="15%" align="right" />
-<h5 align="right"></h5> 
+<h5 align="right"></h5>
 
 PCMDI Metrics Package (PMP)
 ======
@@ -11,9 +11,9 @@ PCMDI Metrics Package (PMP)
 <!--[![CircleCI](https://circleci.com/gh/PCMDI/pcmdi_metrics.svg?style=svg)](https://circleci.com/gh/PCMDI/pcmdi_metrics) -->
 <!--[![Coverage Status](https://coveralls.io/repos/github/PCMDI/pcmdi_metrics/badge.svg)](https://coveralls.io/github/PCMDI/pcmdi_metrics) -->
 
-The PCMDI Metrics Package (PMP) is used to provide "quick-look" objective comparisons of Earth System Models (ESMs) with one another and available observations.  Results are produced in the context of all model simulations contributed to CMIP6 and earlier CMIP phases.  Among other purposes, this enables modeling groups to evaluate changes during the development cycle in the context of the structural error distribution of the multi-model ensemble. Currently, the comparisons emphasize metrics of large- to global-scale annual cycle and both tropcial and extra-tropical modes of variability. Ongoing work in v1.x development branches include established statistics for ENSO, MJO, regional monsoons, and high frequency characteristics of simulated precipitation. 
+The PCMDI Metrics Package (PMP) is used to provide "quick-look" objective comparisons of Earth System Models (ESMs) with one another and available observations.  Results are produced in the context of all model simulations contributed to CMIP6 and earlier CMIP phases.  Among other purposes, this enables modeling groups to evaluate changes during the development cycle in the context of the structural error distribution of the multi-model ensemble. Currently, the comparisons emphasize metrics of large- to global-scale annual cycle and both tropcial and extra-tropical modes of variability. Ongoing work in v1.x development branches include established statistics for ENSO, MJO, regional monsoons, and high frequency characteristics of simulated precipitation.
 
-**PCMDI uses the PMP to produce [quick-look simulation summaries across generations of CMIP](https://cmec.llnl.gov/results/physical.html)** 
+**PCMDI uses the PMP to produce [quick-look simulation summaries across generations of CMIP](https://cmec.llnl.gov/results/physical.html)**
 
 The metrics package consists of four parts: 1) Analysis software, 2) an observationally-based database of global (or near global, land or ocean) [time series and climatologies](https://github.com/PCMDI/PCMDIobs-cmor-tables/tree/master/catalogue), 3) a database of performance metrics computed for CMIP models and 4) [package documentation and interactive demos](http://pcmdi.github.io/pcmdi_metrics/).