Address PR comments for 787 ljw pre commit hook compliant

.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

@@ -3,34 +3,28 @@ 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
 
-    - repo: https://github.com/psf/black
-      rev: 21.9b0
-      hooks:
-          - id: black
+  - repo: https://github.com/psf/black
+    rev: 21.9b0
+    hooks:
+      - id: black
 
-    - repo: https://github.com/timothycrosley/isort
-      rev: 5.9.3
-      hooks:
-          - id: isort
+  - 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]
-
-    - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.910
-      hooks:
-          - id: mypy
-            args: ["--config=setup.cfg"]
+  # 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]

conda-env/dev.yml

@@ -19,6 +19,7 @@ dependencies:
   - eofs=1.4.0
   # Testing
   # ==================
+  - pre_commit=2.15.0
   - pytest=6.2.5
   - pytest-cov=3.0.0
   # Developer Tools

pcmdi_metrics/devel/monsoon_wang/scripts/bar_chart_monsoon_precip_index.py

@@ -182,6 +182,12 @@
     aux_mods = ""
     custom_names = {}
     aux_jsons = []
+
+    # FIXME: Should these be set?
+    mod_name = None
+    numexpts = None
+    ###############################
+
     if aux_json_path:
         print("==> Loading auxillary json file : " + aux_json_path)
         print("...")

pcmdi_metrics/pcmdi/scripts/pcmdi_compute_climatologies-CMOR.py

@@ -218,6 +218,13 @@ def dump_cmor(A, data, time, bounds, season):
     inst = checkCMORAttribute("institution")
     src = checkCMORAttribute("source")
     exp = checkCMORAttribute("experiment_id")
+
+    # FIXME: Should these be set?
+    realization_index = None
+    initialization_index = None
+    physics_index = None
+    ###############################
+
     xtra = {}
     for x in cmor_xtra_args:
         try:
@@ -317,9 +324,16 @@ def dump_cmor(A, data, time, bounds, season):
            "license":                 "CMIP6 model data produced by Lawrence Livermore PCMDI is licensed under a Creative Commons Attribution ShareAlike 4.0 International License (https://creativecommons.org/licenses). Consult https://pcmdi.llnl.gov/CMIP6/TermsOfUse for terms of use governing CMIP6 output, including citation requirements and proper acknowledgment. Further information about this data, including some limitations, can be found via the further_info_url (recorded as a global attribute in this file) and at https:///pcmdi.llnl.gov/. The data producers and data providers make no warranty, either express or implied, including, but not limited to, warranties of merchantability and fitness for a particular purpose. All liabilities arising from the supply of the information (including any liability arising in negligence) are excluded to the fullest extent permitted by law."
 }}
 """.format(
-            A.results_dir, exp, cal_name, r, i, p, inst.split()[0], src
+            A.results_dir,
+            exp,
+            cal_name,
+            realization_index,
+            initialization_index,
+            physics_index,
+            inst.split()[0],
+            src,
         )
-    )  # noqa
+    )
 
     tmp.flush()
     cmor.dataset_json(tmp.name)

setup.cfg

@@ -52,14 +52,6 @@ exclude =
     *__init__.py
     venv
 
-[mypy]
-python_version = 3.8
-check_untyped_defs = True
-ignore_missing_imports = True
-warn_unused_ignores = True
-warn_redundant_casts = True
-warn_unused_configs = True
-
 [aliases]
 # Define setup.py command aliases here
 test = pytest

tests/test_placeholder.py

@@ -0,0 +1,8 @@
+"""
+Placeholder to to suppress `Error: Process completed with exit code 5`,
+which occurs when no tests run. Remove this file when real tests are added.
+"""
+
+
+def test_placeholder():
+    pass