Reformat/restyle files according to rules in .pre-commit-config.yaml

Reformatted the files in the repository according to rules in a new file ".pre-commit-config.yaml". Have to install pre-commit either through pip or conda and then "pre-commit install" to install the git hooks. The pre-commit lints or reformats many file types by using separate linters and autoformaters that are installed as part of pre-commit. Uses "ruff" for Python files, but presently configured only for autoformatting. Turned off "ruff" linting because it found over 300 problems, some of which there weren't easy answers for.
respec · Jul 27, 2024 · 6e1cec2 · 6e1cec2
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diff --git a/.github/workflows/hsp2-pip-install-test.yml b/.github/workflows/hsp2-pip-install-test.yml
@@ -1,87 +1,94 @@
+---
 name: Python application
 
-on:
-  push:
-    branches: [ "master" ]
-  pull_request:
-    branches: [ "master", "develop", "develop-specact" ]
+on:  # yamllint disable-line rule:truthy
+    push:
+        branches: [master]
+    pull_request:
+        branches: [master, develop, develop-specact]
 
 permissions:
-  contents: read
+    contents: read
 
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          cache: "pip"
-      - name: Install dependencies
-        run: |
-          pip install flake8
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --ignore=F821 --show-source --statistics --exclude=build/*
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-  
-  test-pytest:
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    strategy:
-      matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-        pandas-version: [""]
-        include:
-          - python-version: "3.11"
-            pandas-version: "pandas>2.0"
-            coverage: true
-          - python-version: "3.11"
-            pandas-version: "pandas>1.5,<2.0"
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-      - name: Install hsp2
-        run: |
-          # install the hsp2 executable
-          pip install .[dev]
-      - if: ${{ matrix.pandas-version }}
-        run: pip install "${{ matrix.pandas-version }}"
-      - if: ${{ matrix.coverage }}
-        run: |
-          # python coverage
-          NUMBA_DISABLE_JIT=1 pytest --cov --cov-branch --cov-report term-missing
-      - if: ${{ ! matrix.coverage }}
-        run: pytest
-
-  test-cmd:
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    strategy:
-      matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-      - name: Install hsp2
-        run: |
-          # install the hsp2 executable
-          pip install .
-      - name: Run hsp2
-        run: |
-          # TODO: find much shorter test case.
-          hsp2 import_uci ./tests/test10/HSP2results/test10.uci _temp_test10.h5
-          hsp2 run _temp_test10.h5
-   
+    lint:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                  python-version: '3.11'
+                  cache: pip
+            - name: Install dependencies
+              run: |
+                  pip install flake8
+            - name: Lint with flake8
+              run: |
+                  # stop the build if there are Python syntax errors or
+                  # undefined names
+                  flake8 . --count --select=E9,F63,F7,F82 --ignore=F821 \
+                    --show-source --statistics --exclude=build/*
+                  # exit-zero treats all errors as warnings.
+                  # The GitHub editor is 127 chars wide
+                  flake8 . --count --exit-zero --max-complexity=10 \
+                    --max-line-length=127 --statistics
+
+    test-pytest:
+        runs-on: ubuntu-latest
+        continue-on-error: true
+        strategy:
+            matrix:
+                python-version: ['3.9', '3.10', '3.11', '3.12']
+                pandas-version: ['']
+                include:
+                    - python-version: '3.11'
+                      pandas-version: pandas>2.0
+                      coverage: true
+                    - python-version: '3.11'
+                      pandas-version: pandas>1.5,<2.0
+        steps:
+            - uses: actions/checkout@v4
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                  python-version: ${{ matrix.python-version }}
+                  cache: pip
+            - name: Install hsp2
+              run: |
+                  # install the hsp2 executable
+                  pip install .[dev]
+            - if: ${{ matrix.pandas-version }}
+              run: pip install "${{ matrix.pandas-version }}"
+            - if: ${{ matrix.coverage }}
+              run: |
+                  # python coverage
+                  NUMBA_DISABLE_JIT=1 pytest --cov --cov-branch --cov-report \
+                      term-missing
+            - if: ${{ ! matrix.coverage }}
+              run: pytest
+
+    test-cmd:
+        runs-on: ubuntu-latest
+        continue-on-error: true
+        strategy:
+            matrix:
+                python-version: ['3.9', '3.10', '3.11', '3.12']
+        steps:
+            - uses: actions/checkout@v4
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                  python-version: ${{ matrix.python-version }}
+                  cache: pip
+            - name: Install hsp2
+              run: |
+                  # install the hsp2 executable
+                  pip install .
+            - name: Run hsp2
+              run: |
+                  # TODO: find much shorter test case.
+                  hsp2 import_uci \
+                      ./tests/test10/HSP2results/test10.uci \
+                      _temp_test10.h5
+                  hsp2 run _temp_test10.h5
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,96 @@
+---
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+exclude: |
+    (?x)^(
+        .*\.hbn|
+        .*\.wdm|
+        .*\.hdf5|
+        .*\.h5
+        )$
+
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.6.0
+      hooks:
+          - id: check-case-conflict
+          - id: check-docstring-first
+          - id: check-executables-have-shebangs
+          - id: check-json
+          - id: check-merge-conflict
+          - id: check-shebang-scripts-are-executable
+          - id: check-toml
+          - id: check-xml
+          - id: end-of-file-fixer
+            exclude: notebooks/tstoolbox_plot_bash.sh
+          - id: fix-encoding-pragma
+            args: [--remove]
+          - id: mixed-line-ending
+          - id: trailing-whitespace
+            exclude: notebooks/tstoolbox_plot_bash.sh
+
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      # Ruff version.
+      rev: v0.5.5
+      hooks:
+          # Run the linter.
+          # Uncomment the following lines to enable the linter.
+          # Right now way to many things fail.
+          # - id: ruff
+          #   types_or: [python, pyi, jupyter]
+          #   args: [--fix]
+
+          # Run the linter sort imports.
+          - id: ruff
+            types_or: [python, pyi, jupyter]
+            args: [--select, I, --fix]
+
+          # Run the formatter.
+          - id: ruff-format
+            types_or: [python, pyi, jupyter]
+
+    - repo: https://github.com/pappasam/toml-sort
+      rev: v0.23.1
+      hooks:
+          - id: toml-sort-fix
+            args: [--in-place, --spaces-indent-inline-array, '4']
+
+    - repo: https://github.com/adrienverge/yamllint.git
+      rev: v1.35.1
+      hooks:
+          - id: yamllint
+            args: [--format, parsable, --strict]
+
+    - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+      rev: 0.2.3
+      hooks:
+          - id: yamlfmt
+
+    - repo: https://github.com/jumanjihouse/pre-commit-hooks
+      rev: 3.0.0
+      hooks:
+          - id: shellcheck
+            args: [-s, bash]
+
+    - repo: https://github.com/lovesegfault/beautysh
+      rev: v6.2.1
+      hooks:
+          - id: beautysh
+            args: [--indent-size, '4']
+
+    - repo: https://github.com/asottile/blacken-docs
+      rev: 1.18.0
+      hooks:
+          - id: blacken-docs
+
+    - repo: https://github.com/asottile/pyupgrade
+      rev: v3.16.0
+      hooks:
+          - id: pyupgrade
+
+    - repo: https://github.com/commitizen-tools/commitizen
+      rev: v3.28.0
+      hooks:
+          - id: commitizen
+            stages: [commit-msg]
diff --git a/HSP2_Driver.py b/HSP2_Driver.py
@@ -1,30 +1,35 @@
-import os, sys
+import os
+import sys
 
 # print('in HSP2_Driver')
 command_line = ""
 # print('arg count ' + str(len(sys.argv)))
 if len(sys.argv) >= 2:
     # see if anything on command line
     command_line = sys.argv[1]
-    print('command line' + command_line)
+    print("command line" + command_line)
 
 # if given UCI, import to h5 file
 # if given WDM, import to h5 file
 # if given h5, run HSP2
 
-from PyQt5.QtWidgets import QFileDialog, QApplication
+from PyQt5.QtWidgets import QApplication, QFileDialog
 
 application = QApplication(sys.argv)
 
-if command_line == '':
-    file_filter = "Run HDF5 (*.h5) Full Output;;" \
-                  "Run HDF5 (*.h5) Light Output;;" \
-                  "Import UCI to HDF5 (*.uci);;" \
-                  "Import WDM to HDF5 (*.wdm)"
-    filename, filetype = QFileDialog.getOpenFileName(None, 'HSP2 Open File...', '', file_filter)
+if command_line == "":
+    file_filter = (
+        "Run HDF5 (*.h5) Full Output;;"
+        "Run HDF5 (*.h5) Light Output;;"
+        "Import UCI to HDF5 (*.uci);;"
+        "Import WDM to HDF5 (*.wdm)"
+    )
+    filename, filetype = QFileDialog.getOpenFileName(
+        None, "HSP2 Open File...", "", file_filter
+    )
 else:
     filename = command_line
-    filetype = ''
+    filetype = ""
 
 file_ext = filename[-3:]
 dir_name = os.path.dirname(filename)
@@ -33,12 +38,14 @@
 if file_ext.upper() == "UCI":
     h5_name = filename[:-3] + "h5"
     from hsp2.hsp2tools.readUCI import readUCI
+
     readUCI(filename, h5_name)
     # readUCI('HSPF.uci', 'test.h5')
 
 if file_ext.upper() == "WDM":
     h5_name = filename[:-3] + "h5"
     from hsp2.hsp2tools.readWDM import readWDM
+
     readWDM(filename, h5_name)
     # readWDM('GRICM.wdm', 'test.h5')
     # readWDM('ZUMBROSCEN.WDM', 'test.h5')
@@ -52,11 +59,7 @@
     io_manager = IOManager(hdf5_instance)
 
     SaveLevel = True
-    if 'Light' in filetype:
+    if "Light" in filetype:
         SaveLevel = False
     main(io_manager, saveall=SaveLevel, jupyterlab=False)
     # main('test.h5', saveall=True)
-
-
-
-