Merge pull request #162 from ImperialCollegeLondon/dev/pre-commit

dev: Add pre-commit

Author: mfacchinelli

.github/ISSUE_TEMPLATE/bug-report.md

@@ -4,20 +4,21 @@ about: Create a report to help us improve
 title: "[BUG]"
 labels: bug
 assignees: mfacchinelli
-
 ---
+## Describe the Bug
 
-# Describe the Bug
 A clear and concise description of what the bug is.
 
-# To Reproduce
+## To Reproduce
+
 Information to reproduce the behavior:
+
 1. Which data set?
 2. Which processing settings?
 3. Step-by-step description, if applicable.
 4. What is the error?
 
-# Additional Information
+## Additional Information
 
 * Version: vX.X.X
 (Output of `mag.version()`)

.github/workflows/pre-commit_autoupdate.yaml

@@ -0,0 +1,21 @@
+name: Pre-Commit Auto-Update
+
+on:
+  schedule:
+    - cron: "0 0 1 * *" # midnight every first of the month
+
+jobs:
+  auto-update:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - uses: browniebroke/pre-commit-autoupdate-action@main
+      - uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: update/pre-commit-hooks
+          base: main
+          title: "Chore: Update Pre-Commit Hooks"
+          commit-message: "chore: update pre-commit hooks"
+          body: Update versions of pre-commit hooks to latest version.

.github/workflows/test.yml

@@ -10,6 +10,11 @@ concurrency:
   cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
 
 jobs:
+  qa:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pre-commit/[email protected]
 
   test:
     name: Run MATLAB Tests

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-json
+        exclude: resources/codeAnalyzerConfiguration.json|tests/unit/data/imap/test_data/invalid.json
+      - id: check-toml
+      - id: check-yaml
+      - id: check-xml
+      - id: check-merge-conflict
+      - id: trailing-whitespace
+      - id: pretty-format-json
+        args: [--autofix, --indent, "4"]
+        exclude: resources/codeAnalyzerConfiguration.json|tests/unit/data/imap/test_data/invalid.json
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.33.0"
+    hooks:
+      - id: check-github-workflows
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.45.0
+    hooks:
+      - id: markdownlint-fix
+        args: [--ignore, LICENSE.md, --disable, MD013]

.vscode/settings.json

@@ -1,16 +1,4 @@
 {
-    "files.exclude": {
-        "**/._*": true,
-        "**/*.*~": true,
-        "**/*.asv": true,
-        "**/*~": true
-    },
-    "search.exclude": {
-        "**/._*": true,
-        "**/*.*~": true,
-        "**/*.asv": true,
-        "**/*~": true
-    },
     "cSpell.words": [
         "AGROW",
         "Bartington",
@@ -24,5 +12,17 @@
         "SOLARORBITER",
         "Stackedplot",
         "SUPPORTEDEVENTS"
-    ]
-}
+    ],
+    "files.exclude": {
+        "**/*.*~": true,
+        "**/*.asv": true,
+        "**/*~": true,
+        "**/._*": true
+    },
+    "search.exclude": {
+        "**/*.*~": true,
+        "**/*.asv": true,
+        "**/*~": true,
+        "**/._*": true
+    }
+}

README.md

@@ -16,15 +16,17 @@ The following MATLAB toolboxes are required to use the toolbox:
 
 The following external MATLAB libraries are required:
 
-* MATLAB SPICE (MICE): https://naif.jpl.nasa.gov/naif/toolkit_MATLAB.html
-* MATLAB SPDF CDF: https://cdf.gsfc.nasa.gov/html/sw_and_docs.html
+* MATLAB SPICE (MICE): <https://naif.jpl.nasa.gov/naif/toolkit_MATLAB.html>
+* MATLAB SPDF CDF: <https://cdf.gsfc.nasa.gov/html/sw_and_docs.html>
 
 ## Getting Started
 
 The toolbox adds to the path many functions and classes that can be used for data processing and visualization. These can be found under the `mag` namespace; you can use tab-completion to see what is available:
+
 ``` matlab
 mag.<TAB>
 ```
+
 In the sections below you can find more information about some of the functionalities.
 
 ## User Manual
@@ -33,7 +35,7 @@ See [internal documentation](https://imperialcollege.atlassian.net/wiki/spaces/P
 
 ## Development
 
-When developing new features or fixing issues, create a new branch. After finishing development, make sure to write tests to cover any new changes. 
+When developing new features or fixing issues, create a new branch. After finishing development, make sure to write tests to cover any new changes.
 
 To change the version of the toolbox, modify the `MAG_DATA_VISUALIZATION_VERSION` variable in `.env`. This will automatically updated the toolbox version and create a new release with the correct tag.
 Also, update the contents of the `resources/release-notes.md` file by detailing what has changed in the new version.
@@ -43,4 +45,4 @@ Also, update the contents of the `resources/release-notes.md` file by detailing
 MAG Data Visualization Toolbox is released under the [MIT license][license].
 
 [license]: LICENSE.md
-[sml]: http://www.imperial.ac.uk/space-and-atmospheric-physics/research/areas/space-magnetometer-laboratory/
+[sml]: http://www.imperial.ac.uk/space-and-atmospheric-physics/research/areas/space-magnetometer-laboratory/

app/DataVisualization.m

@@ -224,7 +224,7 @@ function resetButtonPushed(app)
 
             for manager = [app.AnalysisManager, app.ResultsManager, app.ExportManager, app.VisualizationManager]
                 manager.reset();
-            end            
+            end
         end
 
         function exportButtonPushed(app)

resources/release-notes.md

@@ -6,3 +6,7 @@
 
 - (All) Add option to specify PNG resolution when saving figures
 - (IMAP) Improve estimation of mode change events
+
+## Project
+
+- Add pre-commit configuration

src/analyze/calibration/README.md

@@ -8,4 +8,4 @@ For temperatures, the following scales apply:
 - Cool Temperature: approx. -10 °C (FM5), 0 °C (FM4)
 - Cold Temperature: approx. -20 °C (FM5), -30 °C (FM4)
 
-Data was extracted from calibration report by IGEP. The misalignment matrix is represented by the reduced transfermatrix, which combines misalignment and scale factor.
+Data was extracted from calibration report by IGEP. The misalignment matrix is represented by the reduced transfermatrix, which combines misalignment and scale factor.

src/analyze/resources/alias.json

@@ -4,4 +4,4 @@
         "OldNames": "mag.process.Filter",
         "WarnOnOldName": false
     }
-}
+}

src/io/+mag/+io/+in/Format.m

@@ -10,7 +10,7 @@
 
         % LOAD Load raw data from file.
         rawData = load(this, fileName)
-    
+
         % PROCESS Process raw data and convert to common data
         % format.
         data = process(this, rawData, varargin)

src/mission/bart/+mag/+bart/+view/Spectrogram.m

@@ -68,7 +68,7 @@ function visualize(this)
             end
 
             if ~isempty(input2) && input2.HasData
-    
+
                 input2Spectrum = mag.spectrogram(input2, FrequencyLimits = this.FrequencyLimits, FrequencyPoints = this.FrequencyPoints, ...
                     Normalize = this.Normalize, Window = this.Window, Overlap = this.Overlap);
 

src/mission/imap/+mag/+imap/+view/Comparison.m

@@ -66,7 +66,7 @@ function visualize(this)
 
                 primaryGraphs = this.generateComparisonGraph(primaryIALiRTComparison, "left");
                 secondaryGraphs = this.generateComparisonGraph(secondaryIALiRTComparison, "right");
-    
+
                 this.Figures(end + 1) = this.Factory.assemble( ...
                     primaryIALiRTComparison, primaryGraphs, secondaryIALiRTComparison, secondaryGraphs, ...
                     Name = "Science vs. I-ALiRT (Closest Vector)", ...
@@ -89,7 +89,7 @@ function visualize(this)
 
                 primaryGraphs = this.generateComparisonGraph(primarySID5Comparison, "left");
                 secondaryGraphs = this.generateComparisonGraph(secondarySID5Comparison, "right");
-    
+
                 this.Figures(end + 1) = this.Factory.assemble( ...
                     primarySID5Comparison, primaryGraphs, secondarySID5Comparison, secondaryGraphs, ...
                     Name = "Science vs. SID5 (Closest Vector)", ...

src/mission/imap/+mag/+imap/+view/Spectrogram.m

@@ -90,7 +90,7 @@ function visualize(this)
 
             transformation.FrequencyLimits = this.FrequencyLimits;
             transformation.FrequencyPoints = this.FrequencyPoints;
-            transformation.Normalize = this.Normalize; 
+            transformation.Normalize = this.Normalize;
             transformation.Window = this.Window;
             transformation.Overlap = this.Overlap;
 

src/mission/imap/resources/alias.json

@@ -40,4 +40,4 @@
             "WarnOnOldName": true
         }
     ]
-}
+}

src/utility/+mag/+buildtool/+task/PackageTask.m

@@ -73,7 +73,7 @@ function packageToolbox(task, ~, version)
         function matlabPath = getMATLABPath()
 
             matlabPath = string(split(path(), pathsep()));
-            
+
             locMAG = contains(matlabPath, "MAG-Data-Visualization") & contains(matlabPath, ["app", "src"]);
             matlabPath = matlabPath(locMAG);
         end

src/utility/+mag/+internal/isThemeable.m

@@ -1,7 +1,7 @@
 function value = isThemeable(figure)
 % ISTHEMEABLE Determine whether figure is themeable (i.e., if setting
 % dark/light mode is supported).
-    
+
     arguments (Input)
         figure (1, 1) matlab.ui.Figure
     end

src/utility/+mag/+mixin/SaveLoad.m

@@ -15,7 +15,7 @@
     methods (Hidden)
 
         function savedObject = saveobj(this)
-            
+
             savedObject = this;
             savedObject.OriginalVersion = this.Version;
         end

tests/system/app/tDataVisualization.m

@@ -82,18 +82,18 @@ function toolbarDebug_noError(testCase)
         end
 
         % function selectMission(testCase, ValidMission)
-        % 
+        %
         %     % Set up.
         %     app = testCase.createAppWithCleanup(ValidMission);
-        % 
+        %
         %     % Exercise.
         %     testCase.press(app.ToolbarManager.MissionPushTool);
-        % 
+        %
         %     testCase.assertNotEmpty(app.SelectMissionDialog, "Mission selection dialog should not be empty.");
-        % 
+        %
         %     testCase.choose(app.SelectMissionDialog.MissionDropDown, ValidMission);
         %     testCase.press(app.SelectMissionDialog.SelectButton);
-        % 
+        %
         %     % Verify.
         %     testCase.verifyEqual(app.Mission, ValidMission, "Mission should be selected.");
         % end