add pre-commit config

.devcontainer/devcontainer.json

@@ -1,122 +1,140 @@
 // For format details, see https://aka.ms/devcontainer.json.
-{
-  "name": "petsird",
-  "build": {
-    "dockerfile": "Dockerfile",
-    "context": ".."
-  },
-  "runArgs": [
-    "--cap-add=SYS_PTRACE",
-    "--security-opt",
-    "seccomp=unconfined",
-    "--platform=linux/amd64"
-  ],
+    {
+      "name": "petsird",
+      "build": {
+        "dockerfile": "Dockerfile",
+        "context": ".."
+      },
+      "runArgs": [
+        "--cap-add=SYS_PTRACE",
+        "--security-opt",
+        "seccomp=unconfined",
+        "--platform=linux/amd64"
+      ],
 
-  // Configure tool-specific properties.
-  "customizations": {
-    // Configure properties specific to VS Code.
-    "vscode": {
-      // Set *default* container specific settings.json values on container create.
-      "settings": {
-        "files.trimFinalNewlines": true,
-        "files.trimTrailingWhitespace": true,
-        "files.insertFinalNewline": true,
+      // Configure tool-specific properties.
+      "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+          // Set *default* container specific settings.json values on container
+          // create.
+          "settings": {
+            "files.trimFinalNewlines": true,
+            "files.trimTrailingWhitespace": true,
+            "files.insertFinalNewline": true,
 
-        "[cpp]": {
-          "editor.formatOnSave": true
-        },
+            "[cpp]": {
+              "editor.formatOnSave": true
+            },
 
-        "[json]": {
-          "editor.defaultFormatter": "esbenp.prettier-vscode",
-          "editor.formatOnSave": true
-        },
+            "[json]": {
+              "editor.defaultFormatter": "esbenp.prettier-vscode",
+              "editor.formatOnSave": true
+            },
 
-        "[jsonc]": {
-          "editor.defaultFormatter": "esbenp.prettier-vscode",
-          "editor.formatOnSave": true
-        },
+            "[jsonc]": {
+              "editor.defaultFormatter": "esbenp.prettier-vscode",
+              "editor.formatOnSave": true
+            },
 
-        "[python]": {
-          "editor.defaultFormatter": "ms-python.black-formatter",
-          "editor.formatOnSave": true
-        },
+            "[python]": {
+              "editor.defaultFormatter": "ms-python.black-formatter",
+              "editor.formatOnSave": true
+            },
 
-        "cmake.sourceDirectory": "${workspaceFolder}/cpp",
-        "cmake.buildDirectory": "${workspaceFolder}/cpp/build",
-        "cmake.configureOnOpen": false,
+            "cmake.sourceDirectory": "${workspaceFolder}/cpp",
+            "cmake.buildDirectory": "${workspaceFolder}/cpp/build",
+            "cmake.configureOnOpen": false,
 
-        "python.defaultInterpreterPath": "/opt/conda/envs/petsird/bin/python",
-        "python.analysis.typeCheckingMode": "strict",
-        "python.analysis.diagnosticMode": "workspace",
-        "python.analysis.diagnosticSeverityOverrides": {
-          "reportUnknownArgumentType": "none",
-          "reportUnknownLambdaType": "none",
-          "reportUnknownMemberType": "none",
-          "reportUnknownParameterType": "none",
-          "reportUnknownVariableType": "none",
-          "reportUnnecessaryIsInstance": "none",
-          "reportUnusedImport": "none"
-        },
-        "python.terminal.activateEnvironment": false, // Disable the extension calling activate when the integrated terminal launches. We take care of this in ~/.bashrc.
+            "python.defaultInterpreterPath":
+                "/opt/conda/envs/petsird/bin/python",
+            "python.analysis.typeCheckingMode": "strict",
+            "python.analysis.diagnosticMode": "workspace",
+            "python.analysis.diagnosticSeverityOverrides": {
+              "reportUnknownArgumentType": "none",
+              "reportUnknownLambdaType": "none",
+              "reportUnknownMemberType": "none",
+              "reportUnknownParameterType": "none",
+              "reportUnknownVariableType": "none",
+              "reportUnnecessaryIsInstance": "none",
+              "reportUnusedImport": "none"
+            },
+            "python.terminal.activateEnvironment": false,
+            // Disable the extension calling activate when the integrated
+            // terminal launches. We take care of this in ~/.bashrc.
 
-        "testMate.cpp.test.executables": "cpp/{build,Build,BUILD,out,Out,OUT}/**/*{test,Test,TEST}*",
+            "testMate.cpp.test.executables":
+                "cpp/{build,Build,BUILD,out,Out,OUT}/**/*{test,Test,TEST}*",
 
-        // enable pretty printing when debugging C++ tests
-        "testMate.cpp.debug.configTemplate": {
-          "type": "cppvsdbg",
-          "linux": { "type": "cppdbg", "MIMode": "gdb" },
-          "darwin": { "type": "cppdbg", "MIMode": "lldb" },
-          "win32": { "type": "cppvsdbg" },
-          "program": "${exec}",
-          "args": "${argsArray}",
-          "cwd": "${cwd}",
-          "env": "${envObj}",
-          "environment": "${envObjArray}",
-          "sourceFileMap": "${sourceFileMapObj}",
-          "setupCommands": [
-            {
-              "description": "Enable pretty-printing for gdb",
-              "text": "-enable-pretty-printing",
-              "ignoreFailures": true
-            }
-          ],
+            // enable pretty printing when debugging C++ tests
+            "testMate.cpp.debug.configTemplate": {
+              "type": "cppvsdbg",
+              "linux": {
+                "type": "cppdbg",
+                "MIMode": "gdb"
+              },
+              "darwin": {
+                "type": "cppdbg",
+                "MIMode": "lldb"
+              },
+              "win32": {
+                "type": "cppvsdbg"
+              },
+              "program": "${exec}",
+              "args": "${argsArray}",
+              "cwd": "${cwd}",
+              "env": "${envObj}",
+              "environment": "${envObjArray}",
+              "sourceFileMap": "${sourceFileMapObj}",
+              "setupCommands": [
+                {
+                  "description": "Enable pretty-printing for gdb",
+                  "text": "-enable-pretty-printing",
+                  "ignoreFailures": true
+                }
+              ],
 
-          "gitlens.showWelcomeOnInstall": false,
-          "gitlens.showWhatsNewAfterUpgrades": false
-        },
+              "gitlens.showWelcomeOnInstall": false,
+              "gitlens.showWhatsNewAfterUpgrades": false
+            },
 
-        "gcovViewer.gcovBinary": "/opt/conda/envs/petsird/bin/x86_64-conda-linux-gnu-gcov",
-        "gcovViewer.buildDirectories": ["${workspaceFolder}/cpp/build"],
+            "gcovViewer.gcovBinary":
+                "/opt/conda/envs/petsird/bin/x86_64-conda-linux-gnu-gcov",
+            "gcovViewer.buildDirectories": [
+              "${workspaceFolder}/cpp/build"
+            ],
+
+            "search.useIgnoreFiles": false,
+            "search.exclude": {
+              "**/cpp/build": true
+            }
+          },
 
-        "search.useIgnoreFiles": false,
-        "search.exclude": {
-          "**/cpp/build": true
+          // Add the IDs of extensions you want installed when the container is
+          // created.
+          "extensions": [
+            "cschlosser.doxdocgen",
+            "eamodio.gitlens",
+            "esbenp.prettier-vscode",
+            "JacquesLucke.gcov-viewer",
+            "matepek.vscode-catch2-test-adapter",
+            "mhutchie.git-graph",
+            "ms-python.black-formatter",
+            "ms-python.python",
+            "ms-vscode.cmake-tools",
+            "ms-vscode.cpptools",
+            "timonwong.shellcheck",
+            "twxs.cmake"
+          ]
         }
       },
 
-      // Add the IDs of extensions you want installed when the container is created.
-      "extensions": [
-        "cschlosser.doxdocgen",
-        "eamodio.gitlens",
-        "esbenp.prettier-vscode",
-        "JacquesLucke.gcov-viewer",
-        "matepek.vscode-catch2-test-adapter",
-        "mhutchie.git-graph",
-        "ms-python.black-formatter",
-        "ms-python.python",
-        "ms-vscode.cmake-tools",
-        "ms-vscode.cpptools",
-        "timonwong.shellcheck",
-        "twxs.cmake"
-      ]
-    }
-  },
-
-  "overrideCommand": false,
-  "mounts": [
-    // Bind mount docker socket under an alias to support docker-from-docker
-    "source=/var/run/docker.sock,target=/var/run/docker-host.sock,type=bind"
-  ],
+      "overrideCommand": false,
+      "mounts": [
+        // Bind mount docker socket under an alias to support
+        // docker-from-docker
+        "source=/var/run/docker.sock,target=/var/run/docker-host.sock,type=bind"
+      ],
 
-  "remoteUser": "vscode"
-}
+      "remoteUser": "vscode"
+    }

.gitattributes

@@ -1,4 +1,4 @@
 # Shell scripts should have LF
 *.bashrc text eol=lf
 *.sh text eol=lf
-*.csh text eol=lf
+*.csh text eol=lf

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,6 +18,6 @@
 
 Please read and adhere to the [contribution guidelines](https://github.com/ETSInitiative/PRDdefinition/blob/master/CONTRIBUTING.md).
 
-Please tick the following: 
+Please tick the following:
 
  - [ ] The content of this Pull Request (the Contribution) is intentionally submitted for inclusion in the ETSI software (the Work) under the terms and conditions of the [Apache-2.0](https://www.apache.org/licenses/LICENSE-2.0) License.

.pre-commit-config.yaml

@@ -0,0 +1,57 @@
+ci:
+  skip: [todo]
+
+default_language_version:
+  python: python3
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+  - id: check-added-large-files
+  - id: check-case-conflict
+  - id: check-docstring-first
+  - id: check-executables-have-shebangs
+  - id: check-toml
+  - id: check-merge-conflict
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: mixed-line-ending
+  - id: sort-simple-yaml
+  - id: trailing-whitespace
+- repo: local
+  hooks:
+  - id: todo
+    name: Check TODO
+    language: pygrep
+    args: [-i]
+    entry: TODO
+    types: [text]
+    exclude: ^.pre-commit-config.yaml$
+- repo: https://github.com/PyCQA/flake8
+  rev: 7.1.1
+  hooks:
+  - id: flake8
+    args: [-j8]
+    additional_dependencies:
+    - flake8-broken-line
+    - flake8-bugbear
+    - flake8-comprehensions
+    - flake8-debugger
+    - flake8-isort
+    - flake8-pyproject
+    - flake8-string-format
+- repo: https://github.com/google/yapf
+  rev: v0.40.2
+  hooks:
+  - id: yapf
+    args: [-i]
+    additional_dependencies: [toml]
+- repo: https://github.com/PyCQA/isort
+  rev: 5.13.2
+  hooks:
+  - id: isort
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: v14.0.6
+  hooks:
+  - id: clang-format

CONTRIBUTING.md

@@ -47,7 +47,7 @@ Please by mindful about the resources used by our Continuous Integration (CI) wo
      - `[actions skip]` does not run GitHub Actions, see [here](https://github.blog/changelog/2021-02-08-github-actions-skip-pull-request-and-push-workflows-with-skip-ci/).
 8. After acceptance of your PR, go home with a nice warm feeling.
 
-Suggested reading: 
+Suggested reading:
 https://help.github.com/articles/fork-a-repo/, https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project or https://guides.github.com/activities/forking/.
 
 ### A note on copyright dates and notices (and licenses)

LICENSE.txt

@@ -37,7 +37,7 @@ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
 You must give any other recipients of the Work or Derivative Works a copy of this License; and
 You must cause any modified files to carry prominent notices stating that You changed the files; and
 You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and
-If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. 
+If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License.
 
 You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License.
 5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions.

README.md

@@ -30,5 +30,3 @@ This codespace/container will contain all necessary tools, including `yardl` its
 
 4. Have a look at (and try!) the examples in the [`cpp`](cpp/README.md) and/or
 [`python`](python/README.md) directories.
-
-

cpp/petsird_analysis.cpp

@@ -96,10 +96,11 @@ main(int argc, char* argv[])
 
   std::cout << "Last time block at " << last_time << " ms\n";
   std::cout << "Number of prompt events: " << num_prompts << std::endl;
-  if (num_prompts > 0) {
-    std::cout << "Average energy_1: " << energy_1 / num_prompts << std::endl;
-    std::cout << "Average energy_2: " << energy_2 / num_prompts << std::endl;
-  }
+  if (num_prompts > 0)
+    {
+      std::cout << "Average energy_1: " << energy_1 / num_prompts << std::endl;
+      std::cout << "Average energy_2: " << energy_2 / num_prompts << std::endl;
+    }
 
   return 0;
 }

environment.yml

@@ -16,6 +16,7 @@ dependencies:
   - ninja>=1.11.0
   - nlohmann_json>=3.11.2
   - numpy>=1.24.3
+  - pre-commit=4.0.1
   - python>=3.11.3
   - shellcheck>=0.8.0
   - xtensor-fftw>=0.2.5

model/DetectionEfficiencies.yml

@@ -56,4 +56,4 @@ DetectionEfficiencies: !record
     modulePairSGIDLUT: ModulePairSGIDLUT?
     # Vector of all modulePairEfficiencies (one for each SGID)
     # Constraint: size(modulePairEfficienciesVector) == max(modulePairSGIDLUT) + 1
-    modulePairEfficienciesVector: ModulePairEfficienciesVector?
+    modulePairEfficienciesVector: ModulePairEfficienciesVector?

model/DetectorInformation.yml

@@ -28,7 +28,7 @@ DetectorModule: !record
 
 # A list of identical modules at different locations
 ReplicatedDetectorModule: ReplicatedObject< DetectorModule >
-    
+
 # Full definition of the geometry of the scanner, consisting of
 # one of more types of modules replicated in space and (optional) other structures (e.g. side-shielding)
 ScannerGeometry: !record

model/ScannerInformation.yml

@@ -22,7 +22,7 @@ ScannerInformation: !record
     # Geometric information for all detector elements
     # All coordinates are in the PET gantry coordinate system.
     scannerGeometry: ScannerGeometry
- 
+
     # List of materials present in the scanner geometry. The `material_id`s there will refer to the
     # identifiers in this list below.
     bulkMaterials: BulkMaterial*