Merge pull request #1 from Yambottle/main

Initial OOP design

+src/+jobs/CatGT.m

@@ -0,0 +1,22 @@
+classdef CatGT < src.jobs.JobBase
+    %CatGT Summary of this class goes here
+    %   Detailed explanation goes here
+
+    properties
+        job_info
+        input
+        output
+    end
+
+    methods
+        function obj = CatGT(job_info, input)
+            obj.job_info = job_info;
+            obj.input = input;
+        end
+
+        function obj = execute(obj)
+            disp(obj.job_info);
+        end
+    end
+end
+

+src/+jobs/JobBase.m

@@ -0,0 +1,15 @@
+classdef (Abstract) JobBase < handle
+    %JOBBASE Summary of this class goes here
+    %   Detailed explanation goes here
+
+    properties (Abstract)
+        job_info
+        input
+        output
+    end
+
+    methods (Abstract)
+        execute(obj)
+    end
+end
+

+src/+jobs/KiloSort.m

@@ -0,0 +1,22 @@
+classdef KiloSort < src.jobs.JobBase
+    %KiloSort Summary of this class goes here
+    %   Detailed explanation goes here
+
+    properties
+        job_info
+        input
+        output
+    end
+
+    methods
+        function obj = KiloSort(job_info, input)
+            obj.job_info = job_info;
+            obj.input = input;
+        end
+
+        function obj = execute(obj)
+           disp(obj.job_info);
+        end
+    end
+end
+

+src/+pipeline/Config.m

@@ -0,0 +1,18 @@
+classdef Config < handle
+    %RunSpec Summary of this class goes here
+    %   Detailed explanation goes here
+
+    properties
+        run_name
+        gate_index
+        concat_trigger
+        probes
+        brain_regions
+    end
+
+    methods
+        function obj=Config()
+        end
+    end
+end
+

+src/+pipeline/Pipeline.m

@@ -0,0 +1,27 @@
+classdef Pipeline < handle
+    %Pipeline Summary of this class goes here
+    %   Detailed explanation goes here
+
+    properties
+        current_stage
+        stages
+    end
+
+    methods
+        function obj = Pipeline()
+            obj.current_stage = -1;
+            obj.stages = {};
+        end
+
+        function execute(obj)
+            % stages have to run in sequence, because of result dependency
+            for stage = obj.stages
+                curr = stage{:};
+                obj.current_stage = curr;
+                disp(obj.current_stage.stage_info);
+                curr.execute();
+            end
+        end
+    end
+end
+

+src/+stage/Stage.m

@@ -0,0 +1,25 @@
+classdef Stage < handle
+    %Stage Summary of this class goes here
+    %   Detailed explanation goes here
+
+    properties
+        stage_info
+        current_job
+        job_queue
+    end
+
+    methods
+        function obj = Stage(stage_info)
+            obj.stage_info = stage_info;
+            obj.job_queue = {};
+        end
+        function obj = execute(obj)
+            % TODO - jobs can run in parallel
+            for job = obj.job_queue
+                curr = job{:};
+                curr.execute();
+            end
+        end
+    end
+end
+

+src/Utils.m

@@ -0,0 +1,16 @@
+classdef Utils
+    %Utils Summary of this class goes here
+    %   Detailed explanation goes here
+
+    methods(Static)
+        function config = load_json(fpath)
+            fid = fopen(fpath); 
+            raw = fread(fid,inf); 
+            config = char(raw'); 
+            fclose(fid);
+            disp(config) % debug
+            config = jsondecode(config);
+        end
+    end
+end
+

.gitignore

@@ -0,0 +1,87 @@
+# Python
+# Sphinx gallery temp dir
+docs/auto_examples/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+test_data/
+cached_data/
+.pytest_cache/
+test-reports/
+.venv/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# pyenv python configuration file
+.python-version
+
+# ide specific 
+.idea/
+.history/
+.vscode/
+
+# matlab
+*.mat
+*.asv
+
+# virtual environment
+.venv/
+
+# macOS
+.DS_Store
+

README.md

@@ -1,2 +1,8 @@
 # neuropixels-toolkit
 (Under construction) Neuropixel Toolkit is a set of unified Matlab tools for manipulating Neuropixel and Kilosort datasets
+
+## Usecase Diagram
+![Here should be a usecase diagram](docs/usecase_diagram.drawio.png)
+
+## Class Diagram
+![Here should be a class diagram](docs/class_diagram.drawio.png)

configs/config.json

@@ -0,0 +1,13 @@
+{
+    "version": "v0.0.1",
+    "type": "text/json",
+    "CatGT": {
+        "v1": 1,
+        "v2": 2
+    },
+    "KiloSort": {
+        "v1": 123,
+        "v2": 345,
+        "v3": 109
+    }
+}