Refactor MAMA and HTIT implementation for improved accuracy and performance

lib/trends/lsma/.github/instructions/codacy.instructions.md

@@ -0,0 +1,79 @@
+---
+    description: Configuration for AI behavior when interacting with Codacy's MCP Server
+    applyTo: '**'
+---
+---
+# Codacy Rules
+Configuration for AI behavior when interacting with Codacy's MCP Server
+
+## using any tool that accepts the arguments: `provider`, `organization`, or `repository`
+- ALWAYS use:
+ - provider: gh
+ - organization: mihakralj
+ - repository: QuanTAlib
+- Avoid calling `git remote -v` unless really necessary
+
+## CRITICAL: After ANY successful `edit_file` or `reapply` operation
+- YOU MUST IMMEDIATELY run the `codacy_cli_analyze` tool from Codacy's MCP Server for each file that was edited, with:
+ - `rootPath`: set to the workspace path
+ - `file`: set to the path of the edited file
+ - `tool`: leave empty or unset
+- If any issues are found in the new edits, propose and apply fixes for them.
+- > NOTE: Failure to follow this rule is considered a critical error.
+
+## When you tried to run the `codacy_cli_analyze` tool and the Codacy CLI is not installed
+- Ask the user 'Codacy CLI is not installed. Would you like me to install it now?'
+- If the user responds with "yes", run the `codacy_cli_install` tool and then continue with the original task
+- If the user responds with "no", instruct the user that they can disable automatic analysis in the extension settings
+- Wait for the user to respond before proceeding with any other actions
+
+## After every response
+- If you made any file edits in this conversation, verify you ran `codacy_cli_analyze` tool from Codacy's MCP Server 
+
+## When there are no Codacy MCP Server tools available, or the MCP Server is not reachable
+- Suggest the user the following troubleshooting steps:
+ - Try to reset the MCP on the extension
+ - If the user is using VSCode, suggest them to review their Copilot > MCP settings in Github, under their organization or personal account. Refer them to Settings > Copilot > Enable MCP servers in Copilot. Suggested URL (https://github.com/settings/copilot/features) or https://github.com/organizations/{organization-name}/settings/copilot/features (This can only be done by their organization admins / owners)
+- If none of the above steps work, suggest the user to contact Codacy support
+
+## Trying to call a tool that needs a rootPath as a parameter
+- Always use the standard, non-URL-encoded file system path
+
+## CRITICAL: Dependencies and Security Checks
+- IMMEDIATELY after ANY of these actions:
+ - Running npm/yarn/pnpm install
+ - Adding dependencies to package.json
+ - Adding requirements to requirements.txt
+ - Adding dependencies to pom.xml
+ - Adding dependencies to build.gradle
+ - Any other package manager operations
+- You MUST run the `codacy_cli_analyze` tool with:
+ - `rootPath`: set to the workspace path
+ - `tool`: set to "trivy"
+ - `file`: leave empty or unset
+- If any vulnerabilities are found because of the newly added packages:
+ - Stop all other operations
+ - Propose and apply fixes for the security issues
+ - Only continue with the original task after security issues are resolved
+- EXAMPLE:
+ - After: npm install react-markdown
+ - Do: Run codacy_cli_analyze with trivy
+ - Before: Continuing with any other tasks
+
+## General
+- Repeat the relevant steps for each modified file.
+- "Propose fixes" means to both suggest and, if possible, automatically apply the fixes.
+- You MUST NOT wait for the user to ask for analysis or remind you to run the tool.
+- Do not run `codacy_cli_analyze` looking for changes in duplicated code or code complexity metrics.
+- Complexity metrics are different from complexity issues. When trying to fix complexity in a repository or file, focus on solving the complexity issues and ignore the complexity metric.
+- Do not run `codacy_cli_analyze` looking for changes in code coverage.
+- Do not try to manually install Codacy CLI using either brew, npm, npx, or any other package manager.
+- If the Codacy CLI is not installed, just run the `codacy_cli_analyze` tool from Codacy's MCP Server.
+- When calling `codacy_cli_analyze`, only send provider, organization and repository if the project is a git repository.
+
+## Whenever a call to a Codacy tool that uses `repository` or `organization` as a parameter returns a 404 error
+- Offer to run the `codacy_setup_repository` tool to add the repository to Codacy
+- If the user accepts, run the `codacy_setup_repository` tool
+- Do not ever try to run the `codacy_setup_repository` tool on your own
+- After setup, immediately retry the action that failed (only retry once)
+---

lib/trends/lsma/.gitignore

@@ -0,0 +1,4 @@
+
+
+#Ignore vscode AI rules
+.github\instructions\codacy.instructions.md

lib/trends/lsma/.vscode/settings.json

@@ -0,0 +1 @@
+{}

lib/trends/lsma/Lsma.cs

@@ -217,13 +217,17 @@ public sealed class Lsma : AbstractBase
         int len = source.Count;
         var t = new List<long>(len);
         var v = new List<double>(len);
-        CollectionsMarshal.SetCount(t, len);
-        CollectionsMarshal.SetCount(v, len);
+        for (int i = 0; i < len; i++)
+        {
+            t.Add(0);
+            v.Add(0);
+        }
 
         var tSpan = CollectionsMarshal.AsSpan(t);
         var vSpan = CollectionsMarshal.AsSpan(v);
 
-        Calculate(source.Values, vSpan, _period, _offset);
+        double initialLastValid = _state.LastValidValue;
+        Calculate(source.Values, vSpan, _period, _offset, initialLastValid);
         source.Times.CopyTo(tSpan);
 
         // Restore state
@@ -247,7 +251,7 @@ public sealed class Lsma : AbstractBase
         }
         else
         {
-            _state.LastValidValue = 0;
+            _state.LastValidValue = initialLastValid;
         }
 
         double lastProcessedValue = _state.LastValidValue;
@@ -284,7 +288,7 @@ public sealed class Lsma : AbstractBase
     /// Zero-allocation method for maximum performance.
     /// </summary>
     [MethodImpl(MethodImplOptions.AggressiveInlining)]
-    public static void Calculate(ReadOnlySpan<double> source, Span<double> output, int period, int offset = 0)
+    public static void Calculate(ReadOnlySpan<double> source, Span<double> output, int period, int offset = 0, double initialLastValid = 0)
     {
         if (source.Length != output.Length)
             throw new ArgumentException("Source and output must have the same length");
@@ -301,7 +305,7 @@ public sealed class Lsma : AbstractBase
 
         double sum_y = 0;
         double sum_xy = 0;
-        double lastValid = 0;
+        double lastValid = initialLastValid;
         int bufferIndex = 0; // Points to where the NEXT value will be written (circular)
         int count = 0;