Merge pull request #56 from royerlab/bug_fixes_aug24

Bug fixes Aug 24

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napari-chatgpt
-version = v2024.5.15
+version = v2024.8.30
 description = A napari plugin to process and analyse images with chatGPT.
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -36,12 +36,13 @@ install_requires =
     scikit-image
     qtpy
     QtAwesome
-    langchain==0.2.0rc2
-    langchain-community==0.2.0rc1
-    langchain-openai==0.1.6
-    langchain-anthropic==0.1.11
-    openai==1.29.0
-    anthropic
+    langchain==0.2.15
+    langchain-community==0.2.14
+    langchain-openai==0.1.23
+    langchain-anthropic==0.1.23
+#    langchain-google-genai==1.0.10
+    openai==1.42.0
+    anthropic==0.34.1
     fastapi
     uvicorn
     websockets
@@ -54,7 +55,7 @@ install_requires =
     xarray
     arbol
     playwright
-    duckduckgo_search==5.3.0b4
+    duckduckgo-search==6.2.11
     ome-zarr
     transformers
     cryptography

src/microplugin/formating/black_formating.py

@@ -1,8 +1,6 @@
 from pathlib import Path
 from typing import Union
 
-from black import FileMode, format_file_in_place, WriteBack
-
 
 def format_code(code: str) -> str:
     """Format the code using black."""
@@ -29,6 +27,9 @@ def format_file(file_path: Union[str, Path]) -> None:
         if isinstance(file_path, str):
             file_path = Path(file_path)
 
+        # Local import to avoid polution of the global namespace:
+        from black import FileMode, format_file_in_place, WriteBack
+
         # Format the file using Black
         format_file_in_place(file_path,
                              fast=False,

src/napari_chatgpt/_widget.py

@@ -17,11 +17,13 @@
 from qtpy.QtWidgets import QVBoxLayout, QComboBox
 
 from microplugin.microplugin_window import MicroPluginMainWindow
+from napari_chatgpt.utils.anthropic.model_list import get_anthropic_model_list
 from napari_chatgpt.utils.configuration.app_configuration import \
     AppConfiguration
 from napari_chatgpt.utils.ollama.ollama_server import is_ollama_running, \
     get_ollama_models
-from napari_chatgpt.utils.openai.model_list import get_openai_model_list
+from napari_chatgpt.utils.openai.model_list import get_openai_model_list, \
+    postprocess_openai_model_list
 from napari_chatgpt.utils.python.installed_packages import \
     is_package_installed
 from napari_chatgpt.utils.qt.one_time_disclaimer_dialog import \
@@ -123,44 +125,15 @@ def _model_selection(self):
 
         if is_package_installed('anthropic'):
             # Add Anthropic models to the combo box:
-            model_list.append('claude-2.1')
-            model_list.append('claude-2.0')
-            model_list.append('claude-instant-1.2')
-            model_list.append('claude-3-sonnet-20240229')
-            model_list.append('claude-3-opus-20240229')
-
+            model_list.extend(get_anthropic_model_list())
 
         if is_ollama_running():
             ollama_models = get_ollama_models()
             for ollama_model in ollama_models:
                 model_list.append('ollama_'+ollama_model)
 
-        # Postprocess model list:
-
-        # Special cases (common prefix):
-        if 'gpt-3.5-turbo' in model_list:
-            model_list.remove('gpt-3.5-turbo')
-
-        # get list of bad models for main LLM:
-        bad_models_filters = ['0613', 'vision', 'turbo-instruct', 'gpt-3.5-turbo-0301', 'gpt-3.5-turbo-16k']
-
-        # get list of best models for main LLM:
-        best_models_filters = ['0314', '0301', '1106', 'gpt-4']
-
-        # Ensure that some 'bad' or unsupported models are excluded:
-        bad_models = [m for m in model_list if any(bm in m for bm in bad_models_filters)]
-        for bad_model in bad_models:
-            if bad_model in model_list:
-                model_list.remove(bad_model)
-                # model_list.append(bad_model)
-
-        # Ensure that the best models are at the top of the list:
-        best_models = [m for m in model_list if any(bm in m for bm in best_models_filters)]
-        model_list = best_models + [m for m in model_list if m not in best_models]
-
-        # Ensure that the very best models are at the top of the list:
-        very_best_models = [m for m in model_list if ('gpt-4-turbo-2024-04-09' in m) ]
-        model_list = very_best_models + [m for m in model_list if m not in very_best_models]
+        # Postprocess OpenAI model list:
+        model_list = postprocess_openai_model_list(model_list)
 
         # normalise list:
         model_list = list(model_list)

src/napari_chatgpt/chat_server/callbacks/callbacks_handle_chat.py

@@ -121,7 +121,19 @@ async def on_agent_action(self, action: AgentAction, **kwargs: Any) -> Any:
         if self.verbose:
             aprint(f"CHAT on_agent_action: {action}")
         tool = camel_case_to_lower_case(action.tool)
-        message = f"I am using the {tool} to tackle your request: '{action.tool_input}'"
+
+        # extract value for args key after checking if action.tool_input is a dict:
+        if isinstance(action.tool_input, dict):
+            argument = action.tool_input.get('args', '')
+
+            # if argument is a singleton list, unpop that single element:
+            if isinstance(argument, list):
+                argument = argument[0]
+
+        else:
+            argument = action.tool_input
+
+        message = f"I am using the {tool} to tackle your request: '{argument}'"
 
         self.last_tool_used = tool
         self.last_tool_input = action.tool_input

src/napari_chatgpt/chat_server/chat_server.py

@@ -30,12 +30,18 @@
 from napari_chatgpt.utils.api_keys.api_key import set_api_key
 from napari_chatgpt.utils.configuration.app_configuration import \
     AppConfiguration
+from napari_chatgpt.utils.network.port_available import \
+    find_first_port_available
 from napari_chatgpt.utils.notebook.jupyter_notebook import JupyterNotebookFile
 from napari_chatgpt.utils.openai.default_model import \
     get_default_openai_model_name
 from napari_chatgpt.utils.python.installed_packages import is_package_installed
 
 
+
+
+
+
 class NapariChatServer:
     def __init__(self,
                  notebook: JupyterNotebookFile,
@@ -71,8 +77,12 @@ def __init__(self,
         # Get configuration
         config = AppConfiguration('omega')
 
-        # port:
-        self.port = config.get('port', 9000)
+        # check if default port is available, if not increment by one until available:
+        default_port = config.get('port', 9000)
+
+        # find first available port:
+        self.port = find_first_port_available(default_port, default_port+1000)
+        aprint(f"Using port: {self.port}")
 
         # Mount static files:
         static_files_path = os.path.join(
@@ -81,9 +91,11 @@ def __init__(self,
         self.app.mount("/static", StaticFiles(directory=static_files_path),
                        name="static")
 
+        # Load templates:
         templates_files_path = os.path.join(
             os.path.dirname(os.path.abspath(__file__)),
             'templates')
+
         # Load Jinja2 templates:
         templates = Jinja2Templates(directory=templates_files_path)
 

src/napari_chatgpt/chat_server/static/marked-highlight.js

@@ -1,62 +1,69 @@
+function markedHighlight(options) {
+  if (typeof options === 'function') {
+    options = {
+      highlight: options,
+    };
+  }
 
-function markedHighlight(options)
-{
-    if (typeof options === 'function') {
-      options = {
-        highlight: options
-      };
-    }
+  if (!options || typeof options.highlight !== 'function') {
+    throw new Error('Must provide highlight function');
+  }
 
-    if (!options || typeof options.highlight !== 'function') {
-      throw new Error('Must provide highlight function');
-    }
+  if (typeof options.langPrefix !== 'string') {
+    options.langPrefix = 'language-';
+  }
 
-    if (typeof options.langPrefix !== 'string') {
-      options.langPrefix = 'language-';
-    }
+  return {
+    async: !!options.async,
+    walkTokens(token) {
+      if (token.type !== 'code') {
+        return;
+      }
 
-    return {
-      async: !!options.async,
-      walkTokens(token) {
-        if (token.type !== 'code') {
-          return;
-        }
+      const lang = getLang(token.lang);
 
-        const lang = getLang(token);
+      if (options.async) {
+        return Promise.resolve(options.highlight(token.text, lang, token.lang || '')).then(updateToken(token));
+      }
 
-        if (options.async) {
-          return Promise.resolve(options.highlight(token.text, lang)).then(updateToken(token));
+      const code = options.highlight(token.text, lang, token.lang || '');
+      if (code instanceof Promise) {
+        throw new Error('markedHighlight is not set to async but the highlight function is async. Set the async option to true on markedHighlight to await the async highlight function.');
+      }
+      updateToken(token)(code);
+    },
+    useNewRenderer: true,
+    renderer: {
+      code(code, infoString, escaped) {
+        // istanbul ignore next
+        if (typeof code === 'object') {
+          escaped = code.escaped;
+          infoString = code.lang;
+          code = code.text;
         }
 
-        const code = options.highlight(token.text, lang);
-        updateToken(token)(code);
+        const lang = getLang(infoString);
+        const classAttr = lang
+          ? ` class="${options.langPrefix}${escape(lang)}"`
+          : '';
+        code = code.replace(/\n$/, '');
+        return `<pre><code${classAttr}>${escaped ? code : escape(code, true)}\n</code></pre>`;
       },
-      renderer: {
-        code(code, infoString, escaped) {
-          const lang = (infoString || '').match(/\S*/)[0];
-          const classAttr = lang
-            ? ` class="${options.langPrefix}${escape(lang)}"`
-            : '';
-          code = code.replace(/\n$/, '');
-          return `<pre><code${classAttr}>${escaped ? code : escape(code, true)}\n</code></pre>`;
-        }
-      }
-    };
+    },
+  };
 }
 
-function getLang(token)
-{
-    return (token.lang || '').match(/\S*/)[0];
+function getLang(lang) {
+  return (lang || '').match(/\S*/)[0];
 }
 
-function updateToken(token)
-{
-    return (code) => {
-      if (typeof code === 'string' && code !== token.text) {
-        token.escaped = true;
-        token.text = code;
-      }
-    };
+function updateToken(token) {
+  return (code) => {
+    if (typeof code === 'string' && code !== token.text) {
+      token.escaped = true;
+      token.text = code;
+    }
+  };
 }
 
 // copied from marked helpers
@@ -65,26 +72,23 @@ const escapeReplace = new RegExp(escapeTest.source, 'g');
 const escapeTestNoEncode = /[<>"']|&(?!(#\d{1,7}|#[Xx][a-fA-F0-9]{1,6}|\w+);)/;
 const escapeReplaceNoEncode = new RegExp(escapeTestNoEncode.source, 'g');
 const escapeReplacements = {
-'&': '&amp;',
-'<': '&lt;',
-'>': '&gt;',
-'"': '&quot;',
-"'": '&#39;'
+  '&': '&amp;',
+  '<': '&lt;',
+  '>': '&gt;',
+  '"': '&quot;',
+  "'": '&#39;',
 };
 const getEscapeReplacement = (ch) => escapeReplacements[ch];
 function escape(html, encode) {
-    if (encode) {
-      if (escapeTest.test(html)) {
-        return html.replace(escapeReplace, getEscapeReplacement);
-      }
-    } else {
-      if (escapeTestNoEncode.test(html)) {
-        return html.replace(escapeReplaceNoEncode, getEscapeReplacement);
-      }
+  if (encode) {
+    if (escapeTest.test(html)) {
+      return html.replace(escapeReplace, getEscapeReplacement);
     }
+  } else {
+    if (escapeTestNoEncode.test(html)) {
+      return html.replace(escapeReplaceNoEncode, getEscapeReplacement);
+    }
+  }
 
-    return html;
-}
-
-//exports.markedHighlight = markedHighlight;
-
+  return html;
+}