refactor: rename modules (I hope this is the last time)

.github/workflows/analyze.yml

@@ -4,7 +4,7 @@ on:
       - main
     paths:
       - evonote/**
-      - doc_in_py/**
+      - docinpy/**
 
 env:
   OPENAI_API_KEY: NAN

docinpy/README.md

@@ -0,0 +1,11 @@
+
+See [DocInPy](https://evonote.org/docinpy) for a project overview.
+
+## Project todos
+
+- Extract variables from module and classes
+- Extract comments for class variables (What should be the format of the comments?)
+- Process code of function and extract comments
+- TODO decorator for functions
+
+- Serialization from structs to Python code

doc_in_py/comment_parser.py → docinpy/comment_parser.py

@@ -3,7 +3,7 @@
 import re
 from typing import List
 
-from doc_in_py import Struct
+from docinpy import Struct
 
 """
 This module is for parse and extract comments

doc_in_py/core.py → docinpy/core.py

@@ -9,8 +9,8 @@
 
 import yaml
 
-from doc_in_py import Struct
-from doc_in_py.comment_parser import prepare_raw_comment_struct, parse_raw_comments
+from docinpy import Struct
+from docinpy.comment_parser import prepare_raw_comment_struct, parse_raw_comments
 
 
 def get_module_members(module) -> Struct:

doc_in_py/test/test_decorator.py → docinpy/test/test_decorator.py

@@ -1,4 +1,4 @@
-from doc_in_py.core import get_module_members
+from docinpy.core import get_module_members
 from utils import to_dict
 
 

doc_in_py/test/test_module_multi.py → docinpy/test/test_module_multi.py

@@ -1,4 +1,4 @@
-from doc_in_py.core import get_module_members
+from docinpy.core import get_module_members
 from utils import to_dict
 
 

doc_in_py/test/test_section.py → docinpy/test/test_section.py

@@ -1,4 +1,4 @@
-from doc_in_py.core import get_module_members
+from docinpy.core import get_module_members
 from utils import to_dict
 
 

doc_in_py/test/testing_module_decorator.py → docinpy/test/testing_module_decorator.py

@@ -1,4 +1,4 @@
-from doc_in_py.decorator import todo, example
+from docinpy.decorator import todo, example
 
 """
 # Todo for the function

doc_in_py/test/utils.py → docinpy/test/utils.py

@@ -1,4 +1,4 @@
-from doc_in_py import Struct
+from docinpy import Struct
 
 
 def to_dict(struct: Struct):

docs/.vuepress/config.ts

@@ -42,6 +42,10 @@ export default defineUserConfig({
                         text: 'Development',
                         link: '/development',
                     },
+                    {
+                        text: 'DocInPy',
+                        link: '/docinpy',
+                    },
                     {
                         text: 'Project tree',
                         link: 'https://evonote.org/html/project_tree.html',

docs/.vuepress/styles/index.scss

@@ -26,7 +26,7 @@
   --c-border-dark: #dfe2e5;
 
   // custom container colors
-  --c-tip: #4a8ee5;
+  --c-tip: #5d98e1;
   --c-tip-bg: var(--c-bg-light);
   --c-tip-title: var(--c-text);
   --c-tip-text: var(--c-text);
@@ -171,7 +171,7 @@ html.dark {
   --c-border-dark: #34404c;
 
   // custom container colors
-  --c-tip: #318a62;
+  --c-tip: #5d83a8;
   --c-warning: #e0ad15;
   --c-warning-bg: #2d2f2d;
   --c-warning-bg-light: #423e2a;

docs/README.md

@@ -1,6 +1,22 @@
+## Website development setup
+
+Install pnpm
+```shell
+curl -fsSL https://get.pnpm.io/install.sh | sh -
+```
+
+Install dependencies
+```shell
+pnpm i
+```
+
 Dev mode for the docs
 ```shell
 pnpm docs:dev
 ```
 
-If you want to edit the sidebars: See `.vuepress/config.ts`.
+## Website content development
+
+Edit sidebars
+
+- See `.vuepress/config.ts`.

docs/development/index.md

@@ -6,7 +6,7 @@ Docstring style: rst
 
 ## DocInPy
 
-Please use the [DocInPy](https://github.com/EvoEvolver/EvoNote/tree/main/doc_in_py) style for adding sections in the codes. 
+Please use the [DocInPy](https://github.com/EvoEvolver/EvoNote/tree/main/docinpy) style for adding sections in the codes. 
 
 ## Installation
 

doc_in_py/README.md → docs/docinpy/index.md

@@ -13,7 +13,7 @@ codebase. It is also important for AI-based agents to understand the codebase an
 ## EvoNote
 
 EvoNote is using DocInPy to document its codebase. You can have a good visualization of EvoNote's codebase by
-running [EvoNote visualization](https://github.com/EvoEvolver/EvoNote/blob/main/playground/visualize_paper.py).
+running [EvoNote visualization](/html/project_tree.html).
 
 ## How to use
 
@@ -82,12 +82,31 @@ def baz():
     pass
 ```
 
+### Section in folder
+
+You add `.tree.yml` file in a folder to add sections in it. For example, in the following folder
+```
+a_folder
+- __init__.py
+- a.py
+- b.py
+- c.py
+- .tree.yml
+```
+You can put `a`,`b` in a section by putting
+```yaml
+sections
+```
+
+
+
+
 ### Mark examples
 
 You can also add examples to your functions and classes. Just use the `@example` decorator. For example,
 
 ```python
-from doc_in_py.decorator import example
+from docinpy.decorator import example
 
 
 @example
@@ -104,7 +123,7 @@ def how_to_use_foo():
 In a similar way, you can also mark todos in your code. Just use the `@todo` decorator. For example,
 
 ```python
-from doc_in_py.decorator import todo
+from docinpy.decorator import todo
 
 @todo
 def todo_foo():
@@ -119,14 +138,6 @@ def buggy_foo():
     foo(a=b)
 ```
 
-## Project todos
-
-- Extract variables from module and classes
-- Extract comments for class variables (What should be the format of the comments?)
-- Process code of function and extract comments
-- TODO decorator for functions
-
-- Serialization from structs to Python code
 
 ## Philosophy behind DocInPy
 
@@ -143,4 +154,4 @@ structure.
 
 DocInPy helps this by adding a zero-cost way to add sections to your functions and classes. It makes another step
 towards a more tree-like structure of the codebase. We believe this will help the programmers to understand the codebase
-better. See [Method of Loci](docs/introduction/2.1 Method of Loci.md) for more details.
+better. See [Method of Loci](/writings/2.1%20Method%20of%20Loci%20and%20sparsity.html) for more details.

evonote/.tree.yml

@@ -1,6 +1,13 @@
 sections:
-  core:
-    - notetree
+  Core:
+    - mindtree
     - indexing
+  Auxiliary:
     - file_helper
-    - model
+    - model
+    - gui
+    - testing
+  Applications:
+    - agent
+    - transform
+    - data_cleaning

evonote/agent/general.py

@@ -1,9 +1,9 @@
-from evonote.notetree import Tree
+from evonote.mindtree import Tree
 
 
 class AgentState:
     def __init__(self):
-        self.root_notetree = Tree(
-            "root notetree that indexes all available notetrees")
+        self.root_tree = Tree(
+            "root tree that indexes all available trees")
         self.objective_stack = []
         self.logs = []

evonote/gui/notetree.py → evonote/gui/mindtree.py

@@ -8,7 +8,7 @@
 from evonote.gui.utlis import hypenate_texts
 
 if TYPE_CHECKING:
-    from evonote.notetree import Note, Tree
+    from evonote.mindtree import Note, Tree
 
 h_en = Hyphenator('en_US')
 
@@ -52,12 +52,12 @@ def get_json_for_treemap(root: Note):
 
 
 def prepare_tree_parameters(root):
-    notetree = root.notetree
+    mindtree = root.tree
     labels = []
     parents = []
     texts = []
     ids = []
-    add_note_to_list(labels, parents, texts, ids, root, notetree)
+    add_note_to_list(labels, parents, texts, ids, root, mindtree)
     line_width = 40
     for i in range(len(texts)):
         if len(texts[i].strip()) == 0:
@@ -67,15 +67,15 @@ def prepare_tree_parameters(root):
     return ids, labels, parents, texts
 
 
-def add_note_to_list(labels, parents, values, ids, note: Note, notetree: Tree):
+def add_note_to_list(labels, parents, values, ids, note: Note, mindtree: Tree):
     i = 1
-    children = notetree.get_children_dict(note)
+    children = mindtree.get_children_dict(note)
     for key, child in children.items():
-        notepath = notetree.get_note_path(child)
+        notepath = mindtree.get_note_path(child)
         label = str(i) + ". " + key if len(children) > 1 else key
         labels.append(label)
         parents.append("/".join(notepath[:-1]))
         values.append(child.content)
         ids.append("/".join(notepath))
-        add_note_to_list(labels, parents, values, ids, child, notetree)
+        add_note_to_list(labels, parents, values, ids, child, mindtree)
         i += 1

evonote/indexing/code_indexer.py

@@ -2,7 +2,7 @@
 from typing import List
 
 from evonote.indexing.core import AbsEmbeddingIndexer, Indexing
-from evonote.notetree import Note
+from evonote.mindtree import Note
 
 
 class CodeParameterIndexer(AbsEmbeddingIndexer):

evonote/indexing/core.py

@@ -10,8 +10,8 @@
 from evonote.model.chat import Chat
 
 if TYPE_CHECKING:
-    from evonote.notetree import Note
-    from evonote.notetree import Tree
+    from evonote.mindtree import Note
+    from evonote.mindtree import Tree
 
 from evonote.file_helper.cache_manage import save_cache, cached_function
 from evonote.model.openai import get_embeddings
@@ -41,11 +41,11 @@ def remove_note(cls, note: Note):
 
 class Indexing:
     def __init__(self, notes: List[Note], indexer: Type[Indexer],
-                 notetree: Tree):
+                 tree: Tree):
         self.notes_without_indexer: List[Note] = notes[:]
         self.indexer: Type[Indexer] = indexer
         self.data: Any = None
-        self.notetree = notetree
+        self.tree = tree
 
     def add_new_note(self, note: Note):
         self.notes_without_indexer.append(note)
@@ -223,7 +223,7 @@ class FragmentedEmbeddingIndexer(AbsEmbeddingIndexer):
     def process_note_with_content(cls, notes: List[Note], indexing: Indexing,
                                   ):
         notes_content = [note.content for note in notes]
-        notetree = indexing.notetree
+        tree = indexing.tree
 
         new_src_list = []
         new_weights = []
@@ -233,9 +233,9 @@ def process_note_with_content(cls, notes: List[Note], indexing: Indexing,
                                    executor.map(process_sent_into_frags, notes_content)):
                 new_src = []
                 new_src.extend(frags)
-                note_path = notetree.get_note_path(note)
+                note_path = tree.get_note_path(note)
                 if len(note_path) > 0:
-                    new_src.append(notetree.get_note_path(note)[-1])
+                    new_src.append(tree.get_note_path(note)[-1])
                 new_src.append(note.content)
 
                 new_src_list.append(new_src)
@@ -274,13 +274,13 @@ def process_note_without_content(cls, notes: List[Note], indexing: Indexing,
     def prepare_src_weight_list(cls, new_notes: List[Note], indexing: Indexing,
                                 ):
 
-        notetree = indexing.notetree
+        tree = indexing.tree
         notes_with_content = []
         notes_content = []
         notes_without_content = []
         for note in new_notes:
             if len(note.content) == 0:
-                keywords_on_path = notetree.get_note_path(note)
+                keywords_on_path = tree.get_note_path(note)
                 if len(keywords_on_path) != 0:
                     notes_without_content.append(note)
                 continue

evonote/notetree/analysis.py → evonote/mindtree/analysis.py

@@ -1,11 +1,11 @@
-from evonote.notetree import Tree
+from evonote.mindtree import Tree
 
 
-def analyze_notetree_sparsity(notetree: Tree):
+def analyze_tree_sparsity(tree: Tree):
     """
     Return the average number of children per note.
     """
-    notes = notetree.get_note_list()
+    notes = tree.get_note_list()
     max_children = -1
     total_children = 0
     n_non_leaf_notes = 0
@@ -16,7 +16,7 @@ def analyze_notetree_sparsity(notetree: Tree):
             total_children += n_children
         max_children = max(max_children, n_children)
     average_children = total_children / n_non_leaf_notes
-    heavy_notes = get_children_heavy_notes(notetree)
+    heavy_notes = get_children_heavy_notes(tree)
     print("Total_notes:", len(notes))
     print("Average children per non-leaf note:", average_children)
     print("Max children per note:", max_children)
@@ -27,11 +27,11 @@ def analyze_notetree_sparsity(notetree: Tree):
         print("Content:", note.content)
         print("")
 
-def get_children_heavy_notes(notetree: Tree, min_children=8):
+def get_children_heavy_notes(tree: Tree, min_children=8):
     """
     Return a list of notes with at least min_children children.
     """
-    notes = notetree.get_note_list()
+    notes = tree.get_note_list()
     heavy_notes = []
     for note in notes:
         n_children = len(note.children())