From 310fafe06aa2851b473c73c04be73ac4a1bdf772 Mon Sep 17 00:00:00 2001
From: bagel897 <ellenagarwal897@gmail.com>
Date: Tue, 9 Jan 2024 12:50:03 -0600
Subject: [PATCH 01/11] rebase onto master

---
 CHANGELOG.md                           |  2 +-
 docs/configuration.rst                 |  9 ++-
 rope/base/prefs.py                     | 10 ++++
 rope/base/versioning.py                |  5 +-
 rope/contrib/autoimport/sqlite.py      | 83 ++++++++++++++++++--------
 rope/contrib/autoimport/utils.py       |  2 +-
 ropetest/contrib/autoimport/deptest.py | 54 +++++++++++++++++
 7 files changed, 136 insertions(+), 29 deletions(-)
 create mode 100644 ropetest/contrib/autoimport/deptest.py

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cd0c47c1a..ab59f07b4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,5 @@
 # **Upcoming release**
-
+- #516 Autoimport Now automatically detects project dependencies and can read TOML configuration
 - #733 skip directories with perm error when building autoimport index (@MrBago)
 - #722, #723 Remove site-packages from packages search tree (@tkrabel)
 - #738 Implement os.PathLike on Resource (@lieryan)
diff --git a/docs/configuration.rst b/docs/configuration.rst
index 5aba53acb..fb703f862 100644
--- a/docs/configuration.rst
+++ b/docs/configuration.rst
@@ -14,6 +14,8 @@ Will be used if [tool.rope] is configured.
 
     [tool.rope]
     split_imports = true
+    [tool.rope.autoimport]
+    underlined = false
 
 config.py
 ---------
@@ -56,9 +58,14 @@ It follows the exact same syntax of the pyproject.toml.
 
 
 Options
--------
+=======
 .. autopytoolconfigtable:: rope.base.prefs.Prefs
 
+Autoimport Options
+------------------
+.. autopytoolconfigtable:: rope.base.prefs.AutoimportPrefs
+
+
 Old Configuration File
 ----------------------
 This is a sample config.py. While this config.py works and all options here should be supported, the above documentation reflects the latest version of rope.
diff --git a/rope/base/prefs.py b/rope/base/prefs.py
index 9d4fd4a43..ae35d7d68 100644
--- a/rope/base/prefs.py
+++ b/rope/base/prefs.py
@@ -12,6 +12,14 @@
 from rope.base.resources import Folder
 
 
+@dataclass
+class AutoimportPrefs:
+    underlined: bool = field(
+        default=False, description="Cache underlined (private) modules")
+    memory: bool = field(default=None, description="Cache in memory instead of disk")
+    parallel: bool = field(default=True, description="Use multiple processes to parse")
+
+
 @dataclass
 class Prefs:
     """Class to store rope preferences."""
@@ -206,6 +214,8 @@ class Prefs:
             Can only be set in config.py.
         """),
     )
+    autoimport: AutoimportPrefs = field(
+        default_factory=lambda: AutoimportPrefs(), description="Preferences for Autoimport")
 
     def set(self, key: str, value: Any):
         """Set the value of `key` preference to `value`."""
diff --git a/rope/base/versioning.py b/rope/base/versioning.py
index 985255e47..4f0615902 100644
--- a/rope/base/versioning.py
+++ b/rope/base/versioning.py
@@ -1,3 +1,4 @@
+import dataclasses
 import hashlib
 import importlib.util
 import json
@@ -31,7 +32,9 @@ def _get_prefs_data(project) -> str:
     del prefs_data["project_opened"]
     del prefs_data["callbacks"]
     del prefs_data["dependencies"]
-    return json.dumps(prefs_data, sort_keys=True, indent=2)
+    return json.dumps(
+        prefs_data, sort_keys=True, indent=2, default=lambda o: o.__dict__
+    )
 
 
 def _get_file_content(module_name: str) -> str:
diff --git a/rope/contrib/autoimport/sqlite.py b/rope/contrib/autoimport/sqlite.py
index 3d5d35977..5e1f9c466 100644
--- a/rope/contrib/autoimport/sqlite.py
+++ b/rope/contrib/autoimport/sqlite.py
@@ -16,7 +16,10 @@
 from threading import local
 from typing import Generator, Iterable, Iterator, List, Optional, Set, Tuple
 
+from packaging.requirements import Requirement
+
 from rope.base import exceptions, libutils, resourceobserver, taskhandle, versioning
+from rope.base.prefs import AutoimportPrefs
 from rope.base.project import Project
 from rope.base.resources import Resource
 from rope.contrib.autoimport import models
@@ -53,18 +56,36 @@ def get_future_names(
 
 
 def filter_packages(
-    packages: Iterable[Package], underlined: bool, existing: List[str]
+    packages: Iterable[Package],
+    underlined: bool,
+    existing: List[str],
+    dependencies: Optional[List[Requirement]],
 ) -> Iterable[Package]:
     """Filter list of packages to parse."""
+    parsed_deps = (
+        [dep.name for dep in dependencies] if dependencies is not None else None
+    )
+
+    def is_dep(package) -> bool:
+        return (
+            parsed_deps is None
+            or package.name in parsed_deps
+            or package.source is not Source.SITE_PACKAGE
+        )
+
     if underlined:
 
         def filter_package(package: Package) -> bool:
-            return package.name not in existing
+            return package.name not in existing and is_dep(package)
 
     else:
 
         def filter_package(package: Package) -> bool:
-            return package.name not in existing and not package.name.startswith("_")
+            return (
+                package.name not in existing
+                and not package.name.startswith("_")
+                and is_dep(package)
+            )
 
     return filter(filter_package, packages)
 
@@ -81,16 +102,15 @@ class AutoImport:
     """
 
     connection: sqlite3.Connection
-    memory: bool
     project: Project
     project_package: Package
-    underlined: bool
+    prefs: AutoimportPrefs
 
     def __init__(
         self,
         project: Project,
         observe: bool = True,
-        underlined: bool = False,
+        underlined: Optional[bool] = None,
         memory: bool = _deprecated_default,
     ):
         """Construct an AutoImport object.
@@ -113,25 +133,29 @@ def __init__(
                 autoimport = AutoImport(..., memory=True)
         """
         self.project = project
+        self.prefs = self.project.prefs.autoimport
         project_package = get_package_tuple(project.root.pathlib, project)
         assert project_package is not None
         assert project_package.path is not None
+        if underlined is not None:
+            self.prefs.underlined = underlined
         self.project_package = project_package
-        self.underlined = underlined
-        self.memory = memory
         if memory is _deprecated_default:
-            self.memory = True
-            warnings.warn(
-                "The default value for `AutoImport(memory)` argument will "
-                "change to use an on-disk database by default in the future. "
-                "If you want to use an in-memory database, you need to pass "
-                "`AutoImport(memory=True)` explicitly.",
-                DeprecationWarning,
-            )
+            if self.prefs.memory is None:
+                self.prefs.memory = True
+                warnings.warn(
+                    "The default value for `AutoImport(memory)` argument will "
+                    "change to use an on-disk database by default in the future. "
+                    "If you want to use an in-memory database, you need to pass "
+                    "`AutoImport(memory=True)` explicitly or set it in the config file.",
+                    DeprecationWarning,
+                )
+        else:
+            self.prefs.memory = memory
         self.thread_local = local()
         self.connection = self.create_database_connection(
             project=project,
-            memory=memory,
+            memory=self.prefs.memory,
         )
         self._setup_db()
         if observe:
@@ -389,12 +413,13 @@ def generate_modules_cache(
         """
         Generate global name cache for external modules listed in `modules`.
 
-        If no modules are provided, it will generate a cache for every module available.
+        If modules is not specified, uses PEP 621 metadata.
+        If modules aren't specified and PEP 621 is not present, caches every package
         This method searches in your sys.path and configured python folders.
         Do not use this for generating your own project's internal names,
         use generate_resource_cache for that instead.
         """
-        underlined = self.underlined if underlined is None else underlined
+        underlined = self.prefs.underlined if underlined is None else underlined
 
         packages: List[Package] = (
             self._get_available_packages()
@@ -403,12 +428,16 @@ def generate_modules_cache(
         )
 
         existing = self._get_packages_from_cache()
-        packages = list(filter_packages(packages, underlined, existing))
-        if not packages:
+        packages = list(
+            filter_packages(
+                packages, underlined, existing, self.project.prefs.dependencies
+            )
+        )
+        if len(packages) == 0:
             return
         self._add_packages(packages)
         job_set = task_handle.create_jobset("Generating autoimport cache", 0)
-        if single_thread:
+        if single_thread or not self.prefs.parallel:
             for package in packages:
                 for module in get_files(package, underlined):
                     job_set.started_job(module.modname)
@@ -512,7 +541,7 @@ def update_resource(
         self, resource: Resource, underlined: bool = False, commit: bool = True
     ):
         """Update the cache for global names in `resource`."""
-        underlined = underlined if underlined else self.underlined
+        underlined = underlined if underlined else self.prefs.underlined
         module = self._resource_to_module(resource, underlined)
         self._del_if_exist(module_name=module.modname, commit=False)
         for name in get_names(module, self.project_package):
@@ -537,7 +566,11 @@ def _del_if_exist(self, module_name, commit: bool = True):
 
     def _get_python_folders(self) -> List[Path]:
         def filter_folders(folder: Path) -> bool:
-            return folder.is_dir() and folder.as_posix() != "/usr/bin"
+            return (
+                folder.is_dir()
+                and folder.as_posix() != "/usr/bin"
+                and str(folder) != self.project.address
+            )
 
         folders = self.project.get_python_path_folders()
         folder_paths = filter(filter_folders, map(Path, folders))
@@ -623,7 +656,7 @@ def _resource_to_module(
         self, resource: Resource, underlined: bool = False
     ) -> ModuleFile:
         assert self.project_package.path
-        underlined = underlined if underlined else self.underlined
+        underlined = underlined if underlined else self.prefs.underlined
         resource_path: Path = resource.pathlib
         # The project doesn't need its name added to the path,
         # since the standard python file layout accounts for that
diff --git a/rope/contrib/autoimport/utils.py b/rope/contrib/autoimport/utils.py
index 5238339de..bc80403c5 100644
--- a/rope/contrib/autoimport/utils.py
+++ b/rope/contrib/autoimport/utils.py
@@ -118,7 +118,7 @@ def get_files(
         yield ModuleFile(package.path, package.path.stem, underlined, False)
     else:
         assert package.path
-        for file in package.path.glob("**/*.py"):
+        for file in package.path.rglob("*.py"):
             if file.name == "__init__.py":
                 yield ModuleFile(
                     file,
diff --git a/ropetest/contrib/autoimport/deptest.py b/ropetest/contrib/autoimport/deptest.py
new file mode 100644
index 000000000..9dcefd132
--- /dev/null
+++ b/ropetest/contrib/autoimport/deptest.py
@@ -0,0 +1,54 @@
+from pathlib import Path
+from typing import Iterable
+
+import pytest
+
+from rope.base.project import Project
+from rope.contrib.autoimport.sqlite import AutoImport
+
+
+@pytest.fixture
+def project(request, tmp_path: Path) -> Iterable[Project]:
+    doc = request.param
+    if doc is not None:
+        file = tmp_path / "pyproject.toml"
+        file.write_text(doc, encoding="utf-8")
+        print(file, doc)
+    project = Project(tmp_path)
+    yield project
+    project.close()
+
+
+@pytest.fixture
+def autoimport(project) -> Iterable[AutoImport]:
+    autoimport = AutoImport(project, memory=True)
+    autoimport.generate_modules_cache()
+    yield autoimport
+    autoimport.close()
+
+
+@pytest.mark.parametrize("project", ((""),), indirect=True)
+def test_blank(project, autoimport):
+    assert project.prefs.dependencies is None
+    assert autoimport.search("pytoolconfig")
+
+
+@pytest.mark.parametrize("project", (("[project]\n dependencies=[]"),), indirect=True)
+def test_empty(project, autoimport):
+    assert len(project.prefs.dependencies) == 0
+    assert [] == autoimport.search("pytoolconfig")
+
+
+FILE = """
+[project]
+dependencies = [
+    "pytoolconfig",
+    "bogus"
+]
+"""
+
+
+@pytest.mark.parametrize("project", ((FILE),), indirect=True)
+def test_not_empty(project, autoimport):
+    assert len(project.prefs.dependencies) == 2
+    assert autoimport.search("pytoolconfig")

From c498523a461231bdcaed7d17ec66bb6d02756558 Mon Sep 17 00:00:00 2001
From: bagel897 <ellenagarwal897@gmail.com>
Date: Tue, 9 Jan 2024 12:55:52 -0600
Subject: [PATCH 02/11] fix some memory things

---
 rope/contrib/autoimport/sqlite.py | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/rope/contrib/autoimport/sqlite.py b/rope/contrib/autoimport/sqlite.py
index 5e1f9c466..6b520d535 100644
--- a/rope/contrib/autoimport/sqlite.py
+++ b/rope/contrib/autoimport/sqlite.py
@@ -141,15 +141,14 @@ def __init__(
             self.prefs.underlined = underlined
         self.project_package = project_package
         if memory is _deprecated_default:
-            if self.prefs.memory is None:
-                self.prefs.memory = True
-                warnings.warn(
-                    "The default value for `AutoImport(memory)` argument will "
-                    "change to use an on-disk database by default in the future. "
-                    "If you want to use an in-memory database, you need to pass "
-                    "`AutoImport(memory=True)` explicitly or set it in the config file.",
-                    DeprecationWarning,
-                )
+            self.prefs.memory = True
+            warnings.warn(
+                "The default value for `AutoImport(memory)` argument will "
+                "change to use an on-disk database by default in the future. "
+                "If you want to use an in-memory database, you need to pass "
+                "`AutoImport(memory=True)` explicitly or set it in the config file.",
+                DeprecationWarning,
+            )
         else:
             self.prefs.memory = memory
         self.thread_local = local()
@@ -211,7 +210,7 @@ def connection(self):
         if not hasattr(self.thread_local, "connection"):
             self.thread_local.connection = self.create_database_connection(
                 project=self.project,
-                memory=self.memory,
+                memory=self.prefs.memory,
             )
         return self.thread_local.connection
 

From 1317549339ab88f97c4cb26053952ecf0ed0f883 Mon Sep 17 00:00:00 2001
From: bagel897 <ellenagarwal897@gmail.com>
Date: Tue, 9 Jan 2024 13:00:57 -0600
Subject: [PATCH 03/11] avoid site-packages

---
 rope/contrib/autoimport/utils.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/rope/contrib/autoimport/utils.py b/rope/contrib/autoimport/utils.py
index bc80403c5..a2e51d990 100644
--- a/rope/contrib/autoimport/utils.py
+++ b/rope/contrib/autoimport/utils.py
@@ -119,6 +119,8 @@ def get_files(
     else:
         assert package.path
         for file in package.path.rglob("*.py"):
+            if "site-packages" in file.parts:
+                continue
             if file.name == "__init__.py":
                 yield ModuleFile(
                     file,

From 8650ff6388df42fe22bd1f0e7f94200aa0e99147 Mon Sep 17 00:00:00 2001
From: bagel897 <ellenagarwal897@gmail.com>
Date: Tue, 9 Jan 2024 13:07:17 -0600
Subject: [PATCH 04/11] pass memory=True for tests

---
 ropetest/contrib/autoimport/autoimporttest.py | 8 ++++----
 ropetest/contrib/autoimporttest.py            | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/ropetest/contrib/autoimport/autoimporttest.py b/ropetest/contrib/autoimport/autoimporttest.py
index 072ab1ed8..f9496db60 100644
--- a/ropetest/contrib/autoimport/autoimporttest.py
+++ b/ropetest/contrib/autoimport/autoimporttest.py
@@ -14,7 +14,7 @@
 
 @pytest.fixture
 def autoimport(project: Project):
-    with closing(AutoImport(project)) as ai:
+    with closing(AutoImport(project, memory=True)) as ai:
         yield ai
 
 
@@ -124,9 +124,9 @@ def foo():
 
 
 def test_connection(project: Project, project2: Project):
-    ai1 = AutoImport(project)
-    ai2 = AutoImport(project)
-    ai3 = AutoImport(project2)
+    ai1 = AutoImport(project, memory=True)
+    ai2 = AutoImport(project, memory=True)
+    ai3 = AutoImport(project2, memory=True)
 
     assert ai1.connection is not ai2.connection
     assert ai1.connection is not ai3.connection
diff --git a/ropetest/contrib/autoimporttest.py b/ropetest/contrib/autoimporttest.py
index 94bb033bb..fb21bbd2b 100644
--- a/ropetest/contrib/autoimporttest.py
+++ b/ropetest/contrib/autoimporttest.py
@@ -11,7 +11,7 @@ def setUp(self):
         self.mod1 = testutils.create_module(self.project, "mod1")
         self.pkg = testutils.create_package(self.project, "pkg")
         self.mod2 = testutils.create_module(self.project, "mod2", self.pkg)
-        self.importer = autoimport.AutoImport(self.project, observe=False)
+        self.importer = autoimport.AutoImport(self.project, observe=False, memory=True)
 
     def tearDown(self):
         testutils.remove_project(self.project)
@@ -86,7 +86,7 @@ def test_not_caching_underlined_names(self):
         self.assertEqual(["mod1"], self.importer.get_modules("_myvar"))
 
     def test_caching_underlined_names_passing_to_the_constructor(self):
-        importer = autoimport.AutoImport(self.project, False, True)
+        importer = autoimport.AutoImport(self.project, False, True, memory=True)
         self.mod1.write("_myvar = None\n")
         importer.update_resource(self.mod1)
         self.assertEqual(["mod1"], importer.get_modules("_myvar"))
@@ -165,7 +165,7 @@ def setUp(self):
         self.mod1 = testutils.create_module(self.project, "mod1")
         self.pkg = testutils.create_package(self.project, "pkg")
         self.mod2 = testutils.create_module(self.project, "mod2", self.pkg)
-        self.importer = autoimport.AutoImport(self.project, observe=True)
+        self.importer = autoimport.AutoImport(self.project, observe=True, memory=True)
 
     def tearDown(self):
         testutils.remove_project(self.project)

From e9fa30d9c5bf8d308419ab191b2ddab787162ce0 Mon Sep 17 00:00:00 2001
From: bagel897 <ellenagarwal897@gmail.com>
Date: Tue, 9 Jan 2024 13:08:51 -0600
Subject: [PATCH 05/11] update site-packages detection

---
 rope/contrib/autoimport/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rope/contrib/autoimport/utils.py b/rope/contrib/autoimport/utils.py
index a2e51d990..85bbef805 100644
--- a/rope/contrib/autoimport/utils.py
+++ b/rope/contrib/autoimport/utils.py
@@ -119,7 +119,7 @@ def get_files(
     else:
         assert package.path
         for file in package.path.rglob("*.py"):
-            if "site-packages" in file.parts:
+            if "site-packages" in file.relative_to(package.path).parts:
                 continue
             if file.name == "__init__.py":
                 yield ModuleFile(

From a05f7d5390b05ec5bc373e74dbfb56b6a73c067e Mon Sep 17 00:00:00 2001
From: bagel897 <ellenagarwal897@gmail.com>
Date: Thu, 11 Jan 2024 11:30:00 -0600
Subject: [PATCH 06/11] use basic suggestions

---
 rope/base/prefs.py                     | 2 +-
 rope/contrib/autoimport/sqlite.py      | 4 ++--
 ropetest/contrib/autoimport/deptest.py | 1 -
 3 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/rope/base/prefs.py b/rope/base/prefs.py
index ae35d7d68..6f3d69c0b 100644
--- a/rope/base/prefs.py
+++ b/rope/base/prefs.py
@@ -215,7 +215,7 @@ class Prefs:
         """),
     )
     autoimport: AutoimportPrefs = field(
-        default_factory=lambda: AutoimportPrefs(), description="Preferences for Autoimport")
+        default_factory=AutoimportPrefs, description="Preferences for Autoimport")
 
     def set(self, key: str, value: Any):
         """Set the value of `key` preference to `value`."""
diff --git a/rope/contrib/autoimport/sqlite.py b/rope/contrib/autoimport/sqlite.py
index 6b520d535..db6758419 100644
--- a/rope/contrib/autoimport/sqlite.py
+++ b/rope/contrib/autoimport/sqlite.py
@@ -17,7 +17,7 @@
 from typing import Generator, Iterable, Iterator, List, Optional, Set, Tuple
 
 from packaging.requirements import Requirement
-
+from copy import deepcopy
 from rope.base import exceptions, libutils, resourceobserver, taskhandle, versioning
 from rope.base.prefs import AutoimportPrefs
 from rope.base.project import Project
@@ -133,7 +133,7 @@ def __init__(
                 autoimport = AutoImport(..., memory=True)
         """
         self.project = project
-        self.prefs = self.project.prefs.autoimport
+        self.prefs = deepcopy(self.project.prefs.autoimport)
         project_package = get_package_tuple(project.root.pathlib, project)
         assert project_package is not None
         assert project_package.path is not None
diff --git a/ropetest/contrib/autoimport/deptest.py b/ropetest/contrib/autoimport/deptest.py
index 9dcefd132..f392c9493 100644
--- a/ropetest/contrib/autoimport/deptest.py
+++ b/ropetest/contrib/autoimport/deptest.py
@@ -13,7 +13,6 @@ def project(request, tmp_path: Path) -> Iterable[Project]:
     if doc is not None:
         file = tmp_path / "pyproject.toml"
         file.write_text(doc, encoding="utf-8")
-        print(file, doc)
     project = Project(tmp_path)
     yield project
     project.close()

From 0a94b9201d23f55952e7eaa0a2d8ad78be58d606 Mon Sep 17 00:00:00 2001
From: bagel897 <ellenagarwal897@gmail.com>
Date: Mon, 22 Jan 2024 09:19:39 -0600
Subject: [PATCH 07/11] modify project fixture

---
 ropetest/conftest.py                   |  6 ++++--
 ropetest/contrib/autoimport/deptest.py | 11 -----------
 ropetest/testutils.py                  |  8 ++++++--
 3 files changed, 10 insertions(+), 15 deletions(-)

diff --git a/ropetest/conftest.py b/ropetest/conftest.py
index ce8a1eab5..53e7b4109 100644
--- a/ropetest/conftest.py
+++ b/ropetest/conftest.py
@@ -7,8 +7,9 @@
 
 
 @pytest.fixture
-def project():
-    project = testutils.sample_project()
+def project(request):
+    pyproject = request.param if hasattr(request, "param") else None
+    project = testutils.sample_project(pyproject=pyproject)
     yield project
     testutils.remove_project(project)
 
@@ -39,6 +40,7 @@ def project2():
 /pkg1/mod2.py       -- mod2
 """
 
+
 @pytest.fixture
 def mod1(project) -> resources.File:
     return testutils.create_module(project, "mod1")
diff --git a/ropetest/contrib/autoimport/deptest.py b/ropetest/contrib/autoimport/deptest.py
index f392c9493..146496176 100644
--- a/ropetest/contrib/autoimport/deptest.py
+++ b/ropetest/contrib/autoimport/deptest.py
@@ -1,21 +1,10 @@
-from pathlib import Path
 from typing import Iterable
 
 import pytest
 
-from rope.base.project import Project
 from rope.contrib.autoimport.sqlite import AutoImport
 
 
-@pytest.fixture
-def project(request, tmp_path: Path) -> Iterable[Project]:
-    doc = request.param
-    if doc is not None:
-        file = tmp_path / "pyproject.toml"
-        file.write_text(doc, encoding="utf-8")
-    project = Project(tmp_path)
-    yield project
-    project.close()
 
 
 @pytest.fixture
diff --git a/ropetest/testutils.py b/ropetest/testutils.py
index 11f58ccfe..80af3f769 100644
--- a/ropetest/testutils.py
+++ b/ropetest/testutils.py
@@ -5,7 +5,7 @@
 import tempfile
 import unittest
 from pathlib import Path
-
+from typing import Optional
 import rope.base.project
 from rope.contrib import generate
 
@@ -14,10 +14,14 @@
 RUN_TMP_DIR = tempfile.mkdtemp(prefix="ropetest-run-")
 
 
-def sample_project(foldername=None, **kwds):
+def sample_project(foldername=None, pyproject: Optional[str] = None, **kwds):
     root = Path(tempfile.mkdtemp(prefix="project-", dir=RUN_TMP_DIR))
     root /= foldername if foldername else "sample_project"
     logging.debug("Using %s as root of the project.", root)
+    root.mkdir(exist_ok=True)
+    if pyproject is not None:
+        file = root / "pyproject.toml"
+        file.write_text(pyproject, encoding="utf-8")
     # Using these prefs for faster tests
     prefs = {
         "save_objectdb": False,

From ef1c0a8b59b6bfea3e63e6c71ea40f4505a38fca Mon Sep 17 00:00:00 2001
From: bagel897 <ellenagarwal897@gmail.com>
Date: Mon, 22 Jan 2024 09:21:45 -0600
Subject: [PATCH 08/11] reformat

---
 ropetest/contrib/autoimport/deptest.py | 2 --
 ropetest/contrib/autoimporttest.py     | 5 +++--
 ropetest/testutils.py                  | 1 +
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/ropetest/contrib/autoimport/deptest.py b/ropetest/contrib/autoimport/deptest.py
index 146496176..7021e3075 100644
--- a/ropetest/contrib/autoimport/deptest.py
+++ b/ropetest/contrib/autoimport/deptest.py
@@ -5,8 +5,6 @@
 from rope.contrib.autoimport.sqlite import AutoImport
 
 
-
-
 @pytest.fixture
 def autoimport(project) -> Iterable[AutoImport]:
     autoimport = AutoImport(project, memory=True)
diff --git a/ropetest/contrib/autoimporttest.py b/ropetest/contrib/autoimporttest.py
index fb21bbd2b..1f2dfed49 100644
--- a/ropetest/contrib/autoimporttest.py
+++ b/ropetest/contrib/autoimporttest.py
@@ -146,9 +146,10 @@ def test_skipping_directories_not_accessible_because_of_permission_error(self):
         # The single thread test takes much longer than the multithread test but is easier to debug
         single_thread = False
         self.importer.generate_modules_cache(single_thread=single_thread)
-        
+
         # Create a temporary directory and set permissions to 000
-        import tempfile, sys
+        import sys
+        import tempfile
         with tempfile.TemporaryDirectory() as dir:
             import os
             os.chmod(dir, 0o000)
diff --git a/ropetest/testutils.py b/ropetest/testutils.py
index 80af3f769..46087ee56 100644
--- a/ropetest/testutils.py
+++ b/ropetest/testutils.py
@@ -6,6 +6,7 @@
 import unittest
 from pathlib import Path
 from typing import Optional
+
 import rope.base.project
 from rope.contrib import generate
 

From f2fd9e6313b13c6c9b1cffaeccb3541e4b6d7cc1 Mon Sep 17 00:00:00 2001
From: bagel897 <ellenagarwal897@gmail.com>
Date: Wed, 31 Jan 2024 22:16:52 -0600
Subject: [PATCH 09/11] update prefs

---
 docs/configuration.rst            |   7 +-
 rope/base/prefs.py                | 102 ++++++++++++++++++++----------
 rope/contrib/autoimport/sqlite.py |  22 +++----
 3 files changed, 81 insertions(+), 50 deletions(-)

diff --git a/docs/configuration.rst b/docs/configuration.rst
index 6d36a980a..f98a489c2 100644
--- a/docs/configuration.rst
+++ b/docs/configuration.rst
@@ -14,12 +14,11 @@ Will be used if [tool.rope] is configured.
 
     [tool.rope]
     split_imports = true
-    [tool.rope.autoimport]
-    underlined = false
     autoimport.aliases = [
         ['dt', 'datetime'],
         ['mp', 'multiprocessing'],
     ]
+    autoimport.underlined = false
 
 config.py
 ---------
@@ -54,9 +53,9 @@ Additionally, you can run an executable function at startup of rope.
 pytool.toml
 -----------
 If neither a config.py or a pyproject.toml is present, rope will use a pytool.toml.
-It follows the exact same syntax as ``pyproject.toml``.
+It follows the exact same syntax of the pyproject.toml.
 
-- Mac OS X: ``~/Library/Application Support/pytool.toml``.
+- Mac OS X: ``~/Library/Application Support/pytool.toml.``
 - Unix: ``~/.config/pytool.toml``` or in $XDG_CONFIG_HOME, if defined
 - Windows: ``C:\Users\<username>\AppData\Local\pytool.toml``
 
diff --git a/rope/base/prefs.py b/rope/base/prefs.py
index 8f7aa3c19..2d04fc5bd 100644
--- a/rope/base/prefs.py
+++ b/rope/base/prefs.py
@@ -15,11 +15,12 @@
 @dataclass
 class AutoimportPrefs:
     underlined: bool = field(
-        default=False, description="Cache underlined (private) modules")
-    memory: bool = field(default=None, description="Cache in memory instead of disk")
-    parallel: bool = field(default=True, description="Use multiple processes to parse")
+        default=False, description="Cache underlined (private) modules"
+    )
+    # memory: bool = field(default=None, description="Cache in memory instead of disk")
+    # parallel: bool = field(default=True, description="Use multiple processes to parse")
     aliases: List[Tuple[str, str]] = field(
-        default_factory=lambda : [
+        default_factory=lambda: [
             ("np", "numpy"),
             ("pd", "pandas"),
             ("plt", "matplotlib.pyplot"),
@@ -28,10 +29,12 @@ class AutoimportPrefs:
             ("sk", "sklearn"),
             ("sm", "statsmodels"),
         ],
-        description=dedent("""
+        description=dedent(
+            """
             Aliases for module names.  For example, `[('np', 'numpy')]` makes rope recommend
             ``import numpy as np``.
-        """),
+        """
+        ),
     )
 
 
@@ -54,7 +57,8 @@ class Prefs:
             ".mypy_cache",
             ".pytest_cache",
         ],
-        description=dedent("""
+        description=dedent(
+            """
             Specify which files and folders to ignore in the project.
             Changes to ignored resources are not added to the history and
             VCSs.  Also they are not returned in `Project.get_files()`.
@@ -64,19 +68,23 @@ class Prefs:
             '.svn': matches 'pkg/.svn' and all of its children
             'build/*.o': matches 'build/lib.o' but not 'build/sub/lib.o'
             'build//*.o': matches 'build/lib.o' and 'build/sub/lib.o'
-        """),
+        """
+        ),
     )
     python_files: List[str] = field(
         default_factory=lambda: ["*.py"],
-        description=dedent("""
+        description=dedent(
+            """
             Specifies which files should be considered python files.  It is
             useful when you have scripts inside your project.  Only files
             ending with ``.py`` are considered to be python files by
             default.
-        """),
+        """
+        ),
     )
     source_folders: List[str] = field(
-        description=dedent("""
+        description=dedent(
+            """
             Custom source folders:  By default rope searches the project
             for finding source folders (folders that should be searched
             for finding modules).  You can add paths to that list.  Note
@@ -85,7 +93,8 @@ class Prefs:
             The folders should be relative to project root and use '/' for
             separating folders regardless of the platform rope is running on.
             'src/my_source_folder' for instance.
-        """),
+        """
+        ),
         default_factory=lambda: [],
     )
     python_path: List[str] = field(
@@ -107,10 +116,12 @@ class Prefs:
     )
     perform_doa: bool = field(
         default=True,
-        description=dedent("""
+        description=dedent(
+            """
             If `False` when running modules or unit tests 'dynamic object analysis' is turned off.
             This makes them much faster.
-        """),
+        """
+        ),
     )
     validate_objectdb: bool = field(
         default=False,
@@ -128,11 +139,13 @@ class Prefs:
 
     indent_size: int = field(
         default=4,
-        description=dedent("""
+        description=dedent(
+            """
             Set the number spaces used for indenting.  According to
             :PEP:`8`, it is best to use 4 spaces.  Since most of rope's
             unit-tests use 4 spaces it is more reliable, too.
-        """),
+        """
+        ),
     )
 
     extension_modules: List[str] = field(
@@ -148,55 +161,68 @@ class Prefs:
     )
     ignore_syntax_errors: bool = field(
         default=False,
-        description=dedent("""
+        description=dedent(
+            """
             If `True` modules with syntax errors are considered to be empty.
             The default value is `False`; When `False` syntax errors raise
             `rope.base.exceptions.ModuleSyntaxError` exception.
-        """),
+        """
+        ),
     )
 
     ignore_bad_imports: bool = field(
         default=False,
-        description=dedent("""
+        description=dedent(
+            """
             If `True`, rope ignores unresolvable imports.  Otherwise, they
             appear in the importing namespace.
-        """),
+        """
+        ),
     )
     prefer_module_from_imports: bool = field(
         default=False,
-        description=dedent("""
+        description=dedent(
+            """
             If `True`, rope will insert new module imports as `from <package> import <module>`by default.
-        """),
+        """
+        ),
     )
 
     split_imports: bool = field(
         default=False,
-        description=dedent("""
+        description=dedent(
+            """
             If `True`, rope will transform a comma list of imports into
             multiple separate import statements when organizing
             imports.
-        """),
+        """
+        ),
     )
 
     pull_imports_to_top: bool = field(
         default=True,
-        description=dedent("""
+        description=dedent(
+            """
             If `True`, rope will remove all top-level import statements and
             reinsert them at the top of the module when making changes.
-        """),
+        """
+        ),
     )
 
     sort_imports_alphabetically: bool = field(
         default=False,
-        description=dedent("""
+        description=dedent(
+            """
             If `True`, rope will sort imports alphabetically by module name instead
             of alphabetically by import statement, with from imports after normal
             imports.
-        """),
+        """
+        ),
     )
     type_hinting_factory: str = field(
         "rope.base.oi.type_hinting.factory.default_type_hinting_factory",
-        description=dedent("""
+        description=dedent(
+            """
             Location of implementation of
             rope.base.oi.type_hinting.interfaces.ITypeHintingFactory In general
             case, you don't have to change this value, unless you're an rope expert.
@@ -204,14 +230,17 @@ class Prefs:
             listed in module rope.base.oi.type_hinting.providers.interfaces
             For example, you can add you own providers for Django Models, or disable
             the search type-hinting in a class hierarchy, etc.
-        """),
+        """
+        ),
     )
     project_opened: Optional[Callable] = field(
         None,
-        description=dedent("""
+        description=dedent(
+            """
             This function is called after opening the project.
             Can only be set in config.py.
-        """),
+        """
+        ),
     )
     py_version: Optional[Tuple[int, int]] = field(
         default=None,
@@ -223,13 +252,16 @@ class Prefs:
     )
     callbacks: Dict[str, Callable[[Any], None]] = field(
         default_factory=lambda: {},
-        description=dedent("""
+        description=dedent(
+            """
             Callbacks run when configuration values are changed.
             Can only be set in config.py.
-        """),
+        """
+        ),
     )
     autoimport: AutoimportPrefs = field(
-        default_factory=AutoimportPrefs, description="Preferences for Autoimport")
+        default_factory=AutoimportPrefs, description="Preferences for Autoimport"
+    )
 
     def set(self, key: str, value: Any):
         """Set the value of `key` preference to `value`."""
diff --git a/rope/contrib/autoimport/sqlite.py b/rope/contrib/autoimport/sqlite.py
index ac8f09423..f18878f35 100644
--- a/rope/contrib/autoimport/sqlite.py
+++ b/rope/contrib/autoimport/sqlite.py
@@ -103,15 +103,17 @@ class AutoImport:
     """
 
     connection: sqlite3.Connection
+    memory: bool
     project: Project
     project_package: Package
     prefs: AutoimportPrefs
+    underlined: bool
 
     def __init__(
         self,
         project: Project,
         observe: bool = True,
-        underlined: Optional[bool] = None,
+        underlined: bool = False,
         memory: bool = _deprecated_default,
     ):
         """Construct an AutoImport object.
@@ -138,24 +140,22 @@ def __init__(
         project_package = get_package_tuple(project.root.pathlib, project)
         assert project_package is not None
         assert project_package.path is not None
-        if underlined is not None:
-            self.prefs.underlined = underlined
         self.project_package = project_package
+        self.underlined = underlined
+        self.memory = memory
         if memory is _deprecated_default:
-            self.prefs.memory = True
+            self.memory = True
             warnings.warn(
                 "The default value for `AutoImport(memory)` argument will "
                 "change to use an on-disk database by default in the future. "
                 "If you want to use an in-memory database, you need to pass "
-                "`AutoImport(memory=True)` explicitly or set it in the config file.",
+                "`AutoImport(memory=True)` explicitly.",
                 DeprecationWarning,
             )
-        else:
-            self.prefs.memory = memory
         self.thread_local = local()
         self.connection = self.create_database_connection(
             project=project,
-            memory=self.prefs.memory,
+            memory=memory,
         )
         self._setup_db()
         if observe:
@@ -211,7 +211,7 @@ def connection(self):
         if not hasattr(self.thread_local, "connection"):
             self.thread_local.connection = self.create_database_connection(
                 project=self.project,
-                memory=self.prefs.memory,
+                memory=self.memory,
             )
         return self.thread_local.connection
 
@@ -440,11 +440,11 @@ def generate_modules_cache(
                 packages, underlined, existing, self.project.prefs.dependencies
             )
         )
-        if len(packages) == 0:
+        if not packages:
             return
         self._add_packages(packages)
         job_set = task_handle.create_jobset("Generating autoimport cache", 0)
-        if single_thread or not self.prefs.parallel:
+        if single_thread:
             for package in packages:
                 for module in get_files(package, underlined):
                     job_set.started_job(module.modname)

From 97cfe933760118d7e52f94f87937adcdb8db2ec5 Mon Sep 17 00:00:00 2001
From: bagel897 <ellenagarwal897@gmail.com>
Date: Wed, 31 Jan 2024 22:23:45 -0600
Subject: [PATCH 10/11] restore files from master

---
 docs/configuration.rst            |  6 +-
 rope/base/prefs.py                | 97 +++++++++++--------------------
 rope/contrib/autoimport/sqlite.py |  9 +--
 3 files changed, 41 insertions(+), 71 deletions(-)

diff --git a/docs/configuration.rst b/docs/configuration.rst
index f98a489c2..b77359765 100644
--- a/docs/configuration.rst
+++ b/docs/configuration.rst
@@ -53,15 +53,15 @@ Additionally, you can run an executable function at startup of rope.
 pytool.toml
 -----------
 If neither a config.py or a pyproject.toml is present, rope will use a pytool.toml.
-It follows the exact same syntax of the pyproject.toml.
+It follows the exact same syntax as ``pyproject.toml``.
 
-- Mac OS X: ``~/Library/Application Support/pytool.toml.``
+- Mac OS X: ``~/Library/Application Support/pytool.toml``.
 - Unix: ``~/.config/pytool.toml``` or in $XDG_CONFIG_HOME, if defined
 - Windows: ``C:\Users\<username>\AppData\Local\pytool.toml``
 
 
 Options
-=======
+-------
 .. autopytoolconfigtable:: rope.base.prefs.Prefs
 
 Autoimport Options
diff --git a/rope/base/prefs.py b/rope/base/prefs.py
index 2d04fc5bd..491746577 100644
--- a/rope/base/prefs.py
+++ b/rope/base/prefs.py
@@ -15,10 +15,10 @@
 @dataclass
 class AutoimportPrefs:
     underlined: bool = field(
-        default=False, description="Cache underlined (private) modules"
-    )
+        default=False, description="Cache underlined (private) modules")
     # memory: bool = field(default=None, description="Cache in memory instead of disk")
     # parallel: bool = field(default=True, description="Use multiple processes to parse")
+
     aliases: List[Tuple[str, str]] = field(
         default_factory=lambda: [
             ("np", "numpy"),
@@ -29,12 +29,10 @@ class AutoimportPrefs:
             ("sk", "sklearn"),
             ("sm", "statsmodels"),
         ],
-        description=dedent(
-            """
+        description=dedent("""
             Aliases for module names.  For example, `[('np', 'numpy')]` makes rope recommend
             ``import numpy as np``.
-        """
-        ),
+        """),
     )
 
 
@@ -57,8 +55,7 @@ class Prefs:
             ".mypy_cache",
             ".pytest_cache",
         ],
-        description=dedent(
-            """
+        description=dedent("""
             Specify which files and folders to ignore in the project.
             Changes to ignored resources are not added to the history and
             VCSs.  Also they are not returned in `Project.get_files()`.
@@ -68,23 +65,19 @@ class Prefs:
             '.svn': matches 'pkg/.svn' and all of its children
             'build/*.o': matches 'build/lib.o' but not 'build/sub/lib.o'
             'build//*.o': matches 'build/lib.o' and 'build/sub/lib.o'
-        """
-        ),
+        """),
     )
     python_files: List[str] = field(
         default_factory=lambda: ["*.py"],
-        description=dedent(
-            """
+        description=dedent("""
             Specifies which files should be considered python files.  It is
             useful when you have scripts inside your project.  Only files
             ending with ``.py`` are considered to be python files by
             default.
-        """
-        ),
+        """),
     )
     source_folders: List[str] = field(
-        description=dedent(
-            """
+        description=dedent("""
             Custom source folders:  By default rope searches the project
             for finding source folders (folders that should be searched
             for finding modules).  You can add paths to that list.  Note
@@ -93,8 +86,7 @@ class Prefs:
             The folders should be relative to project root and use '/' for
             separating folders regardless of the platform rope is running on.
             'src/my_source_folder' for instance.
-        """
-        ),
+        """),
         default_factory=lambda: [],
     )
     python_path: List[str] = field(
@@ -116,12 +108,10 @@ class Prefs:
     )
     perform_doa: bool = field(
         default=True,
-        description=dedent(
-            """
+        description=dedent("""
             If `False` when running modules or unit tests 'dynamic object analysis' is turned off.
             This makes them much faster.
-        """
-        ),
+        """),
     )
     validate_objectdb: bool = field(
         default=False,
@@ -139,13 +129,11 @@ class Prefs:
 
     indent_size: int = field(
         default=4,
-        description=dedent(
-            """
+        description=dedent("""
             Set the number spaces used for indenting.  According to
             :PEP:`8`, it is best to use 4 spaces.  Since most of rope's
             unit-tests use 4 spaces it is more reliable, too.
-        """
-        ),
+        """),
     )
 
     extension_modules: List[str] = field(
@@ -161,68 +149,55 @@ class Prefs:
     )
     ignore_syntax_errors: bool = field(
         default=False,
-        description=dedent(
-            """
+        description=dedent("""
             If `True` modules with syntax errors are considered to be empty.
             The default value is `False`; When `False` syntax errors raise
             `rope.base.exceptions.ModuleSyntaxError` exception.
-        """
-        ),
+        """),
     )
 
     ignore_bad_imports: bool = field(
         default=False,
-        description=dedent(
-            """
+        description=dedent("""
             If `True`, rope ignores unresolvable imports.  Otherwise, they
             appear in the importing namespace.
-        """
-        ),
+        """),
     )
     prefer_module_from_imports: bool = field(
         default=False,
-        description=dedent(
-            """
+        description=dedent("""
             If `True`, rope will insert new module imports as `from <package> import <module>`by default.
-        """
-        ),
+        """),
     )
 
     split_imports: bool = field(
         default=False,
-        description=dedent(
-            """
+        description=dedent("""
             If `True`, rope will transform a comma list of imports into
             multiple separate import statements when organizing
             imports.
-        """
-        ),
+        """),
     )
 
     pull_imports_to_top: bool = field(
         default=True,
-        description=dedent(
-            """
+        description=dedent("""
             If `True`, rope will remove all top-level import statements and
             reinsert them at the top of the module when making changes.
-        """
-        ),
+        """),
     )
 
     sort_imports_alphabetically: bool = field(
         default=False,
-        description=dedent(
-            """
+        description=dedent("""
             If `True`, rope will sort imports alphabetically by module name instead
             of alphabetically by import statement, with from imports after normal
             imports.
-        """
-        ),
+        """),
     )
     type_hinting_factory: str = field(
         "rope.base.oi.type_hinting.factory.default_type_hinting_factory",
-        description=dedent(
-            """
+        description=dedent("""
             Location of implementation of
             rope.base.oi.type_hinting.interfaces.ITypeHintingFactory In general
             case, you don't have to change this value, unless you're an rope expert.
@@ -230,17 +205,14 @@ class Prefs:
             listed in module rope.base.oi.type_hinting.providers.interfaces
             For example, you can add you own providers for Django Models, or disable
             the search type-hinting in a class hierarchy, etc.
-        """
-        ),
+        """),
     )
     project_opened: Optional[Callable] = field(
         None,
-        description=dedent(
-            """
+        description=dedent("""
             This function is called after opening the project.
             Can only be set in config.py.
-        """
-        ),
+        """),
     )
     py_version: Optional[Tuple[int, int]] = field(
         default=None,
@@ -252,16 +224,13 @@ class Prefs:
     )
     callbacks: Dict[str, Callable[[Any], None]] = field(
         default_factory=lambda: {},
-        description=dedent(
-            """
+        description=dedent("""
             Callbacks run when configuration values are changed.
             Can only be set in config.py.
-        """
-        ),
+        """),
     )
     autoimport: AutoimportPrefs = field(
-        default_factory=AutoimportPrefs, description="Preferences for Autoimport"
-    )
+        default_factory=AutoimportPrefs, description="Preferences for Autoimport")
 
     def set(self, key: str, value: Any):
         """Set the value of `key` preference to `value`."""
diff --git a/rope/contrib/autoimport/sqlite.py b/rope/contrib/autoimport/sqlite.py
index f18878f35..bdec6fb5f 100644
--- a/rope/contrib/autoimport/sqlite.py
+++ b/rope/contrib/autoimport/sqlite.py
@@ -2,30 +2,31 @@
 
 import contextlib
 import json
-from hashlib import sha256
-import secrets
 import re
+import secrets
 import sqlite3
 import sys
 import warnings
 from collections import OrderedDict
 from concurrent.futures import Future, ProcessPoolExecutor, as_completed
+from copy import deepcopy
 from datetime import datetime
+from hashlib import sha256
 from itertools import chain
 from pathlib import Path
 from threading import local
 from typing import Generator, Iterable, Iterator, List, Optional, Set, Tuple
 
 from packaging.requirements import Requirement
-from copy import deepcopy
+
 from rope.base import exceptions, libutils, resourceobserver, taskhandle, versioning
 from rope.base.prefs import AutoimportPrefs
 from rope.base.project import Project
 from rope.base.resources import Resource
 from rope.contrib.autoimport import models
 from rope.contrib.autoimport.defs import (
-    ModuleFile,
     Alias,
+    ModuleFile,
     Name,
     NameType,
     Package,

From 5b78bb9f2c42186c88bcae11651d601ec794d4d3 Mon Sep 17 00:00:00 2001
From: bagel897 <ellenagarwal897@gmail.com>
Date: Wed, 31 Jan 2024 22:26:09 -0600
Subject: [PATCH 11/11] cleanup

---
 rope/contrib/autoimport/sqlite.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/rope/contrib/autoimport/sqlite.py b/rope/contrib/autoimport/sqlite.py
index bdec6fb5f..21139b670 100644
--- a/rope/contrib/autoimport/sqlite.py
+++ b/rope/contrib/autoimport/sqlite.py
@@ -2,16 +2,15 @@
 
 import contextlib
 import json
-import re
+from hashlib import sha256
 import secrets
+import re
 import sqlite3
 import sys
 import warnings
 from collections import OrderedDict
 from concurrent.futures import Future, ProcessPoolExecutor, as_completed
-from copy import deepcopy
 from datetime import datetime
-from hashlib import sha256
 from itertools import chain
 from pathlib import Path
 from threading import local
@@ -671,7 +670,7 @@ def _resource_to_module(
         self, resource: Resource, underlined: bool = False
     ) -> ModuleFile:
         assert self.project_package.path
-        underlined = underlined if underlined else self.prefs.underlined
+        underlined = underlined if underlined else self.underlined
         resource_path: Path = resource.pathlib
         # The project doesn't need its name added to the path,
         # since the standard python file layout accounts for that