From 0c51f00596762df885d4c284f73c5ea64b04a309 Mon Sep 17 00:00:00 2001
From: sneakers-the-rat <sneakers-the-rat@protonmail.com>
Date: Tue, 20 Aug 2024 20:26:00 -0700
Subject: [PATCH] aha fix black formatting include, generate core by cloning
 into tmp directory

---
 nwb_linkml/src/nwb_linkml/providers/git.py |  9 ++++---
 pyproject.toml                             |  2 +-
 scripts/generate_core.py                   | 28 +++++++++++++++-------
 3 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/nwb_linkml/src/nwb_linkml/providers/git.py b/nwb_linkml/src/nwb_linkml/providers/git.py
index 8219aaf..77afc59 100644
--- a/nwb_linkml/src/nwb_linkml/providers/git.py
+++ b/nwb_linkml/src/nwb_linkml/providers/git.py
@@ -117,7 +117,11 @@ class GitRepo:
             path (:class:`pathlib.Path`): A directory to clone to -
                 if ``None``, use :attr:`~.Config.git_dir` / :attr:`.NamespaceRepo.name`
         """
-        self._temp_directory = path
+        if path is None:
+            self._base_directory = Config().git_dir
+        else:
+            self._base_directory = Path(path)
+        self._temp_directory = None
         self.namespace = namespace
         self._commit = commit
 
@@ -135,8 +139,7 @@ class GitRepo:
         Temporary directory where this repository will be cloned to
         """
         if self._temp_directory is None:
-            git_dir = Config().git_dir
-            self._temp_directory = git_dir / self.namespace.name
+            self._temp_directory = self._base_directory / self.namespace.name
             if not self._temp_directory.exists():
                 self._temp_directory.mkdir(parents=True)
 
diff --git a/pyproject.toml b/pyproject.toml
index 30d5e43..99b5e1f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -101,5 +101,5 @@ warn_unreachable = true
 target-version = ['py38', 'py39', 'py310', 'py311']
 enable-unstable-feature = ["string_processing"]
 preview = true
-include = "nwb_linkml/.*\\.py$|nwb_schema_language/.*\\.py$"
+include = "nwb_linkml/.*\\.py$|nwb_schema_language/.*\\.py$|nwb_models/.*\\.py$"
 line-length = 100
\ No newline at end of file
diff --git a/scripts/generate_core.py b/scripts/generate_core.py
index 620d9d4..ad593cf 100644
--- a/scripts/generate_core.py
+++ b/scripts/generate_core.py
@@ -50,6 +50,18 @@ def generate_core_pydantic(yaml_path: Path, output_path: Path, dry_run: bool = F
                 pfile.write(gen_pydantic)
 
 
+def make_tmp_dir(clear: bool = False) -> Path:
+    # use a directory underneath this one as the temporary directory rather than
+    # the default hidden one
+    tmp_dir = Path(__file__).parent / "__tmp__"
+    if tmp_dir.exists() and clear:
+        for p in tmp_dir.iterdir():
+            if p.is_dir() and not p.name == "git":
+                shutil.rmtree(tmp_dir)
+    tmp_dir.mkdir(exist_ok=True)
+    return tmp_dir
+
+
 def generate_versions(
     yaml_path: Path,
     pydantic_path: Path,
@@ -64,12 +76,7 @@ def generate_versions(
     # repo.clone(force=True)
     repo.clone()
 
-    # use a directory underneath this one as the temporary directory rather than
-    # the default hidden one
-    tmp_dir = Path(__file__).parent / "__tmp__"
-    if tmp_dir.exists():
-        shutil.rmtree(tmp_dir)
-    tmp_dir.mkdir()
+    tmp_dir = make_tmp_dir()
 
     linkml_provider = LinkMLProvider(path=tmp_dir, verbose=False)
     pydantic_provider = PydanticProvider(path=tmp_dir, verbose=False)
@@ -227,10 +234,15 @@ def parser() -> ArgumentParser:
 
 def main():
     args = parser().parse_args()
+
+    tmp_dir = make_tmp_dir(clear=True)
+    git_dir = tmp_dir / "git"
+    git_dir.mkdir(exist_ok=True)
+
     if args.hdmf:
-        repo = GitRepo(HDMF_COMMON_REPO)
+        repo = GitRepo(HDMF_COMMON_REPO, path=git_dir)
     else:
-        repo = GitRepo(NWB_CORE_REPO)
+        repo = GitRepo(NWB_CORE_REPO, path=git_dir)
 
     if not args.dry_run:
         args.yaml.mkdir(exist_ok=True)