uw-ssec · pre-commit-ci · Aug 31, 2026 · Aug 31, 2026
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -20,14 +20,14 @@ repos:
   #         - tags
   #         - slideshow
   #         - --
-  - repo: https://github.com/psf/black
-    rev: 24.10.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.5.1
     hooks:
       - id: black
       - id: black-jupyter
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v5.0.0"
+    rev: "v6.0.0"
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -50,14 +50,14 @@ repos:
       - id: rst-inline-touching-normal
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.8.4"
+    rev: "v0.16.5"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: "v0.23"
+    rev: "0.26"
     hooks:
       - id: validate-pyproject
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
@@ -70,13 +70,13 @@ repos:
         args: [--prose-wrap=always]
 
   - repo: https://github.com/codespell-project/codespell
-    rev: "v2.3.0"
+    rev: "v2.4.3"
     hooks:
       - id: codespell
         args: ["-L", "precessing"]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: "0.30.0"
+    rev: "0.38.0"
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

diff --git a/AI_Postdoc_Workshop/appendix/astrophysics-dataset-creation.ipynb b/AI_Postdoc_Workshop/appendix/astrophysics-dataset-creation.ipynb
@@ -27,8 +27,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from tqdm import tqdm\n",
-    "import pandas as pd"
+    "import pandas as pd\n",
+    "from tqdm import tqdm"
    ]
   },
   {

diff --git a/AI_Postdoc_Workshop/appendix/langchain-document-loaders.ipynb b/AI_Postdoc_Workshop/appendix/langchain-document-loaders.ipynb
@@ -190,6 +190,7 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "\n",
     "from langchain_community.document_loaders import PyMuPDFLoader\n",
     "\n",
     "pdf_folder_path = \"/your/folder/path/\"  # update path to point to the relevant directory\n",

diff --git a/AI_Postdoc_Workshop/appendix/qdrant-vector-database-creation.ipynb b/AI_Postdoc_Workshop/appendix/qdrant-vector-database-creation.ipynb
@@ -16,11 +16,11 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "\n",
     "from getpass import getpass\n",
+    "\n",
+    "import pandas as pd\n",
     "from langchain_huggingface import HuggingFaceEmbeddings\n",
     "from langchain_qdrant import Qdrant\n",
-    "import pandas as pd\n",
     "from qdrant_client import QdrantClient"
    ]
   },
@@ -42,12 +42,12 @@
     "from ssec_tutorials import (\n",
     "    ASTROPH_ARXIV_ABSTRACTS,\n",
     "    ASTROPY_GITHUB,\n",
+    "    QDRANT_COLLECTION_NAME,\n",
+    "    QDRANT_PATH,\n",
     "    download_astroph_arxiv_abstracts,\n",
     "    download_astropy_github_documents,\n",
-    "    fetch_and_process_github_rst_files,\n",
     "    download_qdrant_data,\n",
-    "    QDRANT_COLLECTION_NAME,\n",
-    "    QDRANT_PATH,\n",
+    "    fetch_and_process_github_rst_files,\n",
     ")\n",
     "from ssec_tutorials.scipy_conf import load_docs_from_jsonl"
    ]

diff --git a/AI_Postdoc_Workshop/module1/4-algorithms-prompting-with-olmo.ipynb b/AI_Postdoc_Workshop/module1/4-algorithms-prompting-with-olmo.ipynb
@@ -175,12 +175,10 @@
    "source": [
     "# Test the prompt you want to send to OLMo.\n",
     "question = \"What is the best method for multiplying large numbers?\"\n",
-    "input_content = textwrap.dedent(\n",
-    "    f\"\"\"\\\n",
+    "input_content = textwrap.dedent(f\"\"\"\\\n",
     "    You are an algorithms expert. Please answer the following question on algorithms.\n",
     "    Question: {question}\n",
-    "\"\"\"\n",
-    ")\n",
+    "\"\"\")\n",
     "input_messages = [\n",
     "    {\n",
     "        \"role\": \"user\",\n",
@@ -271,13 +269,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "input_prompt_template = textwrap.dedent(\n",
-    "    \"\"\"\\\n",
+    "input_prompt_template = textwrap.dedent(\"\"\"\\\n",
     "{instruction}\n",
     "\n",
     "Question: {question}\n",
-    "\"\"\"\n",
-    ")"
+    "\"\"\")"
    ]
   },
   {

diff --git a/AI_Postdoc_Workshop/module2/1-retrieval-augmented-text-generation.ipynb b/AI_Postdoc_Workshop/module2/1-retrieval-augmented-text-generation.ipynb
@@ -459,6 +459,7 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "\n",
     "from langchain_community.document_loaders import PyMuPDFLoader\n",
     "\n",
     "pdf_folder_path = \".\"  # update path to point to the relevant directory\n",
@@ -513,10 +514,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import shutil\n",
+    "\n",
     "from langchain_qdrant import Qdrant\n",
     "from qdrant_client import QdrantClient\n",
     "from ssec_tutorials import TUTORIAL_CACHE\n",
-    "import shutil\n",
     "\n",
     "qdrant_collection = \"algorithms_book\"\n",
     "qdrant_path = TUTORIAL_CACHE / \"algorithms_book\"\n",

diff --git a/AI_Postdoc_Workshop/module2/2-olmo-chat-rag.ipynb b/AI_Postdoc_Workshop/module2/2-olmo-chat-rag.ipynb
@@ -58,19 +58,16 @@
    "outputs": [],
    "source": [
     "import textwrap\n",
-    "from uuid import uuid4\n",
     "import warnings\n",
+    "from uuid import uuid4\n",
     "\n",
-    "\n",
-    "from langchain_core.runnables import RunnablePassthrough\n",
-    "from langchain_core.callbacks import CallbackManager, BaseCallbackHandler\n",
-    "from langchain_core.prompts import PromptTemplate\n",
     "from langchain_community.llms import LlamaCpp\n",
-    "from langchain_qdrant import Qdrant\n",
+    "from langchain_core.callbacks import BaseCallbackHandler, CallbackManager\n",
+    "from langchain_core.prompts import PromptTemplate\n",
+    "from langchain_core.runnables import RunnablePassthrough\n",
     "from langchain_huggingface import HuggingFaceEmbeddings\n",
-    "\n",
-    "from ssec_tutorials import TUTORIAL_CACHE\n",
-    "from ssec_tutorials import download_olmo_model"
+    "from langchain_qdrant import Qdrant\n",
+    "from ssec_tutorials import TUTORIAL_CACHE, download_olmo_model"
    ]
   },
   {
@@ -342,15 +339,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "input_prompt_template = textwrap.dedent(\n",
-    "    \"\"\"\\\n",
+    "input_prompt_template = textwrap.dedent(\"\"\"\\\n",
     "You are an algorithms expert. Please answer the question on algorithms based on the following context:\n",
     "\n",
     "{context}\n",
     "\n",
     "Question: {question}\n",
-    "\"\"\"\n",
-    ")"
+    "\"\"\")"
    ]
   },
   {

diff --git a/Archive/SciPy2024/appendix/astrophysics-dataset-creation.ipynb b/Archive/SciPy2024/appendix/astrophysics-dataset-creation.ipynb
@@ -27,8 +27,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from tqdm import tqdm\n",
-    "import pandas as pd"
+    "import pandas as pd\n",
+    "from tqdm import tqdm"
    ]
   },
   {

diff --git a/Archive/SciPy2024/appendix/langchain-document-loaders.ipynb b/Archive/SciPy2024/appendix/langchain-document-loaders.ipynb
@@ -190,6 +190,7 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "\n",
     "from langchain_community.document_loaders import PyMuPDFLoader\n",
     "\n",
     "pdf_folder_path = \"/your/folder/path/\"  # update path to point to the relevant directory\n",

diff --git a/Archive/SciPy2024/appendix/qdrant-vector-database-creation.ipynb b/Archive/SciPy2024/appendix/qdrant-vector-database-creation.ipynb
@@ -16,11 +16,11 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "\n",
     "from getpass import getpass\n",
+    "\n",
+    "import pandas as pd\n",
     "from langchain_huggingface import HuggingFaceEmbeddings\n",
     "from langchain_qdrant import Qdrant\n",
-    "import pandas as pd\n",
     "from qdrant_client import QdrantClient"
    ]
   },
@@ -42,12 +42,12 @@
     "from ssec_tutorials import (\n",
     "    ASTROPH_ARXIV_ABSTRACTS,\n",
     "    ASTROPY_GITHUB,\n",
+    "    QDRANT_COLLECTION_NAME,\n",
+    "    QDRANT_PATH,\n",
     "    download_astroph_arxiv_abstracts,\n",
     "    download_astropy_github_documents,\n",
-    "    fetch_and_process_github_rst_files,\n",
     "    download_qdrant_data,\n",
-    "    QDRANT_COLLECTION_NAME,\n",
-    "    QDRANT_PATH,\n",
+    "    fetch_and_process_github_rst_files,\n",
     ")\n",
     "from ssec_tutorials.scipy_conf import load_docs_from_jsonl"
    ]

diff --git a/Archive/SciPy2024/module1/1-introduction-to-language-models.ipynb b/Archive/SciPy2024/module1/1-introduction-to-language-models.ipynb
@@ -101,10 +101,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from collections import defaultdict\n",
-    "import nltk\n",
     "import random\n",
     "import re\n",
+    "from collections import defaultdict\n",
+    "\n",
+    "import nltk\n",
     "import numpy as np\n",
     "import pandas as pd"
    ]
@@ -332,7 +333,7 @@
    "outputs": [],
    "source": [
     "# Removing extra spaces\n",
-    "abstracts = re.sub(\"\\s+\", \" \", abstracts)"
+    "abstracts = re.sub(r\"\\s+\", \" \", abstracts)"
    ]
   },
   {

diff --git a/Archive/SciPy2024/module2/2-astrophysics-prompting-with-olmo.ipynb b/Archive/SciPy2024/module2/2-astrophysics-prompting-with-olmo.ipynb
@@ -204,12 +204,10 @@
    "source": [
     "# Test the prompt you want to send to OLMo.\n",
     "question = \"What is dark matter?\"\n",
-    "input_content = textwrap.dedent(\n",
-    "    f\"\"\"\\\n",
+    "input_content = textwrap.dedent(f\"\"\"\\\n",
     "    You are an astrophysics expert. Please answer the following question on astrophysics.\n",
     "    Question: {question}\n",
-    "\"\"\"\n",
-    ")\n",
+    "\"\"\")\n",
     "input_messages = [\n",
     "    {\n",
     "        \"role\": \"user\",\n",
@@ -330,13 +328,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "input_prompt_template = textwrap.dedent(\n",
-    "    \"\"\"\\\n",
+    "input_prompt_template = textwrap.dedent(\"\"\"\\\n",
     "{instruction}\n",
     "\n",
     "Question: {question}\n",
-    "\"\"\"\n",
-    ")"
+    "\"\"\")"
    ]
   },
   {

diff --git a/Archive/SciPy2024/module2/3-retrieval-augmented-text-generation.ipynb b/Archive/SciPy2024/module2/3-retrieval-augmented-text-generation.ipynb
@@ -539,7 +539,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ssec_tutorials import download_qdrant_data, QDRANT_COLLECTION_NAME"
+    "from ssec_tutorials import QDRANT_COLLECTION_NAME, download_qdrant_data"
    ]
   },
   {

diff --git a/Archive/SciPy2024/module3/1-olmo-chat-rag.ipynb b/Archive/SciPy2024/module3/1-olmo-chat-rag.ipynb
@@ -80,19 +80,20 @@
    "outputs": [],
    "source": [
     "import textwrap\n",
-    "from uuid import uuid4\n",
     "import warnings\n",
+    "from uuid import uuid4\n",
     "\n",
-    "\n",
-    "from langchain_core.runnables import RunnablePassthrough\n",
-    "from langchain_core.callbacks import CallbackManager, BaseCallbackHandler\n",
-    "from langchain_core.prompts import PromptTemplate\n",
     "from langchain_community.llms import LlamaCpp\n",
-    "from langchain_qdrant import Qdrant\n",
+    "from langchain_core.callbacks import BaseCallbackHandler, CallbackManager\n",
+    "from langchain_core.prompts import PromptTemplate\n",
+    "from langchain_core.runnables import RunnablePassthrough\n",
     "from langchain_huggingface import HuggingFaceEmbeddings\n",
-    "\n",
-    "from ssec_tutorials import QDRANT_COLLECTION_NAME\n",
-    "from ssec_tutorials import download_olmo_model, download_qdrant_data"
+    "from langchain_qdrant import Qdrant\n",
+    "from ssec_tutorials import (\n",
+    "    QDRANT_COLLECTION_NAME,\n",
+    "    download_olmo_model,\n",
+    "    download_qdrant_data,\n",
+    ")"
    ]
   },
   {
@@ -364,15 +365,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "input_prompt_template = textwrap.dedent(\n",
-    "    \"\"\"\\\n",
+    "input_prompt_template = textwrap.dedent(\"\"\"\\\n",
     "You are an astrophysics expert. Please answer the question on astrophysics based on the following context:\n",
     "\n",
     "{context}\n",
     "\n",
     "Question: {question}\n",
-    "\"\"\"\n",
-    ")"
+    "\"\"\")"
    ]
   },
   {