diff --git a/poetry.lock b/poetry.lock
index 53ef8b09d..516b0bbf5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1047,33 +1047,13 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "debugpy"
-version = "1.8.2"
+version = "1.8.3"
 description = "An implementation of the Debug Adapter Protocol for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "debugpy-1.8.3.zip", hash = "sha256:0f5a6326d9fc375b864ed368d06cddf2dabe5135511e71cde3758be699847d36"},
 ]
 
 [[package]]
@@ -1162,26 +1142,6 @@ files = [
     {file = "distro-1.9.0.tar.gz", hash = "sha256:2fa77c6fd8940f116ee1d6b94a2f90b13b5ea8d019b98bc8bafdcabcdd9bdbed"},
 ]
 
-[[package]]
-name = "dnspython"
-version = "2.6.1"
-description = "DNS toolkit"
-optional = true
-python-versions = ">=3.8"
-files = [
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-
-[package.extras]
-dev = ["black (>=23.1.0)", "coverage (>=7.0)", "flake8 (>=7)", "mypy (>=1.8)", "pylint (>=3)", "pytest (>=7.4)", "pytest-cov (>=4.1.0)", "sphinx (>=7.2.0)", "twine (>=4.0.0)", "wheel (>=0.42.0)"]
-dnssec = ["cryptography (>=41)"]
-doh = ["h2 (>=4.1.0)", "httpcore (>=1.0.0)", "httpx (>=0.26.0)"]
-doq = ["aioquic (>=0.9.25)"]
-idna = ["idna (>=3.6)"]
-trio = ["trio (>=0.23)"]
-wmi = ["wmi (>=1.5.1)"]
-
 [[package]]
 name = "docopt"
 version = "0.6.2"
@@ -1269,21 +1229,6 @@ files = [
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 ]
 
-[[package]]
-name = "email-validator"
-version = "2.2.0"
-description = "A robust email address syntax and deliverability validation library."
-optional = true
-python-versions = ">=3.8"
-files = [
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-
-[package.dependencies]
-dnspython = ">=2.0.0"
-idna = ">=2.0.0"
-
 [[package]]
 name = "entrypoints"
 version = "0.4"
@@ -1406,45 +1351,23 @@ cli = ["requests"]
 
 [[package]]
 name = "fastapi"
-version = "0.111.1"
+version = "0.112.0"
 description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
 optional = true
 python-versions = ">=3.8"
 files = [
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+    {file = "fastapi-0.112.0-py3-none-any.whl", hash = "sha256:3487ded9778006a45834b8c816ec4a48d522e2631ca9e75ec5a774f1b052f821"},
+    {file = "fastapi-0.112.0.tar.gz", hash = "sha256:d262bc56b7d101d1f4e8fc0ad2ac75bb9935fec504d2b7117686cec50710cf05"},
 ]
 
 [package.dependencies]
-email_validator = ">=2.0.0"
-fastapi-cli = ">=0.0.2"
-httpx = ">=0.23.0"
-jinja2 = ">=2.11.2"
 pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0 || >2.0.0,<2.0.1 || >2.0.1,<2.1.0 || >2.1.0,<3.0.0"
-python-multipart = ">=0.0.7"
 starlette = ">=0.37.2,<0.38.0"
 typing-extensions = ">=4.8.0"
-uvicorn = {version = ">=0.12.0", extras = ["standard"]}
-
-[package.extras]
-all = ["email_validator (>=2.0.0)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)", "jinja2 (>=2.11.2)", "orjson (>=3.2.1)", "pydantic-extra-types (>=2.0.0)", "pydantic-settings (>=2.0.0)", "python-multipart (>=0.0.7)", "pyyaml (>=5.3.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0)", "uvicorn[standard] (>=0.12.0)"]
-
-[[package]]
-name = "fastapi-cli"
-version = "0.0.4"
-description = "Run and manage FastAPI apps from the command line with FastAPI CLI. 🚀"
-optional = true
-python-versions = ">=3.8"
-files = [
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-]
-
-[package.dependencies]
-typer = ">=0.12.3"
 
 [package.extras]
-standard = ["fastapi", "uvicorn[standard] (>=0.15.0)"]
+all = ["email_validator (>=2.0.0)", "fastapi-cli[standard] (>=0.0.5)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)", "jinja2 (>=2.11.2)", "orjson (>=3.2.1)", "pydantic-extra-types (>=2.0.0)", "pydantic-settings (>=2.0.0)", "python-multipart (>=0.0.7)", "pyyaml (>=5.3.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0)", "uvicorn[standard] (>=0.12.0)"]
+standard = ["email_validator (>=2.0.0)", "fastapi-cli[standard] (>=0.0.5)", "httpx (>=0.23.0)", "jinja2 (>=2.11.2)", "python-multipart (>=0.0.7)", "uvicorn[standard] (>=0.12.0)"]
 
 [[package]]
 name = "fastjsonschema"
@@ -2044,54 +1967,6 @@ http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
 trio = ["trio (>=0.22.0,<0.26.0)"]
 
-[[package]]
-name = "httptools"
-version = "0.6.1"
-description = "A collection of framework independent HTTP protocol utils."
-optional = true
-python-versions = ">=3.8.0"
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-]
-
-[package.extras]
-test = ["Cython (>=0.29.24,<0.30.0)"]
-
 [[package]]
 name = "httpx"
 version = "0.27.0"
@@ -3279,13 +3154,13 @@ requests = "*"
 
 [[package]]
 name = "litellm"
-version = "1.42.8"
+version = "1.42.11"
 description = "Library to easily interface with LLM API providers"
 optional = false
 python-versions = "!=2.7.*,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,!=3.7.*,>=3.8"
 files = [
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 [package.dependencies]
@@ -4333,13 +4208,13 @@ tests = ["coverage", "pytest", "unittest-templates"]
 
 [[package]]
 name = "openai"
-version = "1.37.1"
+version = "1.38.0"
 description = "The official Python library for the openai API"
 optional = false
 python-versions = ">=3.7.1"
 files = [
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 ]
 
 [package.dependencies]
@@ -5285,20 +5160,6 @@ files = [
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-version = "0.0.9"
-description = "A streaming multipart parser for Python"
-optional = true
-python-versions = ">=3.8"
-files = [
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-
 [[package]]
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 version = "0.6.23"
@@ -5886,24 +5747,6 @@ files = [
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-
-[package.extras]
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 [[package]]
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 [[package]]
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 version = "2.9.0.20240316"
@@ -7373,74 +7188,23 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
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+version = "0.30.5"
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 [[package]]
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 version = "0.33.0"
@@ -7530,93 +7294,6 @@ files = [
 [package.extras]
 watchmedo = ["PyYAML (>=3.10)"]
 
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 [[package]]
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 version = "0.2.13"
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 optional = ["python-socks", "wsaccel"]
 test = ["websockets"]
 
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-]
-
 [[package]]
 name = "werkzeug"
 version = "3.0.3"
diff --git a/pyproject.toml b/pyproject.toml
index 2364f58c8..48e09b2f6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ontogpt"
-version = "1.0.0"
+version = "1.0.1"
 description = "OntoGPT"
 authors = ["Chris Mungall <cjmungall@lbl.gov>", "J. Harry Caufield <jhc@lbl.gov>"]
 license = "BSD-3"
diff --git a/src/ontogpt/clients/llm_client.py b/src/ontogpt/clients/llm_client.py
index dec2838aa..ae5af59f6 100644
--- a/src/ontogpt/clients/llm_client.py
+++ b/src/ontogpt/clients/llm_client.py
@@ -37,7 +37,7 @@ def __post_init__(self):
         # Get appropriate API key for the model source
         # and other details if needed
         if self.model.startswith("ollama"):
-            self.api_key = "" # Don't need an API key
+            self.api_key = ""  # Don't need an API key
         if not self.api_key and not self.custom_llm_provider:
             self.api_key = get_apikey_value("openai")
         elif self.custom_llm_provider == "anthropic":
diff --git a/src/ontogpt/conf/synonymizer-conf.yaml b/src/ontogpt/conf/synonymizer-conf.yaml
index 6d4428df5..6a950f6d2 100644
--- a/src/ontogpt/conf/synonymizer-conf.yaml
+++ b/src/ontogpt/conf/synonymizer-conf.yaml
@@ -22,4 +22,3 @@ rules:
       match: "(.*) food product"
       match_scope: "FOODON"
       replacement: "\\1"
-
diff --git a/src/ontogpt/engines/generic_engine.py b/src/ontogpt/engines/generic_engine.py
index 9c4d3eb05..123e6d76d 100644
--- a/src/ontogpt/engines/generic_engine.py
+++ b/src/ontogpt/engines/generic_engine.py
@@ -1,4 +1,5 @@
-"""Synonym engine."""
+"""Generic engine."""
+
 import logging
 from copy import deepcopy
 from dataclasses import dataclass
diff --git a/src/ontogpt/engines/pheno_engine.py b/src/ontogpt/engines/pheno_engine.py
index c8ca3407a..389e1d489 100644
--- a/src/ontogpt/engines/pheno_engine.py
+++ b/src/ontogpt/engines/pheno_engine.py
@@ -1,4 +1,4 @@
-"""Reasoner engine."""
+"""Pheno engine."""
 
 import json
 import logging
diff --git a/src/ontogpt/io/json_wrapper.py b/src/ontogpt/io/json_wrapper.py
index c474f8b33..85ba5ada5 100644
--- a/src/ontogpt/io/json_wrapper.py
+++ b/src/ontogpt/io/json_wrapper.py
@@ -25,6 +25,7 @@ def eliminate_empty(obj: Any, preserve=False) -> Any:
     else:
         return obj
 
+
 def dump_minimal_json(obj: Any, minimize=True, file: Optional[TextIO] = None) -> str:
     """Dump a JSON string, but eliminate Nones and empty lists and dicts."""
     if not file: