update pyproject.toml

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "monarch-ingest"
-version = "0.7.2"
+version = "0.8.0"
 description = ""
 authors = [
     "The Monarch Initiative <info@monarchinitiative.org>",
@@ -16,37 +16,37 @@ packages = [
 
 [tool.poetry.dependencies]
 python = ">=3.10,<3.12"
-kghub-downloader = "^0.3.2"
-koza = "^0.3.0"
+# Monarch & Related Dependencies
+biolink-model = { git = "https://github.com/biolink/biolink-model/", branch = "master" } # "^3.5.0"
+bmt = "^1.0.15"
 cat-merge = ">=0.2.0"
 closurizer = "0.4.1"
+kghub-downloader = "^0.3.2"
 kgx = ">=2.1"
+koza = "^0.5.0"
+linkml = "^1.5.7"
+linkml-runtime = "1.6.1"
+linkml-solr = {git = "https://github.com/linkml/linkml-solr.git", branch = "main"} # "^0.1.3"
+linkml-validator = "^0.4.5"
 multi-indexer = "0.0.5"
+# Other Dependencies
 botocore = "^1.31"
-biolink-model = "^3.5.0"
-linkml = "^1.5.7"
-#linkml-solr = "^0.1.3"
-linkml-solr = {git = "https://github.com/linkml/linkml-solr.git", branch = "top_class"}
 importlib-metadata = ">=4.6.1"
+loguru = "*"
+pydantic = "^2.5"
 sh = "^1.14.3"
 typer = "^0.7"
 typer-cli = "^0.0.13"
-loguru = "*"
-linkml-validator = "^0.4.5"
-bmt = "^1.0.15"
-linkml-runtime = "1.6.0"
 
 [tool.poetry.group.dev]
 optional = true
 
 [tool.poetry.group.dev.dependencies]
-autoflake = "^1.4"
-flake8 = "^3.9.2"
-isort = "^5.9.1"
+pytest = "^7.1.1"
 mkdocs = "^1.3.0"
 mkdocs-material = "^8.2.9"
-pytest = "^7.1.1"
-black = "^23.3.0"
+black = "^23.10.0"
+ruff = "*"
 
 [tool.poetry.scripts]
 ingest = "monarch_ingest.main:typer_app"
@@ -59,8 +59,8 @@ build-backend = "poetry.core.masonry.api"
 line_length = 120
 skip-string-normalization = true
 
-[tool.isort]
-profile = "black"
-line_length = 120
-multi_line_output = 3
-include_trailing_comma = true
+[tool.ruff]
+line-length = 120
+ignore = [
+    "F541", # f-strings with no placeholders
+]