Resync pip compile and pyproject

pydatalab/Pipfile

@@ -4,41 +4,6 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [packages]
-#Flask = "~=3.0"
-#Flask-Cors = "*"
-#Flask-Dance = "*"
-#Flask-Login = "*"
-#Flask-PyMongo = "*"
-#Flask-Mail = "~= 0.9, < 0.10"
-#Werkzeug = "~=3.0"
-#bokeh = "<3"
-#pandas = "*"
-#scipy = "~= 1.13, < 1.14"
-#matplotlib = "*"
-#pymongo = "~= 4.7, < 5"
-#openpyxl = "*"
-#nmrglue = "*"
-#python-dotenv = "*"
-#pydantic = {extras = ["email"], version = "<2.0"}
-#blinker = "*"
-#pint = "~= 0.23, < 0.24"
-#periodictable = "*"
-#flask-compress = "*"
-#pillow = "*"
-#tiktoken = "~= 0.7, < 0.8"
-#galvani = "~= 0.4"
-#navani = {git = "git+https://github.com/the-grey-group/[email protected]"}
-#NewareNDA = ">= 2024"
-#python-dateutil = "*"
-#pybaselines = "*"
-#rosettasciio = "~= 0.3, < 0.4"
-#pyjwt = "*"
-#invoke = "*"
-#paramiko = "*"
-#langchain = "==0.2.6"
-#langchain-openai = "*"
-#langchain-anthropic = "*"
-#transformers = "~= 4.42, < 5"
 datalab-server = {path = ".", extras = ["all"]}
 
 [dev-packages]

pydatalab/pyproject.toml

@@ -63,32 +63,26 @@ server = [
     "Flask-Cors",
     "Flask-Dance",
     "Flask-PyMongo",
-    "Flask-Mail",
+    "Flask-Mail ~= 0.9",
     "Flask-Compress",
     "Werkzeug ~= 3.0",
     "pandas[excel] ~= 2.2",
-    "scipy ~= 1.13",
     "matplotlib ~= 3.8",
-    "nmrglue",
     "python-dotenv",
     "blinker",  # not sure if needed anymore,
     "pint",
     "periodictable",
     "pillow",
-    "tiktoken", # not sure if needed
-    "galvani ~= 0.4",
-    "NewareNDA >= 2024",
     "python-dateutil",
     "pybaselines",
-    "rosettasciio ~= 0.3, < 0.4",
     "pyjwt",
     "invoke",
     "paramiko",
 ]
 
 apps = [
     # General
-    "scipy ~= 1.11",
+    "scipy ~= 1.13",
     # NMR
     "nmrglue ~= 0.10",
     # Electrochemistry
@@ -102,10 +96,11 @@ apps = [
 ]
 
 chat = [
-    "langchain ~= 0.1",
+    "langchain == 0.2.6",
     "langchain-openai ~= 0.1",
     "langchain-anthropic ~= 0.1",
-    "transformers ~= 4.40"
+    "tiktoken ~= 0.7",
+    "transformers ~= 4.42"
 ]
 
 

pydatalab/requirements/requirements-all-dev.txt

@@ -1,12 +1,10 @@
 # This file was autogenerated by uv via the following command:
 #    uv pip compile pyproject.toml -o requirements/requirements-all-dev.txt --extra all --extra dev
 aiohttp==3.9.5
-    # via
-    #   langchain
-    #   langchain-community
+    # via langchain
 aiosignal==1.3.1
     # via aiohttp
-anthropic==0.25.7
+anthropic==0.31.2
     # via langchain-anthropic
 anyio==4.3.0
     # via
@@ -65,10 +63,6 @@ cycler==0.12.1
     # via matplotlib
 dask==2024.4.2
     # via rosettasciio
-dataclasses-json==0.6.5
-    # via
-    #   langchain
-    #   langchain-community
 defusedxml==0.7.1
     # via
     #   langchain-anthropic
@@ -134,7 +128,7 @@ httpx==0.27.0
     # via
     #   anthropic
     #   openai
-huggingface-hub==0.22.2
+huggingface-hub==0.24.0
     # via
     #   tokenizers
     #   transformers
@@ -161,32 +155,28 @@ jinja2==3.1.3
     #   mkdocs
     #   mkdocs-material
     #   mkdocstrings
+jiter==0.5.0
+    # via anthropic
 jsonpatch==1.33
-    # via
-    #   langchain
-    #   langchain-core
+    # via langchain-core
 jsonpointer==2.4
     # via jsonpatch
 kiwisolver==1.4.5
     # via matplotlib
-langchain==0.1.17
-langchain-anthropic==0.1.11
-langchain-community==0.0.36
-    # via langchain
-langchain-core==0.1.48
+langchain==0.2.6
+langchain-anthropic==0.1.20
+langchain-core==0.2.22
     # via
     #   langchain
     #   langchain-anthropic
-    #   langchain-community
     #   langchain-openai
     #   langchain-text-splitters
-langchain-openai==0.1.4
-langchain-text-splitters==0.0.1
+langchain-openai==0.1.17
+langchain-text-splitters==0.2.2
     # via langchain
-langsmith==0.1.52
+langsmith==0.1.93
     # via
     #   langchain
-    #   langchain-community
     #   langchain-core
 locket==1.0.0
     # via partd
@@ -204,8 +194,6 @@ markupsafe==2.1.5
     #   mkdocs-autorefs
     #   mkdocstrings
     #   werkzeug
-marshmallow==3.21.1
-    # via dataclasses-json
 matplotlib==3.8.4
     # via navani
 mergedeep==1.3.4
@@ -235,8 +223,6 @@ multidict==6.0.5
     # via
     #   aiohttp
     #   yarl
-mypy-extensions==1.0.0
-    # via typing-inspect
 natsort==8.4.0
     # via mkdocs-awesome-pages-plugin
 navani @ git+https://github.com/the-grey-group/navani.git@32aa742c3b84aa63fb4e3bd7b1824acb89e2b61d
@@ -252,7 +238,6 @@ numpy==1.26.4
     #   dask
     #   galvani
     #   langchain
-    #   langchain-community
     #   matplotlib
     #   navani
     #   nmrglue
@@ -268,7 +253,7 @@ oauthlib==3.2.2
     #   requests-oauthlib
 odfpy==1.4.1
     # via pandas
-openai==1.25.0
+openai==1.36.1
     # via langchain-openai
 openpyxl==3.1.2
     # via
@@ -282,7 +267,6 @@ packaging==23.2
     #   dask
     #   huggingface-hub
     #   langchain-core
-    #   marshmallow
     #   matplotlib
     #   mkdocs
     #   mongomock
@@ -368,7 +352,6 @@ pyyaml==6.0.1
     #   dask
     #   huggingface-hub
     #   langchain
-    #   langchain-community
     #   langchain-core
     #   mkdocs
     #   mkdocs-get-deps
@@ -389,7 +372,6 @@ requests==2.31.0
     #   flask-dance
     #   huggingface-hub
     #   langchain
-    #   langchain-community
     #   langsmith
     #   mkdocs-material
     #   requests-oauthlib
@@ -420,15 +402,12 @@ sniffio==1.3.1
     #   httpx
     #   openai
 sqlalchemy==2.0.29
-    # via
-    #   langchain
-    #   langchain-community
+    # via langchain
 tenacity==8.2.3
     # via
     #   langchain
-    #   langchain-community
     #   langchain-core
-tiktoken==0.6.0
+tiktoken==0.7.0
     # via langchain-openai
 tokenizers==0.19.1
     # via
@@ -449,7 +428,7 @@ tqdm==4.66.2
     #   huggingface-hub
     #   openai
     #   transformers
-transformers==4.40.2
+transformers==4.42.4
 typing-extensions==4.11.0
     # via
     #   anthropic
@@ -460,9 +439,6 @@ typing-extensions==4.11.0
     #   pint
     #   pydantic
     #   sqlalchemy
-    #   typing-inspect
-typing-inspect==0.9.0
-    # via dataclasses-json
 tzdata==2024.1
     # via pandas
 urllib3==2.2.1