From e4624fd5334bfb7f9417e559fac70804740c5ebb Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Mon, 7 Oct 2024 12:01:04 +0100 Subject: [PATCH 1/2] Rearrange dependencies to include more as 'core' --- pydatalab/pyproject.toml | 12 ++++++------ pydatalab/uv.lock | 32 +++++++++++++------------------- 2 files changed, 19 insertions(+), 25 deletions(-) diff --git a/pydatalab/pyproject.toml b/pydatalab/pyproject.toml index bb926d2fb..c2e3c177f 100644 --- a/pydatalab/pyproject.toml +++ b/pydatalab/pyproject.toml @@ -18,8 +18,14 @@ classifiers = [ requires-python = ">= 3.10, < 3.12" dependencies = [ + "bokeh ~= 2.4, < 3.0", + "matplotlib ~= 3.8", # Slightly confusing, but git dependencies cannot be included as extra by uv at the moment "navani @ git+https://github.com/the-grey-group/navani.git@v0.1.5", + "periodictable ~= 1.7", + "pydantic[email, dotenv] < 2.0", + "pint ~= 0.24", + "pandas[excel] ~= 2.2", ] [project.urls] @@ -55,9 +61,7 @@ dev = [ ] server = [ - "pydantic[email, dotenv] < 2.0", "pymongo ~= 4.7", - "bokeh ~= 2.4, < 3.0", "Flask ~= 3.0", "Flask-Login ~= 0.6", "Flask-Cors ~= 5.0", @@ -66,11 +70,7 @@ server = [ "Flask-Mail ~= 0.10", "Flask-Compress ~= 1.15", "Werkzeug ~= 3.0", - "pandas[excel] ~= 2.2", - "matplotlib ~= 3.8", "python-dotenv ~= 1.0", - "pint ~= 0.24", - "periodictable ~= 1.7", "pillow ~= 10.4", "pyjwt ~= 2.9", "invoke ~= 2.2", diff --git a/pydatalab/uv.lock b/pydatalab/uv.lock index 0ef969050..4a0e0371c 100644 --- a/pydatalab/uv.lock +++ b/pydatalab/uv.lock @@ -662,15 +662,20 @@ array = [ [[package]] name = "datalab-server" -version = "0.5.0rc5.dev33+g788a185.d20241001" +version = "0.5.0rc5.dev49+gce95aea.d20241007" source = { editable = "." } dependencies = [ + { name = "bokeh" }, + { name = "matplotlib" }, { name = "navani" }, + { name = "pandas", extra = ["excel"] }, + { name = "periodictable" }, + { name = "pint" }, + { name = "pydantic", extra = ["dotenv", "email"] }, ] [package.optional-dependencies] all = [ - { name = "bokeh" }, { name = "flask" }, { name = "flask-compress" }, { name = "flask-cors" }, @@ -683,16 +688,11 @@ all = [ { name = "langchain" }, { name = "langchain-anthropic" }, { name = "langchain-openai" }, - { name = "matplotlib" }, { name = "newarenda" }, { name = "nmrglue" }, - { name = "pandas", extra = ["excel"] }, { name = "paramiko" }, - { name = "periodictable" }, { name = "pillow" }, - { name = "pint" }, { name = "pybaselines" }, - { name = "pydantic", extra = ["dotenv", "email"] }, { name = "pyjwt" }, { name = "pymongo" }, { name = "python-dateutil" }, @@ -731,7 +731,6 @@ dev = [ { name = "pytest-dependency" }, ] server = [ - { name = "bokeh" }, { name = "flask" }, { name = "flask-compress" }, { name = "flask-cors" }, @@ -740,13 +739,8 @@ server = [ { name = "flask-mail" }, { name = "flask-pymongo" }, { name = "invoke" }, - { name = "matplotlib" }, - { name = "pandas", extra = ["excel"] }, { name = "paramiko" }, - { name = "periodictable" }, { name = "pillow" }, - { name = "pint" }, - { name = "pydantic", extra = ["dotenv", "email"] }, { name = "pyjwt" }, { name = "pymongo" }, { name = "python-dotenv" }, @@ -755,7 +749,7 @@ server = [ [package.metadata] requires-dist = [ - { name = "bokeh", marker = "extra == 'server'", specifier = "~=2.4,<3.0" }, + { name = "bokeh", specifier = "~=2.4,<3.0" }, { name = "datalab-server", extras = ["apps", "chat", "server"], marker = "extra == 'all'" }, { name = "flask", marker = "extra == 'server'", specifier = "~=3.0" }, { name = "flask-compress", marker = "extra == 'server'", specifier = "~=1.15" }, @@ -769,7 +763,7 @@ requires-dist = [ { name = "langchain", marker = "extra == 'chat'", specifier = "==0.2.6" }, { name = "langchain-anthropic", marker = "extra == 'chat'", specifier = "~=0.1" }, { name = "langchain-openai", marker = "extra == 'chat'", specifier = "~=0.1" }, - { name = "matplotlib", marker = "extra == 'server'", specifier = "~=3.8" }, + { name = "matplotlib", specifier = "~=3.8" }, { name = "mkdocs", marker = "extra == 'dev'", specifier = "~=1.6" }, { name = "mkdocs-awesome-pages-plugin", marker = "extra == 'dev'", specifier = "~=2.9" }, { name = "mkdocs-material", marker = "extra == 'dev'", specifier = "~=9.5" }, @@ -778,14 +772,14 @@ requires-dist = [ { name = "navani", git = "https://github.com/the-grey-group/navani.git?rev=v0.1.5" }, { name = "newarenda", marker = "extra == 'apps'", specifier = ">=2024" }, { name = "nmrglue", marker = "extra == 'apps'", specifier = "~=0.10" }, - { name = "pandas", extras = ["excel"], marker = "extra == 'server'", specifier = "~=2.2" }, + { name = "pandas", extras = ["excel"], specifier = "~=2.2" }, { name = "paramiko", marker = "extra == 'server'", specifier = "~=3.4" }, - { name = "periodictable", marker = "extra == 'server'", specifier = "~=1.7" }, + { name = "periodictable", specifier = "~=1.7" }, { name = "pillow", marker = "extra == 'server'", specifier = "~=10.4" }, - { name = "pint", marker = "extra == 'server'", specifier = "~=0.24" }, + { name = "pint", specifier = "~=0.24" }, { name = "pre-commit", marker = "extra == 'dev'", specifier = "~=3.7" }, { name = "pybaselines", marker = "extra == 'apps'", specifier = "~=1.1" }, - { name = "pydantic", extras = ["dotenv", "email"], marker = "extra == 'server'", specifier = "<2.0" }, + { name = "pydantic", extras = ["dotenv", "email"], specifier = "<2.0" }, { name = "pyjwt", marker = "extra == 'server'", specifier = "~=2.9" }, { name = "pymongo", marker = "extra == 'server'", specifier = "~=4.7" }, { name = "pytest", marker = "extra == 'dev'", specifier = "~=8.2" }, From 2b94694f460c7cc9ba5442b1eec06b76b0cfdb0b Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Mon, 7 Oct 2024 12:02:34 +0100 Subject: [PATCH 2/2] Update navani to 0.1.7 and move it to apps extra now uv supports it --- pydatalab/pyproject.toml | 3 +-- pydatalab/requirements/requirements-all-dev.txt | 2 +- pydatalab/requirements/requirements-all.txt | 2 +- pydatalab/uv.lock | 9 +++++---- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/pydatalab/pyproject.toml b/pydatalab/pyproject.toml index c2e3c177f..88b8a6afd 100644 --- a/pydatalab/pyproject.toml +++ b/pydatalab/pyproject.toml @@ -20,8 +20,6 @@ requires-python = ">= 3.10, < 3.12" dependencies = [ "bokeh ~= 2.4, < 3.0", "matplotlib ~= 3.8", - # Slightly confusing, but git dependencies cannot be included as extra by uv at the moment - "navani @ git+https://github.com/the-grey-group/navani.git@v0.1.5", "periodictable ~= 1.7", "pydantic[email, dotenv] < 2.0", "pint ~= 0.24", @@ -83,6 +81,7 @@ apps = [ # NMR "nmrglue ~= 0.10", # Electrochemistry + "navani @ git+https://github.com/the-grey-group/navani.git@v0.1.7", "galvani ~= 0.4, < 0.5", "NewareNDA >= 2024", # Raman diff --git a/pydatalab/requirements/requirements-all-dev.txt b/pydatalab/requirements/requirements-all-dev.txt index 1320524df..b7e5e2379 100644 --- a/pydatalab/requirements/requirements-all-dev.txt +++ b/pydatalab/requirements/requirements-all-dev.txt @@ -260,7 +260,7 @@ multidict==6.1.0 # yarl natsort==8.4.0 # via mkdocs-awesome-pages-plugin -navani @ git+https://github.com/the-grey-group/navani.git@32aa742c3b84aa63fb4e3bd7b1824acb89e2b61d +navani @ git+https://github.com/the-grey-group/navani.git@d171781b483f0a17a0ada7a043c8f1e243499245 # via datalab-server (pyproject.toml) newarenda==2024.10.1 # via diff --git a/pydatalab/requirements/requirements-all.txt b/pydatalab/requirements/requirements-all.txt index ecdb178cf..eac41c04c 100644 --- a/pydatalab/requirements/requirements-all.txt +++ b/pydatalab/requirements/requirements-all.txt @@ -191,7 +191,7 @@ multidict==6.1.0 # via # aiohttp # yarl -navani @ git+https://github.com/the-grey-group/navani.git@32aa742c3b84aa63fb4e3bd7b1824acb89e2b61d +navani @ git+https://github.com/the-grey-group/navani.git@d171781b483f0a17a0ada7a043c8f1e243499245 # via datalab-server (pyproject.toml) newarenda==2024.10.1 # via diff --git a/pydatalab/uv.lock b/pydatalab/uv.lock index 4a0e0371c..52a2cbcbd 100644 --- a/pydatalab/uv.lock +++ b/pydatalab/uv.lock @@ -662,12 +662,11 @@ array = [ [[package]] name = "datalab-server" -version = "0.5.0rc5.dev49+gce95aea.d20241007" +version = "0.5.0rc5.dev49+gc73904f.d20241007" source = { editable = "." } dependencies = [ { name = "bokeh" }, { name = "matplotlib" }, - { name = "navani" }, { name = "pandas", extra = ["excel"] }, { name = "periodictable" }, { name = "pint" }, @@ -688,6 +687,7 @@ all = [ { name = "langchain" }, { name = "langchain-anthropic" }, { name = "langchain-openai" }, + { name = "navani" }, { name = "newarenda" }, { name = "nmrglue" }, { name = "paramiko" }, @@ -705,6 +705,7 @@ all = [ ] apps = [ { name = "galvani" }, + { name = "navani" }, { name = "newarenda" }, { name = "nmrglue" }, { name = "pybaselines" }, @@ -769,7 +770,7 @@ requires-dist = [ { name = "mkdocs-material", marker = "extra == 'dev'", specifier = "~=9.5" }, { name = "mkdocstrings", extras = ["python-legacy"], marker = "extra == 'dev'", specifier = "~=0.25" }, { name = "mongomock", marker = "extra == 'dev'", specifier = "~=4.1" }, - { name = "navani", git = "https://github.com/the-grey-group/navani.git?rev=v0.1.5" }, + { name = "navani", marker = "extra == 'apps'", git = "https://github.com/the-grey-group/navani.git?rev=v0.1.7" }, { name = "newarenda", marker = "extra == 'apps'", specifier = ">=2024" }, { name = "nmrglue", marker = "extra == 'apps'", specifier = "~=0.10" }, { name = "pandas", extras = ["excel"], specifier = "~=2.2" }, @@ -1880,7 +1881,7 @@ wheels = [ [[package]] name = "navani" version = "0.1.5" -source = { git = "https://github.com/the-grey-group/navani.git?rev=v0.1.5#32aa742c3b84aa63fb4e3bd7b1824acb89e2b61d" } +source = { git = "https://github.com/the-grey-group/navani.git?rev=v0.1.7#d171781b483f0a17a0ada7a043c8f1e243499245" } dependencies = [ { name = "galvani" }, { name = "matplotlib" },