napistu 0.1.0__tar.gz → 0.2.4.dev2__tar.gz

napistu-0.2.4.dev2/PKG-INFO

@@ -0,0 +1,84 @@
+Metadata-Version: 2.4
+Name: napistu
+Version: 0.2.4.dev2
+Summary: Connecting high-dimensional data to curated pathways
+Home-page: https://github.com/napistu/napistu-py
+Author: Sean Hackett
+Author-email: seanmchackett@gmail.com
+Project-URL: Documentation, https://napistu.readthedocs.io
+Project-URL: Source, https://github.com/napistu/napistu-py
+Project-URL: Tracker, https://github.com/napistu/napistu-py/issues
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: Jinja2
+Requires-Dist: PyYAML<7.0.0,>=6.0.0
+Requires-Dist: click<9.0.0,>=8.0.0
+Requires-Dist: click-logging
+Requires-Dist: fs<3.0.0,>=2.4.0
+Requires-Dist: fs-gcsfs<2.0.0,>=1.5.0
+Requires-Dist: igraph
+Requires-Dist: matplotlib<4.0.0,>=3.5.0
+Requires-Dist: numpy<3.0.0,>=1.24.0
+Requires-Dist: pandas<3.0.0,>=1.5.0
+Requires-Dist: pydantic<3.0.0,>=2.0.0
+Requires-Dist: python-libsbml
+Requires-Dist: requests>=2.25.0
+Requires-Dist: scipy<2.0.0,>=1.10.0
+Requires-Dist: tqdm
+Requires-Dist: zeep<4.0.0,>=3.0.0
+Provides-Extra: dev
+Requires-Dist: black>=24.0.0; extra == "dev"
+Requires-Dist: ipykernel; extra == "dev"
+Requires-Dist: pre-commit<4.0.0,>=3.0.0; extra == "dev"
+Requires-Dist: pytest<8.0.0,>=7.0.0; extra == "dev"
+Requires-Dist: pytest-asyncio; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: testcontainers; extra == "dev"
+Provides-Extra: mcp
+Requires-Dist: fastmcp<3.0.0,>=2.0.0; extra == "mcp"
+Requires-Dist: mcp<2.0.0,>=1.0.0; extra == "mcp"
+Requires-Dist: httpx>=0.24.0; extra == "mcp"
+Requires-Dist: beautifulsoup4<5.0.0,>=4.11.0; extra == "mcp"
+Requires-Dist: markdown>=3.4.0; extra == "mcp"
+Requires-Dist: jupyter-client>=7.0.0; extra == "mcp"
+Requires-Dist: nbformat>=5.0.0; extra == "mcp"
+Provides-Extra: rpy2
+Requires-Dist: pyarrow<19.0.0,>=15.0.0; extra == "rpy2"
+Requires-Dist: rpy2<4.0.0,>=3.5.0; extra == "rpy2"
+Requires-Dist: rpy2-arrow<1.0.0,>=0.1.0; extra == "rpy2"
+Dynamic: license-file
+
+# Napistu Python Library
+
+[![Documentation Status](https://readthedocs.org/projects/napistu/badge/?version=latest)](https://napistu.readthedocs.io/en/latest/?badge=latest)
+
+This Python package hosts the majority of the algorithmic code for the [Napistu project](https://github.com/napistu/napistu).
+
+## Setup
+
+Napistu is available on [PyPI](https://pypi.org/project/napistu) so the recommended way to use it is just to pip install with:
+
+```bash
+pip install napistu
+```
+
+Alternatively, you can clone this repository and perform a local install. e.g., from this directory:
+
+```bash
+pip install .
+```
+
+## Documentation
+📘 **Full Documentation**: [https://napistu.readthedocs.io](https://napistu.readthedocs.io)
+** Wiki **: [napistu/wiki](https://github.com/napistu/napistu/wiki)
+
+### Quick Links
+- [Installation Guide](https://napistu.readthedocs.io/en/latest/installation.html)
+- [API Reference](https://napistu.readthedocs.io/en/latest/api.html)
+- [Usage Examples](https://napistu.readthedocs.io/en/latest/usage.html)

napistu-0.2.4.dev2/README.md

@@ -0,0 +1,28 @@
+# Napistu Python Library
+
+[![Documentation Status](https://readthedocs.org/projects/napistu/badge/?version=latest)](https://napistu.readthedocs.io/en/latest/?badge=latest)
+
+This Python package hosts the majority of the algorithmic code for the [Napistu project](https://github.com/napistu/napistu).
+
+## Setup
+
+Napistu is available on [PyPI](https://pypi.org/project/napistu) so the recommended way to use it is just to pip install with:
+
+```bash
+pip install napistu
+```
+
+Alternatively, you can clone this repository and perform a local install. e.g., from this directory:
+
+```bash
+pip install .
+```
+
+## Documentation
+📘 **Full Documentation**: [https://napistu.readthedocs.io](https://napistu.readthedocs.io)
+** Wiki **: [napistu/wiki](https://github.com/napistu/napistu/wiki)
+
+### Quick Links
+- [Installation Guide](https://napistu.readthedocs.io/en/latest/installation.html)
+- [API Reference](https://napistu.readthedocs.io/en/latest/api.html)
+- [Usage Examples](https://napistu.readthedocs.io/en/latest/usage.html)

{napistu-0.1.0 → napistu-0.2.4.dev2}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napistu
-version = 0.1.0
+version = 0.2.4.dev2
 description = Connecting high-dimensional data to curated pathways
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -14,27 +14,29 @@ classifiers =
 	Programming Language :: Python :: 3
 	Programming Language :: Python :: 3 :: Only
 project_urls = 
-	Bug Tracker = https://github.com/napistu/napistu-py/issues
+	Documentation = https://napistu.readthedocs.io
+	Source = https://github.com/napistu/napistu-py
+	Tracker = https://github.com/napistu/napistu-py/issues
 
 [options]
 packages = find:
 install_requires = 
 	Jinja2
-	PyYAML==6.*
-	click==8.*
+	PyYAML>=6.0.0,<7.0.0
+	click>=8.0.0,<9.0.0
 	click-logging
-	fs==2.4.*
-	fs-gcsfs==1.5.*
+	fs>=2.4.0,<3.0.0
+	fs-gcsfs>=1.5.0,<2.0.0
 	igraph
-	matplotlib==3.*
-	numpy==1.26.*
-	pandas==1.5.*
-	pydantic==2.*
+	matplotlib>=3.5.0,<4.0.0
+	numpy>=1.24.0,<3.0.0
+	pandas>=1.5.0,<3.0.0
+	pydantic>=2.0.0,<3.0.0
 	python-libsbml
-	requests>=2
-	scipy==1.14.*
+	requests>=2.25.0
+	scipy>=1.10.0,<2.0.0
 	tqdm
-	zeep==3.*
+	zeep>=3.0.0,<4.0.0
 python_requires = >=3.11
 package_dir = 
 	= src
@@ -48,17 +50,30 @@ console_scripts =
 
 [options.extras_require]
 dev = 
-	black==25.*
+	black>=24.0.0
 	ipykernel
-	pre-commit==3.3.*
-	pytest==7.*
+	pre-commit>=3.0.0,<4.0.0
+	pytest>=7.0.0,<8.0.0
+	pytest-asyncio
 	pytest-cov
 	ruff
 	testcontainers
+mcp = 
+	fastmcp>=2.0.0,<3.0.0
+	mcp>=1.0.0,<2.0.0
+	httpx>=0.24.0
+	beautifulsoup4>=4.11.0,<5.0.0
+	markdown>=3.4.0
+	jupyter-client>=7.0.0
+	nbformat>=5.0.0
 rpy2 = 
-	pyarrow==18.0.0
-	rpy2==3.5.*
-	rpy2-arrow==0.1.1
+	pyarrow>=15.0.0,<19.0.0
+	rpy2>=3.5.0,<4.0.0
+	rpy2-arrow>=0.1.0,<1.0.0
+
+[tool:pytest]
+filterwarnings = 
+	ignore::DeprecationWarning
 
 [egg_info]
 tag_build = 

{napistu-0.1.0 → napistu-0.2.4.dev2}/src/napistu/__init__.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version
 
-__version__ = "0.2.0"
+__version__ = "0.2.2"
 
 try:
     __version__ = version("calicolabs-cpr")