scez 0.0.1__tar.gz → 0.1.1__tar.gz

scez-0.1.1/PKG-INFO

@@ -0,0 +1,67 @@
+Metadata-Version: 2.1
+Name: scez
+Version: 0.1.1
+Summary: Single Cell Analysis, Easy Mode!
+License: MIT
+Author: Abe Arab
+Author-email: abarbiology@gmail.com
+Requires-Python: >=3.9,<4.0
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: adjustText (>=0.7.3,<0.8.0)
+Requires-Dist: adpbulk (>=0.1.4,<0.2.0)
+Requires-Dist: anndata (>=0.8.0,<0.9.0)
+Requires-Dist: blitzgsea (>=1.3.0,<2.0.0)
+Requires-Dist: bottleneck (>=1.3.6,<2.0.0)
+Requires-Dist: matplotlib (>=3.7,<4.0)
+Requires-Dist: numpy (>=1.26.0,<2.0.0)
+Requires-Dist: pandas (>=2.1.4,<3.0.0)
+Requires-Dist: pydeseq2 (>=0.4.0,<0.5.0)
+Requires-Dist: pytdc (>=1.0.0,<2.0.0)
+Requires-Dist: scanpy (>=1.9.6,<2.0.0)
+Requires-Dist: seaborn (>=0.12.2,<0.13.0)
+Requires-Dist: tomli
+Requires-Dist: tqdm
+Project-URL: Source, https://github.com/abearab/scez
+Description-Content-Type: text/markdown
+
+## scez – single cell, easy mode
+[![package](https://github.com/abearab/scez/actions/workflows/main.yml/badge.svg)](https://github.com/abearab/scez/actions/workflows/main.yml)
+[![PyPI version](https://badge.fury.io/py/scez.svg)](https://badge.fury.io/py/scez)
+[![Downloads](https://static.pepy.tech/badge/scez)](https://pepy.tech/project/scez)
+[![Downloads](https://static.pepy.tech/badge/scez/month)](https://pepy.tech/project/scez)
+
+
+### Description
+There are many tools available for single-cell RNA-seq analysis, but they often require a lot of understanding of the underlying algorithms, reading of documentation, and setting up analysis environments. This takes time and effort, and can be a barrier to entry for many projects. [Single-Cell Best Practices](https://github.com/theislab/single-cell-best-practices) is a great resource for learning about the best practices for single-cell analysis. `scez` aims to provide functionalities for single-cell analysis through definitions of analysis "tasks" and implementation of these "best practices" in a user-friendly way.
+
+This is more a personal effort to streamline my own analysis workflows, but I hope it can be useful to others as well.
+
+
+### Installation
+Make sure you have mamba installed in your base environment. If not, install it with:
+```bash
+conda install mamba -n base -c conda-forge
+```
+Then, create a new conda environment with the provided `environment.yml` file and activate it. This will install all necessary dependencies for scez.
+```bash
+conda env create -f https://raw.githubusercontent.com/abearab/scez/main/environment.yml
+
+conda activate scez
+```
+Finally, install scez with:
+
+```bash
+pip install scez
+```
+
+___
+Or, if you want to install the latest version from the repository:
+```bash
+pip install git+https://github.com/abearab/scez.git
+```
+

scez-0.1.1/README.md

@@ -0,0 +1,35 @@
+## scez – single cell, easy mode
+[![package](https://github.com/abearab/scez/actions/workflows/main.yml/badge.svg)](https://github.com/abearab/scez/actions/workflows/main.yml)
+[![PyPI version](https://badge.fury.io/py/scez.svg)](https://badge.fury.io/py/scez)
+[![Downloads](https://static.pepy.tech/badge/scez)](https://pepy.tech/project/scez)
+[![Downloads](https://static.pepy.tech/badge/scez/month)](https://pepy.tech/project/scez)
+
+
+### Description
+There are many tools available for single-cell RNA-seq analysis, but they often require a lot of understanding of the underlying algorithms, reading of documentation, and setting up analysis environments. This takes time and effort, and can be a barrier to entry for many projects. [Single-Cell Best Practices](https://github.com/theislab/single-cell-best-practices) is a great resource for learning about the best practices for single-cell analysis. `scez` aims to provide functionalities for single-cell analysis through definitions of analysis "tasks" and implementation of these "best practices" in a user-friendly way.
+
+This is more a personal effort to streamline my own analysis workflows, but I hope it can be useful to others as well.
+
+
+### Installation
+Make sure you have mamba installed in your base environment. If not, install it with:
+```bash
+conda install mamba -n base -c conda-forge
+```
+Then, create a new conda environment with the provided `environment.yml` file and activate it. This will install all necessary dependencies for scez.
+```bash
+conda env create -f https://raw.githubusercontent.com/abearab/scez/main/environment.yml
+
+conda activate scez
+```
+Finally, install scez with:
+
+```bash
+pip install scez
+```
+
+___
+Or, if you want to install the latest version from the repository:
+```bash
+pip install git+https://github.com/abearab/scez.git
+```

{scez-0.0.1 → scez-0.1.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "scez"
-version = "0.0.1"
+version = "0.1.1"
 authors = [
 	"Abe Arab <abarbiology@gmail.com>"
 ]
@@ -17,24 +17,23 @@ packages = [
 [tool.poetry.urls]
 Source = "https://github.com/abearab/scez"
 
-# [tool.poetry.dependencies]
-# dependencies = [
-# 	"anndata>=0.7.4",
-# 	"numpy>=1.17.0",
-# 	"pandas>=0.21,<2.0",
-# 	"matplotlib<3.7",
-#  	"seaborn==0.12.2",
-# 	"scvi-tools",
-# 	"scar",
-# 	"scanpy",
-# 	"adjustText",
-#  	"adpbulk",
-# 	"pydeseq2",
-# 	"pytdc",
-# 	"blitzgsea",
-# 	"tqdm",
-# 	"pytest"
-# ]
+[tool.poetry.dependencies]
+python = "^3.9 <4.0"
+numpy = "^1.26.0"
+pandas = "^2.1.4 <3.0.0"
+bottleneck = "^1.3.6"
+tqdm = "*"
+tomli = "*"
+matplotlib = "^3.7"
+seaborn = "^0.12.2"
+adjustText = "^0.7.3"
+scanpy = "^1.9.6"
+anndata = "^0.8.0"
+adpbulk  = "^0.1.4"
+pydeseq2 = "^0.4.0"
+pytdc = "^1.0.0"
+blitzgsea = "^1.3.0"
+
 
 [tool.poetry.group.test.dependencies]
 pytest = "*"

{scez-0.0.1 → scez-0.1.1}/scez/__init__.py

@@ -8,8 +8,9 @@ import scanpy as sc
 import matplotlib.pyplot as plt
 
 import tomli
+from pathlib import Path
 
-toml_dict = tomli.load(open('pyproject.toml','rb'))
+toml_dict = tomli.load(open(Path(__file__).parent.parent / 'pyproject.toml','rb'))
 __version__ = toml_dict['tool']['poetry']['version']
 
 

scez-0.0.1/PKG-INFO

@@ -1,48 +0,0 @@
-Metadata-Version: 2.1
-Name: scez
-Version: 0.0.1
-Summary: Single Cell Analysis, Easy Mode!
-License: MIT
-Author: Abe Arab
-Author-email: abarbiology@gmail.com
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 2
-Classifier: Programming Language :: Python :: 2.7
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.4
-Classifier: Programming Language :: Python :: 3.5
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Project-URL: Source, https://github.com/abearab/scez
-Description-Content-Type: text/markdown
-
-## scez – single cell, easy mode
-[![package](https://github.com/abearab/scez/actions/workflows/main.yml/badge.svg)](https://github.com/abearab/scez/actions/workflows/main.yml)
-
-### Installation
-Make sure you have mamba installed in your base environment. If not, install it with:
-```bash
-conda install mamba -n base -c conda-forge
-```
-Then, create a new conda environment with the provided `environment.yml` file and activate it. This will install all necessary dependencies for scez.
-```bash
-conda env create -f environment.yml
-
-conda activate scez
-```
-Finally, install scez with:
-
-```bash
-pip install scez
-```
-
-Or, if you want to install the latest version from the repository:
-```bash
-pip install git+https://github.com/abearab/scez.git
-```
-

scez-0.0.1/README.md

@@ -1,24 +0,0 @@
-## scez – single cell, easy mode
-[![package](https://github.com/abearab/scez/actions/workflows/main.yml/badge.svg)](https://github.com/abearab/scez/actions/workflows/main.yml)
-
-### Installation
-Make sure you have mamba installed in your base environment. If not, install it with:
-```bash
-conda install mamba -n base -c conda-forge
-```
-Then, create a new conda environment with the provided `environment.yml` file and activate it. This will install all necessary dependencies for scez.
-```bash
-conda env create -f environment.yml
-
-conda activate scez
-```
-Finally, install scez with:
-
-```bash
-pip install scez
-```
-
-Or, if you want to install the latest version from the repository:
-```bash
-pip install git+https://github.com/abearab/scez.git
-```