Rename package from pygreta to gretapy

- Rename src/pygreta/ to src/gretapy/
- Update all imports from `import pygreta as pg` to `import gretapy as gt`
- Update pyproject.toml with new package name and URLs
- Update all documentation and API references
- Update CI/CD workflows and issue templates
- Rename GitHub repository to saezlab/gretapy

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: PauBadiaM

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Propose a new feature for pygreta
+description: Propose a new feature for gretapy
 type: Enhancement
 body:
   - type: textarea

.github/workflows/release.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/pygreta
+      url: https://pypi.org/p/gretapy
     permissions:
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:

README.md

@@ -1,4 +1,4 @@
-# pygreta - Evaluation and analysis of Gene Regulatory Networks (GRNs)
+# gretapy - Evaluation and analysis of Gene Regulatory Networks (GRNs)
 <img src="https://drive.google.com/uc?id=1DFGeAuSp8w1kDlMaS4zyeXfepKVW14Ym" align="right" width="120" class="no-scaled-link" alt='GRETA logo' />
 
 [![Tests][badge-tests]][tests]
@@ -15,18 +15,18 @@
 [![Conda version][badge-condav]][conda]
 [![Conda downloads][badge-condad]][conda]
 
-[badge-tests]: https://img.shields.io/github/actions/workflow/status/saezlab/pygreta/test.yaml?branch=main
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/saezlab/gretapy/test.yaml?branch=main
 [badge-docs]: https://img.shields.io/readthedocs/gretapy
-[badge-condav]: https://img.shields.io/conda/vn/conda-forge/pygreta.svg
-[badge-condad]: https://img.shields.io/conda/dn/conda-forge/pygreta.svg
-[badge-issues]: https://img.shields.io/github/issues/saezlab/pygreta
-[badge-coverage]: https://codecov.io/gh/saezlab/pygreta/branch/main/graph/badge.svg
-[badge-pypi]: https://img.shields.io/pypi/v/pygreta.svg
-[badge-mdown]: https://static.pepy.tech/badge/pygreta/month
-[badge-adown]: https://static.pepy.tech/badge/pygreta
-[badge-stars]: https://img.shields.io/github/stars/saezlab/pygreta?style=flat&logo=github&color=yellow
+[badge-condav]: https://img.shields.io/conda/vn/conda-forge/gretapy.svg
+[badge-condad]: https://img.shields.io/conda/dn/conda-forge/gretapy.svg
+[badge-issues]: https://img.shields.io/github/issues/saezlab/gretapy
+[badge-coverage]: https://codecov.io/gh/saezlab/gretapy/branch/main/graph/badge.svg
+[badge-pypi]: https://img.shields.io/pypi/v/gretapy.svg
+[badge-mdown]: https://static.pepy.tech/badge/gretapy/month
+[badge-adown]: https://static.pepy.tech/badge/gretapy
+[badge-stars]: https://img.shields.io/github/stars/saezlab/gretapy?style=flat&logo=github&color=yellow
 
-`pygreta` is a comprehensive framework for benchmarking and evaluating gene regulatory networks (GRNs) inferred from single-cell multiome (RNA+ATAC) data. It provides a systematic evaluation across four complementary dimensions: prior knowledge validation (TF markers, known TF-TF interactions, reference networks), genomic annotations (TF binding sites, cis-regulatory elements, chromatin-gene links), predictive performance (pathway enrichment, expression correlation), and mechanistic validation (perturbation forecasting, Boolean network simulations). The package includes built-in GRN inference methods, curated benchmark datasets, and visualization tools to facilitate rigorous comparison of network inference approaches.
+`gretapy` is a comprehensive framework for benchmarking and evaluating gene regulatory networks (GRNs) inferred from single-cell multiome (RNA+ATAC) data. It provides a systematic evaluation across four complementary dimensions: prior knowledge validation (TF markers, known TF-TF interactions, reference networks), genomic annotations (TF binding sites, cis-regulatory elements, chromatin-gene links), predictive performance (pathway enrichment, expression correlation), and mechanistic validation (perturbation forecasting, Boolean network simulations). The package includes built-in GRN inference methods, curated benchmark datasets, and visualization tools to facilitate rigorous comparison of network inference approaches.
 
 ## Getting started
 
@@ -38,30 +38,30 @@ in particular, the [API documentation][].
 You need to have Python 3.11 or newer installed on your system.
 If you don't have Python installed, we recommend installing [uv][].
 
-There are several alternative options to install pygreta:
+There are several alternative options to install gretapy:
 
 1. Install the latest stable release from [PyPI][pypi] with minimal dependancies:
 
 ```bash
-pip install pygreta
+pip install gretapy
 ```
 
 2. Install the latest stable full release from [PyPI][pypi] with extra dependancies:
 
 ```bash
-pip install pygreta[full]
+pip install gretapy[full]
 ```
 
-3. Install the latest stable version from [conda-forge][conda] using mamba or conda (pay attention to the `-py` suffix at the end):
+3. Install the latest stable version from [conda-forge][conda] using mamba or conda:
 
 ```bash
-mamba create -n=dcp conda-forge::pygreta
+mamba create -n=greta conda-forge::gretapy
 ```
 
 4. Install the latest development version:
 
 ```bash
-pip install git+https://github.com/saezlab/pygreta.git@main
+pip install git+https://github.com/saezlab/gretapy.git@main
 ```
 
 ## Release notes
@@ -79,12 +79,12 @@ If you found a bug, please use the [issue tracker][].
 
 [uv]: https://github.com/astral-sh/uv
 [scverse discourse]: https://discourse.scverse.org/
-[issue tracker]: https://github.com/PauBadiaM/pygreta/issues
-[tests]: https://github.com/PauBadiaM/pygreta/actions/workflows/test.yaml
+[issue tracker]: https://github.com/saezlab/gretapy/issues
+[tests]: https://github.com/saezlab/gretapy/actions/workflows/test.yaml
 [documentation]: https://gretapy.readthedocs.io
-[changelog]: https://pygreta.readthedocs.io/en/latest/changelog.html
-[api documentation]: https://pygreta.readthedocs.io/en/latest/api.html
-[pypi]: https://pypi.org/project/pygreta
-[down]: https://pepy.tech/project/pygreta
-[conda]: https://anaconda.org/conda-forge/pygreta-py
-[codecoverage]: https://codecov.io/gh/saezlab/pygreta
+[changelog]: https://gretapy.readthedocs.io/en/latest/changelog.html
+[api documentation]: https://gretapy.readthedocs.io/en/latest/api.html
+[pypi]: https://pypi.org/project/gretapy
+[down]: https://pepy.tech/project/gretapy
+[conda]: https://anaconda.org/conda-forge/gretapy
+[codecoverage]: https://codecov.io/gh/saezlab/gretapy

docs/api/ds.md

@@ -3,8 +3,8 @@
 Functions for downloading and reading datasets and databases.
 
 ```{eval-rst}
-.. module:: pygreta.ds
-.. currentmodule:: pygreta.ds
+.. module:: gretapy.ds
+.. currentmodule:: gretapy.ds
 
 .. autosummary::
     :toctree: generated

docs/api/index.md

@@ -1,16 +1,16 @@
 # API
 
-Import pygreta as:
+Import gretapy as:
 
 ```
-import pygreta as pg
+import gretapy as gt
 ```
 
 ## General Functions
 
 ```{eval-rst}
-.. module:: pygreta
-.. currentmodule:: pygreta
+.. module:: gretapy
+.. currentmodule:: gretapy
 
 .. autosummary::
     :toctree: generated

docs/api/mt.md

@@ -3,8 +3,8 @@
 Methods for inferring gene regulatory networks.
 
 ```{eval-rst}
-.. module:: pygreta.mt
-.. currentmodule:: pygreta.mt
+.. module:: gretapy.mt
+.. currentmodule:: gretapy.mt
 
 .. autosummary::
     :toctree: generated

docs/api/pl.md

@@ -3,8 +3,8 @@
 Plotting functions for visualizing GRN analysis results.
 
 ```{eval-rst}
-.. module:: pygreta.pl
-.. currentmodule:: pygreta.pl
+.. module:: gretapy.pl
+.. currentmodule:: gretapy.pl
 
 .. autosummary::
     :toctree: generated

docs/api/tl.md

@@ -5,8 +5,8 @@ Tools for benchmarking and analyzing gene regulatory networks.
 ## Benchmarking
 
 ```{eval-rst}
-.. module:: pygreta.tl
-.. currentmodule:: pygreta.tl
+.. module:: gretapy.tl
+.. currentmodule:: gretapy.tl
 
 .. autosummary::
     :toctree: generated

docs/conf.py

@@ -21,7 +21,7 @@
 
 # NOTE: If you installed your project in editable mode, this might be stale.
 #       If this is the case, reinstall it to refresh the metadata
-info = metadata("pygreta")
+info = metadata("gretapy")
 project = info["Name"]
 author = info["Author"]
 copyright = f"{datetime.now():%Y}, {author}."

pyproject.toml

@@ -3,7 +3,7 @@ build-backend = "hatchling.build"
 requires = [ "hatchling" ]
 
 [project]
-name = "pygreta"
+name = "gretapy"
 version = "0.0.1"
 description = "Package to evaluate gene regulatory networks (GRNs)."
 readme = "README.md"
@@ -31,9 +31,9 @@ dependencies = [
   "session-info2",
 ]
 # https://docs.pypi.org/project_metadata/#project-urls
-urls.Documentation = "https://pygreta.readthedocs.io/"
-urls.Homepage = "https://github.com/PauBadiaM/pygreta"
-urls.Source = "https://github.com/PauBadiaM/pygreta"
+urls.Documentation = "https://gretapy.readthedocs.io/"
+urls.Homepage = "https://github.com/PauBadiaM/gretapy"
+urls.Source = "https://github.com/PauBadiaM/gretapy"
 
 [dependency-groups]
 dev = [
@@ -138,7 +138,7 @@ addopts = [
 ]
 
 [tool.coverage.run]
-source = [ "pygreta" ]
+source = [ "gretapy" ]
 patch = [ "subprocess" ]
 omit = [
   "**/test_*.py",