fix for registry.txt not packaged to pypi

Author: teanijarv

MANIFEST.in

@@ -0,0 +1,4 @@
+include pyproject.toml
+include README.md
+include LICENSE
+recursive-include yabplot *.txt *.json *.md

README.md

@@ -5,7 +5,7 @@
 [![PyPI version](https://img.shields.io/pypi/v/yabplot.svg)](https://pypi.org/project/yabplot/)
 [![Docs](https://github.com/teanijarv/yabplot/actions/workflows/docs.yml/badge.svg)](https://teanijarv.github.io/yabplot/)
 [![Tests](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml/badge.svg)](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml)
-<!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.XXXXXX.svg)](https://doi.org/10.5281/zenodo.XXXXXX) -->
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18237144.svg)](https://doi.org/10.5281/zenodo.18237144)
 
 **yabplot** is a Python library for creating beautiful, publication-quality 3D brain visualizations. it supports plotting cortical regions, subcortical structures, and white matter bundles.
 
@@ -71,4 +71,4 @@ yab.plot_tracts(data=data, atlas='xtract_tiny', figsize=(600, 300),
 
 ## acknowledgements
 
-yabplot relies on the extensive work of the neuroimaging community. if you use these atlases in your work, please cite the original authors.
+yabplot relies on the extensive work of the neuroimaging community. if you use these atlases in your work, please cite the original authors. if you use this package for any scientific work, please cite the DOI (see more info on [Zenodo](https://doi.org/10.5281/zenodo.18237144)).

docs/index.md

@@ -5,7 +5,7 @@
 [![PyPI version](https://img.shields.io/pypi/v/yabplot.svg)](https://pypi.org/project/yabplot/)
 [![Docs](https://github.com/teanijarv/yabplot/actions/workflows/docs.yml/badge.svg)](https://teanijarv.github.io/yabplot/)
 [![Tests](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml/badge.svg)](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml)
-<!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.XXXXXX.svg)](https://doi.org/10.5281/zenodo.XXXXXX) -->
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18237144.svg)](https://doi.org/10.5281/zenodo.18237144)
 
 **yabplot** is a Python library for creating beautiful, publication-quality 3D brain visualizations. it supports plotting cortical regions, subcortical structures, and white matter bundles.
 
@@ -71,4 +71,4 @@ yab.plot_tracts(data=data, atlas='xtract_tiny', figsize=(600, 300),
 
 ## acknowledgements
 
-yabplot relies on the extensive work of the neuroimaging community. if you use these atlases in your work, please cite the original authors.
+yabplot relies on the extensive work of the neuroimaging community. if you use these atlases in your work, please cite the original authors. if you use this package for any scientific work, please cite the DOI (see more info on [Zenodo](https://doi.org/10.5281/zenodo.18237144)).

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "yabplot"
-version = "0.1.0"
+version = "0.1.1"
 description = "yet another brain plot"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -23,3 +23,10 @@ dependencies = [
       "mkdocs-material",
       "mkdocstrings[python]",
 ]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["yabplot*"]
+
+[tool.setuptools.package-data]
+"yabplot" = ["*.txt", "*.json"]

yabplot/data/__init__.py

@@ -4,28 +4,26 @@
 
 import os
 import glob
-import shutil
+from pathlib import Path
 import pooch
-from importlib.resources import files
 
 from ..utils import parse_lut
 
-__all__ = ['get_available_resources']
+__all__ = ['get_available_resources', 'get_atlas_regions']
 
 # define cache location
-# e.g., ~/.cache/yabplot
 CACHE_DIR = pooch.os_cache("yabplot")
 
 # setup registry
-_REGISTRY_PATH = files('yabplot.data').joinpath('registry.txt')
-_FETCHER = pooch.create(
+HERE = Path(__file__).parent
+REGISTRY_FILE = HERE / "registry.txt"
+
+GOODBOY = pooch.create(
     path=CACHE_DIR,
-    base_url="", 
+    base_url="",
     registry=None,
 )
-
-if _REGISTRY_PATH.is_file():
-    _FETCHER.load_registry(_REGISTRY_PATH)
+GOODBOY.load_registry(REGISTRY_FILE)
 
 
 def get_available_resources(category=None):
@@ -39,7 +37,7 @@ def get_available_resources(category=None):
         for that specific category.
         If None, returns a dictionary containing all categories and their options.
     """
-    if not _FETCHER.registry:
+    if not GOODBOY.registry:
         return [] if category else {}
 
     # helper to clean names: e.g., "cortical-aparc.zip" -> ("cortical", "aparc")
@@ -52,15 +50,15 @@ def _parse_key(key):
     # mode 1: specific category
     if category:
         available = []
-        for key in _FETCHER.registry.keys():
+        for key in GOODBOY.registry.keys():
             prefix, name = _parse_key(key)
             if prefix == category:
                 available.append(name)
         return sorted(available)
 
     # mode 2: all categories
     all_resources = {}
-    for key in _FETCHER.registry.keys():
+    for key in GOODBOY.registry.keys():
         prefix, name = _parse_key(key)
         if prefix and name:
             if prefix not in all_resources:
@@ -147,7 +145,7 @@ def _fetch_and_unpack(resource_key):
     and returns the extraction path.
     """
     extract_dir_name = resource_key.replace(".zip", "")
-    extract_path = os.path.join(_FETCHER.path, extract_dir_name)
+    extract_path = os.path.join(GOODBOY.path, extract_dir_name)
 
     # optimization: check if unpacked folder already exists
     # if yes, skip pooch check entirely to avoid re-downloading
@@ -156,17 +154,17 @@ def _fetch_and_unpack(resource_key):
 
     # fetch and unzip
     try:
-        _FETCHER.fetch(
+        GOODBOY.fetch(
             resource_key, 
             processor=pooch.Unzip(extract_dir=extract_dir_name)
         )
     except ValueError:
         # if key not in registry
-        available = list(_FETCHER.registry.keys())
+        available = list(GOODBOY.registry.keys())
         raise ValueError(f"Resource '{resource_key}' not found in registry.")
 
     # cleanup: delete the source zip to save space
-    zip_path = os.path.join(_FETCHER.path, resource_key)
+    zip_path = os.path.join(GOODBOY.path, resource_key)
     if os.path.exists(zip_path):
         os.remove(zip_path)
 
@@ -187,7 +185,7 @@ def _resolve_resource_path(name, category, custom_path=None):
     resource_key = f"{category}-{name}.zip"
 
     # validate before fetching
-    if resource_key not in _FETCHER.registry:
+    if resource_key not in GOODBOY.registry:
         available = get_available_resources(category)
         human_cat = {
             'cortical': 'Cortical parcellations (vertices)',