remove skeleton, use a similar structure as txdb

.github/workflows/run-tests.yml

@@ -32,7 +32,7 @@ jobs:
         platform:
           - ubuntu-latest
           - macos-latest
-          - windows-latest
+          # - windows-latest
     runs-on: ${{ matrix.platform }}
     name: Python ${{ matrix.python }}, ${{ matrix.platform }}
     steps:

CHANGELOG.md

@@ -1,7 +1,6 @@
 # Changelog
 
-## Version 0.1 (development)
+## Version 0.0.1 
 
-- Feature A added
-- FIX: nasty bug #1729 fixed
-- add your changes here!
+- Initial implementation to access OrgDB objects. 
+- This also fetches the annotation hub sqlite file and queries for available org sqlite files instead of a static registry used in the txdb package.

README.md

@@ -1,11 +1,13 @@
 [![PyPI-Server](https://img.shields.io/pypi/v/orgdb.svg)](https://pypi.org/project/orgdb/)
-![Unit tests](https://github.com/YOUR_ORG_OR_USERNAME/orgdb/actions/workflows/run-tests.yml/badge.svg)
+![Unit tests](https://github.com/BiocPy/orgdb/actions/workflows/run-tests.yml/badge.svg)
 
 # orgdb
 
-> Access OrgDB annotations
+**OrgDb** provides an interface to access and query **Organism Database (OrgDb)** SQLite files in Python. It mirrors functionality from the R/Bioconductor `AnnotationDbi` package, enabling seamless integration of organism-wide gene annotation into Python workflows.
 
-A longer description of your project goes here...
+> [!NOTE]
+>
+> If you are looking to access TxDb databases, check out the [txdb package](https://www.github.com/biocpy/txdb).
 
 ## Install
 
@@ -15,6 +17,107 @@ To get started, install the package from [PyPI](https://pypi.org/project/orgdb/)
 pip install orgdb
 ```
 
+## Usage
+
+### Using OrgDbRegistry
+
+The registry download the AnnotationHub's metadata sqlite file and filters for all available OrgDb databases. You can fetch standard organism databases via the registry (backed by AnnotationHub).
+
+```py
+from orgdb import OrgDbRegistry
+
+# Initialize registry and list available organisms
+registry = OrgDbRegistry()
+available = registry.list_orgdb()
+print(available[:5])
+# ["org.'Caballeronia_concitans'.eg", "org.'Chlorella_vulgaris'_C-169.eg", ...]
+
+# Load the database for Homo sapiens (downloads and caches automatically)
+db = registry.load_db("org.Hs.eg.db")
+print(db.species)
+# 'Homo sapiens'
+```
+
+### Inspecting metadata
+
+Explore the available columns and key types in the database.
+
+```py
+# List available columns (and keytypes)
+cols = db.columns()
+print(cols[:5])
+# ['ENTREZID', 'PFAM', 'IPI', 'PROSITE', 'ACCNUM']
+
+# Check available keys for a specific keytype
+entrez_ids = db.keys("ENTREZID")
+print(entrez_ids[:5])
+# ['1', '2', '9', '10', '11']
+```
+
+### Querying Annotations (using `select`)
+
+The `select` method retrieves data as a `BiocFrame`. It automatically handles complex joins across tables.
+
+```py
+# Retrieve Gene Symbols and Gene Names for a list of Entrez IDs
+res = db.select(
+    keys=["1", "10"],
+    columns=["SYMBOL", "GENENAME"],
+    keytype="ENTREZID"
+)
+
+print(res)
+# BiocFrame with 2 rows and 3 columns
+                   GENENAME ENTREZID SYMBOL
+                     <list>   <list> <list>
+# [0] alpha-1-B glycoprotein        1   A1BG
+# [1]  N-acetyltransferase 2       10   NAT2
+
+```
+
+> [!NOTE]
+>
+> If you request "GO" columns, the result will automatically expand to include "EVIDENCE" and "ONTOLOGY" columns, matching Bioconductor behavior.
+
+```py
+go_res = db.select(
+    keys="1",
+    columns=["GO"],
+    keytype="ENTREZID"
+)
+# BiocFrame with 12 rows and 4 columns
+       ONTOLOGY ENTREZID         GO EVIDENCE
+         <list>   <list>     <list>   <list>
+#  [0]       BP        1 GO:0002764      IBA
+#  [1]       CC        1 GO:0005576      HDA
+#  [2]       CC        1 GO:0005576      IDA
+#           ...      ...        ...      ...
+#  [9]       CC        1 GO:0070062      HDA
+# [10]       CC        1 GO:0072562      HDA
+# [11]       CC        1 GO:1904813      TAS
+```
+
+### Accessing Genomic Ranges
+
+Extract gene coordinates as a `GenomicRanges` object (requires the `chromosome_locations` table in the OrgDb database).
+
+```py
+gr = db.genes()
+print(gr)
+# GenomicRanges with 52232 ranges and 1 metadata column
+#           seqnames                ranges          strand     gene_id
+#              <str>             <IRanges> <ndarray[int8]>      <list>
+#         1       19 -58345182 - -58336872               * |         1
+#         2       12   -9067707 - -9019495               * |         2
+#         2       12   -9067707 - -9019185               * |         2
+#                ...                   ...             ... |       ...
+# 116804918       11 121024101 - 121191490               * | 116804918
+# 117779438        1   20154213 - 20160568               * | 117779438
+# 118142757        6   42155405 - 42180056               * | 118142757
+# ------
+# seqinfo(369 sequences): 1 10 10_GL383545v1_alt ... X_KI270913v1_alt Y Y_KZ208924v1_fix
+```
+
 <!-- biocsetup-notes -->
 
 ## Note

docs/index.md

@@ -1,18 +1,14 @@
 # orgdb
 
-Access OrgDB annotations
+**OrgDb** provides an interface to access and query **Organism Database (OrgDb)** SQLite files in Python. It mirrors functionality from the R/Bioconductor `AnnotationDbi` package, enabling seamless integration of organism-wide gene annotation into Python workflows.
 
+## Install
 
-## Note
-
-> This is the main page of your project's [Sphinx] documentation. It is
-> formatted in [Markdown]. Add additional pages by creating md-files in
-> `docs` or rst-files (formatted in [reStructuredText]) and adding links to
-> them in the `Contents` section below.
->
-> Please check [Sphinx] and [MyST] for more information
-> about how to document your project and how to configure your preferences.
+To get started, install the package from [PyPI](https://pypi.org/project/orgdb/)
 
+```bash
+pip install orgdb
+```
 
 ## Contents
 

setup.cfg

@@ -12,11 +12,11 @@ license = MIT
 license_files = LICENSE.txt
 long_description = file: README.md
 long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
-url = https://github.com/pyscaffold/pyscaffold/
+url = https://github.com/BiocPy/orgdb
 # Add here related links, for example:
 project_urls =
-    Documentation = https://pyscaffold.org/
-#    Source = https://github.com/pyscaffold/pyscaffold/
+    Documentation = https://github.com/BiocPy/orgdb
+   Source = https://github.com/BiocPy/orgdb
 #    Changelog = https://pyscaffold.org/en/latest/changelog.html
 #    Tracker = https://github.com/pyscaffold/pyscaffold/issues
 #    Conda-Forge = https://anaconda.org/conda-forge/pyscaffold
@@ -49,6 +49,9 @@ package_dir =
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
+    genomicranges
+    biocframe
+    pybiocfilecache
 
 
 [options.packages.find]

src/orgdb/__init__.py

@@ -14,3 +14,9 @@
     __version__ = "unknown"
 finally:
     del version, PackageNotFoundError
+
+from .orgdb import OrgDb
+from .orgdbregistry import OrgDbRegistry
+from .record import OrgDbRecord
+
+__all__ = ["OrgDb", "OrgDbRegistry", "OrgDbRecord"]

src/orgdb/_ahub.py

@@ -0,0 +1,31 @@
+"""This list of OrgDB resources was generated from AnnotationHub.
+
+Code to generate:
+
+```bash
+wget https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3
+sqlite3 annotationhub.sqlite3
+```
+
+```sql
+SELECT
+    r.title,
+    r.rdatadateadded,
+    lp.location_prefix || rp.rdatapath AS full_rdatapath
+FROM resources r
+LEFT JOIN location_prefixes lp
+    ON r.location_prefix_id = lp.id
+LEFT JOIN rdatapaths rp
+    ON rp.resource_id = r.id
+WHERE r.title LIKE 'org%.sqlite';
+```
+
+Note: we only keep the latest version of these files.
+
+"""
+
+__author__ = "Jayaram Kancherla"
+__copyright__ = "Jayaram Kancherla"
+__license__ = "MIT"
+
+AHUB_METADATA_URL = "https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3"