pymetadata 0.5.5__tar.gz → 0.5.6__tar.gz

{pymetadata-0.5.5 → pymetadata-0.5.6}/.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.5.5"
+current_version = "0.5.6"
 commit = true
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]

{pymetadata-0.5.5 → pymetadata-0.5.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymetadata
-Version: 0.5.5
+Version: 0.5.6
 Summary: pymetadata are python utilities for working with metadata.
 Author-email: Matthias König <konigmatt@googlemail.com>
 Maintainer-email: Matthias König <konigmatt@googlemail.com>
@@ -53,9 +53,9 @@ metadata in the context of COMBINE standards with source code available from
 
 Features include among others
 
-- [core](src/pymetadata/core)COMBINE archive version 1 support (OMEX)
+- COMBINE archive version 1 support (OMEX)
 - annotation classes and helpers
-- SBO and KISAO ontology enums
+- SBO, KISAO and ECO ontology enums
 
 If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/pymetadata/issues).
 
@@ -66,8 +66,6 @@ see [omex_example.py](src/pymetadata/examples/omex_example.py).
 # How to cite
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg)](https://doi.org/10.5281/zenodo.5308801)
 
-# Contributing
-Contributions are always welcome! Please read the [contributing guidelines](https://github.com/matthiaskoenig/pymetadata/blob/develop/.github/CONTRIBUTING.rst) to get started.
 
 # License
 - Source Code: [MIT](https://opensource.org/license/MIT)
@@ -84,19 +82,6 @@ can be installed via
 pip install pymetadata
 ```
 
-## Develop version
-The latest develop version can be installed via
-```bash
-pip install git+https://github.com/matthiaskoenig/pymetadata.git@develop
-```
-
-Or via cloning the repository and installing via
-```bash
-git clone https://github.com/matthiaskoenig/pymetadata.git
-cd pymetadata
-pip install -e .
-```
-
 # Cache path
 `pymetadata` caches some information for faster retrieval. The cache path is set to
 

{pymetadata-0.5.5 → pymetadata-0.5.6}/README.md

@@ -13,9 +13,9 @@ metadata in the context of COMBINE standards with source code available from
 
 Features include among others
 
-- [core](src/pymetadata/core)COMBINE archive version 1 support (OMEX)
+- COMBINE archive version 1 support (OMEX)
 - annotation classes and helpers
-- SBO and KISAO ontology enums
+- SBO, KISAO and ECO ontology enums
 
 If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/pymetadata/issues).
 
@@ -26,8 +26,6 @@ see [omex_example.py](src/pymetadata/examples/omex_example.py).
 # How to cite
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg)](https://doi.org/10.5281/zenodo.5308801)
 
-# Contributing
-Contributions are always welcome! Please read the [contributing guidelines](https://github.com/matthiaskoenig/pymetadata/blob/develop/.github/CONTRIBUTING.rst) to get started.
 
 # License
 - Source Code: [MIT](https://opensource.org/license/MIT)
@@ -44,19 +42,6 @@ can be installed via
 pip install pymetadata
 ```
 
-## Develop version
-The latest develop version can be installed via
-```bash
-pip install git+https://github.com/matthiaskoenig/pymetadata.git@develop
-```
-
-Or via cloning the repository and installing via
-```bash
-git clone https://github.com/matthiaskoenig/pymetadata.git
-cd pymetadata
-pip install -e .
-```
-
 # Cache path
 `pymetadata` caches some information for faster retrieval. The cache path is set to
 

pymetadata-0.5.6/release-notes/0.5.6.md

@@ -0,0 +1,10 @@
+# Release notes for pymetadata 0.5.6
+![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
+
+We are pleased to release the next version of pymetadata including the
+following changes:
+
+## Features & fixes
+- bugfix compact ids when id starts with namespace
+
+Your pymetadata team

{pymetadata-0.5.5 → pymetadata-0.5.6}/src/pymetadata/__init__.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 __author__ = "Matthias Koenig"
-__version__ = "0.5.5"
+__version__ = "0.5.6"
 
 
 program_name: str = "pymetadata"

{pymetadata-0.5.5 → pymetadata-0.5.6}/src/pymetadata/core/annotation.py

@@ -184,7 +184,7 @@ class RDFAnnotation:
         namespace = REGISTRY.ns_dict.get(collection, None)
         if namespace and not namespace.namespaceEmbeddedInLui:
             # shorter term
-            if term.lower().startswith(collection):
+            if term.lower().startswith(f"{collection}:"):
                 tokens = term.split(":")
                 term = ":".join(tokens[1:])
 
@@ -399,10 +399,14 @@ if __name__ == "__main__":
     for annotation in [
         RDFAnnotation(
             qualifier=BQB.IS_VERSION_OF,
-            resource="https://bioregistry.io/chebi:15996",
+            resource="hmdb/HMDB0000122",
         ),
         # RDFAnnotation(
         #     qualifier=BQB.IS_VERSION_OF,
+        #     resource="https://bioregistry.io/chebi:15996",
+        # ),
+        # RDFAnnotation(
+        #     qualifier=BQB.IS_VERSION_OF,
         #     resource="NCIT:C75913",
         # ),
         # RDFAnnotation(

{pymetadata-0.5.5 → pymetadata-0.5.6}/tests/core/test_annotation.py

@@ -144,6 +144,16 @@ rdf_annotation_data = [
         "https://bioregistry.io/chebi:15996",
         "RDFAnnotation(BQB.IS|None|https://bioregistry.io/chebi:15996|bioregistry.io)",
     ),
+    (
+        BQB.IS,
+        "hmdb/HMDB0000122",
+        "RDFAnnotation(BQB.IS|hmdb|HMDB0000122|identifiers.org)",
+    ),
+    (
+        BQB.IS,
+        "hmdb:HMDB0000122",
+        "RDFAnnotation(BQB.IS|hmdb|HMDB0000122|identifiers.org)",
+    ),
 ]