Merge pull request #25 from NatalieThurlby/dev

Dev

.gitignore

@@ -7,3 +7,4 @@ tests/data/
 __pycache__/
 *.egg-info/
 .idea/
+docs/contents/api

docs/conf.py

@@ -16,6 +16,7 @@
 from distutils.util import convert_path
 
 sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('..'))
 
 # get version:
 ns = {}
@@ -41,8 +42,12 @@
 # extensions coming with Sphinx (named 'sphinx._ext.*') or your custom
 # ones.
 extensions += [
-    'myst_nb'
+    'myst_nb',
+    # "sphinxarg.ext",
+    'sphinx.ext.autosummary',
 ]
+autosummary_generate = True
+
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -63,8 +68,24 @@
 html_theme_options = {
     'github_url': 'https://github.com/NatalieThurlby/ontolopy',
     'twitter_url': 'https://twitter.com/hashtag/ontolopy',
-    'search_bar_text': 'Search this site...',
-    'search_bar_position': 'navbar',
+    'search_bar_text': 'Search the docs...',
+    "icon_links": [
+        {
+            "name": "PyPI",
+            "url": "https://pypi.org/project/ontolopy",
+            "icon": "fas fa-box-open",
+        }
+    ],
+    "search_bar_position": "navbar"
+}
+
+html_sidebars = {
+    'index': [],
+    'contents/changelog': [],
+    'contents/installation': [],
+    'contents/quickstart': [],
+    'contents/develop': [],
+    'contents/roadmap': [],
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,

docs/contents/changelog.md

@@ -2,6 +2,28 @@
 
 [//]: # (TODO: Link to GitHub releases)
 
+## [1.1.0-beta](https://github.com//NatalieThurlby/ontolopy/compare/1.0.2-beta...1.1.0-beta)
+- New functionality:
+    - `Obo()` class:
+        - Added `opy.Obo.merge()`: merge one ontology into another.
+        - Added `opy.Obo.from_dict()`: create `Obo()` from a dictionary.
+        - Added `opy.Obo.copy()`: copies `Obo()` object.
+        - Separated `load_obo` from `Obo()` class.
+        - Added local functions that are used to extract synonyms and synonym types from synonym strings.
+    - new `opy.uberon` module, containing:
+        - `Uberon()` class that inherits from `Obo()`, including `sample_map_by_ont` method.
+        - `uberon_from_obo` function
+    - new `Relations.format_all` method.
+- Refactoring:
+    - Made the static class variables for reading ontologies private variables.
+    - Refactored `opy.relations.Relations` class to subclass Pandas DataFrame.
+- Testing:    
+    - Added test for `obo.Obo.merge()`.
+    - Updated tests to include new behaviour for synonyms
+- Documentation:
+    - Improved docstrings for `Obo()` class.
+    - Set up sphinx autodoc and used to document `Obo()` class.
+
 ## [1.0.2-beta](https://github.com//NatalieThurlby/ontolopy/compare/1.0.1-beta...1.0.2-beta)
 - Fixed GitHub action for versioned docs [[#9](https://github.com/NatalieThurlby/ontolopy/issues/9)]
 

docs/contents/reference.md

@@ -0,0 +1,21 @@
+# API Reference
+
+```{admonition} What's an API?
+API stands for "Application Programming Interface". Ontolopy's API Reference describes everything you needs to know about Ontolopy to know how to use it. It describes all public objects, modules, and functions.
+```
+
+## `ontolopy.obo`
+
+The `ontolopy.obo` module contains code for creating and working with the `Obo` class: objects that represent ontologies.
+
+```{eval-rst}
+.. currentmodule:: ontolopy.obo
+
+.. autosummary::
+   :toctree: api/
+
+   Obo
+   Obo.merge   
+   download_obo
+   load_obo
+```

docs/contents/roadmap.md

@@ -1,4 +1,4 @@
-# Road map
+# Road-map
 
 This road map is subject to change, but exists to give an outline of plans for Ontolopy in the near future:
 - Increase test coverage

docs/index.md

@@ -17,4 +17,5 @@ contents/quickstart
 contents/changelog
 contents/roadmap
 contents/develop
+contents/reference
 ```

ontolopy/__init__.py

@@ -1,2 +1,3 @@
-from .obo import Obo, validate_term, get_obo
-from .relations import Relations
+from .obo import Obo, download_obo, load_obo
+from .relations import Relations, relation_path_to_text
+from .uberon import Uberon, uberon_from_obo