Merge pull request #70 from ielis/release-v0.5.1

Make release `v0.5.1`
ielis · May 20, 2024 · 5912542 · 5912542
2 parents c3dea26 + e53ca09
commit 5912542
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diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml
@@ -24,12 +24,7 @@ jobs:
             python-version: ${{ matrix.python }}
         - name: Install hpo-toolkit
           run: |
-            python3 -m pip install --editable .[test,docs]
-        - name: Run tests
+            python3 -m pip install --editable .[test]
+        - name: Run all tests
           run: |
-            pytest
-        - name: Run documentation tests
-          run: |
-            cd docs
-            sphinx-apidoc --separate --module-first -d 2 -H "API reference" -o apidocs ../src/hpotk
-            make doctest
+            pytest src docs tests
diff --git a/README.md b/README.md
@@ -1,8 +1,9 @@
 # hpo-toolkit
 
-![Build status](https://img.shields.io/github/actions/workflow/status/TheJacksonLaboratory/hpo-toolkit/python_ci.yml)
-![PyPi downloads](https://img.shields.io/pypi/dm/hpo-toolkit.svg?label=Pypi%20downloads)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/hpo-toolkit)
+![PyPi downloads](https://img.shields.io/pypi/dm/hpo-toolkit.svg?label=Pypi%20downloads)
+![Build status](https://img.shields.io/github/actions/workflow/status/ielis/hpo-toolkit/python_ci.yml)
+[![GitHub release](https://img.shields.io/github/release/ielis/hpo-toolkit.svg)](https://github.com/ielis/hpo-toolkit/releases)
 
 A toolkit for working with Human Phenotype Ontology (HPO) and HPO disease annotations in Python.
 
@@ -38,5 +39,5 @@ You got yourself phenotype annotations of 12,468 rare diseases.
 
 Find more info in our detailed documentation:
 
-- [Stable documentation](https://thejacksonlaboratory.github.io/hpo-toolkit/stable) (last release on `main` branch)
-- [Latest documentation](https://thejacksonlaboratory.github.io/hpo-toolkit/latest) (bleeding edge, latest commit on `development` branch)
+- [Stable documentation](https://ielis.github.io/hpo-toolkit/stable) (last release on `main` branch)
+- [Latest documentation](https://ielis.github.io/hpo-toolkit/latest) (bleeding edge, latest commit on `development` branch)
diff --git a/docs/conf.py b/docs/conf.py
@@ -3,7 +3,7 @@
 
 hpotk_src = os.path.abspath(os.path.join('..', 'src'))
 sys.path.insert(0, hpotk_src)
-# The import order is crucial to prevent having to install the library before generating documetation.
+# The import order is crucial to prevent having to install the library before generating documentation.
 import hpotk
 
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -28,5 +28,5 @@ Feedback
 --------
 
 The best place to leave feedback, ask questions, and report bugs is the
-`HPO Toolkit's Issue Tracker <https://github.com/TheJacksonLaboratory/hpo-toolkit/issues>`_.
+`HPO Toolkit's Issue Tracker <https://github.com/ielis/hpo-toolkit/issues>`_.
 
diff --git a/docs/setup.rst b/docs/setup.rst
@@ -20,7 +20,7 @@ The bleeding edge code
 
 To access the bleeding edge features, the development version can be installed by::
 
-  git clone https://github.com/TheJacksonLaboratory/hpo-toolkit.git
+  git clone https://github.com/ielis/hpo-toolkit.git
   cd hpo-toolkit
   git checkout development && git pull
   python3 -m pip install .
@@ -33,23 +33,14 @@ Run tests
 
 The contributors may want to run the unit tests and the integration tests to ensure all features work as expected.
 
-Before running tests, make sure you install HPO toolkit with `test` and `docs` dependencies::
+Before running tests, make sure you install HPO toolkit with `test` dependencies::
 
-  python3 -m pip install .[test,docs]
+  python3 -m pip install .[test]
 
-The unit tests and the integration tests can the be running by invoking the `pytest` runner::
+The unit tests, integration tests, doctests, and the tutorial scripts can the be running by invoking the `pytest` runner::
 
   pytest
 
-We go extra mile to ensure the documentation is always up-to-date, and, therefore, we also run the documentation tests.
-The documentation tests are run by::
-
-  cd docs
-  sphinx-apidoc --separate --module-first -d 2 -H "API reference" -o apidocs ../src/hpotk
-  make doctest
-
-.. note::
-
   The library *must* be installed in the environment before running all tests. Otherwise, the test discovery will fail.
 
 Run benches
@@ -58,7 +49,7 @@ Run benches
 Bench suites provide an idea about the performance of the library.
 Running a bench requires checking out the GitHub repository and installing HPO toolkit with `bench` dependencies::
 
-  git clone https://github.com/TheJacksonLaboratory/hpo-toolkit.git
+  git clone https://github.com/ielis/hpo-toolkit.git
   cd hpo-toolkit
   python3 -m pip install .[bench]
 

diff --git a/docs/user-guide/sort-term-ids.rst b/docs/user-guide/sort-term-ids.rst
@@ -10,16 +10,15 @@ HPO toolkit provides logic for sorting HPO terms such that the similar terms are
 
 Let's illustrate this on example. Suppose having a subject annotated with the following terms:
 
-.. doctest:: sort-term-ids
-
-  >>> subject = (
-  ...   'HP:0001744',  # Splenomegaly
-  ...   'HP:0020221',  # Clonic seizure
-  ...   'HP:0001238',  # Slender finger
-  ...   'HP:0011153',  # Focal motor seizure
-  ...   'HP:0002240'   # Hepatomegaly
-  ... )
-  >>> term_ids = tuple(TermId.from_curie(curie) for curie in subject)
+>>> import hpotk
+>>> subject = (
+...   'HP:0001744',  # Splenomegaly
+...   'HP:0020221',  # Clonic seizure
+...   'HP:0001238',  # Slender finger
+...   'HP:0011153',  # Focal motor seizure
+...   'HP:0002240'   # Hepatomegaly
+... )
+>>> term_ids = tuple(hpotk.TermId.from_curie(curie) for curie in subject)
 
 
 The order of HPO annotations does not reflect that *Splenomegaly* is more "similar" to *Hepatomegaly* than
@@ -39,18 +38,18 @@ The algorithm iteratively chooses the most similar term ID pairs and places them
 
 We'll use a toy HPO with several terms to present the functionality:
 
-.. doctest:: sort-term-ids
+>>> import os
+>>> fpath_hpo = os.path.join('docs', 'data', 'hp.toy.json')
+>>> hpo = hpotk.load_minimal_ontology(fpath_hpo)
 
-  >>> from hpotk.util.sort import HierarchicalEdgeTermIdSorting
-  >>> hpo = hpotk.load_minimal_ontology('data/hp.toy.json')
-  >>> sorting = HierarchicalEdgeTermIdSorting(hpo)
+>>> from hpotk.util.sort import HierarchicalEdgeTermIdSorting
+>>> sorting = HierarchicalEdgeTermIdSorting(hpo)
 
 We can obtain the indices that will sort the HPO terms and prepare a `tuple` with sorted terms:
 
-.. doctest:: sort-term-ids
 
-  >>> indices = sorting.argsort(term_ids)
-  >>> ordered = tuple(term_ids[idx] for idx in indices)
+>>> indices = sorting.argsort(term_ids)
+>>> ordered = tuple(term_ids[idx] for idx in indices)
 
 Now let's look at the order. Originally, the HPO terms were ordered as follows::
 
@@ -62,14 +61,13 @@ Now let's look at the order. Originally, the HPO terms were ordered as follows::
 
 After the sorting, we get this order:
 
-.. doctest:: sort-term-ids
 
-  >>> for term_id in ordered:
-  ...   print(hpo.get_term(term_id).name)
-  Focal motor seizure
-  Clonic seizure
-  Hepatomegaly
-  Splenomegaly
-  Slender finger
+>>> for term_id in ordered:
+...   print(hpo.get_term(term_id).name)
+Focal motor seizure
+Clonic seizure
+Hepatomegaly
+Splenomegaly
+Slender finger
 
 which is much better, right?
diff --git a/docs/user-guide/use-hierarchy.rst b/docs/user-guide/use-hierarchy.rst
@@ -14,12 +14,13 @@ HPO toolkit enables accessing the ontology hierarchy through the :class:`hpotk.g
 in turn available through :class:`hpotk.ontology.MinimalOntology`. In other words, each ontology has the ontology graph
 as a property:
 
-.. doctest:: traverse-hierarchy
+>>> import os
+>>> import hpotk
 
-  >>> import hpotk
-  >>> hpo = hpotk.load_minimal_ontology('data/hp.toy.json')
-  >>> hpo.graph
-  CsrIndexedOntologyGraph(root=HP:0000001, n_nodes=393)
+>>> fpath_hpo = os.path.join('docs', 'data', 'hp.toy.json')
+>>> hpo = hpotk.load_minimal_ontology(fpath_hpo)
+>>> hpo.graph
+CsrIndexedOntologyGraph(root=HP:0000001, n_nodes=393)
 
 
 We can leverage the hierarchy to infer a lot of extra information about the concepts, and, for instance,
@@ -37,23 +38,19 @@ a term instead of successor/predecessors of a node. Let's illustrate this on a c
 We can get term IDs of the *parents* of a term, such as `Seizure <https://hpo.jax.org/app/browse/term/HP:0001250>`_
 [`HP:0001250`] by calling:
 
-.. doctest:: traverse-hierarchy
-
-  >>> for parent in hpo.graph.get_parents('HP:0001250'):
-  ...   print(parent)
-  HP:0012638
+>>> for parent in hpo.graph.get_parents('HP:0001250'):
+...   print(parent)
+HP:0012638
 
 `HP:0012638` corresponds to
 `Abnormal nervous system physiology <https://hpo.jax.org/app/browse/term/HP:0012638>`_.
 
 *Children* are accessed in a similar fashion:
 
-.. doctest:: traverse-hierarchy
-
-  >>> for child in hpo.graph.get_children('HP:0001250'):
-  ...   print(child)
-  HP:0020219
-  HP:0007359
+>>> for child in hpo.graph.get_children('HP:0001250'):
+...   print(child)
+HP:0020219
+HP:0007359
 
 
 We will leave finding the ancestors or descendants of a term as an exercise for the interested reader.
@@ -66,13 +63,11 @@ ancestors/descendants of each other.
 
 We can test if Seizure [`HP:0001250`] is a parent or an ancestor of Clonic seizure [`HP:0020221`]:
 
-.. doctest:: traverse-hierarchy
-
-  >>> hpo.graph.is_parent_of('HP:0001250', 'HP:0020221')
-  False
+>>> hpo.graph.is_parent_of('HP:0001250', 'HP:0020221')
+False
 
-  >>> hpo.graph.is_ancestor_of('HP:0001250', 'HP:0020221')
-  True
+>>> hpo.graph.is_ancestor_of('HP:0001250', 'HP:0020221')
+True
 
 Similar methods exist for checking if a term is a child or a descendant of another term.