refacgtor and fixed test

README.md

@@ -1,14 +1,14 @@
 <!--
 <p align="center">
-  <img src="https://github.com/hrshdhgd/ontobot-change-agent/raw/main/docs/source/logo.png" height="150">
+  <img src="https://github.com/INCATools/ontobot-change-agent/raw/main/docs/source/logo.png" height="150">
 </p>
 -->
 
 Update ontologies using change language.
 
 ## Getting Started
 
-[Read the docs](https://hrshdhgd.github.io/ontobot-change-agent/index.html)
+[Read the docs](https://INCATools.github.io/ontobot-change-agent/index.html)
 
 <!-- IMPLEMENTERS_START -->
 

docs/developers.rst

@@ -9,7 +9,7 @@ To install in development mode, use the following:
 .. code-block:: shell
 
     $ pip install poetry
-    $ git clone git+https://github.com/hrshdhgd/ontobot-change-agent.git
+    $ git clone git+https://github.com/INCATools/ontobot-change-agent.git
     $ cd ontobot-change-agent
     $ poetry install
 
@@ -23,4 +23,4 @@ the unit tests in the :code:`tests/` folder can be run reproducibly with:
 
     $ tox
 
-Additionally, these tests are automatically re-run with each commit in a `GitHub Action <https://github.com/hrshdhgd/ontobot-change-agent/actions?query=workflow%3ATests>`_.
+Additionally, these tests are automatically re-run with each commit in a `GitHub Action <https://github.com/INCATools/ontobot-change-agent/actions?query=workflow%3ATests>`_.

docs/implementation.rst

@@ -9,7 +9,7 @@ repository.
 
 1. Choosing of a GitHub workflow depends on the type of resource one is trying to edit:
 
-    - **OBO Resource**: The template for the workflow is provided by `this YAML file <https://github.com/hrshdhgd/ontobot-change-agent/blob/main/.github/workflows/new-pr.yml>`_.
+    - **OBO Resource**: The template for the workflow is provided by `this YAML file <https://github.com/INCATools/ontobot-change-agent/blob/main/.github/workflows/new-pr.yml>`_.
     Just uncomment the code and change the following:
 
     Update the resource (:code:`*.obo` file) path in the ontology's repository.
@@ -20,7 +20,7 @@ repository.
             echo "resource=src/ontology/YOUR-RESOURCE-FILENAME.obo" >> $GITHUB_ENV
             
 
-    - **OWL Resource**: The template for the workflow is provided by `this YAML file <https://github.com/hrshdhgd/ontobot-change-agent/blob/main/.github/workflows/new-pr-java.yml>`_.
+    - **OWL Resource**: The template for the workflow is provided by `this YAML file <https://github.com/INCATools/ontobot-change-agent/blob/main/.github/workflows/new-pr-java.yml>`_.
     Just uncomment the code and change the following:
 
     Update the resource (:code:`*.owl` file) path in the ontology's repository.
@@ -38,8 +38,8 @@ repository.
 
         - Use a standalone JAR file which combines both ROBOT and :code:`kgcl-java`.
 
-        We highly recommend using the standard option (#1). For this you should just uncomment `this code block <https://github.com/hrshdhgd/ontobot-change-agent/blob/b60d32375941c19672deace22b74814e04a73284/.github/workflows/new-pr-java.yml#L56-L62>`_
-        and delete `this code block <https://github.com/hrshdhgd/ontobot-change-agent/blob/b60d32375941c19672deace22b74814e04a73284/.github/workflows/new-pr-java.yml#L63-L68>`_
+        We highly recommend using the standard option (#1). For this you should just uncomment `this code block <https://github.com/INCATools/ontobot-change-agent/blob/b60d32375941c19672deace22b74814e04a73284/.github/workflows/new-pr-java.yml#L56-L62>`_
+        and delete `this code block <https://github.com/INCATools/ontobot-change-agent/blob/b60d32375941c19672deace22b74814e04a73284/.github/workflows/new-pr-java.yml#L63-L68>`_
 
 2. Create a `personal access token <https://docs.github.com/en/[email protected]/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token>`_ 
 and enter it in the "Secrets" section of the ontology repository `as explained here <https://docs.github.com/en/actions/security-guides/encrypted-secrets>`_.

docs/installation.rst

@@ -11,12 +11,12 @@ The most recent code and data can be installed directly from GitHub with:
 
 .. code-block:: shell
 
-    $ pip install git+https://github.com/hrshdhgd/ontobot-change-agent.git
+    $ pip install git+https://github.com/INCATools/ontobot-change-agent.git
 
 To install in development mode, use the following:
 
 .. code-block:: shell
 
-    $ git clone git+https://github.com/hrshdhgd/ontobot-change-agent.git
+    $ git clone git+https://github.com/INCATools/ontobot-change-agent.git
     $ cd ontobot-change-agent
     $ poetry install

src/ontobot_change_agent/api.py

@@ -28,7 +28,7 @@
 ONTOLOGY_RESOURCE = TESTS / "resources/fbbt.obo"
 # RESOURCE_DICT = {
 #     "hrshdhgd/mondo": "src/ontology/mondo-edit.obo",
-#     "hrshdhgd/ontobot-change-agent": ONTOLOGY_RESOURCE,
+#     "INCATools/ontobot-change-agent": ONTOLOGY_RESOURCE,
 # }
 
 # Token.txt unique to every user.

tests/test_api.py

@@ -14,7 +14,7 @@ class TestAPI(unittest.TestCase):
 
     def setUp(self) -> None:
         """Set up variables."""
-        self.repo_name = "hrshdhgd/ontobot-change-agent"
+        self.repo_name = "INCATools/ontobot-change-agent"
         self.label = "test"
         self.issue_title = "Test issue"
 
@@ -56,4 +56,4 @@ def test_get_all_labels_from_repo(self):
         label_dict = {}
         label_dict = get_all_labels_from_repo(self.repo_name)
 
-        self.assertEqual(len(label_dict), 12)
+        self.assertEqual(len(label_dict), 13)

tests/test_cli.py

@@ -17,7 +17,7 @@ def setUp(self):
         """Set up variables."""
         runner = CliRunner(mix_stderr=False)
         self.runner = runner
-        self.repo_name = "hrshdhgd/ontobot-change-agent"
+        self.repo_name = "INCATools/ontobot-change-agent"
         self.resource = str(ONTOLOGY_RESOURCE)
         self.output = TESTS / "resources/tmp/test.obo"