Remove reliance on locally stored CITATION.cff file:

- Use `requests` to get the `CITATION.cff` file from GitHub rather than locally in the project directory
- If there are network issues display a minimal splash screen with just ASCII art
- Update unit tests to ensure all new functionality is covered

Author: harryswift01

CodeEntropy/run.py

@@ -3,6 +3,7 @@
 import pickle
 
 import MDAnalysis as mda
+import requests
 import yaml
 from art import text2art
 from MDAnalysis.analysis.base import AnalysisFromFunction
@@ -95,71 +96,91 @@ def create_job_folder():
         # Return the path of the newly created folder
         return new_folder_path
 
-    def load_citation_data(self, path="CITATION.cff"):
-        """"""
-        with open(path, "r", encoding="utf-8") as file:
-            return yaml.safe_load(file)
+    def load_citation_data(self):
+        """
+        Load CITATION.cff from GitHub into memory.
+        Return empty dict if offline.
+        """
+        url = (
+            "https://raw.githubusercontent.com/CCPBioSim/"
+            "CodeEntropy/refs/heads/main/CITATION.cffs"
+        )
+        try:
+            response = requests.get(url, timeout=10)
+            response.raise_for_status()
+            return yaml.safe_load(response.text)
+        except requests.exceptions.RequestException:
+            return None
 
     def show_splash(self):
-        """"""
+        """Render splash screen with optional citation metadata."""
         citation = self.load_citation_data()
 
-        # ASCII Title
-        ascii_title = text2art(citation.get("title", "CodeEntropy"))
-        ascii_render = Align.center(Text(ascii_title, style="bold white"))
-
-        # Metadata
-        version = citation.get("version", "?")
-        release_date = citation.get("date-released", "?")
-        url = citation.get("url", citation.get("repository-code", ""))
-
-        version_text = Align.center(
-            Text(f"Version {version} | Released {release_date}", style="green")
-        )
-        url_text = Align.center(Text(url, style="blue underline"))
-
-        # Description block
-        abstract = citation.get("abstract", "No description available.")
-        description_title = Align.center(
-            Text("Description", style="bold magenta underline")
-        )
-        description_body = Align.center(
-            Padding(Text(abstract, style="white", justify="left"), (0, 4))
-        )
-
-        # Contributors table
-        contributors_title = Align.center(
-            Text("Contributors", style="bold magenta underline")
-        )
+        if citation:
+            # ASCII Title
+            ascii_title = text2art(citation.get("title", "CodeEntropy"))
+            ascii_render = Align.center(Text(ascii_title, style="bold white"))
+
+            # Metadata
+            version = citation.get("version", "?")
+            release_date = citation.get("date-released", "?")
+            url = citation.get("url", citation.get("repository-code", ""))
+
+            version_text = Align.center(
+                Text(f"Version {version} | Released {release_date}", style="green")
+            )
+            url_text = Align.center(Text(url, style="blue underline"))
+
+            # Description block
+            abstract = citation.get("abstract", "No description available.")
+            description_title = Align.center(
+                Text("Description", style="bold magenta underline")
+            )
+            description_body = Align.center(
+                Padding(Text(abstract, style="white", justify="left"), (0, 4))
+            )
+
+            # Contributors table
+            contributors_title = Align.center(
+                Text("Contributors", style="bold magenta underline")
+            )
+
+            author_table = Table(
+                show_header=True, header_style="bold yellow", box=None, pad_edge=False
+            )
+            author_table.add_column("Name", style="bold", justify="center")
+            author_table.add_column("Affiliation", justify="center")
+
+            for author in citation.get("authors", []):
+                name = (
+                    f"{author.get('given-names', '')} {author.get('family-names', '')}"
+                ).strip()
+                affiliation = author.get("affiliation", "")
+                author_table.add_row(name, affiliation)
+
+            contributors_table = Align.center(Padding(author_table, (0, 4)))
+
+            # Full layout
+            splash_content = Group(
+                ascii_render,
+                Rule(style="cyan"),
+                version_text,
+                url_text,
+                Text(),
+                description_title,
+                description_body,
+                Text(),
+                contributors_title,
+                contributors_table,
+            )
+        else:
+            # ASCII Title
+            ascii_title = text2art("CodeEntropy")
+            ascii_render = Align.center(Text(ascii_title, style="bold white"))
 
-        author_table = Table(
-            show_header=True, header_style="bold yellow", box=None, pad_edge=False
-        )
-        author_table.add_column("Name", style="bold", justify="center")
-        author_table.add_column("Affiliation", justify="center")
-
-        for author in citation.get("authors", []):
-            name = (
-                f"{author.get('given-names', '')} {author.get('family-names', '')}"
-            ).strip()
-            affiliation = author.get("affiliation", "")
-            author_table.add_row(name, affiliation)
-
-        contributors_table = Align.center(Padding(author_table, (0, 4)))
-
-        # Full layout
-        splash_content = Group(
-            ascii_render,
-            Rule(style="cyan"),
-            version_text,
-            url_text,
-            Text(),
-            description_title,
-            description_body,
-            Text(),
-            contributors_title,
-            contributors_table,
-        )
+            splash_content = Group(
+                ascii_render,
+            )
 
         splash_panel = Panel(
             splash_content,

tests/test_CodeEntropy/test_run.py

@@ -2,9 +2,13 @@
 import shutil
 import tempfile
 import unittest
+from io import StringIO
 from unittest.mock import MagicMock, mock_open, patch
 
 import numpy as np
+import requests
+import yaml
+from rich.console import Console
 
 from CodeEntropy.run import RunManager
 
@@ -45,8 +49,8 @@ def setup_citation_file(self, mock_file):
         """
         citation_content = """\
     authors:
-    - given-names: Name1
-      family-names: Name2
+    - given-names: Alice
+      family-names: Smith
     """
 
         mock_file.return_value = mock_open(read_data=citation_content).return_value
@@ -122,18 +126,129 @@ def test_create_job_folder_with_invalid_job_suffix(
         self.assertEqual(new_folder_path, expected_path)
         mock_makedirs.assert_called_once_with(expected_path, exist_ok=True)
 
-    @patch("builtins.open", new_callable=mock_open)
-    def test_load_citation_data(self, mock_file):
+    @patch("requests.get")
+    def test_load_citation_data_success(self, mock_get):
+        """Should return parsed dict when CITATION.cff loads successfully."""
+        mock_yaml = """
+        authors:
+          - given-names: Alice
+            family-names: Smith
+        title: TestProject
+        version: 1.0
+        date-released: 2025-01-01
         """
-        Test loading the citation data from CITATION.cff.
-        """
-        self.setup_citation_file(mock_file)
-        instance = RunManager("dummy")  # replace with your class
-        data = instance.load_citation_data("CITATION.cff")
+        mock_response = MagicMock()
+        mock_response.status_code = 200
+        mock_response.text = mock_yaml
+        mock_get.return_value = mock_response
+
+        instance = RunManager("dummy")
+        data = instance.load_citation_data()
+
+        self.assertIsInstance(data, dict)
+        self.assertEqual(data["title"], "TestProject")
+        self.assertEqual(data["authors"][0]["given-names"], "Alice")
+
+    @patch("requests.get")
+    def test_load_citation_data_network_error(self, mock_get):
+        """Should return None if network request fails."""
+        mock_get.side_effect = requests.exceptions.ConnectionError("Network down")
+
+        instance = RunManager("dummy")
+        data = instance.load_citation_data()
+
+        self.assertIsNone(data)
+
+    @patch("requests.get")
+    def test_load_citation_data_http_error(self, mock_get):
+        """Should return None if HTTP response is non-200."""
+        mock_response = MagicMock()
+        mock_response.status_code = 404
+        mock_response.raise_for_status.side_effect = requests.exceptions.HTTPError()
+        mock_get.return_value = mock_response
+
+        instance = RunManager("dummy")
+        data = instance.load_citation_data()
+
+        self.assertIsNone(data)
+
+    @patch("requests.get")
+    def test_load_citation_data_invalid_yaml(self, mock_get):
+        """Should raise YAML error if file content is invalid YAML."""
+        mock_response = MagicMock()
+        mock_response.status_code = 200
+        mock_response.text = "invalid: [oops"
+        mock_get.return_value = mock_response
+
+        instance = RunManager("dummy")
+
+        with self.assertRaises(yaml.YAMLError):
+            instance.load_citation_data()
+
+    @patch.object(RunManager, "load_citation_data")
+    def test_show_splash_with_citation(self, mock_load):
+        """Should render full splash screen when citation data is present."""
+        mock_load.return_value = {
+            "title": "TestProject",
+            "version": "1.0",
+            "date-released": "2025-01-01",
+            "url": "https://example.com",
+            "abstract": "This is a test abstract.",
+            "authors": [
+                {"given-names": "Alice", "family-names": "Smith", "affiliation": "Uni"}
+            ],
+        }
+
+        buf = StringIO()
+        test_console = Console(file=buf, force_terminal=False, width=80)
+
+        instance = RunManager("dummy")
+        with patch("CodeEntropy.run.console", test_console):
+            instance.show_splash()
+
+        output = buf.getvalue()
+
+        self.assertIn("Version 1.0", output)
+        self.assertIn("2025-01-01", output)
+        self.assertIn("https://example.com", output)
+        self.assertIn("This is a test abstract.", output)
+        self.assertIn("Alice Smith", output)
+
+    @patch.object(RunManager, "load_citation_data", return_value=None)
+    def test_show_splash_without_citation(self, mock_load):
+        """Should render minimal splash screen when no citation data."""
+        buf = StringIO()
+        test_console = Console(file=buf, force_terminal=False, width=80)
+
+        instance = RunManager("dummy")
+        with patch("CodeEntropy.run.console", test_console):
+            instance.show_splash()
+
+        output = buf.getvalue()
+
+        self.assertNotIn("Version", output)
+        self.assertNotIn("Contributors", output)
+        self.assertIn("Welcome to CodeEntropy", output)
+
+    @patch.object(RunManager, "load_citation_data")
+    def test_show_splash_missing_fields(self, mock_load):
+        """Should gracefully handle missing optional fields in citation data."""
+        mock_load.return_value = {
+            "title": "PartialProject",
+            # no version, no date, no authors, no abstract
+        }
+
+        buf = StringIO()
+        test_console = Console(file=buf, force_terminal=False, width=80)
+
+        instance = RunManager("dummy")
+        with patch("CodeEntropy.run.console", test_console):
+            instance.show_splash()
+
+        output = buf.getvalue()
 
-        self.assertIn("authors", data)
-        self.assertEqual(data["authors"][0]["given-names"], "Name1")
-        self.assertEqual(data["authors"][0]["family-names"], "Name2")
+        self.assertIn("Version ?", output)
+        self.assertIn("No description available.", output)
 
     def test_run_entropy_workflow(self):
         """