Fix CI, fix tests, bidirectional type bug, typos

.github/workflows/tests.yml

@@ -18,20 +18,22 @@ jobs:
         python-version: ['3.12']
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v7
 
     - name: Install uv
-      uses: astral-sh/setup-uv@v5
+      uses: astral-sh/setup-uv@v10.0.1
       with:
         python-version: ${{ matrix.python-version }}
         enable-cache: true
 
     - name: Install dependencies
-      run: |
-        uv sync
+      run: uv sync
 
-    - uses: astral-sh/ruff-action@v3
+    - name: Check formatting
+      run: uv run ruff format --check --diff .
+
+    - name: Check linting
+      run: uv run ruff check .
 
     - name: Run tests
-      run: |
-        uv run pytest
+      run: uv run pytest

README.md

@@ -24,9 +24,9 @@ To upgrade Lycophron:
 uv tool upgrade lycophron
 ```
 
-### Initalize a local project
+### Initialize a local project
 
-Let's initalize a local project named `monkeys`:
+Let's initialize a local project named `monkeys`:
 
 ```bash
 lycophron init monkeys
@@ -173,7 +173,7 @@ This command validates the current project. I.e. it checks whether the applicati
 
 **new-template**
 
-This command generates a CSV file from the default template, containing all the required headers. The template can either be generated with all the fields or by explicitely adding custom fields on top of the required ones.
+This command generates a CSV file from the default template, containing all the required headers. The template can either be generated with all the fields or by explicitly adding custom fields on top of the required ones.
 
 `new-template --file`                                       : creates the output file in the given path and name.
 `new-template --all`                                        : creates a template using all fields (required and custom fields).

src/lycophron/errors.py

@@ -54,7 +54,7 @@ class DatabaseNotFound(DatabaseError):
 
 
 class DatabaseResourceNotModified(DatabaseError):
-    message = "Datbase resource not modified."
+    message = "Database resource not modified."
 
 
 class RecordError(LycophronError):

src/lycophron/references.py

@@ -65,7 +65,7 @@ def store_references(self, record_id: str, references: list[dict]) -> None:
                 target_record_id=ref["target_record_id"],
                 source_field=ref["source_field"],
                 target_field=ref["target_field"],
-                bidirectional=str(ref["bidirectional"]),
+                bidirectional=ref["bidirectional"],
             )
             self.session.add(reference)
 

src/lycophron/tasks/__init__.py

@@ -43,7 +43,7 @@ def init_celery_app():
     app.conf.max_memory_per_child = 100000
     app.conf.update(imports=["lycophron.tasks.tasks"])
     app.conf.beat_schedule = {
-        "record-dispathcer": {
+        "record-dispatcher": {
             "task": "lycophron.tasks.tasks.record_dispatcher",
             "schedule": 5,
             "args": (20,),

tests/conftest.py

@@ -7,6 +7,8 @@
 
 import pytest
 
+from lycophron.cli import lycophron
+
 
 @pytest.fixture(autouse=True)
 def reset_singleton():
@@ -23,3 +25,16 @@ def reset_singleton():
 
     # Restore original instances after test
     SingletonMeta._instances = original_instances
+
+
+def init(runner, token="", project_name=None):
+    # Skip the token prompt by providing an empty string token by default.
+    cli_args = ["init", "--token", token]
+    if project_name:
+        cli_args.append(project_name)
+    result = runner.invoke(lycophron, cli_args)
+
+    assert result.exit_code == 0
+    assert "Project initialized in directory" in result.output
+
+    return result

tests/test_cli.py

@@ -6,12 +6,14 @@
 """Test Lycophron CLI commands."""
 
 import csv
+import json
 import os
 import sqlite3
 import tempfile
 from pathlib import Path
 
 from click.testing import CliRunner
+from conftest import init
 
 from lycophron.cli import lycophron
 
@@ -21,10 +23,7 @@ def test_init_command_with_name():
     runner = CliRunner()
     with tempfile.TemporaryDirectory() as tmpdir:
         os.chdir(tmpdir)
-        result = runner.invoke(lycophron, ["init", "testproject"])
-
-        assert result.exit_code == 0
-        assert "Project initialized in directory" in result.output
+        init(runner, project_name="testproject")
 
         # Verify project structure
         project_dir = Path(tmpdir) / "testproject"
@@ -39,11 +38,7 @@ def test_init_command_default_directory():
     runner = CliRunner()
     with tempfile.TemporaryDirectory() as tmpdir:
         os.chdir(tmpdir)
-        # Skip the token prompt by providing an empty token
-        result = runner.invoke(lycophron, ["init", "--token", ""])
-
-        assert result.exit_code == 0
-        assert "Project initialized in directory" in result.output
+        init(runner)
 
         # Verify project structure
         assert (Path(tmpdir) / "files").exists()
@@ -56,10 +51,7 @@ def test_init_command_with_token():
     runner = CliRunner()
     with tempfile.TemporaryDirectory() as tmpdir:
         os.chdir(tmpdir)
-        result = runner.invoke(lycophron, ["init", "--token", "test_token123"])
-
-        assert result.exit_code == 0
-        assert "Project initialized in directory" in result.output
+        init(runner, token="test_token123")
 
         # Verify token in config
         config_path = Path(tmpdir) / "lycophron.cfg"
@@ -77,7 +69,7 @@ def test_new_template_default():
         os.chdir(tmpdir)
 
         # Initialize project first
-        runner.invoke(lycophron, ["init"])
+        init(runner)
 
         # Generate template
         result = runner.invoke(lycophron, ["new-template"])
@@ -105,7 +97,7 @@ def test_new_template_with_options():
         os.chdir(tmpdir)
 
         # Initialize project first
-        runner.invoke(lycophron, ["init"])
+        init(runner)
 
         # Generate template with options
         custom_path = os.path.join(tmpdir, "custom_template.csv")
@@ -146,7 +138,7 @@ def test_new_template_minimal():
         os.chdir(tmpdir)
 
         # Initialize project first
-        runner.invoke(lycophron, ["init"])
+        init(runner)
 
         # Generate minimal template
         result = runner.invoke(lycophron, ["new-template", "--minimal"])
@@ -178,7 +170,7 @@ def test_load_command():
         os.chdir(tmpdir)
 
         # Initialize project
-        runner.invoke(lycophron, ["init"])
+        init(runner)
 
         # Create a simple CSV file with required fields
         csv_path = os.path.join(tmpdir, "test_data.csv")
@@ -225,7 +217,7 @@ def test_load_db_objects():
         os.chdir(tmpdir)
 
         # Initialize project
-        runner.invoke(lycophron, ["init"])
+        init(runner)
 
         # Create test file
         files_dir = Path(tmpdir) / "files"
@@ -292,7 +284,7 @@ def test_load_db_objects():
         assert record["id"] == "record1"
 
         # Verify input_metadata
-        metadata = eval(record["input_metadata"])
+        metadata = json.loads(record["input_metadata"])
         assert metadata["metadata"]["title"] == "Test Record"
         assert metadata["metadata"]["publication_date"] == "2023-01-01"
         assert metadata["metadata"]["resource_type"]["id"] == "image"
@@ -335,7 +327,7 @@ def test_load_multiple_records():
         os.chdir(tmpdir)
 
         # Initialize project
-        runner.invoke(lycophron, ["init"])
+        init(runner)
 
         # Create CSV file with multiple records
         csv_path = os.path.join(tmpdir, "test_multi.csv")
@@ -414,13 +406,13 @@ def test_load_multiple_records():
         # Verify first record metadata
         cursor.execute("SELECT * FROM record WHERE id = ?", ("record1",))
         record1 = cursor.fetchone()
-        metadata1 = eval(record1["input_metadata"])
+        metadata1 = json.loads(record1["input_metadata"])
         assert metadata1["metadata"]["title"] == "First Record"
 
         # Verify second record metadata
         cursor.execute("SELECT * FROM record WHERE id = ?", ("record2",))
         record2 = cursor.fetchone()
-        metadata2 = eval(record2["input_metadata"])
+        metadata2 = json.loads(record2["input_metadata"])
         assert metadata2["metadata"]["title"] == "Second Record"
         assert metadata2["metadata"]["resource_type"]["id"] == "publication"
         assert (
@@ -438,7 +430,7 @@ def test_load_update_record():
         os.chdir(tmpdir)
 
         # Initialize project
-        runner.invoke(lycophron, ["init"])
+        init(runner)
 
         # Create initial CSV file
         csv_path = os.path.join(tmpdir, "initial.csv")
@@ -539,7 +531,7 @@ def test_load_update_record():
 
         cursor.execute("SELECT * FROM record WHERE id = ?", ("record1",))
         record = cursor.fetchone()
-        metadata = eval(record["input_metadata"])
+        metadata = json.loads(record["input_metadata"])
 
         # Check updated fields
         assert metadata["metadata"]["title"] == "Updated Title"

tests/test_references.py

@@ -10,9 +10,9 @@
 from unittest.mock import MagicMock, patch
 
 from click.testing import CliRunner
+from conftest import init
 
 from lycophron.app import LycophronApp
-from lycophron.cli import lycophron
 from lycophron.models import Record, RecordStatus, Reference
 from lycophron.template import LazyReference, TemplateEngine
 
@@ -79,7 +79,7 @@ def test_bidirectional_references():
         os.chdir(tmpdir)
 
         # Initialize project
-        runner.invoke(lycophron, ["init"])
+        init(runner)
 
         # Create test records with bidirectional references
         app = LycophronApp()
@@ -157,7 +157,7 @@ def test_bidirectional_references():
         assert len(specimen_refs) == 1
         assert specimen_refs[0].target_record_id == "figure1"
         assert specimen_refs[0].target_field == "doi"
-        assert specimen_refs[0].bidirectional == "True"
+        assert specimen_refs[0].bidirectional
 
 
 def test_reference_parsing_without_schema():
@@ -305,7 +305,7 @@ def test_two_phase_processing(mock_publish, mock_upload, mock_update, mock_creat
         os.chdir(tmpdir)
 
         # Initialize project
-        runner.invoke(lycophron, ["init"])
+        init(runner)
         app = LycophronApp()
 
         # Mock draft creation to set upload_id