.github/workflows/build.yml

@@ -8,13 +8,13 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     env:
       GITHUB_EVENT_NAME: ${{ github.event_name }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.12"]
     timeout-minutes: 15
 
     steps:

.pre-commit-config.yaml

@@ -2,8 +2,8 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.12.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
@@ -24,7 +24,7 @@ repos:
               docs/notes/
           )
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.9.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
@@ -44,7 +44,7 @@ repos:
       - id: trailing-whitespace
       - id: check-case-conflict
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.1
+    rev: v1.14.1
     hooks:
       - id: mypy
         args: [--no-strict-optional, --ignore-missing-imports]

docs/changelog.md

@@ -3,6 +3,9 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+💚 Remove references to deleted migrations | [14](https://github.com/laminlabs/omop/pull/14) | [falexwolf](https://github.com/falexwolf) | 2025-02-16 |
+⬆️ Lamindb v1 | [12](https://github.com/laminlabs/omop/pull/12) | [Zethson](https://github.com/Zethson) | 2025-02-05 |
+♻️ Clean up | [10](https://github.com/laminlabs/omop/pull/10) | [sunnyosun](https://github.com/sunnyosun) | 2024-11-21 |
 🎨 Set blank=True | [9](https://github.com/laminlabs/omop/pull/9) | [sunnyosun](https://github.com/sunnyosun) | 2024-11-17 |
 ✨Add typehints and validation | [8](https://github.com/laminlabs/omop/pull/8) | [Zethson](https://github.com/Zethson) | 2024-10-09 |
 🎨 Fix DecimalField | [4](https://github.com/laminlabs/omop/pull/4) | [sunnyosun](https://github.com/sunnyosun) | 2024-09-16 |

docs/notes/inspectdb.ipynb

@@ -65,12 +65,13 @@
    ],
    "source": [
     "for file in [\n",
-    "    \"OMOPCDM_postgresql_5.4_ddl.sql\", \n",
-    "    \"OMOPCDM_postgresql_5.4_indices.sql\", \n",
-    "    \"OMOPCDM_postgresql_5.4_primary_keys.sql\", \n",
-    "    \"OMOPCDM_postgresql_5.4_constraints.sql\"]:\n",
+    "    \"OMOPCDM_postgresql_5.4_ddl.sql\",\n",
+    "    \"OMOPCDM_postgresql_5.4_indices.sql\",\n",
+    "    \"OMOPCDM_postgresql_5.4_primary_keys.sql\",\n",
+    "    \"OMOPCDM_postgresql_5.4_constraints.sql\",\n",
+    "]:\n",
     "    print(\"Executing file:\", file)\n",
-    "    with open(file, \"r\") as sql_file:\n",
+    "    with open(file) as sql_file:\n",
     "        sql_statements = sql_file.read()\n",
     "\n",
     "    statements = sql_statements.split(\";\")\n",
@@ -1144,33 +1145,29 @@
    "outputs": [],
    "source": [
     "def remove_lnchema_classes(file_path):\n",
-    "    \"\"\"\n",
-    "    Removes entire classes starting with \"Lnschema\" from a Python file.\n",
+    "    \"\"\"Removes entire classes starting with \"Lnschema\" from a Python file.\n",
     "\n",
     "    Args:\n",
     "    file_path: Path to the Python file.\n",
     "\n",
     "    Returns:\n",
     "    A string containing the modified code without \"Lnschema\" classes.\n",
     "    \"\"\"\n",
-    "\n",
-    "    with open(file_path, \"r\") as f:\n",
+    "    with open(file_path) as f:\n",
     "        content = f.readlines()\n",
     "\n",
     "    # Flag to track if inside a class definition\n",
     "    in_class = False\n",
-    "    class_name = None\n",
     "    modified_lines = []\n",
     "\n",
     "    for line in content:\n",
     "        if line.strip().startswith(\"class Lnschema\"):\n",
     "            # Start of a class with \"Lnschema\" prefix\n",
     "            in_class = True\n",
-    "            class_name = line.split()[1]  # Extract class name\n",
+    "            line.split()[1]  # Extract class name\n",
     "        elif line.strip() == \"}\" and in_class:\n",
     "            # End of the class with \"Lnschema\" prefix\n",
     "            in_class = False\n",
-    "            class_name = None\n",
     "        elif not in_class:\n",
     "            # Lines outside a class or not starting with \"Lnschema\" class\n",
     "            modified_lines.append(line)\n",
@@ -1180,6 +1177,7 @@
     "\n",
     "    return \"\".join(modified_lines)\n",
     "\n",
+    "\n",
     "# Example usage\n",
     "file_path = \"your_models.py\"  # Replace with your actual file path\n",
     "modified_code = remove_lnchema_classes(file_path)\n",

docs/quickstart.ipynb

@@ -79,7 +79,9 @@
    },
    "outputs": [],
    "source": [
-    "df = pd.read_csv(\"./mimic-iv-demo-data-in-the-omop-common-data-model-0.9/1_omop_data_csv/2b_concept.csv\")\n",
+    "df = pd.read_csv(\n",
+    "    \"./mimic-iv-demo-data-in-the-omop-common-data-model-0.9/1_omop_data_csv/2b_concept.csv\"\n",
+    ")\n",
     "df.columns = df.columns.str.lower()\n",
     "df.rename(columns={\"concept_class_id\": \"concept_class\"}, inplace=True)\n",
     "df.head()"
@@ -105,7 +107,7 @@
     "concepts = [op.Concept(**row.to_dict()) for _, row in df.iterrows()]\n",
     "for concept in concepts:\n",
     "    concept.save()\n",
-    "op.Concept.df()"
+    "op.Concept.filter().first()"
    ]
   },
   {
@@ -121,7 +123,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "op.Concept.validate([\"Stroke Volume Variation\", \"this concept does not exist\"], field=op.Concept.concept_name)"
+    "op.Concept.validate(\n",
+    "    [\"Stroke Volume Variation\", \"this concept does not exist\"],\n",
+    "    field=op.Concept.concept_name,\n",
+    ")"
    ]
   }
  ],
@@ -141,7 +146,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

noxfile.py

@@ -15,7 +15,7 @@ def lint(session: nox.Session) -> None:
 
 @nox.session()
 def build(session):
-    install_lamindb(session, branch="main")
+    install_lamindb(session, branch="release")
     session.run(*"uv pip install --system .[dev]".split())
     run_pytest(session)
     build_docs(session, strict=True)

omop/__init__.py

@@ -54,7 +54,7 @@
    Vocabulary
 """
 
-__version__ = "0.1.2"  # denote a pre-release for 0.1.0 with 0.1rc1
+__version__ = "0.2.1"  # denote a pre-release for 0.1.0 with 0.1rc1
 
 from lamindb_setup import _check_instance_setup
 

omop/migrations/0001_initial.py

@@ -7,7 +7,9 @@
 class Migration(migrations.Migration):
     initial = True
 
-    dependencies: list = []
+    dependencies: list = [
+        ("lamindb", "0081_revert_textfield_collection"),
+    ]
 
     operations = [
         migrations.CreateModel(