build(medcat): CU-869aujr7h Add nightly workflow to check library stability

.github/workflows/medcat-v2-lib-stabiliy.yml

@@ -0,0 +1,58 @@
+name: MedCAT-nightly-stability-check
+permissions:
+  contents: read
+on:
+  schedule:
+    - cron: "0 3 * * *"  # every day at 3am UTC
+  workflow_dispatch:     # allow manual runs
+  pull_request:
+    paths:
+      - ".github/workflows/medcat-v2-lib-stabiliy.yml"
+
+defaults:
+  run:
+    working-directory: ./medcat-v2
+
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [ "3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install with latest deps
+        shell: bash
+        run: |
+          uv run --python ${{ matrix.python-version }} python -m ensurepip
+          uv run --python ${{ matrix.python-version }} python -m pip install --upgrade pip
+          # install cpu-only torch for MacOS
+          if [[ "$RUNNER_OS" == "macOS" ]]; then
+            uv run --python ${{ matrix.python-version }} python -m pip install torch --index-url https://download.pytorch.org/whl/cpu
+          fi
+          uv run --python ${{ matrix.python-version }} python -m pip install ".[spacy,deid,meta-cat,rel-cat,dict-ner,dev]"
+
+      - name: Check types
+        run: |
+          uv run --python ${{ matrix.python-version }} python -m mypy --follow-imports=normal medcat
+
+      - name: Ruff linting
+        run: |
+          uv run --python ${{ matrix.python-version }} python -m ruff check medcat --preview
+
+      - name: Test
+        run: |
+          uv run --python ${{ matrix.python-version }} python -m unittest discover
+        timeout-minutes: 45
+
+      - name: Model regression
+        run: |
+          uv run --python ${{ matrix.python-version }} bash tests/backwards_compatibility/run_current.sh

medcat-v2/medcat/utils/cdb_state.py

@@ -3,6 +3,7 @@
 from typing import TypedDict, cast
 import tempfile
 import dill
+import os
 
 from copy import deepcopy
 
@@ -216,7 +217,10 @@ def on_disk_memory_capture(cdb):
     Yields:
         None
     """
-    with tempfile.NamedTemporaryFile() as tf:
-        save_cdb_state(cdb, tf.name)
+    # NOTE: using temporary directory so that it also works on Windows
+    #       otherwise you can't reopen a temporary file in Windows (apparently)
+    with tempfile.TemporaryDirectory() as temp_dir:
+        temp_file_name = os.path.join(temp_dir, "cdb_state.dat")
+        save_cdb_state(cdb, temp_file_name)
         yield
-        load_and_apply_cdb_state(cdb, tf.name)
+        load_and_apply_cdb_state(cdb, temp_file_name)

medcat-v2/pyproject.toml

@@ -57,7 +57,8 @@ classifiers = [
 # For an analysis of this field vs pip's requirements files see:
 # https://packaging.python.org/discussions/install-requires-vs-requirements/
 dependencies = [ # Optional
-  "numpy>2.0",
+  "numpy>=2.1; python_version >= '3.13'",
+  "numpy>=2.0; python_version < '3.13'",
   "dill",
   "pandas>=2.2,<3.0",
   "tqdm>=4.64,<5.0",
@@ -102,6 +103,8 @@ dict_ner = [
 ]
 deid = [
   "datasets>=2.2.2,<3.0.0",
+  # Transformers 4.57 doesn't support 3.9
+  "transformers!=4.57.0; python_version == '3.9'",
   "transformers>=4.41.0,<5.0", # avoid major bump
   # Transformers 4.57 doesn't support 3.9
   "transformers!=4.57.0; python_version == '3.9'",
@@ -112,6 +115,8 @@ deid = [
   "scipy>=1.14; python_version >= '3.13'",
 ]
 rel_cat = [
+  # Transformers 4.57 doesn't support 3.9
+  "transformers!=4.57.0; python_version == '3.9'",
   "transformers>=4.41.0,<5.0", # avoid major bump
   # Transformers 4.57 doesn't support 3.9
   "transformers!=4.57.0; python_version == '3.9'",

medcat-v2/tests/components/helper.py

@@ -40,13 +40,32 @@ def setUpClass(cls):
         cls.vtokenizer = FTokenizer()
         cls.comp_cnf: ComponentConfig = getattr(
             cls.cnf.components, cls.comp_type.name)
+        if isinstance(cls.default_creator, Type):
+            cls._def_creator_name_opts = (cls.default_creator.__name__,)
+        else:
+            # classmethod
+            cls._def_creator_name_opts = (".".join((
+                # etiher class.method_name
+                cls.default_creator.__self__.__name__,
+                cls.default_creator.__name__)),
+                # or just method_name
+                cls.default_creator.__name__
+                )
 
     def test_has_default(self):
         avail_components = types.get_registered_components(self.comp_type)
         self.assertEqual(len(avail_components), self.expected_def_components)
         name, cls_name = avail_components[0]
-        self.assertEqual(name, self.default)
-        self.assertIs(cls_name, self.default_creator.__name__)
+        # 1 name / cls name
+        eq_name = [name == self.default for name, _ in avail_components]
+        eq_cls = [cls_name in self._def_creator_name_opts
+                  for _, cls_name in avail_components]
+        self.assertEqual(sum(eq_name), 1)
+        # NOTE: for NER both the default as well as the Dict based NER
+        #       have the came class name, so may be more than 1
+        self.assertGreaterEqual(sum(eq_cls), 1)
+        # needs to have the same class where name is equal
+        self.assertTrue(eq_cls[eq_name.index(True)])
 
     def test_can_create_def_component(self):
         component = types.create_core_component(

medcat-v2/tests/components/ner/trf/test_transformers_ner.py

@@ -14,12 +14,13 @@
 from medcat.model_creation.cdb_maker import CDBMaker
 from transformers import TrainerCallback
 
-from unittest import TestCase
+from unittest import TestCase, skipIf
 import unittest.mock
 
 from ...addons.meta_cat.test_meta_cat import FakeTokenizer
 from ....pipeline.test_pipeline import FakeCDB, Config
 from .... import RESOURCES_PATH
+from ....utils.ner.test_deid import is_macos_on_ci
 
 
 class TransformersNERTests(TestCase):
@@ -280,6 +281,8 @@ def test_ignore_extra_labels(self):
         )
 
 
+@skipIf(not is_macos_on_ci(),
+        "MacOS on workflow doesn't have enough memory")
 class AdditionalTransfromersNERTests(TestCase):
     TOKENIZER = FakeTokenizer()
     CNF = ConfigTransformersNER()

medcat-v2/tests/utils/ner/test_deid.py

@@ -36,6 +36,10 @@
 cnf.general.nlp.provider = 'spacy'
 
 
+def is_macos_on_ci() -> bool:
+    return os.getenv("RUNNER_OS", "None").lower() != "macos"
+
+
 def _get_def_cdb():
     return CDB(config=cnf)
 
@@ -112,13 +116,16 @@ def _train_model_once() -> tuple[tuple[Any, Any, Any], deid.DeIdModel]:
     return retval, model
 
 
-_TRAINED_MODEL_AND_INFO = _train_model_once()
+if is_macos_on_ci():
+    _TRAINED_MODEL_AND_INFO = _train_model_once()
 
 
 def train_model_once() -> tuple[tuple[Any, Any, Any], deid.DeIdModel]:
     return _TRAINED_MODEL_AND_INFO
 
 
+@unittest.skipIf(not is_macos_on_ci(),
+                 "MacOS on workflow doesn't have enough memory")
 class DeIDModelTests(unittest.TestCase):
     save_folder = os.path.join("results", "final_model")
 
@@ -171,6 +178,8 @@ def test_add_new_concepts(self):
 '''  # noqa
 
 
+@unittest.skipIf(not is_macos_on_ci(),
+                 "MacOS on workflow doesn't have enough memory")
 class DeIDModelWorks(unittest.TestCase):
     save_folder = os.path.join("results", "final_model")
 

medcat-v2/tests/utils/test_cdb_state.py

@@ -113,18 +113,19 @@ def test_state_restored(self):
 
 class StateSavedOnDiskTests(StateSavedTests):
     on_disk = True
-    _named_tempory_file = tempfile.NamedTemporaryFile
+    _named_tempory_directory = tempfile.TemporaryDirectory
 
     @classmethod
     def saved_name_temp_file(cls):
-        tf = cls._named_tempory_file()
-        cls.temp_file_name = tf.name
+        tf = cls._named_tempory_directory()
+        cls.temp_file_name = os.path.join(tf.name, "cdb_state.dat")
         return tf
 
     @classmethod
     def setUpClass(cls) -> None:
-        with mock.patch("builtins.open", side_effect=open) as cls.popen:
-            with mock.patch("tempfile.NamedTemporaryFile",
+        with mock.patch("medcat.utils.cdb_state.open", side_effect=open
+                        ) as cls.popen:
+            with mock.patch("tempfile.TemporaryDirectory",
                             side_effect=cls.saved_name_temp_file) as cls.pntf:
                 return super().setUpClass()