chore: updating CI

AstraZeneca · Dec 24, 2024 · 76edc83 · 76edc83
1 parent 0132c39
commit 76edc83
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Showing 17 changed files with 174 additions and 323 deletions.
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
@@ -9,10 +9,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - run: python -m pip install poetry
+      - name: Install uv
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+      - name: "Set up Python"
+        run: uv python install
       - run: |
-          python -m poetry install --only docs
-          poetry run mkdocs gh-deploy --force
+          uv sync --only-group docs
+          uv run mkdocs gh-deploy --force
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -15,10 +15,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: 3.8
-      - run: python -m pip install poetry
       - run: |
           # Download the binary
           curl -sLO https://github.com/argoproj/argo-workflows/releases/download/v3.5.4/argo-linux-amd64.gz
@@ -39,9 +35,7 @@ jobs:
         run: curl -LsSf https://astral.sh/uv/install.sh | sh
 
       - name: "Set up Python"
-        uses: actions/setup-python@v5
-        with:
-          python-version-file: ".python-version"
+        run: uv python install
 
       - name: Install the project
         run: uv sync --all-extras --dev

diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -18,13 +18,12 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
-        with:
-          python-version: 3.9
-      - run: python -m pip install poetry
+      - name: Install uv
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+      - name: "Set up Python"
+        run: uv python install
       - run: |
           uv sync --only-group release
-
       - name: Figure version
         continue-on-error: true
         env:

diff --git a/tests/extensions/catalog/test_catalog_extension.py b/tests/extensions/catalog/test_catalog_extension.py
@@ -1,4 +1,4 @@
-from extensions.catalog import is_catalog_out_of_sync
+from runnable.catalog import is_catalog_out_of_sync
 
 
 def test_is_catalog_out_of_sync_returns_true_for_empty_synced_catalogs():

diff --git a/tests/extensions/catalog/test_file_system.py b/tests/extensions/catalog/test_file_system.py
@@ -3,8 +3,8 @@
 
 import pytest
 
-import extensions.catalog.file_system as implementation
-from extensions.catalog.file_system.implementation import FileSystemCatalog
+from extensions.catalog import file_system as module
+from extensions.catalog.file_system import FileSystemCatalog
 from runnable import defaults
 
 
@@ -38,7 +38,7 @@ def mock_does_dir_exist(dir_name):
             return True
         return False
 
-    monkeypatch.setattr(implementation.utils, "does_dir_exist", mock_does_dir_exist)
+    monkeypatch.setattr(module.utils, "does_dir_exist", mock_does_dir_exist)
 
     catalog_handler = FileSystemCatalog(catalog_location="this_location")
     with pytest.raises(Exception, match="Expected Catalog to be present at"):
@@ -62,13 +62,13 @@ def test_file_system_catalog_get_copies_files_from_catalog_to_compute_folder_wit
 
     with tempfile.TemporaryDirectory() as catalog_location:
         with tempfile.TemporaryDirectory(dir=".") as compute_folder:
-            catalog_location_path = implementation.Path(catalog_location)
+            catalog_location_path = module.Path(catalog_location)
             run_id = "testing"
-            implementation.Path(catalog_location_path / run_id / compute_folder).mkdir(
+            module.Path(catalog_location_path / run_id / compute_folder).mkdir(
                 parents=True
             )
             with open(
-                implementation.Path(catalog_location)
+                module.Path(catalog_location)
                 / run_id
                 / compute_folder
                 / "catalog_file",
@@ -101,13 +101,13 @@ def test_file_system_catalog_get_copies_files_from_catalog_to_compute_folder_wit
 
     with tempfile.TemporaryDirectory() as catalog_location:
         with tempfile.TemporaryDirectory(dir=".") as compute_folder:
-            catalog_location_path = implementation.Path(catalog_location)
+            catalog_location_path = module.Path(catalog_location)
             run_id = "testing"
-            implementation.Path(catalog_location_path / run_id / compute_folder).mkdir(
+            module.Path(catalog_location_path / run_id / compute_folder).mkdir(
                 parents=True
             )
             with open(
-                implementation.Path(catalog_location)
+                module.Path(catalog_location)
                 / run_id
                 / compute_folder
                 / "catalog_file",
@@ -116,10 +116,7 @@ def test_file_system_catalog_get_copies_files_from_catalog_to_compute_folder_wit
                 fw.write("hello")
 
             with open(
-                implementation.Path(catalog_location)
-                / run_id
-                / compute_folder
-                / "not_catalog",
+                module.Path(catalog_location) / run_id / compute_folder / "not_catalog",
                 "w",
             ) as fw:
                 fw.write("hello")
@@ -136,7 +133,7 @@ def test_file_system_catalog_put_copies_files_from_compute_folder_to_catalog_if_
     mocker, monkeypatch
 ):
     monkeypatch.setattr(
-        implementation, "is_catalog_out_of_sync", mocker.MagicMock(return_value=True)
+        module, "is_catalog_out_of_sync", mocker.MagicMock(return_value=True)
     )
     mock_run_store = mocker.MagicMock()
     mock_context = mocker.MagicMock()
@@ -150,11 +147,11 @@ def test_file_system_catalog_put_copies_files_from_compute_folder_to_catalog_if_
 
     with tempfile.TemporaryDirectory() as catalog_location:
         with tempfile.TemporaryDirectory(dir=".") as compute_folder:
-            catalog_location_path = implementation.Path(catalog_location)
+            catalog_location_path = module.Path(catalog_location)
             run_id = "testing"
-            implementation.Path(catalog_location_path / run_id).mkdir(parents=True)
+            module.Path(catalog_location_path / run_id).mkdir(parents=True)
 
-            with open(implementation.Path(compute_folder) / "catalog_file", "w") as fw:
+            with open(module.Path(compute_folder) / "catalog_file", "w") as fw:
                 fw.write("hello")
 
             catalog_handler = FileSystemCatalog(catalog_location=catalog_location)
@@ -169,7 +166,7 @@ def test_file_system_catalog_put_copies_files_from_compute_folder_to_catalog_if_
     mocker, monkeypatch
 ):
     monkeypatch.setattr(
-        implementation, "is_catalog_out_of_sync", mocker.MagicMock(return_value=True)
+        module, "is_catalog_out_of_sync", mocker.MagicMock(return_value=True)
     )
     mock_run_store = mocker.MagicMock()
     mock_context = mocker.MagicMock()
@@ -182,15 +179,13 @@ def test_file_system_catalog_put_copies_files_from_compute_folder_to_catalog_if_
     )
     with tempfile.TemporaryDirectory() as catalog_location:
         with tempfile.TemporaryDirectory(dir=".") as compute_folder:
-            catalog_location_path = implementation.Path(catalog_location)
+            catalog_location_path = module.Path(catalog_location)
             run_id = "testing"
-            implementation.Path(catalog_location_path / run_id).mkdir(parents=True)
-            with open(implementation.Path(compute_folder) / "catalog_file", "w") as fw:
+            module.Path(catalog_location_path / run_id).mkdir(parents=True)
+            with open(module.Path(compute_folder) / "catalog_file", "w") as fw:
                 fw.write("hello")
 
-            with open(
-                implementation.Path(compute_folder) / "not_catalog_file", "w"
-            ) as fw:
+            with open(module.Path(compute_folder) / "not_catalog_file", "w") as fw:
                 fw.write("hello")
 
             catalog_handler = FileSystemCatalog(catalog_location=catalog_location)
@@ -206,7 +201,7 @@ def test_file_system_catalog_put_copies_files_from_compute_folder_to_catalog_if_
     mocker, monkeypatch
 ):
     monkeypatch.setattr(
-        implementation, "is_catalog_out_of_sync", mocker.MagicMock(return_value=False)
+        module, "is_catalog_out_of_sync", mocker.MagicMock(return_value=False)
     )
     mock_run_store = mocker.MagicMock()
     mock_context = mocker.MagicMock()
@@ -220,15 +215,13 @@ def test_file_system_catalog_put_copies_files_from_compute_folder_to_catalog_if_
 
     with tempfile.TemporaryDirectory() as catalog_location:
         with tempfile.TemporaryDirectory(dir=".") as compute_folder:
-            catalog_location_path = implementation.Path(catalog_location)
+            catalog_location_path = module.Path(catalog_location)
             run_id = "testing"
-            implementation.Path(catalog_location_path / run_id).mkdir(parents=True)
-            with open(implementation.Path(compute_folder) / "catalog_file", "w") as fw:
+            module.Path(catalog_location_path / run_id).mkdir(parents=True)
+            with open(module.Path(compute_folder) / "catalog_file", "w") as fw:
                 fw.write("hello")
 
-            with open(
-                implementation.Path(compute_folder) / "not_catalog_file", "w"
-            ) as fw:
+            with open(module.Path(compute_folder) / "not_catalog_file", "w") as fw:
                 fw.write("hello")
 
             catalog_handler = FileSystemCatalog(catalog_location=catalog_location)
@@ -242,42 +235,42 @@ def test_file_system_catalog_put_copies_files_from_compute_folder_to_catalog_if_
 
 def test_file_system_catalog_put_uses_compute_folder_by_default(monkeypatch, mocker):
     mock_safe_make_dir = mocker.MagicMock()
-    monkeypatch.setattr(implementation.utils, "safe_make_dir", mock_safe_make_dir)
+    monkeypatch.setattr(module.utils, "safe_make_dir", mock_safe_make_dir)
 
     mock_does_dir_exist = mocker.MagicMock(side_effect=Exception())
-    monkeypatch.setattr(implementation.utils, "does_dir_exist", mock_does_dir_exist)
+    monkeypatch.setattr(module.utils, "does_dir_exist", mock_does_dir_exist)
 
     catalog_handler = FileSystemCatalog(catalog_location="this_location")
     with pytest.raises(Exception):
         catalog_handler.put("testing", run_id="dummy_run_id")
 
-    mock_does_dir_exist.assert_called_once_with(implementation.Path("."))
+    mock_does_dir_exist.assert_called_once_with(module.Path("."))
 
 
 def test_file_system_catalog_put_uses_compute_folder_provided(monkeypatch, mocker):
     mock_safe_make_dir = mocker.MagicMock()
-    monkeypatch.setattr(implementation.utils, "safe_make_dir", mock_safe_make_dir)
+    monkeypatch.setattr(module.utils, "safe_make_dir", mock_safe_make_dir)
 
     mock_does_dir_exist = mocker.MagicMock(side_effect=Exception())
-    monkeypatch.setattr(implementation.utils, "does_dir_exist", mock_does_dir_exist)
+    monkeypatch.setattr(module.utils, "does_dir_exist", mock_does_dir_exist)
 
     catalog_handler = FileSystemCatalog(catalog_location="this_location")
     with pytest.raises(Exception):
         catalog_handler.put(
             "testing", run_id="dummy_run_id", compute_data_folder="not_data"
         )
 
-    mock_does_dir_exist.assert_called_once_with(implementation.Path("not_data"))
+    mock_does_dir_exist.assert_called_once_with(module.Path("not_data"))
 
 
 def test_file_system_catalog_put_raises_exception_if_compute_data_folder_does_not_exist(
     monkeypatch, mocker
 ):
     mock_safe_make_dir = mocker.MagicMock()
-    monkeypatch.setattr(implementation.utils, "safe_make_dir", mock_safe_make_dir)
+    monkeypatch.setattr(module.utils, "safe_make_dir", mock_safe_make_dir)
 
     mock_does_dir_exist = mocker.MagicMock(return_value=False)
-    monkeypatch.setattr(implementation.utils, "does_dir_exist", mock_does_dir_exist)
+    monkeypatch.setattr(module.utils, "does_dir_exist", mock_does_dir_exist)
 
     catalog_handler = FileSystemCatalog(catalog_location="this_location")
     with pytest.raises(Exception):
@@ -290,29 +283,29 @@ def test_file_system_catalog_put_creates_catalog_location_using_run_id(
     monkeypatch, mocker
 ):
     mock_safe_make_dir = mocker.MagicMock()
-    monkeypatch.setattr(implementation.utils, "safe_make_dir", mock_safe_make_dir)
+    monkeypatch.setattr(module.utils, "safe_make_dir", mock_safe_make_dir)
 
     mock_does_dir_exist = mocker.MagicMock(side_effect=Exception())
-    monkeypatch.setattr(implementation.utils, "does_dir_exist", mock_does_dir_exist)
+    monkeypatch.setattr(module.utils, "does_dir_exist", mock_does_dir_exist)
 
     catalog_handler = FileSystemCatalog(catalog_location="this_location")
 
     with pytest.raises(Exception):
         catalog_handler.put("testing", run_id="dummy_run_id")
 
     mock_safe_make_dir.assert_called_once_with(
-        implementation.Path("this_location") / "dummy_run_id"
+        module.Path("this_location") / "dummy_run_id"
     )
 
 
 def test_file_system_sync_between_runs_raises_exception_if_previous_catalog_does_not_exist(
     monkeypatch, mocker
 ):
     mock_safe_make_dir = mocker.MagicMock()
-    monkeypatch.setattr(implementation.utils, "safe_make_dir", mock_safe_make_dir)
+    monkeypatch.setattr(module.utils, "safe_make_dir", mock_safe_make_dir)
 
     mock_does_dir_exist = mocker.MagicMock(return_value=False)
-    monkeypatch.setattr(implementation.utils, "does_dir_exist", mock_does_dir_exist)
+    monkeypatch.setattr(module.utils, "does_dir_exist", mock_does_dir_exist)
 
     catalog_handler = FileSystemCatalog(catalog_location="this_location")
     with pytest.raises(Exception):

diff --git a/tests/extensions/catalog/test_k8s_pvc.py b/tests/extensions/catalog/test_k8s_pvc.py
diff --git a/tests/extensions/catalog/test_k8s_pvc_integration.py b/tests/extensions/catalog/test_k8s_pvc_integration.py
diff --git a/tests/extensions/executor/test_argo_executor.py b/tests/extensions/executor/test_argo_executor.py
@@ -1,6 +1,6 @@
 import pytest
 
-from runnable.extensions.executor.argo import implementation
+from extensions.executor import argo as implementation
 
 
 def test_secret_env_var_has_value_from_field():