WIP hatch

Dockerfile

@@ -5,9 +5,6 @@ LABEL maintainer="dan.leehr@duke.edu"
 RUN apt-get update && apt-get install -y nodejs
 
 RUN mkdir -p /app
-COPY . /app
-RUN pip install /app
-WORKDIR /app
 
 # Create a default user and home directory
 ENV HOME=/home/calrissian
@@ -19,4 +16,16 @@ RUN useradd -u 1001 -r -g 0 -m -d ${HOME} -s /sbin/nologin \
   chmod g+rwx ${HOME}
 
 USER calrissian
+RUN pip install hatch 
+ENV PATH="${HOME}/.local/bin:${PATH}"
+
+COPY . /app
+WORKDIR /app
+
+ENV VIRTUAL_ENV=/app/envs/calrissian
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+
+RUN hatch env prune && \
+    hatch env create prod
+
 CMD ["calrissian"]

calrissian/__about__.py

@@ -0,0 +1 @@
+version="0.17.3"

pyproject.toml

@@ -0,0 +1,90 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "calrissian"
+dynamic = ["version"]
+description = 'CWL runner for Kubernetes'
+readme = "README.md"
+requires-python = ">=3.8"
+license = "MIT"
+keywords = []
+authors = [
+  { name = "Fabrice Brito", email = "fabrice.brito@terradue.com" },
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: Implementation :: CPython",
+  "Programming Language :: Python :: Implementation :: PyPy",
+]
+dependencies = []
+
+[project.urls]
+Documentation = "https://github.com/Duke-GCB/calrissian#readme"
+Issues = "https://github.com/Duke-GCB/calrissian/issues"
+Source = "https://github.com/Duke-GCB/calrissian"
+
+[tool.hatch.version]
+path = "calrissian/__about__.py"
+
+[tool.hatch.envs.types]
+extra-dependencies = [
+  "mypy>=1.0.0",
+]
+[tool.hatch.envs.types.scripts]
+check = "mypy --install-types --non-interactive {args:src/calrissian tests}"
+
+[tool.coverage.run]
+source_pkgs = ["calrissian", "tests"]
+branch = true
+parallel = true
+omit = [
+  "calrissian/__about__.py",
+]
+
+[tool.coverage.paths]
+calrissian = ["calrissian"]
+tests = ["tests"]
+
+[tool.coverage.report]
+exclude_lines = [
+  "no cov",
+  "if __name__ == .__main__.:",
+  "if TYPE_CHECKING:",
+]
+
+
+[tool.hatch.envs.default]
+skip-install = false
+dependencies = [
+  "urllib3==1.26.18",
+  "kubernetes==28.1.0",
+  "cwltool==3.1.20231114134824",
+  "tenacity==8.2.3",
+  "importlib-metadata==6.8.0",
+  "msgpack==1.0.7",
+  "typing-extensions==4.8.0",
+  "freezegun==1.2.2"
+]
+
+[tool.hatch.envs.prod]
+path = "/app/envs/calrissian"
+
+
+
+[project.scripts]
+calrissian = "calrissian.main:main"
+
+[tool.hatch.envs.test]
+skip-install = false
+
+dependencies = [
+  "nose2"
+]
+
+[tool.hatch.envs.test.env-vars]
+RETRY_ATTEMPTS="0"
+

tests/test_job.py

@@ -520,7 +520,8 @@ def test_makes_tmpdir_when_not_exists(self, mock_os, mock_volume_builder, mock_c
         job = self.make_job()
         job.make_tmpdir()
         self.assertTrue(mock_os.path.exists.called)
-        self.assertTrue(mock_os.makedirs.called_with(job.tmpdir))
+        #self.assertTrue(mock_os.makedirs.assert_called_with(job.tmpdir))
+        mock_os.makedirs.assert_called_with(job.tmpdir)
 
     @patch('calrissian.job.os')
     def test_not_make_tmpdir_when_exists(self, mock_os, mock_volume_builder, mock_client):
@@ -681,7 +682,8 @@ def test_execute_kubernetes_pod(self, mock_volume_builder, mock_client):
         job = self.make_job()
         k8s_pod = Mock()
         job.execute_kubernetes_pod(k8s_pod)
-        self.assertTrue(mock_client.return_value.submit_pod.called_with(k8s_pod))
+        # self.assertTrue(mock_client.return_value.submit_pod.assert_called_with(k8s_pod))
+        mock_client.return_value.submit_pod.assert_called_with(k8s_pod)
 
     def test_add_file_or_directory_volume_ro(self, mock_volume_builder, mock_client):
         mock_add_volume_binding = mock_volume_builder.return_value.add_volume_binding

tests/test_k8s.py

@@ -95,7 +95,6 @@ def test_wait_calls_watch_pod_with_pod_name_field_selector(self, mock_watch, moc
         mock_stream = mock_watch.Watch.return_value.stream
         self.assertEqual(mock_stream.call_args, call(kc.core_api_instance.list_namespaced_pod, kc.namespace,
                                                      field_selector='metadata.name=test123'))
-
     @patch('calrissian.k8s.watch', autospec=True)
     def test_wait_calls_watch_pod_with_imcomplete_status(self, mock_watch, mock_get_namespace, mock_client):
         self.setup_mock_watch(mock_watch)