add orjson as dep and pytest fix gha

.github/workflows/run_workflows.yml

@@ -168,18 +168,18 @@ jobs:
 
     - name: cwl-docker-extract (i.e. recursively docker pull)
       if: always()
-      run: cd workflow-inference-compiler/ && pytest -k test_cwl_docker_extract
+      run: cd workflow-inference-compiler/ && pytest tests/test_examples.py -k test_cwl_docker_extract
       # For self-hosted runners, make sure the docker cache is up-to-date.
 
     - name: PyTest Run Workflows
       if: always()
       # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
-      run: cd workflow-inference-compiler/ && pytest -k test_run_workflows_on_push --workers 8 --cwl_runner cwltool # --cov
+      run: cd workflow-inference-compiler/ && pytest tests/test_examples.py -k test_run_workflows_on_push --workers 8 --cwl_runner cwltool # --cov
 
-    - name: PyTest Run REST core Tests
+    - name: PyTest Run REST Core Tests
       if: always()
       # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
-      run: cd workflow-inference-compiler/ && pytest -k test_rest_core --cwl_runner cwltool
+      run: cd workflow-inference-compiler/ && pytest tests/test_rest_core.py -k test_rest_core --cwl_runner cwltool
 
     # NOTE: The steps below are for repository_dispatch only. For all other steps, please insert above
     # this comment.

install/system_deps.yml

@@ -35,8 +35,10 @@ dependencies:
 # Similarly, toil[cwl] depends on ruamel.yaml.clib for performance.
 # Install it with conda/mamba here.
   - ruamel.yaml.clib
-# Simiarly, cryptography needs to build binary wheels
+# Similarly, cryptography needs to build binary wheels
   - cryptography
 # Needs binary PyQt5 dependencies.
   - kubernetes-helm
   - zstandard
+# Needed for orjson wheels
+  - orjson