Merge pull request #285 from pyiron/flux_integration_test

Add flux integration test

.github/workflows/coverage.yml

@@ -21,7 +21,7 @@ jobs:
       - name: Setup environment
         run: |
           cp .ci_support/environment.yml environment.yml
-          echo "- flux-core" >> environment.yml
+          echo "- flux-core =0.59.0" >> environment.yml
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -32,12 +32,18 @@ jobs:
           activate-environment: my-env
           environment-file: environment.yml
           use-mamba: true
-      - name: Test
+      - name: Install
         shell: bash -l {0}
         run: |
           pip install versioneer[toml]==0.29
           pip install . --no-deps --no-build-isolation
+      - name: Test
+        shell: bash -l {0}
+        run: >
+          flux start
           coverage run  --omit="pysqa/_version.py,tests/*" -m unittest discover tests
-          coverage xml
+      - name: Collect Coverage
+        shell: bash -l {0}
+        run: coverage xml
       - name: Coveralls
         uses: coverallsapp/github-action@v2

pysqa/wrapper/flux.py

@@ -43,5 +43,6 @@ def convert_queue_status(queue_status_output: str) -> pandas.DataFrame:
         )
         df.loc[df.status == "R", "status"] = "running"
         df.loc[df.status == "S", "status"] = "pending"
+        df.loc[df.status == "C", "status"] = "error"
         df.loc[df.status == "CD", "status"] = "finished"
         return df

tests/test_flux.py

@@ -2,7 +2,9 @@
 # Copyright (c) Jan Janssen
 
 import os
+from time import sleep
 import unittest
+
 import pandas
 from pysqa import QueueAdapter
 
@@ -92,3 +94,15 @@ def execute_command(
 echo hello"""
         self.assertEqual(content, output)
         os.remove("run_queue.sh")
+
+    def test_flux_integration(self):
+        job_id = self.flux.submit_job(
+            queue="flux",
+            job_name="test",
+            working_directory=".",
+            cores=1,
+            command="sleep 1"
+        )
+        self.assertEqual(self.flux.get_status_of_job(process_id=job_id), 'running')
+        self.flux.delete_job(process_id=job_id)
+        self.assertEqual(self.flux.get_status_of_job(process_id=job_id), 'error')