test flux workflow

this might take me a few tries :)

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

.github/workflows/test-flux.yaml

@@ -0,0 +1,42 @@
+name: Test Flux Executor
+on:
+  pull_request: []
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      packages: read
+    strategy:
+      fail-fast: false
+      matrix:
+        container: ['fluxrm/flux-sched:focal']
+
+    container:
+      image: ${{ matrix.container }}
+      options: "--platform=linux/amd64"
+
+    name: ${{ matrix.container }}
+    steps:
+      - name: Make Space
+        run: |        
+          rm -rf /usr/share/dotnet
+          rm -rf /opt/ghc
+
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Install Snakemake
+        run: |
+          # We are fluxuser in the container (added to sudo)
+          sudo wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh           
+          sudo /bin/bash ~/miniconda.sh -b -p /opt/conda
+          export PATH=/opt/conda:/bin:$PATH
+          # Install snakemake
+          pip install .
+
+      - name: Start Flux and Test Workflow
+        run: |
+          cd examples/flux
+          flux start --test-size=4
+          snakemake --flux --jobs=1

snakemake/executors/flux.py

@@ -130,17 +130,7 @@ def _get_jobname(self, job):
         return "snakejob-%s-%s-%s" % (self.run_namespace, job.name, job.jobid)
 
     def _generate_environment(self):
-        """
-        Loop through envvars (keys to host environment) and add
-        any that are requested for the runtime environment
-        """
-        envvars = dict(os.environ)
-        for key in self.envvars:
-            try:
-                envvars[key] = os.environ[key]
-            except Exception:
-                continue
-        return envvars
+        return {os.environ[key] for key in self.envvars}
 
     def format_job_exec(self, job):
         """