[*] Fix a bug with inline configuration of executables.

[*] Add tests for new features.

Author: royjacobson

.github/workflows/nextflow-plugin.yml

@@ -22,6 +22,9 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: '3.10'
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        miniconda-version: latest
     - name: Install Nextflow
       run: |
         wget -qO- https://get.nextflow.io | bash
@@ -46,5 +49,18 @@ jobs:
         cp -r build/plugins/nf-python-${{ env.PLUGIN_VERSION }} ~/.nextflow/plugins/
     - name: Run Nextflow workflow test
       run: |
-        cd test
+        source $CONDA/etc/profile.d/conda.sh
+
+        pushd test/test-datatypes
         nextflow run test_flow.nf -plugins "nf-python@${{ env.PLUGIN_VERSION }}"
+        popd
+
+        pushd test/test-conda
+        nextflow run test_conda_config.nf -plugins "nf-python@${{ env.PLUGIN_VERSION }}" -config conda.config
+        nextflow run test_conda_inline.nf -plugins "nf-python@${{ env.PLUGIN_VERSION }}"
+        popd
+
+        pushd test/test-executable
+        nextflow run test_executable_config.nf -plugins "nf-python@${{ env.PLUGIN_VERSION }}" -config executable.config
+        nextflow run test_executable_inline.nf -plugins "nf-python@${{ env.PLUGIN_VERSION }}"
+        popd

plugins/nf-python/src/main/nextflow/python/PythonExtension.groovy

@@ -130,7 +130,7 @@ from nf_python import nf
 
         executable = this.executable
         if (args.containsKey('_executable') || args.containsKey('_conda_env')) {
-            executable = getExecutableFromConfigVals(args._executable, args._conda_env)
+            executable = getExecutableFromConfigVals(args._executable ?: '', args._conda_env ?: '')
         }
 
         File infile = File.createTempFile('nfpy_in', '.json')

test/nextflow.config

@@ -0,0 +1,7 @@
+plugins {
+  id 'nf-python'
+}
+
+nf_python {
+    conda_env='six'
+}

test/test-conda/conda.config

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { pyFunction } from 'plugin/nf-python'
+
+workflow {
+    assert pyFunction('''
+    import six
+    print("Package 'six' available!")
+    nf.output(True)
+''') == [true]
+}

test/test-conda/test_conda_config.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { pyFunction } from 'plugin/nf-python'
+
+workflow {
+    assert pyFunction('''
+    import six
+    print("Package 'six' available!")
+    nf.output(True)
+''', _conda_env: 'six') == [true]
+
+}

test/test-conda/test_conda_inline.nf

@@ -0,0 +1,7 @@
+plugins {
+  id 'nf-python'
+}
+
+nf_python {
+    executable='doesntexist'
+}

test/echo_kwargs.py renamed to test/test-datatypes/echo_kwargs.py

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { pyFunction } from 'plugin/nf-python'
+
+workflow {
+    try {
+        pyFunction('test')
+        assert false, "Should always throw"
+    } catch (java.lang.reflect.InvocationTargetException e) {
+        def cause = e.getCause()
+        assert cause.message.startsWith('Cannot run program "doesntexist"')
+    }
+}