Merge pull request #73 from hexylena/hexylena-patch-1

.github/workflows/ci.yml

@@ -0,0 +1,56 @@
+name: Lint Code
+
+on: [pull_request]
+
+jobs:
+  lint-workflows:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 1
+
+      # BEGIN Dependencies
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
+          architecture: 'x64'
+
+      - name: Install dependencies
+        run: |
+            pip install -r requirements.txt
+            pip install -U setuptools
+            pip install -U planemo
+            pip install -U flake8
+            pip install -U xmldiff
+      # END Dependencies
+
+      - name: Lint 🔍👁👁
+        run: |
+            python setup.py install
+            flake8 argparse2tool --ignore=E2,E3,E4,E5,W3,W505
+            PYTHONPATH=$(argparse2tool) python examples/example.py --generate_galaxy_xml > tmp.xml
+            xmldiff tmp.xml examples/example.xml
+            planemo lint --report_level all --fail_level error --xsd tmp.xml
+
+            # Galaxy tool generation for example with subparsers -- generating one large (invalid) tool
+            echo '<root>' > tmp-sub.xml # wrap in extra level
+            PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_galaxy_xml >> tmp-sub.xml
+            echo '</root>' >> tmp-sub.xml
+            xmldiff tmp-sub.xml <(echo "<root>"; cat examples/example-sub.xml; echo "</root>")
+
+            # Galaxy tool generation for example with subparsers -- generating separate tools
+            PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_galaxy_xml --command foo > tmp-sub-foo.xml
+            PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_galaxy_xml --command bar > tmp-sub-bar.xml
+            xmldiff tmp-sub-foo.xml examples/example-sub-foo.xml
+            planemo lint --report_level all --fail_level error --xsd tmp-sub-foo.xml
+            xmldiff tmp-sub-bar.xml examples/example-sub-bar.xml
+            planemo lint --report_level all --fail_level error --xsd tmp-sub-bar.xml
+
+            PYTHONPATH=$(argparse2tool) python examples/example.py --generate_cwl_tool > tmp.cwl
+            PYTHONPATH=$(argparse2tool) python examples/example-sub.py --generate_cwl_tool > tmp-sub.cwl
+            sed -i 's/argparse2tool .*/argparse2tool/g' tmp.cwl tmp-sub.cwl
+            diff tmp.cwl examples/example.cwl
+            diff tmp-sub.cwl examples/example-sub.cwl
+            PYTHONPATH=$(argparse2tool) python examples/example-click.py --generate_cwl_tool > tmp-click.cwl
+            diff tmp-click.cwl examples/example-click.cwl

.github/workflows/publish.yml

@@ -0,0 +1,42 @@
+name: Publish
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  lint-workflows:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 1
+
+      # BEGIN Dependencies
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
+          architecture: 'x64'
+
+      - name: Install dependencies
+        run: |
+            pip install -r requirements.txt
+            pip install -U setuptools
+            pip install -U planemo
+            pip install -U flake8
+            pip install -U xmldiff
+      # END Dependencies
+
+      - name: Install dependencies
+        run: pip install wheel
+
+      - name: Build package
+        run: python setup.py sdist bdist_wheel
+
+      - name: Publish a Python distribution to PyPI
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

argparse2tool/dropins/argparse/argparse_galaxy_translation.py

@@ -30,7 +30,7 @@ def __gxtp_param_from_type(self, param, flag, label, num_dashes, gxparam_extra_k
             gxparam = gxtp.DataParam(flag, label=label, num_dashes=num_dashes, **gxparam_extra_kwargs)
         elif isinstance(param.type, FileType):
             if 'w' in param.type._mode:
-                gxparam = gxtp.OutputParameter(
+                gxparam = gxtp.OutputData(
                     flag, format='data', default=default, label=label,
                     num_dashes=num_dashes, **gxparam_extra_kwargs
                 )