Merge pull request #39 from hexylena/gha

Extract GHA From #37

.github/workflows/deploy.yml

@@ -0,0 +1,31 @@
+name: Release (by Tag Push)
+
+'on':
+  push:
+    tags:
+      - '*'
+
+jobs:
+
+  deploy:
+    name: Deploy
+    needs: [lint, test]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7']
+    steps:
+    - uses: actions/checkout@v1
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}
+    - uses: casperdcl/deploy-pypi@v2
+      with:
+        password: ${{ secrets.PYPI_TOKEN }}
+        build: --sdist --wheel --outdir dist .

.github/workflows/pr.yml

@@ -0,0 +1,58 @@
+name: Test Pull Request
+
+on: [pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8']
+    steps:
+    - uses: actions/checkout@v1
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}
+    - name: Install package
+      run: pip install -r requirements.txt black==23.3 flake8==6.0
+    - name: Flake8
+      run: flake8 --ignore=C901,W503
+    - name: Black
+      uses: psf/[email protected]
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8']
+    steps:
+    - uses: actions/checkout@v1
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}
+    - name: install package
+      run: python -m pip install .
+    - name: install packages for testing
+      run: pip install nose xmldiff
+      # TODO: replace with tox tests from #38
+      #- name: run nosetests
+      #  run: nosetests --with-coverage --cover-package=galaxyxml
+
+    - name: Run smoke test on example
+      run: |
+        python examples/example.py > tmp.xml
+        xmldiff --check tmp.xml examples/tool.xml
+        python examples/example_macros.py > tmp.xml
+        xmldiff --check tmp.xml examples/example_macros.xml

examples/example.py

@@ -88,7 +88,7 @@
 outputs.append(param)
 # Collection
 collection = gxtp.OutputCollection("supercollection", label="a small label")
-discover = gxtp.DiscoverDatasets("(?P<designation>.+)\.pdf.fasta", format="fasta")
+discover = gxtp.DiscoverDatasets("(?P<designation>.+).pdf.fasta", format="fasta")
 collection.append(discover)
 outputs.append(collection)
 
@@ -111,7 +111,7 @@
 rep_out.append(param)
 test_a.append(rep_out)
 test_coll = gxtp.TestOutputCollection(name="pdf_out")
-test_elem = gxtp.TestOCElement(name="apdf",file="apdf",ftype="pdf")
+test_elem = gxtp.TestOCElement(name="apdf", file="apdf", ftype="pdf")
 test_coll.append(test_elem)
 test_a.append(test_coll)
 rep_out = gxtp.TestRepeat(name="output_repeat")

examples/example_macros.py

@@ -3,7 +3,7 @@
 import galaxyxml.tool.parameters as gxtp
 
 # examplify the use of MacrosTool
-# 
+#
 
 tool = gxt.MacrosTool(
     name="aragorn",
@@ -57,6 +57,7 @@
 param_max.command_line_override = ""
 param_min.space_between_arg = " "
 param_max.space_between_arg = " "
+
 inputs.append(param_min)
 inputs.append(param_max)
 inputs.append(posint)
@@ -84,7 +85,7 @@
 outputs.append(param)
 # Collection
 collection = gxtp.OutputCollection("supercollection", label="a small label")
-discover = gxtp.DiscoverDatasets("(?P<designation>.+)\.pdf.fasta", format="fasta")
+discover = gxtp.DiscoverDatasets("(?P<designation>.+).pdf.fasta", format="fasta")
 collection.append(discover)
 outputs.append(collection)
 

test/unit_test_import_xml.py

@@ -19,6 +19,7 @@ def test_stdio(self):
         self.assertEqual(std.attrib["level"], "fatal")
         self.assertEqual(std.attrib["range"], "1:")
 
+
 class TestOverrides(TestImport):
     def test_override(self):
         co = "bash foo.sh > output1"
@@ -199,20 +200,20 @@ def test_collection_output(self):
 
     def test_repeat(self):
         repeat = self.tool.tests.children[0].node[3]
-        self.assertEqual(repeat.attrib["name"],"testrepeat")
+        self.assertEqual(repeat.attrib["name"], "testrepeat")
         # test param within repeat
         self.assertEqual(repeat[0].attrib["name"], "repeatchild")
         self.assertEqual(repeat[0].attrib["value"], "foo")
         # test output within repeat
         output = self.tool.tests.children[0].node[4]
-        self.assertEqual(output.attrib["name"],"output_repeat")
+        self.assertEqual(output.attrib["name"], "output_repeat")
         self.assertEqual(output[0].attrib["file"], "outputchild")
         self.assertEqual(output[0].attrib["name"], "bar")
 
     def test_ocr(self):
         # test outputcollection within repeat - who knows...
         output = self.tool.tests.children[0].node[5]
-        self.assertEqual(output.attrib["name"],"collection_repeat")
+        self.assertEqual(output.attrib["name"], "collection_repeat")
         collection = output[0]
         self.assertEqual(collection.attrib["name"], "collectionchild")
         element = collection[0]