Collection of improvements

.github/workflows/pr.yml

@@ -0,0 +1,87 @@
+name: Test Pull Request
+
+on: [push,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 isort==5.12
+    - name: Flake8
+      run: flake8 --ignore=C901,W503
+    - name: Check import order
+      uses: isort/isort-action@v1
+      with:
+        isort-version: 5.12.0
+        configuration: --check --diff --profile black
+    - 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
+    - name: run nosetests
+      run: nosetests --with-coverage --cover-package=galaxyxml
+
+    - name: Run smoke test on example
+      run: |
+        python examples/example.py > tmp.xml
+        xmldiff tmp.xml examples/tool.xml
+        python examples/example_macros.py > tmp.xml
+        xmldiff tmp.xml examples/example_macros.xml
+
+
+  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 .
+        # only upload if a tag is pushed (otherwise just build & check)
+        upload: ${{ github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') }}

examples/example.py

@@ -29,10 +29,14 @@
 
 # A float in a section
 section = gxtp.Section("float_section", "Float section")
-param = gxtp.FloatParam("float", value=0, label="Float label", help="Float help", num_dashes=1)
+param = gxtp.FloatParam(
+    "float", value=0, label="Float label", help="Float help", num_dashes=1
+)
 param.space_between_arg = " "
 section.append(param)
-param = gxtp.FloatParam(None, argument="--float-fromarg", value=0, label="Float label", help="Float help")
+param = gxtp.FloatParam(
+    None, argument="--float-fromarg", value=0, label="Float label", help="Float help"
+)
 section.append(param)
 inputs.append(section)
 
@@ -41,16 +45,29 @@
 param.append(gxtp.SelectParam("Select", options={"hi": "1", "bye": "2"}))
 when_a = gxtp.When(value="hi")
 when_b = gxtp.When(value="bye")
-when_b.append(gxtp.IntegerParam("some_int", value=0, num_dashes=1, label="Advanced value"))
+when_b.append(
+    gxtp.IntegerParam("some_int", value=0, num_dashes=1, label="Advanced value")
+)
 param.append(when_a)
 param.append(when_b)
 inputs.append(param)
 
 # Integer parameters
-param_min = gxtp.IntegerParam("int_min", label="int_min label", help="int_min help", value=0, num_dashes=1)
-param_max = gxtp.IntegerParam("int_max", label="int_max label", help="int_max help", value=0, num_dashes=1)
+param_min = gxtp.IntegerParam(
+    "int_min", label="int_min label", help="int_min help", value=0, num_dashes=1
+)
+param_max = gxtp.IntegerParam(
+    "int_max", label="int_max label", help="int_max help", value=0, num_dashes=1
+)
 
-posint = gxtp.IntegerParam("posint", label="posint label", positional=True, help="posinthelp", value=0, num_dashes=2)
+posint = gxtp.IntegerParam(
+    "posint",
+    label="posint label",
+    positional=True,
+    help="posinthelp",
+    value=0,
+    num_dashes=2,
+)
 
 param_min.command_line_override = "-i$int_min,$int_max"
 param_max.command_line_override = ""
@@ -70,10 +87,21 @@
 filter_a = gxtp.Filter("sort_by", name="sorted", column="1")
 options.append(filter_a)
 param.append(options)
+validator = gxtp.ValidatorParam(type="regex")
+validator.node.text = ".*"
+param.append(validator)
 inputs.append(param)
 
 param = gxtp.Repeat("repeat", "repeat title")
-data = gxtp.DataParam("data", argument="--data", optional=True, format="fasta", multiple=True, label="data label", help="data help")
+data = gxtp.DataParam(
+    "data",
+    argument="--data",
+    optional=True,
+    format="fasta",
+    multiple=True,
+    label="data label",
+    help="data help",
+)
 param.append(data)
 inputs.append(param)
 
@@ -88,7 +116,9 @@
 outputs.append(param)
 # Collection
 collection = gxtp.OutputCollection("supercollection", label="a small label")
-discover = gxtp.DiscoverDatasets("(?P<designation>.+)\.pdf.fasta", format="fasta")
+discover = gxtp.DiscoverDatasets(
+    r"(?P<designation>.+)\.pdf.fasta", format="fasta"
+)
 collection.append(discover)
 outputs.append(collection)
 
@@ -111,7 +141,7 @@
 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 +3,6 @@
 import galaxyxml.tool.parameters as gxtp
 
 # examplify the use of MacrosTool
-# 
 
 tool = gxt.MacrosTool(
     name="aragorn",
@@ -32,7 +31,9 @@
 
 # A float in a section
 section = gxtp.Section("float_section", "Float section")
-param = gxtp.FloatParam("float", label="Float label", help="Float help", value=0, num_dashes=1)
+param = gxtp.FloatParam(
+    "float", label="Float label", help="Float help", value=0, num_dashes=1
+)
 param.space_between_arg = " "
 section.append(param)
 inputs.append(section)
@@ -42,16 +43,29 @@
 param.append(gxtp.SelectParam("Select", options={"hi": "1", "bye": "2"}))
 when_a = gxtp.When(value="hi")
 when_b = gxtp.When(value="bye")
-when_b.append(gxtp.IntegerParam("some_int", value=0, num_dashes=1, label="Advanced value"))
+when_b.append(
+    gxtp.IntegerParam("some_int", value=0, num_dashes=1, label="Advanced value")
+)
 param.append(when_a)
 param.append(when_b)
 inputs.append(param)
 
 # Integer parameters
-param_min = gxtp.IntegerParam("int_min", label="int_min label", help="int_min help", value=0, num_dashes=1)
-param_max = gxtp.IntegerParam("int_max", label="int_max label", help="int_max help", value=0, num_dashes=1)
+param_min = gxtp.IntegerParam(
+    "int_min", label="int_min label", help="int_min help", value=0, num_dashes=1
+)
+param_max = gxtp.IntegerParam(
+    "int_max", label="int_max label", help="int_max help", value=0, num_dashes=1
+)
 
-posint = gxtp.IntegerParam("posint", label="posint label", positional=True, help="posinthelp", value=0, num_dashes=2)
+posint = gxtp.IntegerParam(
+    "posint",
+    label="posint label",
+    positional=True,
+    help="posinthelp",
+    value=0,
+    num_dashes=2,
+)
 
 param_min.command_line_override = "-i$int_min,$int_max"
 param_max.command_line_override = ""
@@ -84,7 +98,9 @@
 outputs.append(param)
 # Collection
 collection = gxtp.OutputCollection("supercollection", label="a small label")
-discover = gxtp.DiscoverDatasets("(?P<designation>.+)\.pdf.fasta", format="fasta")
+discover = gxtp.DiscoverDatasets(
+    r"(?P<designation>.+)\.pdf.fasta", format="fasta"
+)
 collection.append(discover)
 outputs.append(collection)
 

examples/tool.xml

@@ -52,6 +52,7 @@ select_local $select_local
         <column name="value" index="1"/>
         <filter name="sorted" type="sort_by" column="1"/>
       </options>
+      <validator type="regex">.*</validator>
     </param>
     <repeat name="repeat" title="repeat title">
       <param name="data" argument="--data" type="data" optional="true" label="data label" help="data help" format="fasta" multiple="true"/>

galaxyxml/__init__.py

@@ -1,7 +1,4 @@
-from builtins import (
-    object,
-    str
-)
+from builtins import object, str
 
 from lxml import etree
 
@@ -25,7 +22,11 @@ def coerce(cls, data, kill_lists=False):
         - kill_lists: True -> replace lists by their first element
         """
         if isinstance(data, dict):
-            return {k: cls.coerce(v, kill_lists=kill_lists) for k, v in list(data.items()) if v is not None}
+            return {
+                k: cls.coerce(v, kill_lists=kill_lists)
+                for k, v in list(data.items())
+                if v is not None
+            }
         elif isinstance(data, list):
             if kill_lists:
                 return cls.coerce(data[0])
@@ -36,8 +37,7 @@ def coerce(cls, data, kill_lists=False):
 
     @classmethod
     def coerce_value(cls, obj):
-        """Make everything a string!
-        """
+        """Make everything a string!"""
         if isinstance(obj, bool):
             if obj:
                 return "true"