add github workflow

missing deploy so far

.github/workflows/pr.yml

@@ -0,0 +1,61 @@
+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 flake8
+    - 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

examples/example.py

@@ -91,7 +91,7 @@
 outputs.append(param)
 # Collection
 collection = gxtp.OutputCollection("supercollection", label="a small label")
-discover = gxtp.DiscoverDatasets("(?P<designation>.+)\.pdf.fasta", format="fasta")
+discover = gxtp.DiscoverDatasets(r"(?P<designation>.+)\.pdf.fasta", format="fasta")
 collection.append(discover)
 outputs.append(collection)
 
@@ -114,7 +114,7 @@
 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",
@@ -84,7 +83,7 @@
 outputs.append(param)
 # Collection
 collection = gxtp.OutputCollection("supercollection", label="a small label")
-discover = gxtp.DiscoverDatasets("(?P<designation>.+)\.pdf.fasta", format="fasta")
+discover = gxtp.DiscoverDatasets(r"(?P<designation>.+)\.pdf.fasta", format="fasta")
 collection.append(discover)
 outputs.append(collection)
 

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"

galaxyxml/tool/__init__.py

@@ -1,6 +1,8 @@
 import copy
 import logging
 
+from lxml import etree
+
 from galaxyxml import GalaxyXML, Util
 from galaxyxml.tool.parameters import (
     Expand,
@@ -9,11 +11,9 @@
     Macro,
     Macros,
     Outputs,
-    XMLParam
+    XMLParam,
 )
 
-from lxml import etree
-
 VALID_TOOL_TYPES = ("data_source", "data_source_async")
 VALID_URL_METHODS = ("get", "post")
 
@@ -63,15 +63,19 @@ def __init__(
 
         if tool_type is not None:
             if tool_type not in VALID_TOOL_TYPES:
-                raise Exception("Tool type must be one of %s" % ",".join(VALID_TOOL_TYPES))
+                raise Exception(
+                    "Tool type must be one of %s" % ",".join(VALID_TOOL_TYPES)
+                )
             else:
                 kwargs["tool_type"] = tool_type
 
                 if URL_method is not None:
                     if URL_method in VALID_URL_METHODS:
                         kwargs["URL_method"] = URL_method
                     else:
-                        raise Exception("URL_method must be one of %s" % ",".join(VALID_URL_METHODS))
+                        raise Exception(
+                            "URL_method must be one of %s" % ",".join(VALID_URL_METHODS)
+                        )
 
         description_node = etree.SubElement(self.root, "description")
         description_node.text = description
@@ -169,13 +173,18 @@ def export(self, keep_old_command=False):
             if getattr(self, "command", None):
                 command_node.text = etree.CDATA(export_xml.command)
             else:
-                logger.warning("The tool does not have any old command stored. Only the command line is written.")
+                logger.warning(
+                    "The tool does not have any old command stored. Only the command line is written."
+                )
                 command_node.text = export_xml.executable
         else:
             if self.command_override:
                 actual_cli = export_xml.clean_command_string(command_line)
             else:
-                actual_cli = "%s %s" % (export_xml.executable, export_xml.clean_command_string(command_line),)
+                actual_cli = "%s %s" % (
+                    export_xml.executable,
+                    export_xml.clean_command_string(command_line),
+                )
             command_node.text = etree.CDATA(actual_cli.strip())
         export_xml.append(command_node)
 
@@ -227,13 +236,13 @@ class MacrosTool(Tool):
 
     TODO all other elements, like requirements are currently ignored
     """
+
     def __init__(self, *args, **kwargs):
         super(MacrosTool, self).__init__(*args, **kwargs)
-        self.root = etree.Element('macros')
+        self.root = etree.Element("macros")
         self.inputs = Macro("%s_inmacro" % self.id)
         self.outputs = Macro("%s_outmacro" % self.id)
 
-
     def export(self, keep_old_command=False):  # noqa
 
         export_xml = copy.deepcopy(self)
@@ -252,7 +261,9 @@ def export(self, keep_old_command=False):  # noqa
             raise
 
         # Add command section
-        command_node = etree.SubElement(export_xml.root, 'token', {"name": "%s_INMACRO" % self.id.upper()})
+        command_node = etree.SubElement(
+            export_xml.root, "token", {"name": "%s_INMACRO" % self.id.upper()}
+        )
         actual_cli = "%s" % (export_xml.clean_command_string(command_line))
         command_node.text = etree.CDATA(actual_cli.strip())
 
@@ -261,7 +272,9 @@ def export(self, keep_old_command=False):  # noqa
             command_line.append(export_xml.outputs.cli())
         except Exception:
             pass
-        command_node = etree.SubElement(export_xml.root, 'token', {"name": "%s_OUTMACRO" % self.id.upper()})
+        command_node = etree.SubElement(
+            export_xml.root, "token", {"name": "%s_OUTMACRO" % self.id.upper()}
+        )
         actual_cli = "%s" % (export_xml.clean_command_string(command_line))
         command_node.text = etree.CDATA(actual_cli.strip())
 

galaxyxml/tool/import_xml.py

@@ -77,8 +77,8 @@ def _load_stdio(self, tool, stdio_root):
         """
         tool.stdios = gxtp.Stdios()
         for std in stdio_root:
-            slevel = std.attrib['level']
-            srange = std.attrib['range']
+            slevel = std.attrib["level"]
+            srange = std.attrib["range"]
             tool.stdios.append(gxtp.Stdio(level=slevel, range=srange))
         logger.info("<stdio> loaded.")
 
@@ -119,7 +119,9 @@ def _load_requirements(self, tool, requirements_root):
             value = req.text
             if req.tag == "requirement":
                 version = req.attrib.get("version", None)
-                tool.requirements.append(gxtp.Requirement(req_type, value, version=version))
+                tool.requirements.append(
+                    gxtp.Requirement(req_type, value, version=version)
+                )
             elif req.tag == "container":
                 tool.requirements.append(gxtp.Container(req_type, value))
             else:
@@ -352,7 +354,9 @@ def _load_option_select(self, root, option):
         """
         root.append(
             gxtp.SelectOption(
-                option.attrib.get("value", None), option.text, selected=option.attrib.get("selected", False)
+                option.attrib.get("value", None),
+                option.text,
+                selected=option.attrib.get("selected", False),
             )
         )
 
@@ -432,9 +436,13 @@ def _load_select_param(self, root, sel_param):
         # Deal with child nodes (usually option and options)
         for sel_child in sel_param:
             try:
-                getattr(self, "_load_{}_select".format(sel_child.tag))(select_param, sel_child)
+                getattr(self, "_load_{}_select".format(sel_child.tag))(
+                    select_param, sel_child
+                )
             except AttributeError:
-                logger.warning(sel_child.tag + " tag is not processed for <param type='select'>.")
+                logger.warning(
+                    sel_child.tag + " tag is not processed for <param type='select'>."
+                )
         root.append(select_param)
 
     def _load_param(self, root, param_root):
@@ -535,7 +543,12 @@ def load_inputs(self, root, inputs_root):
             try:
                 getattr(self, "_load_{}".format(inp_child.tag))(root, inp_child)
             except AttributeError:
-                logger.warning(inp_child.tag + " tag is not processed for <" + inputs_root.tag + "> tag.")
+                logger.warning(
+                    inp_child.tag
+                    + " tag is not processed for <"
+                    + inputs_root.tag
+                    + "> tag."
+                )
 
 
 class OutputsParser(object):
@@ -580,7 +593,9 @@ def _load_change_format(self, root, chfmt_root):
         for chfmt_child in chfmt_root:
             change_format.append(
                 gxtp.ChangeFormatWhen(
-                    chfmt_child.attrib["input"], chfmt_child.attrib["format"], chfmt_child.attrib["value"]
+                    chfmt_child.attrib["input"],
+                    chfmt_child.attrib["format"],
+                    chfmt_child.attrib["value"],
                 )
             )
         root.append(change_format)
@@ -607,7 +622,9 @@ def _load_collection(self, outputs_root, coll_root):
             try:
                 getattr(self, "_load_{}".format(coll_child.tag))(collection, coll_child)
             except AttributeError:
-                logger.warning(coll_child.tag + " tag is not processed for <collection>.")
+                logger.warning(
+                    coll_child.tag + " tag is not processed for <collection>."
+                )
         outputs_root.append(collection)
 
     def _load_discover_datasets(self, root, disc_root):
@@ -727,11 +744,12 @@ def _load_element(self, test_root, element_root):
         :param repeat_root: root of <output_collection> tag.
         :param repeat_root: :class:`xml.etree._Element`
         """
-        test_root.append(gxtp.TestOCElement(
-            name=element_root.attrib.get("name", None),
-            ftype=element_root.attrib.get("ftype", None),
-            file=element_root.attrib.get("file", None)
-        )
+        test_root.append(
+            gxtp.TestOCElement(
+                name=element_root.attrib.get("name", None),
+                ftype=element_root.attrib.get("ftype", None),
+                file=element_root.attrib.get("file", None),
+            )
         )
 
     def _load_repeat(self, test_root, repeat_root):
@@ -747,7 +765,7 @@ def _load_repeat(self, test_root, repeat_root):
             repeat_root.attrib.get("title", None),
             min=repeat_root.attrib.get("min", None),
             max=repeat_root.attrib.get("max", None),
-            default=repeat_root.attrib.get("default", None)
+            default=repeat_root.attrib.get("default", None),
         )
         # Deal with child nodes
         self.load_inputs(repeat, repeat_root)
@@ -765,7 +783,12 @@ def load_inputs(self, repeat, repeat_root):
             try:
                 getattr(self, "_load_{}".format(rep_child.tag))(repeat, rep_child)
             except AttributeError:
-                logger.warning(rep_child.tag + " tag is not processed for <" + repeat_root.tag + "> tag.")
+                logger.warning(
+                    rep_child.tag
+                    + " tag is not processed for <"
+                    + repeat_root.tag
+                    + "> tag."
+                )
 
     def load_tests(self, root, tests_root):
         """
@@ -781,5 +804,7 @@ def load_tests(self, root, tests_root):
                 try:
                     getattr(self, "_load_{}".format(test_child.tag))(test, test_child)
                 except AttributeError:
-                    logger.warning(test_child.tag + " tag is not processed within <test>.")
+                    logger.warning(
+                        test_child.tag + " tag is not processed within <test>."
+                    )
             root.append(test)