feat: update lems scripts to include version and commit information

scripts/lems/asttemplates.py

@@ -25,7 +25,8 @@
     ---
     {%- endif %}
 
-    Generated on {{ todays_date }}.
+    Schema against which LEMS based on these should be valid: [LEMS_v{{ lems_version }}.xsd](https://github.com/LEMS/LEMS/tree/{{ lems_branch }}/Schemas/LEMS/LEMS_v{{ lems_version }}.xsd).
+    Generated on {{ lems_date }} from [this](https://github.com/LEMS/LEMS/commit/{{ lems_commit }}) commit.
     Please file any issues or questions at the [issue tracker here](https://github.com/LEMS/LEMS/issues).
 
     ---

scripts/lems/requirements.txt

@@ -0,0 +1,3 @@
+lxml
+xmltodict
+jinja2

scripts/lems/xml2md.py

@@ -7,6 +7,11 @@
 Copyright 2023 NeuroML contributors
 """
 
+import tempfile
+import subprocess
+import re
+import lxml
+import lxml.etree as ET
 import xmltodict
 from datetime import date
 import asttemplates
@@ -28,83 +33,169 @@
     "components": ["Defining Components", ""]
 }
 
-todays_date = date.today().strftime("%d/%m/%y")
+lems_branch = "master"
+lems_version = "0.7.6"
+GitHubRepo = "https://github.com/LEMS/LEMS.git"
+lems_date = date.today().strftime("%d/%m/%y")
+lems_commit = ""
+
 parsed_data = {}
 
 srcfile = "sourceannotations.xml"
-destdir = "../../source/Userdocs/LEMS_elements/"
-
-# populate our page info
-with open(srcfile, 'r') as ast_doc:
-    elementtypes = xmltodict.parse(ast_doc.read())['ElementTypes']['ElementType']
-    for et in elementtypes:
-        try:
-            parsed_data[et['@section']].append(et)
-        except KeyError:
-            parsed_data[et['@section']] = []
-            parsed_data[et['@section']].append(et)
-
-# add Include
-parsed_data['root'].append(
-    OrderedDict(
-        {
-            '@name': 'Include',
-            'Info': 'Include LEMS files in other LEMS files. Files are included where the Include declaration occurs.  The enclosing Lems block is stripped off and the rest of the content included as is',
-            'Property': OrderedDict(
-                {
-                    '@name': 'file',
-                    '@type': 'String',
-                    '#text': 'the name or relative path of a file to be included'
-                }
-            )
-        }
-    )
-)
-
-print(parsed_data)
-
-# render templates
-for pg, pginfo in sections_pages.items():
-    outputfile = "{}/{}.md".format(destdir, pginfo[0].replace(" ", ""))
-    with open(outputfile, 'w') as ast_doc:
-        print(
-            asttemplates.page_header.render(section_data=pginfo, todays_date=todays_date),
-            file=ast_doc)
-        for et in parsed_data[pg]:
-            print(f"Rendering {et['@name']}")
-            print(
-                asttemplates.elementtype.render(et=et),
-                file=ast_doc)
-            if 'Property' in et or 'ListProperty' in et:
-                print("""`````{tab-set}""", end="", file=ast_doc)
 
+comp_type_schema = {}
+
+def get_schema_doc(schemafile):
+    """Get schemas for everything
+
+    :param schemafile: path to the XSD schema file
+    """
+    print(ET.__file__)
+    parser = lxml.etree.XMLParser(remove_comments=True,
+                                  remove_blank_text=True, ns_clean=True)
+    try:
+        tree = ET.parse(schemafile, parser=parser)
+        root = tree.getroot()
+    except ET.XMLSyntaxError as e:
+        print(f"Could not parse file {schemafile}: {e}")
+    namespaces = root.nsmap
+
+    # currently unused
+    for simple_type in root.findall("xs:simpleType", namespaces=namespaces):
+        simple_type_str = ET.tostring(simple_type, pretty_print=True,
+                                      encoding="unicode",
+                                      xml_declaration=False)
+
+        # needs to be lowerCamelCase to match XML core types
+        type_name = simple_type.attrib['name'].lower().replace("nml2quantity_", "")
+        comp_type_schema[type_name] = re.sub(r"Type.*name=",r"Type name=", simple_type_str)
+
+    for complex_type in root.findall("xs:complexType", namespaces=namespaces):
+        for node in complex_type:
+            if "annotation" in str(node.tag) or "documentation" in str(node.tag):
+                complex_type.remove(node)
+
+        complex_type_str = ET.tostring(complex_type, pretty_print=True,
+                                       encoding="unicode",
+                                       xml_declaration=False)
+        # needs to be lowerCamelCase to match XML core types
+        type_name = complex_type.attrib['name'].lower()
+        comp_type_schema[type_name] = re.sub(r"Type.*name=",r"Type name=", complex_type_str)
+
+
+def main(srcdir, destdir):
+    """TODO: Docstring for main.
+
+    :param arg1: TODO
+    :returns: TODO
+
+    """
+    # If not defined or empty, download a new copy to a temporary directory
+    if not srcdir or src == "":
+        print("No src directory specified. Cloning NeuroML2 repo")
+        tempdir = tempfile.TemporaryDirectory()
+        tmpsrcdir = tempdir.name
+        print("Temporariy directory: {}".format(tmpsrcdir))
+        clone_command = ["git", "clone", "--depth", "1", "--branch", lems_branch, GitHubRepo, tmpsrcdir]
+        subprocess.run(clone_command)
+    else:
+        tmpsrcdir = srcdir
+
+    # TODO: add LEMS examples
+    #  exampledirs = [tmpsrcdir + "/examples/", tmpsrcdir + "/LEMSexamples/"]
+    exampledirs = [tmpsrcdir + "/examples/"]
+    xsdsrc = tmpsrcdir + f"/Schemas/LEMS/LEMS_v{lems_version}.xsd"
+
+    # Get current commit
+    commit_command = ["git", "log", "-1", "--pretty=format:%H"]
+    output = subprocess.run(commit_command, capture_output=True,
+                            cwd=tmpsrcdir, text=True)
+    lems_commit = output.stdout
+
+    # start
+    get_schema_doc(xsdsrc)
+
+    # populate our page info
+    with open(srcfile, 'r') as ast_doc:
+        elementtypes = xmltodict.parse(ast_doc.read())['ElementTypes']['ElementType']
+        for et in elementtypes:
             try:
-                if type(et['Property']) == list:
-                    props=et['Property']
-                else:
-                    props=[et['Property']]
-                print(f" - {len(props)} properties: {props}")
-                print(
-                    asttemplates.prop.render(props=props),
-                    file=ast_doc)
+                parsed_data[et['@section']].append(et)
             except KeyError:
-                pass
+                parsed_data[et['@section']] = []
+                parsed_data[et['@section']].append(et)
+
+    # add Include
+    parsed_data['root'].append(
+        OrderedDict(
+            {
+                '@name': 'Include',
+                'Info': 'Include LEMS files in other LEMS files. Files are included where the Include declaration occurs.  The enclosing Lems block is stripped off and the rest of the content included as is',
+                'Property': OrderedDict(
+                    {
+                        '@name': 'file',
+                        '@type': 'String',
+                        '#text': 'the name or relative path of a file to be included'
+                    }
+                )
+            }
+        )
+    )
 
-            try:
-                if type(et['ListProperty']) == list:
-                    lprops=et['ListProperty']
-                else:
-                    lprops=[et['ListProperty']]
-                print(f" - {len(lprops)} properties: {lprops}")
+    print(parsed_data)
+
+    # render templates
+    for pg, pginfo in sections_pages.items():
+        outputfile = "{}/{}.md".format(destdir, pginfo[0].replace(" ", ""))
+        with open(outputfile, 'w') as ast_doc:
+            print(
+                asttemplates.page_header.render(section_data=pginfo,
+                                                lems_date=lems_date,
+                                                lems_commit=lems_commit,
+                                                lems_version=lems_version,
+                                                lems_branch=lems_branch),
+                file=ast_doc)
+            for et in parsed_data[pg]:
+                print(f"Rendering {et['@name']}")
                 print(
-                    asttemplates.listprop.render(lprops=lprops),
+                    asttemplates.elementtype.render(et=et),
                     file=ast_doc)
-            except KeyError:
-                pass
-
-            # process them, close tab-set
-            if 'Property' in et or 'ListProperty' in et:
-                print("""`````""", end="", file=ast_doc)
+                if 'Property' in et or 'ListProperty' in et:
+                    print("""`````{tab-set}""", end="", file=ast_doc)
+
+                try:
+                    if isinstance(et['Property'], list):
+                        props=et['Property']
+                    else:
+                        props=[et['Property']]
+                    print(f" - {len(props)} properties: {props}")
+                    print(
+                        asttemplates.prop.render(props=props),
+                        file=ast_doc)
+                except KeyError:
+                    pass
+
+                try:
+                    if isinstance(et['ListProperty'], list):
+                        lprops=et['ListProperty']
+                    else:
+                        lprops=[et['ListProperty']]
+                    print(f" - {len(lprops)} properties: {lprops}")
+                    print(
+                        asttemplates.listprop.render(lprops=lprops),
+                        file=ast_doc)
+                except KeyError:
+                    pass
+
+                # process them, close tab-set
+                if 'Property' in et or 'ListProperty' in et:
+                    print("""`````""", end="", file=ast_doc)
 
 
 # print(parsed_data)
+
+if __name__ == "__main__":
+    # src = "/home/asinha/Documents/02_Code/00_mine/NeuroML/software/NeuroML2/"
+    src = None
+    destdir = "../../source/Userdocs/LEMS_elements/"
+    main(src, destdir)