Merge pull request #507 from hed-standard/develop

Updated requirements so documentation displays properly.
hed-standard · Apr 14, 2023 · aed176e · aed176e
2 parents ff67689 + 1ab7df5
commit aed176e
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Showing 35 changed files with 309 additions and 295 deletions.
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,3 +1,14 @@
-Sphinx>=5.2.2
-myst-parser>=0.18.1
+Jinja2>=3.1.2
+MarkupSafe>=2.1.1
+portalocker>=2.4.0
+python-dateutil>=2.8.2
+pytz>=2022.1
+semantic_version>=2.10.0
+six>=1.16.0
+Sphinx>=4.5.0
+SphinxExtensions>=0.2.0
 sphinx_rtd_theme>=1.0.0
+Werkzeug>=2.1.2
+WTForms>=3.0.1
+xlrd>=2.0.1
+myst-parser>=0.18.1
diff --git a/docs/source/Appendix_B.md b/docs/source/Appendix_B.md
@@ -237,7 +237,8 @@ for additional information on the tag extension rules.
 ### TAG_EXTENSION_INVALID 
 
 **a.**  A tag extension term is already in the schema.   
-**b.**  A tag extension term does not comply with rules for schema nodes.   
+**b.**  A tag extension term does not comply with rules for schema nodes.
+**c.**  A tag has extension, but an extension is not allowed.
 
 See [**3.2.5 Tag extensions**](./03_HED_formats.md#325-tag-extensions)
 for additional information on the tag extension rules.

diff --git a/docs/source/_static/data/error_tests/CHARACTER_INVALID.json b/docs/source/_static/data/error_tests/CHARACTER_INVALID.json
diff --git a/docs/source/_template/layout.html b/docs/source/_template/layout.html
@@ -3,7 +3,7 @@
   {% block menu %}
     {{ super() }}
     <p class="caption" role="heading">
-      <span class="caption-text">Other HED resources:</span>
+      <span class="caption-text">HED resources:</span>
     </p>
     <ul>
       <li class="toctree-li">
@@ -12,6 +12,8 @@
         <a href="https://www.youtube.com/channel/UCYu8B1eFb-gRemamXod-exQ">HED YouTube channel</a></li>
       <li class="toctree-li">
         <a href="https://hed-examples.readthedocs.io/en/latest/DocumentationSummary.html">Documentation summary</a></li>
+      <li class="toctree-li">
+        <a href="https://hed-specification.readthedocs.io/en/latest/index.html">Specification</a></li>
       <li class="toctree-li"><a href="https://hedtools.ucsd.edu/hed">Online tools</a></li>
       <li class="toctree-li"><a href="https://hed-python.readthedocs.io/en/latest/">HEDTools API</a></li>
       <li class="toctree-li"><a href="https://hed-web.readthedocs.io/en/latest/">Web deployment</a></li>

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -52,7 +52,7 @@
 autodoc_default_flags = ['members', 'inherited-members']
 add_module_names = False
 myst_all_links_external = False
-myst_heading_anchors = 5
+myst_heading_anchors = 4
 myst_enable_extensions = ["deflist"]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -85,7 +85,7 @@
     # Toc options
     'collapse_navigation': True,
     'sticky_navigation': True,
-    'navigation_depth': 5,
+    'navigation_depth': 4,
     'includehidden': True,
     'titles_only': False
 }

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -19,9 +19,9 @@ HED specification
 
    * `HED project homepage <https://www.hedtags.org/>`_
 
-|
-|
-|
+
+Specification role
+******************
 
 The HED specification document formalizes the syntax and behavior of
 HED (Hierarchical Event Descriptors) vocabulary, annotations, and supporting tools. The specification supports three versions of the specification:
@@ -33,6 +33,7 @@ HED (Hierarchical Event Descriptors) vocabulary, annotations, and supporting too
 For more information about HED see `The HED project homepage <https://www.hedtags.org>`_ and
 the `HED resources page <https://www.hed-resources.org>`_.
 
+
 .. toctree::
    :maxdepth: 4
    :caption: Contents:
@@ -52,5 +53,4 @@ Indices and tables
 ==================
 
 * :ref:`genindex`
-* :ref:`modindex`
 * :ref:`search`
diff --git a/readthedocs.yml b/readthedocs.yml
@@ -15,7 +15,7 @@ sphinx:
 
 # Optionally set the version of Python and requirements required to _build your docs
 python:
-  version: "3.8"
+  version: "3.7"
   install:
     - requirements: docs/requirements.txt
   system_packages: true
diff --git a/tests/json_tests/CHARACTER_INVALID.json b/tests/json_tests/CHARACTER_INVALID.json
@@ -0,0 +1,90 @@
+ [
+    {
+        "error_code": "CHARACTER_INVALID",
+        "name": "character-invalid-utf-8",
+        "description": "The HED string contains a UTF-8 character.",
+        "schema": "8.1.0",
+        "definitions": ["(Definition/Acc/#, (Acceleration/#, Red))", "(Definition/MyColor, (Label/Pie))"],
+        "tests": {
+            "string_tests": {
+                "fails": [
+                    "Collection/[x]",
+                    "Description/This is a ʰ bad character"
+                ],
+                "passes": [
+                    "Red, Blue, Description/Red"
+                ]
+            },
+            "sidecar_tests": {
+                "fails": [
+                    {
+                        "event_code": {
+                            "HED": {
+                                "show": "Red, Label/a ʰ bad"
+                            }
+                        }
+                    }
+                ],
+                "passes": [
+                    {
+                        "event_code": {
+                            "HED": {
+                                "show": "Red, Label/Good"
+                            }
+                        }
+                    }
+                ]
+            },
+            "event_tests": {
+                "fails": [
+                    [
+                        ["onset", "duration", "HED"],
+                        [ 4.5, 0, "Label/a ʰ bad"]
+                    ]
+                ],
+                "passes": [
+                    [
+                        ["onset", "duration", "HED"],
+                        [ 4.5, 0, "Label/Temp"]
+                    ]
+                ]
+            },
+            "combo_tests": {
+                "fails": [
+                    {
+                        "sidecar":  {
+                            "event_code": {
+                                "HED": {
+                                    "show": "Red, Label/a ʰ bad",
+                                    "ball": "Def/Acc/4.5 m-per-s^2"
+                                }
+                            }
+                        },
+                        "events": 
+                            [
+                                ["onset", "duration", "event_code", "HED"],
+                                [ 4.5, 0, "show", "Description/a ʰ good"],
+                                [ 5.0, 0, "ball", "Blue"]
+                            ]
+                    }
+                ],
+                "passes": [
+                    {
+                         "sidecar":  {
+                            "event_code": {
+                                "HED": {
+                                    "show": "Red, Label/a"
+                                }
+                            }
+                        },
+                        "events": 
+                            [
+                                ["onset", "duration", "event_code", "HED"],
+                                [ 4.5, 0, "show", "Description/goodness"]
+                            ]
+                    }
+                ]
+            }
+        }
+    }
+]    
diff --git a/...tatic/data/error_tests/COMMA_MISSING.json → tests/json_tests/COMMA_MISSING.json b/...tatic/data/error_tests/COMMA_MISSING.json → tests/json_tests/COMMA_MISSING.json
diff --git a/.../data/error_tests/DEFINITION_INVALID.json → tests/json_tests/DEFINITION_INVALID.json b/.../data/error_tests/DEFINITION_INVALID.json → tests/json_tests/DEFINITION_INVALID.json
@@ -12,7 +12,6 @@
                     "Definition/Blech, (Red)"
                 ],
                 "passes": [
-                    "(Definition/Blech, (Red))"
                 ]
             },
             "sidecar_tests": {
@@ -716,7 +715,7 @@
         "name": "definition-not-allowed-here",
         "description": "A definition appears in an unexpected place such as an events file.",
         "schema": "8.1.0",
-        "definitions": ["(Definition/Acc/#, (Acceleration/#, Red))", "(Definition/MyColor, (Event-context, Item, (Label/Pie)))"],
+        "definitions": ["(Definition/Acc/#, (Acceleration/#, Red))", "(Definition/MyColor, (Item, (Label/Pie)))"],
         "tests": {
             "string_tests": {
                 "fails": [