Merge pull request #1096 from effigies/deep_magic

sappelhoff · web-flow · commit a4a03ddfcc7a · 2022-04-29T08:40:14.000+02:00
[INFRA] Fix internal links implicitly
diff --git a/macros_doc.md b/macros_doc.md
@@ -78,7 +78,7 @@ consistency.
 ## What macros are available?
 
 All the macros we use are in listed in this
-[python file](https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py).
+[Python file](https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py).
 
 | Name                    | Purpose                                                                                | Uses schema | Example                                                                                                                                                                                     |
 | ----------------------- | -------------------------------------------------------------------------------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
diff --git a/pdf_build_src/process_markdowns.py b/pdf_build_src/process_markdowns.py
@@ -10,6 +10,7 @@
 from datetime import datetime
 import json
 import os
+import posixpath
 import re
 import subprocess
 import sys
@@ -562,6 +563,13 @@ def edit_titlepage():
         file.writelines(data)
 
 
+class MockPage:
+    pass
+
+class MockFile:
+    pass
+
+
 def process_macros(duplicated_src_dir_path):
     """Search for mkdocs macros in the specification, run the embedded
     functions, and replace the macros with their outputs.
@@ -594,6 +602,17 @@ def process_macros(duplicated_src_dir_path):
             with open(filename, "r") as fo:
                 contents = fo.read()
 
+            # Create a mock MkDocs Page object that has a "file" attribute,
+            # which is a mock MkDocs File object with a str "src_path" attribute
+            # The src_path
+            mock_file = MockFile()
+            mock_file.src_path = posixpath.sep.join(filename.split(os.sep)[1:])
+
+            page = MockPage()
+            page.file = mock_file
+
+            _Context__self = {"page": page}
+
             # Replace code snippets in the text with their outputs
             matches = re.findall(re_code_snippets, contents)
             for m in matches:
diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
@@ -3,7 +3,7 @@ HED:
   name: HED
   description: |
     Hierarchical Event Descriptor (HED) Tag.
-    See [Appendix III](/99-appendices/03-hed.html) for details.
+    See [Appendix III](SPEC_ROOT/99-appendices/03-hed.md) for details.
   type: string
 abbreviation:
   name: abbreviation
@@ -16,14 +16,16 @@ acq_time__scans:
     Acquisition time refers to when the first data point in each run was acquired.
     Furthermore, if this header is provided, the acquisition times of all files
     from the same recording MUST be identical.
-    Datetime format and their anonymization are described in [Units](/02-common-principles.html#units).
+    Datetime format and their anonymization are described in
+    [Units](SPEC_ROOT/02-common-principles.md#units).
   type: string
   format: datetime
 acq_time__sessions:
   name: acq_time
   description: |
     Acquisition time refers to when the first data point of the first run was acquired.
-    Datetime format and their anonymization are described in [Units](/02-common-principles.html#units).
+    Datetime format and their anonymization are described in
+    [Units](SPEC_ROOT/02-common-principles.md#units).
   type: string
   format: datetime
 age:
@@ -563,7 +565,7 @@ units:
   description: |
     Physical unit of the value represented in this channel,
     for example, `V` for Volt, or `fT/cm` for femto Tesla per centimeter
-    (see [Units](/02-common-principles.html#units)).
+    (see [Units](SPEC_ROOT/02-common-principles.md#units)).
   type: string
   format: unit
 value:
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
@@ -61,7 +61,7 @@ AnatomicalLandmarkCoordinateSystem:
   name: AnatomicalLandmarkCoordinateSystem
   description: |
     Defines the coordinate system for the anatomical landmarks.
-    See [Appendix VIII](/99-appendices/08-coordinate-systems.html)
+    See [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `"AnatomicalLandmarkCoordinateSystemDescription"`.
@@ -262,7 +262,7 @@ BodyPartDetails:
 BodyPartDetailsOntology:
   name: BodyPartDetailsOntology
   description: |
-    [URI](/02-common-principles.html#uniform-resource-indicator) of ontology used for
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator) of ontology used for
     BodyPartDetails (for example: `"https://www.ebi.ac.uk/ols/ontologies/uberon"`).
   type: string
   format: uri
@@ -378,7 +378,7 @@ ChunkTransformationMatrixAxis:
 Code:
   name: Code
   description: |
-    [URI](/02-common-principles.html#uniform-resource-indicator)
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
     of the code used to present the stimuli.
     Persistent identifiers such as DOIs are preferred.
     If multiple versions of code may be hosted at the same location,
@@ -388,15 +388,15 @@ Code:
 CogAtlasID:
   name: CogAtlasID
   description: |
-    [URI](/02-common-principles.html#uniform-resource-indicator)
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
     of the corresponding [Cognitive Atlas](https://www.cognitiveatlas.org/)
     Task term.
   type: string
   format: uri
 CogPOID:
   name: CogPOID
   description: |
-    [URI](/02-common-principles.html#uniform-resource-indicator)
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
     of the corresponding [CogPO](http://www.cogpo.org/) term.
   type: string
   format: uri
@@ -446,9 +446,9 @@ DatasetDOI:
   description: |
     The Digital Object Identifier of the dataset (not the corresponding paper).
     DOIs SHOULD be expressed as a valid
-    [URI](/02-common-principles.html#uniform-resource-indicator);
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator);
     bare DOIs such as `10.0.2.3/dfjj.10` are
-    [DEPRECATED](/02-common-principles.html#definitions).
+    [DEPRECATED](SPEC_ROOT/02-common-principles.md#definitions).
   type: string
   format: uri
 DatasetType:
@@ -547,7 +547,7 @@ DigitizedHeadPointsCoordinateSystem:
   description: |
     Defines the coordinate system for the digitized head points.
     See
-    [Appendix VIII](/99-appendices/08-coordinate-systems.html)
+    [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `"DigitizedHeadPointsCoordinateSystemDescription"`.
@@ -637,7 +637,7 @@ EEGCoordinateSystem:
     Defines the coordinate system for the EEG sensors.
 
     See
-    [Appendix VIII](/99-appendices/08-coordinate-systems.html)
+    [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `EEGCoordinateSystemDescription`.
@@ -706,13 +706,13 @@ EchoTime:
     (please note that the DICOM term is in milliseconds not seconds).
     The data type number may apply to files from any MRI modality concerned with
     a single value for this field, or to the files in a
-    [file collection](/99-appendices/10-file-collections.html)
+    [file collection](SPEC_ROOT/99-appendices/10-file-collections.md)
     where the value of this field is iterated using the
-    [echo entity](/99-appendices/09-entities.html#echo).
+    [echo entity](SPEC_ROOT/99-appendices/09-entities.md#echo).
     The data type array provides a value for each volume in a 4D dataset and
     should only be used when the volume timing is critical for interpretation
     of the data, such as in
-    [ASL](/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#\
+    [ASL](SPEC_ROOT/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#\
     arterial-spin-labeling-perfusion-data)
     or variable echo time fMRI sequences.
   anyOf:
@@ -823,7 +823,7 @@ FiducialsCoordinateSystem:
     Defines the coordinate system for the fiducials.
     Preferably the same as the `"EEGCoordinateSystem"`.
     See
-    [Appendix VIII](/99-appendices/08-coordinate-systems.html)
+    [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `"FiducialsCoordinateSystemDescription"`.
@@ -881,13 +881,13 @@ FlipAngle:
     Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
     The data type number may apply to files from any MRI modality concerned with
     a single value for this field, or to the files in a
-    [file collection](/99-appendices/10-file-collections.html)
+    [file collection](SPEC_ROOT/99-appendices/10-file-collections.md)
     where the value of this field is iterated using the
-    [flip entity](/99-appendices/09-entities.html#flip).
+    [flip entity](SPEC_ROOT/99-appendices/09-entities.md#flip).
     The data type array provides a value for each volume in a 4D dataset and
     should only be used when the volume timing is critical for interpretation of
     the data, such as in
-    [ASL](/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#\
+    [ASL](SPEC_ROOT/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#\
     arterial-spin-labeling-perfusion-data)
     or variable flip angle fMRI sequences.
   anyOf:
@@ -968,14 +968,14 @@ GeneticLevel:
 Genetics.Database:
   name: Genetics.Database
   description: |
-    [URI](/02-common-principles.html#uniform-resource-indicator)
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
     of database where the dataset is hosted.
   type: string
   format: uri
 Genetics.Dataset:
   name: Genetics.Dataset
   description: |
-    [URI](/02-common-principles.html#uniform-resource-indicator)
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
     where data can be retrieved.
   type: string
   format: uri
@@ -984,7 +984,7 @@ Genetics.Descriptors:
   description: |
     List of relevant descriptors (for example, journal articles) for dataset
     using a valid
-    [URI](/02-common-principles.html#uniform-resource-indicator)
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
     when possible.
   anyOf:
   - type: string
@@ -1015,7 +1015,7 @@ HED:
   name: HED
   description: |
     Hierarchical Event Descriptor (HED) information,
-    see: [Appendix III](/99-appendices/03-hed.html) for details.
+    see: [Appendix III](SPEC_ROOT/99-appendices/03-hed.md) for details.
   anyOf:
   - type: string
   - type: object
@@ -1067,7 +1067,7 @@ HeadCoilCoordinateSystem:
   description: |
     Defines the coordinate system for the head coils.
     See
-    [Appendix VIII](/99-appendices/08-coordinate-systems.html)
+    [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `HeadCoilCoordinateSystemDescription`.
@@ -1139,7 +1139,7 @@ ImageAcquisitionProtocol:
   name: ImageAcquisitionProtocol
   description: |
     Description of the image acquisition protocol or
-    [URI](/02-common-principles.html#uniform-resource-indicator)
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
     (for example from [protocols.io](https://www.protocols.io/)).
   type: string
 ImageDecayCorrected:
@@ -1440,7 +1440,7 @@ License:
   description: |
     The license for the dataset.
     The use of license name abbreviations is RECOMMENDED for specifying a license
-    (see [Appendix II](/99-appendices/02-licenses.html)).
+    (see [Appendix II](SPEC_ROOT/99-appendices/02-licenses.md)).
     The corresponding full license text MAY be specified in an additional
     `LICENSE` file.
   type: string
@@ -1487,7 +1487,7 @@ MEGCoordinateSystem:
   name: MEGCoordinateSystem
   description: |
     Defines the coordinate system for the MEG sensors.
-    See [Appendix VIII](/99-appendices/08-coordinate-systems.html)
+    See [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `"MEGCoordinateSystemDescription"`.
@@ -2119,7 +2119,7 @@ ReferencesAndLinks:
   description: |
     List of references to publications that contain information on the dataset.
     A reference may be textual or a
-    [URI](/02-common-principles.html#uniform-resource-indicator).
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator).
   items:
     type: string
   type: array
@@ -2175,7 +2175,7 @@ RepetitionTimePreparation:
     The data type array provides a value for each volume in a 4D dataset and
     should only be used when the volume timing is critical for interpretation of
     the data, such as in
-    [ASL](/04-modality-specific-files/01-magnetic-resonance-imaging-data.html\
+    [ASL](SPEC_ROOT/04-modality-specific-files/01-magnetic-resonance-imaging-data.md\
     #arterial-spin-labeling-perfusion-data).
   anyOf:
   - type: number
@@ -2228,7 +2228,7 @@ SampleExtractionProtocol:
   name: SampleExtractionProtocol
   description: |
     Description of the sample extraction protocol or
-    [URI](/02-common-principles.html#uniform-resource-indicator)
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
     (for example from [protocols.io](https://www.protocols.io/)).
   type: string
 SampleFixation:
@@ -2313,7 +2313,7 @@ ScanDate:
   description: |
     Date of scan in the format `"YYYY-MM-DD[Z]"`.
     This field is DEPRECATED, and this metadata SHOULD be recorded in the `acq_time` column of the
-    corresponding [Scans file](/03-modality-agnostic-files.html#scans-file).
+    corresponding [Scans file](SPEC_ROOT/03-modality-agnostic-files.md#scans-file).
   type: string
   format: date
 ScanOptions:
@@ -2477,7 +2477,7 @@ SourceDatasets:
   description: |
     Used to specify the locations and relevant attributes of all source datasets.
     Valid keys in each object include `"URL"`, `"DOI"` (see
-    [URI](/02-common-principles.html#uniform-resource-indicator)), and
+    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)), and
     `"Version"` with
     [string](https://www.w3schools.com/js/js_json_datatypes.asp)
     values.
@@ -2775,7 +2775,7 @@ Units:
   description: |
     Measurement units for the associated file.
     SI units in CMIXF formatting are RECOMMENDED
-    (see [Units](/02-common-principles.html#units)).
+    (see [Units](SPEC_ROOT/02-common-principles.md#units)).
   type: string
   format: unit
 VascularCrushing:
@@ -2934,7 +2934,7 @@ iEEGCoordinateSystem:
   description: |
     Defines the coordinate system for the iEEG sensors.
     See
-    [Appendix VIII](/99-appendices/08-coordinate-systems.html)
+    [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `iEEGCoordinateSystemDescription`.
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
@@ -463,7 +463,7 @@ blood:
   name: Blood recording data
   description: |
     Blood measurements of radioactivity stored in
-    [tabular files](/02-common-principles.html#tabular-files)
+    [tabular files](SPEC_ROOT/02-common-principles.md#tabular-files)
     and located in the `pet/` directory along with the corresponding PET data.
 bold:
   name: Blood-Oxygen-Level Dependent image
@@ -579,11 +579,11 @@ pet:
 phase:
   name: Phase image
   description: |
-    [DEPRECATED](/02-common-principles.html#definitions).
+    [DEPRECATED](SPEC_ROOT/02-common-principles.md#definitions).
     Phase information associated with magnitude information stored in BOLD
     contrast.
     This suffix should be replaced by the
-    [`part-phase`](/99-appendices/09-entities.html#part)
+    [`part-phase`](SPEC_ROOT/99-appendices/09-entities.md#part)
     in conjunction with the `bold` suffix.
   anyOf:
   - unit: arbitrary
diff --git a/tools/mkdocs_macros_bids/macros.py b/tools/mkdocs_macros_bids/macros.py
diff --git a/tools/schemacode/schemacode/render.py b/tools/schemacode/schemacode/render.py
