Merge pull request #43 from ocefpaf/link_checker

add dependabot for GHA and linkchecker

.github/workflows/md-link-check.yml

@@ -0,0 +1,26 @@
+name: Check Markdown links
+
+on:
+  pull_request:
+  push:
+    branches:
+      - gh-pages
+
+jobs:
+  markdown-link-check:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Check Links
+      uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        use-quiet-mode: 'yes'
+        use-verbose-mode: 'yes'
+        config-file: '.mlc_config.json'
+        file-path: './README.md'
+        folder-path: '_docs/'

.mlc_config.json

@@ -0,0 +1,18 @@
+{
+  "ignorePatterns": [
+    {
+      "pattern": "://localhost"
+    }
+  ],
+  "replacementPatterns": [
+    {
+      "pattern": "^/(.*)",
+      "replacement": "https://ioos.github.io/$1"
+    },
+    {
+      "pattern": "^\\s*{{\\s*site.baseurl\\s*}}\\s*/(.*)",
+      "replacement": "https://ioos.github.io/$1"
+    }
+],
+  "aliveStatusCodes": [200, 400, 403, 0]
+}

_docs/gold-standard-examples.md

@@ -10,7 +10,7 @@ summary:  Describes gold standard examples for various dataset types and scenari
 
 ## **Overview**
 
-The page provides links to example datasets that satisfy the [IOOS Metadata Profile 1.2](ioos-metadata-profile-v1-2.html).
+The page provides links to example datasets that satisfy the [IOOS Metadata Profile 1.2](ioos-metadata-profile-v1-2).
 
 Since the IOOS standard builds off of the [**NOAA NCEI NetCDF Templates**](https://www.nodc.noaa.gov/data/formats/netcdf/), the NCEI "Gold Standard" examples ([HTTP](https://data.nodc.noaa.gov/ncei/example/data/netcdf/), [THREDDS](https://data.nodc.noaa.gov/thredds/catalog/example/catalog.html)) provide a great starting point.
 

_docs/index.md

@@ -9,7 +9,7 @@ summary: The IOOS Metadata Profile contains dataset attribution guidelines and e
 
 ## **Current Profile Version**
 
-### [**IOOS Metadata Profile 1.2**](ioos-metadata-profile-v1-2.html)
+### [**IOOS Metadata Profile 1.2**](ioos-metadata-profile-v1-2)
 
 Looking for the latest version?  Follow the link above for details on requirements to implement the IOOS Metadata Profile for publishing data according to the latest IOOS guidelines.
 
@@ -29,7 +29,7 @@ Individual releases of the IOOS Metadata Profile (e.g. 1.0, 1.1, 1.2) target spe
 
 ## Profile Versions:
 
-### [**IOOS Metadata Profile, Version 1.2** (Current)](ioos-metadata-profile-v1-2.html)
+### [**IOOS Metadata Profile, Version 1.2** (Current)](ioos-metadata-profile-v1-2)
 
 IOOS Metadata Profile Version 1.2 (released in 2020) is the current **valid**{: style="color: green"} profile, and is based upon the following convention versions:
 
@@ -58,15 +58,15 @@ Version 1.2 of the Metadata Profile targets ERDDAP as the future platform for IO
 Data providers wishing to maintain ncSOS/IOOS SOS compatibility can refer to this list and add all required IOOS attributes from deprecated Metadata Profile 1.1 and or duplicate attributes where appropriate.
 
 
-### [**IOOS Metadata Profile, Version 1.1**](ioos-metadata-profile-v1-1.html)
+### [**IOOS Metadata Profile, Version 1.1**](ioos-metadata-profile-v1-1)
 
 IOOS Metadata Profile Version 1.1 (**deprecated in 2019**{: style="color: red"}) is based upon the following convention versions:
 
 - [Climate and Forecast Conventions (CF) 1.6](http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html)
 - [Attribute Convention for Data Discovery 1.3](http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3)
 - [NOAA NCEI NetCDF Templates 2.0](https://www.nodc.noaa.gov/data/formats/netcdf/v2.0/)
 
-### [**IOOS Metadata Profile, Version 1.0**](ioos-metadata-profile-v1-0.html)
+### [**IOOS Metadata Profile, Version 1.0**](ioos-metadata-profile-v1-0)
 
 IOOS Metadata Profile Version 1.0 (**deprecated in 2016**{: style="color: red"}) is based upon the following convention versions:
 

_docs/ioos-metadata-profile-v1-0.md

@@ -4,7 +4,7 @@ keywords: [ioos, metadata, netCDF, 1.0]
 tags: [ioos, metadata, netCDF, 1.0]
 toc: false
 #permalink: index.html
-summary: Deprecated 2016.  Visit the [1.2 Metadata Profile](./ioos-metadata-profile-v1-2.html) page for the current version.
+summary: Deprecated 2016.  Visit the [1.2 Metadata Profile](ioos-metadata-profile-v1-2) page for the current version.
 ---
 
 
@@ -18,14 +18,14 @@ summary: Deprecated 2016.  Visit the [1.2 Metadata Profile](./ioos-metadata-prof
  2. Each attribute in the Profile is either **required** or **recommended**.
  3. All **required** attributes must have meaningful values assigned to them in accordance with the rules prescribed by the corresponding Convention or Template.
  4. Each and all of the **recommended** attributes may be omitted; however, it is highly desirable that these attributes are included into the NetcDF metadata ***AND*** have meaningful values assigned to them.
- 5. The **`platform_variable:ioos_code`** and **`platform_variable:short_name`** are the only **interchangeable** attributes - either a single **`platform_variable:ioos_code`** or a combination of **`platform_variable:short_name`** with **`naming_authority`** is **required** to ensure that ncSOS will be able to produce the IOOS SOS Asset Identifier for the specific platform (see the [NetCDF to IOOS SOS Crosswalk](https://github.com/ioos/ioos-metadata/blob/master/docs/NetCDF-to-SOS%20Mappings_clean_2016-04-07a.xlsx) for details). The rest of attributes ***may not*** be substituted for one another.
+ 5. The **`platform_variable:ioos_code`** and **`platform_variable:short_name`** are the only **interchangeable** attributes - either a single **`platform_variable:ioos_code`** or a combination of **`platform_variable:short_name`** with **`naming_authority`** is **required** to ensure that ncSOS will be able to produce the IOOS SOS Asset Identifier for the specific platform (see the [NetCDF to IOOS SOS Crosswalk](https://github.com/ioos/ioos-metadata/raw/gh-pages/_docs/NetCDF-to-SOS%20Mappings_clean_2016-04-07a.xlsx) for details). The rest of attributes ***may not*** be substituted for one another.
  6. The **`platform_vocabulary`** attribute is at the moment the only pure ACDD v1.3 attribute that is included in the Profile.
  7. This document only describes a fraction of the Profile:
    - attributes that are IOOS-specific;
    - attributes with a different role in the Templates; for example, the attribute **`_FillValue`** is required by the NODC Template; however, the Profile just recommends to use it because it is optional in the IOOS SOS metadata set (whether the Template requirement should prevail, is beyond the scope of the Profile description);
    - attributes that are **required** by the Profile regardless of their role in the Templates.
  8.  Other Profile attributes are described in the [**NOAA NODC NetCDF Templates v1.1**](http://www.nodc.noaa.gov/data/formats/netcdf/v1.1/).  A set of "Gold Standard" example NetCDF files, which precisely follow the NODC/NCEI Templates, may be found [here](http://data.nodc.noaa.gov/ncei/example/data/netcdf/) or [here](http://data.nodc.noaa.gov/thredds/catalog/example/catalog.html).
- 9.  The [**U.S. IOOS National Glider Data Assembly Center**](https://gliders.ioos.us/index.html) currently uses a slightly different [NetCDF Metadata Profile](https://github.com/ioos/ioosngdac/wiki/NGDAC-NetCDF-File-Format-Version-2); work is in progress to harmonize the NGDAC and IOOS NetCDF Profiles.
+ 9.  The [**U.S. IOOS National Glider Data Assembly Center**](https://gliders.ioos.us/) currently uses a slightly different [NetCDF Metadata Profile](https://github.com/ioos/ioosngdac/wiki/NGDAC-NetCDF-File-Format-Version-2); work is in progress to harmonize the NGDAC and IOOS NetCDF Profiles.
 
 
 ## **IOOS NetCDF Metadata Profile Attributes**
@@ -40,13 +40,13 @@ creator_country | IOOS | Country of the person or organization that operates a p
 creator_email  | ACDD | Email address of the person or institution that collected the data. | global | required
 creator_name  | ACDD | Name of the person or organization that collected the data. | global | recommended
 creator_phone | IOOS | The phone number of the person or group that collected the data. | global | recommended
-creator_sector | IOOS | [IOOS classifier](http://mmisw.org/orr/#http://mmisw.org/ont/ioos/sector) that best describes the platform (network) operator's societal sector. <br><br>Example: **`creator_sector = "academic"`** | global |required
+creator_sector | IOOS | [IOOS classifier](https://mmisw.org/ont/ioos/sector) that best describes the platform (network) operator's societal sector. <br><br>Example: **`creator_sector = "academic"`** | global |required
 creator_state | IOOS | State of the person or organization that collected the data.  | global | recommended
 creator_url  | ACDD | The URL of the institution that collected the data. | global | recommended
 creator_zipcode | IOOS | ZIP code of the person or organization that collected the data.  | global | recommended
 featureType | CF | CF attribute for identifying the featureType, e.g. featureType = "timeSeries". | global | required
 geophysical_variable:_FillValue<br>geospatial_variable:_FillValue | CF | This value is considered to be a special value that indicates undefined or missing data, and is returned when reading values that were not written: {::nomarkdown}<i><ul>  <li>time:_FillValue = 0.0f    <li>lat:_FillValue = 0.0f    <li>on:_FillValue = 0.0f    <li>z:_FillValue = 0.0f    <li>sea_water_temperature:_FillValue = 0.0f</ul></i>{:/} | variable | recommended
-geophysical_variable:standard_name | CF | Standardized field which uses the [CF Standard Names](http://www.cfconventions.org/documents.html/). If a variables does not have an existing standard_name in the CF-managed list, this attribute should not be used. In these cases, a standard name can be proposed to the CF community for consideration and acceptance. | variable | required
+geophysical_variable:standard_name | CF | Standardized field which uses the [CF Standard Names](https://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html). If a variables does not have an existing standard_name in the CF-managed list, this attribute should not be used. In these cases, a standard name can be proposed to the CF community for consideration and acceptance. | variable | required
 id | ACDD | An identifier for the data set, provided by and unique within its naming authority. The combination of the **`naming authority`** and the **`id`** should be globally unique, but the **`id`** can be globally unique by itself also. IDs can be URLs, URNs, DOIs, meaningful text strings, a local key, or any other unique string of characters. The **`id`** should not include blanks. | global | required
 institution  | ACDD | The institution of the person or group that collected the data. | global | required
 instrument_variable:discriminant | IOOS | The value of a **`discriminant`** applies to the like-named field in the IOOS SOS Asset Identifier URN; it ensures that in case of multiple sensors measuring the same **`observedProperty`**, each sensor has a unique ID. <br><br>Examples: {::nomarkdown}<i><ul> <li>sea_water_temperature:<b>top</b> <li> sea_water_temperature:<b>bottom</b> <li> sea_water_temperature:<b>nortek_adp_514</b></i></ul>{:/}| variable | required, if applicable
@@ -57,8 +57,8 @@ platform | NODC Templates<br>(ACDD 1.3) | Name of the platform(s) that supported
 platform_variable:ioos_code | IOOS | Provides IOOS asset identification similar to **`wmo_code`** and **`nodc_code`**. The attribute is a URN that should follow the "[IOOS Convention for Asset Identification](http://ioos.github.io/conventions-for-observing-asset-identifiers/ioos-assets-v1-0.html)" with a general pattern of _**`urn:ioos:asset_type:authority:label[:discriminant]`**_.  <br><br>Examples: {::nomarkdown}<i><ul> <li> <b><code>urn:ioos:glider:wmo:4801902:20160218T1913Z</code></b> <li><b><code>urn:ioos:station:us.glos:45024</code></b> </ul></i>{:/} <br>**NOTE:** interchangeable with **`platform_variable:short_name`** | variable | required
 platform_variable:long_name | NODC Templates | Provide a descriptive, long name for this variable. | variable | required
 platform_variable:short_name | IOOS | Provide a short name for the platform.  Similar to ID, a **`short_name`** can be any unique string of characters that does not include blanks. <br><br>Examples: {::nomarkdown}<i><ul> <li> <b><code>station_1:short_name = “carquinez”</code></b> <li><b><code>station_1:short_name = “cb0102</code></b></i> </ul>{:/} <br>**NOTE:** interchangeable with **`platform_variable:ioos_code`** | variable | required
-platform_variable:type | IOOS | In  conjunction with a **`platform_vocabulary`** attribute, identifies platform's type as defined in the [IOOS Platform Categories vocabulary](https://mmisw.org/orr/#http://mmisw.org/ont/ioos/platform), or [SeaVoX Platform Categories vocabulary](http://vocab.nerc.ac.uk/collection/L06/current/"), or any other vocabulary. The URL of the actual vocabulary must be published in the **`platform_vocabulary`** global attribute. <br><br>Alternatively, the **`platform`** and **`platform_vocabulary`** pair of attributes may be used; however, this option is not recommended (see details in the **`platform_vocabulary`** description.) | variable | required
-platform_vocabulary | ACDD 1.3<br>(NCEI Templates v2.0) | Controlled vocabulary for the names used in the "platform" attribute.<br><br> It is recommended that this attribute is used in conjunction with the **`platform_variable:type`** attribute. In that case, the recommended value for the **`platform_vocabulary`** attribute is a URL to either the [IOOS Platform Category vocabulary](https://mmisw.org/orr/#http://mmisw.org/ont/ioos/platform), or [SeaVoX Platform Categories vocabulary](http://vocab.nerc.ac.uk/collection/L06/current/). <br><br>Example: **`platform_vocabulary = "https://mmisw.org/orr/#http://mmisw.org/ont/ioos/platform"`**<br><br>As an alternative (although not recommended), a NetCDF file may follow the NCEI Template v2.0, which suggests the use of "NASA GCMD Platform Keywords Version 8.1" string as the fixed value for the **`platform_vocabulary`**, and does not stipulate for the **`platform_variable:type`**. Instead, the actual type of the platform must be placed in the global **`platform`** attribute as described in the Science Keyword Rules (http://gcmd.nasa.gov/learn/rules.html) for NASA Global Change Master Directory (GCMD) Keywords (http://gcmd.nasa.gov/learn/keywords.html). <br><br>Example: **`platform: In Situ Ocean-based Platforms > MOORINGS`** | global | required
+platform_variable:type | IOOS | In  conjunction with a **`platform_vocabulary`** attribute, identifies platform's type as defined in the [IOOS Platform Categories vocabulary](https://mmisw.org/ont/ioos/platform), or [SeaVoX Platform Categories vocabulary](http://vocab.nerc.ac.uk/collection/L06/current/), or any other vocabulary. The URL of the actual vocabulary must be published in the **`platform_vocabulary`** global attribute. <br><br>Alternatively, the **`platform`** and **`platform_vocabulary`** pair of attributes may be used; however, this option is not recommended (see details in the **`platform_vocabulary`** description.) | variable | required
+platform_vocabulary | ACDD 1.3<br>(NCEI Templates v2.0) | Controlled vocabulary for the names used in the "platform" attribute.<br><br> It is recommended that this attribute is used in conjunction with the **`platform_variable:type`** attribute. In that case, the recommended value for the **`platform_vocabulary`** attribute is a URL to either the [IOOS Platform Category vocabulary](https://mmisw.org/ont/ioos/platform), or [SeaVoX Platform Categories vocabulary](http://vocab.nerc.ac.uk/collection/L06/current/). <br><br>Example: **`platform_vocabulary = "https://mmisw.org/ont/ioos/platform"`**<br><br>As an alternative (although not recommended), a NetCDF file may follow the NCEI Template v2.0, which suggests the use of "NASA GCMD Platform Keywords Version 8.1" string as the fixed value for the **`platform_vocabulary`**, and does not stipulate for the **`platform_variable:type`**. Instead, the actual type of the platform must be placed in the global **`platform`** attribute as described in the Science Keyword Rules (http://gcmd.nasa.gov/learn/rules.html) for NASA Global Change Master Directory (GCMD) Keywords (http://gcmd.nasa.gov/learn/keywords.html). <br><br>Example: **`platform: In Situ Ocean-based Platforms > MOORINGS`** | global | required
 publisher_address | IOOS | Street address of the person or organization that distributes the data.   | global | recommended
 publisher_city | IOOS | City of the person or organization that distributes the data.   | global | recommended
 publisher_country | IOOS | Country of the person or organization that distributes the data.   | global | required
@@ -68,7 +68,7 @@ publisher_phone | IOOS | The phone number of the person or group that distribute
 publisher_state | IOOS | State of the person or organization that distributes the data.   | global | recommended
 publisher_url  | ACDD | URL of the person or group that distributes the data files. | global | recommended
 publisher_zipcode | IOOS | ZIP code of the person or organization that distributes the data.   | global | recommended
-standard_name_vocabulary  | ACDD | Standardized field which uses the [CF Standard Names](http://www.cfconventions.org/documents.html/). If a variables does not have an existing standard_name in the CF-managed list, this attribute should not be used. In these cases, a standard name can be proposed to the CF community for consideration and acceptance. | global | required
+standard_name_vocabulary  | ACDD | Standardized field which uses the [CF Standard Names](https://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html). If a variables does not have an existing standard_name in the CF-managed list, this attribute should not be used. In these cases, a standard name can be proposed to the CF community for consideration and acceptance. | global | required
 summary  | ACDD | One paragraph describing the data set. |  global | recommended
 title  | ACDD | One sentence about the data contained within the file. | global | required
 units  | CF | Required for most all variables that represent dimensional quantities. The value should come from [**`udunits`**](http://www.unidata.ucar.edu/software/udunits/) authoritative vocabulary, which is documented in the CF standard name table with it's corresponding standard name. The **`udunits`** package includes a file `udunits.dat` which lists its supported unit names. | variable | required