Fix broken links

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

@@ -0,0 +1,35 @@
+name: Check Markdown links
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  markdown-link-check:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    - name: Check gh-pages
+      if: github.ref == 'refs/heads/gh-pages'
+      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/'
+
+    - name: Check main
+      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'

.pre-commit-config.yaml

@@ -0,0 +1,31 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      # - id: trailing-whitespace
+      # - id: end-of-file-fixer
+      - id: check-added-large-files
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.5
+    hooks:
+      - id: codespell
+        exclude: >
+            (?x)^(
+                .*\.yaml|
+                .*\.yml|
+            )$
+        args:
+          - --ignore-words-list=nd,ot,adn,redict
+
+
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+        for more information, see https://pre-commit.ci
+    autofix_prs: false
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: monthly
+    skip: []
+    submodules: false

_docs/faqs.md

@@ -27,14 +27,9 @@ Either way works.
 
 ## Can I submit variables other than the core CTD variables?
 
-Yes! The DAC now accepts any science variables that have a valid [CF Standard Name](http://cfconventions.org/standard-names.html). Any ancillary variables (as specified in the variable attribute `ancillary_variables`) will also be ingested into ERDDAP.
+Yes! The DAC now accepts any science variables that have a valid [CF Standard Name](https://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html). Any ancillary variables (as specified in the variable attribute `ancillary_variables`) will also be ingested into ERDDAP.
 
 
 ## What is the current procedure for sending data to the Global Telecommunications System (GTS)?
 
 The National Data Buoy Center harvests new profile observations from the [DAC's ERDDAP server](https://gliders.ioos.us/erddap/index.html) once per hour, encodes the profiles in to a modified drifting buoy BUFR format and releases the messages to the GTS.  The development of a glider specific BUFR format is currently being developed and finalized.
-
-
-<!-- 2. Can I submit raw glider files to the DAC? -->
-
-<!-- At the moment no, you must convert the raw files to netCDF following the DAC [metadata conventions](/ioosngdac/ngdac-netcdf-file-format-version-2.html). But we're in the process of developing a raw data upload tool that will enable users to  -->

_docs/glider-background-and-sampling-terminology.md

@@ -8,30 +8,20 @@ toc: false
 #permalink: index.html
 summary: This page defines glider and sampling terminology used throughout the rest of the Wiki.
 ---
-<!--
-> [Wiki](https://github.com/kerfoot/ioosngdac/wiki) ▸ **Glider Background and Sampling Terminology**
-
-## Contents
-
-+ [Glider Types](#glider-types)
-+ [Sampling Pattern Terminology](#sampling-pattern-terminology)
-+ [NetCDF File Format Description](ngdac-netcdf-file-format-version-2.html)
--->
 
 ## Glider Types
 As of this writing, there are 3 major buoyancy driven glider types that are currently utilized by IOOS Regional Associations:
- + [Seaglider](http://www.apl.washington.edu/project/project.php?id=seaglider#:~:text=The%20AUV%20Seaglider%20is%20the,time%20via%20satellite%20data%20telemetry.): originally designed and built through a collaboration with the University of Washington's [Applied Physics Lab](http://www.apl.washington.edu/) and [School of Oceanography](http://www.ocean.washington.edu/).  The Seaglider is now manufactured by [Hydroid](https://www.hydroid.com/seaglider)
- + [Spray](http://spray.ucsd.edu/pub/rel/info/spray_description.php): originally designed by [Scripps Institution of Oceanography](https://scripps.ucsd.edu/) and [Woods Hole Oceangraphic Institution](http://www.whoi.edu/) with funding provided by the [Office of Naval Research](http://www.onr.navy.mil/), the Spray glider is now manufactured by [Bluefin Robotics](http://www.bluefinrobotics.com/products/spray-glider/).
- + [Slocum](http://www.webbresearch.com/slocumglider.aspx): designed and built by [Teledyne Webb Research Corporation](http://www.webbresearch.com/).
+ + [Seaglider](https://apl.uw.edu/project/project.php?id=seaglider): originally designed and built through a collaboration with the University of Washington's [Applied Physics Lab](https://apl.uw.edu/) and [School of Oceanography](https://www.ocean.washington.edu/).
+ + [Spray](https://spray.ucsd.edu/pub/rel/info/spray_description.php): originally designed by [Scripps Institution of Oceanography](https://scripps.ucsd.edu/) and [Woods Hole Oceanographic Institution](http://www.whoi.edu/) with funding provided by the [Office of Naval Research](https://www.nre.navy.mil/), the Spray glider is now manufactured by [Bluefin Robotics](https://gdmissionsystems.com/underwater-vehicles/bluefin-robotics/).
+ + [Slocum](https://www.teledynemarine.com/en-us/products/product-line/Pages/Autonomous-Underwater-Glider.aspx): designed and built by [Teledyne Webb Research Corporation](https://www.teledynemarine.com/brands/webb-research/).
 
 ## Sampling Pattern Terminology
 
 The schematic and definitions below define the sampling terminology of a profiling glider.  While all of the terms defined below are commonly used in the glider community, the 2 fundamental terms used by the **NGDAC** to organize data are the **profile** and **trajectory**.  The **NGDAC** receives glider data as individual, sequentially numbered **profiles** and aggregates files from the same **trajectory** into a single data set representing the deployment.
 
-<!-- ![Glider Sampling Patterns and Terms](https://raw.githubusercontent.com/kerfoot/ioosngdac/master/doco/glider-sampling-terminology.png) -->
 ![Glider Sampling Patterns and Terms](/glider-dac/glider-sampling-terminology.png)
 
- + **Profile**: A single vertically oriented track of a glider, either upward or downward through the water column.  A profile is one-half of a **dive**.  The profile is the fundamental atomic data type used by the **NGDAC**.  All data submitted to the **NGDAC** is submitted as individual profiles, containing the various water column properties or sensor values.  Examples of the file format description can be found as [CDL](https://github.com/kerfoot/ioosngdac/blob/master/nc/template/IOOS_Glider_NetCDF_v2.0.cdl), [NetCDF file](https://github.com/kerfoot/ioosngdac/blob/master/nc/template/IOOS_Glider_NetCDF_v2.0.nc) and [ncml](https://github.com/kerfoot/ioosngdac/blob/master/nc/template/IOOS_Glider_NetCDF_v2.0.ncml) can be found [here](https://github.com/kerfoot/ioosngdac/tree/master/nc/template).
+ + **Profile**: A single vertically oriented track of a glider, either upward or downward through the water column.  A profile is one-half of a **dive**.  The profile is the fundamental atomic data type used by the **NGDAC**.  All data submitted to the **NGDAC** is submitted as individual profiles, containing the various water column properties or sensor values.  Examples of the file format description can be found as [CDL](/glider-dac/nc/template/IOOS_Glider_NetCDF_v2.0.cdl), [NetCDF file](/glider-dac/nc/template/IOOS_Glider_NetCDF_v2.0.nc) and [ncml](/glider-dac/nc/template/IOOS_Glider_NetCDF_v2.0.ncml) can be found [here](https://github.com/ioos/glider-dac/tree/gh-pages/nc/template).
  + **Dive**: A single vertical <strong>profile</strong> to depth followed by a vertical **profile** towards the surface.  A dive does not necessarily begin with or terminate with a surfacing and/or gps fix.
  + **Segment**: The set of data collected between 2 gps fixes obtained while the glider is on the surface of the water.  The first gps fix is acquired prior to the beginning of a dive and the second gps fix is acquired following the completion of at least one dive.  Glider **segments** always consist of at least one, and possibly many **dives**.
  + **Trajectory** or **Deployment**: A series of one or more **segments** completed by a glider between the time of deployment and the time of recovery.

_docs/index.md

@@ -9,34 +9,20 @@ toc: false
 summary: This wiki is a collection of documents and resources describing the NetCDF file specification, data provider registration and data set submission processes for contributing real-time and delayed-mode glider data sets to the U.S. IOOS National Glider Data Assembly Center (NGDAC).
 ---
 
-<!--
-This wiki is a collection of documents and resources describing the NetCDF file specification, data provider registration and data set submission processes for contributing real-time and delayed-mode glider data sets to the U.S. IOOS <b>N</b>ational <b>G</b>lider <b>D</b>ata <b>A</b>ssembly <b>C</b>enter (__NGDAC__).
-
-## Wiki Contents
-
-+ [Introduction](#introduction)
-+ [Glider Background and Sampling Terminology](/ioosngdac/glider-background-and-sampling-terminology.html)
-+ [NetCDF file format description](ngdac-netcdf-file-format-version-2.html)
-+ [Links for Data Providers](/ioosngdac/useful-links.html)
-+ [NGDAC Architecture](/ioosngdac/ngdac-architecture.html)
-+ [NGDAC NetCDF File Submission Process](/ioosngdac/ngdac-netcdf-file-submission-process.html)
-+ [Backup and Recovery](/ioosngdac/data-backup-recovery)
--->
-
 ## Introduction
 
 The goals of the <b>U.S. IOOS National Glider Data Assembly Center</b>:
 
- + Develop a simple, fully self-describing [NetCDF](http://en.wikipedia.org/wiki/NetCDF) file specification that preserves the resolution of the original glider data sets.
+ + Develop a simple, fully self-describing [NetCDF](https://docs.unidata.ucar.edu/netcdf-c/current/) file specification that preserves the resolution of the original glider data sets.
  + Provide glider operators with a simple process for registering and submitting glider data sets to a centralized storage location.
  + Provide public access to glider data sets via existing web services and standards, in a variety of well-known formats.
- + Facilitate the distribution of glider data sets on the [Global Telecommunication System](http://www.wmo.int/pages/prog/www/TEM/GTS/index_en.html).
+ + Facilitate the distribution of glider data sets on the [Global Telecommunication System](https://community.wmo.int/en/activity-areas/global-telecommunication-system-gts).
  + Work with the [National Centers for Environmental Information](https://www.ncei.noaa.gov/) to create a permanent data archive.
 
-The **NGDAC** accepts a [simple NetCDF file](/ioosngdac/ngdac-netcdf-file-format-version-2.html) containing water column measurements collected by a glider during a single profile (see glider sampling terminology [here](glider-background-and-sampling-terminology.html#sampling-pattern-terminology)).  Groups of these NetCDF files, gathered during a deployment (also known as a [**trajectory**](glider-background-and-sampling-terminology.html#sampling-pattern-terminology)), are uploaded to the **NGDAC** by individual glider operators.  Once they arrive at the **NGDAC**, the files are validated for compliance, aggregated into a single dataset representing the **deployment/trajectory** and distributed via [ERDDAP](http://coastwatch.pfeg.noaa.gov/erddap/information.html) and [THREDDS](http://www.unidata.ucar.edu/software/thredds/current/tds/TDS.html) end-points.  The data sets served by the **NGDAC** provide access to the **trajectory/deployment** data both as time-series and on a profile-by-profile basis.
+The **NGDAC** accepts a [simple NetCDF file](/glider-dac/ngdac-netcdf-file-format-version-2.html) containing water column measurements collected by a glider during a single profile (see glider sampling terminology [here](glider-background-and-sampling-terminology.html#sampling-pattern-terminology)).  Groups of these NetCDF files, gathered during a deployment (also known as a [**trajectory**](glider-background-and-sampling-terminology.html#sampling-pattern-terminology)), are uploaded to the **NGDAC** by individual glider operators.  Once they arrive at the **NGDAC**, the files are validated for compliance, aggregated into a single dataset representing the **deployment/trajectory** and distributed via [ERDDAP](https://coastwatch.pfeg.noaa.gov/erddap/information.html) and [THREDDS](https://www.unidata.ucar.edu/software/tds/) end-points.  The data sets served by the **NGDAC** provide access to the **trajectory/deployment** data both as time-series and on a profile-by-profile basis.
 
-Transmission of the data sets via the [Global Telecommunication System](http://www.wmo.int/pages/prog/www/TEM/GTS/index_en.html) is made possible by the [National Data Buoy Center](http://www.ndbc.noaa.gov/), which accesses the data sets from the **ERDDAP** and/or **THREDDS** end-points. After performing some internal quality checks, the profiles are encoded into [BUFR](http://en.wikipedia.org/wiki/BUFR) format and released on the [Global Telecommunication System](http://www.wmo.int/pages/prog/www/TEM/GTS/index_en.html), making them available for assimilation by regional and global scale ocean forecasting models.
+Transmission of the data sets via the [Global Telecommunication System](https://community.wmo.int/en/activity-areas/global-telecommunication-system-gts) is made possible by the [National Data Buoy Center](http://www.ndbc.noaa.gov/), which accesses the data sets from the **ERDDAP** and/or **THREDDS** end-points. After performing some internal quality checks, the profiles are encoded into [BUFR](http://en.wikipedia.org/wiki/BUFR) format and released on the [Global Telecommunication System](https://community.wmo.int/en/activity-areas/global-telecommunication-system-gts), making them available for assimilation by regional and global scale ocean forecasting models.
 
-Please read the documentation **thoroughly** before beginning the data submission process.  Additional questions and information requests should be directed to:
+Additional questions and information requests should be directed to:
 
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[email protected]](mailto:[email protected]?subject=GliderDAC%20Support)

_docs/ngdac-architecture.md

@@ -9,15 +9,6 @@ toc: false
 summary: This page presents an in-depth description and discussion of the U.S. IOOS National Data Assembly Center architecture.
 ---
 
-<!--
-> [Wiki](https://github.com/kerfoot/ioosngdac/wiki) ▸ **NGDAC Architecture**
-
-# Contents
-
-+ [Data Assembly Center Architecture](#data-assembly-center-architecture)
-
--->
-
 ## Data Assembly Center Architecture
 
 The following diagram illustrates the architecture of the <b>U.S. IOOS National Glider Data Assembly Center</b> and end-to-end data flow pathway.