Merge pull request #4 from cchdo:submission_guide

Add Submission Guide

docs/conf.py

@@ -22,6 +22,7 @@
 myst_enable_extensions = [
     "fieldlist",
     "dollarmath",
+    "attrs_block",
 ]
 
 templates_path = ['_templates']
@@ -30,6 +31,9 @@
 # Just include the notebooks as is
 jupyter_execute_notebooks = "off"
 
+# Automatically number any captioned figures, tables, and code blocks
+numfig = True
+
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output

docs/getting_started/index.md

@@ -5,4 +5,5 @@
 :hidden:
 
 submission
+submission_detailed
 ```

docs/getting_started/submission.md

@@ -1 +1,94 @@
-# Submission Guidelines
+# CCHDO Summary Data Submission Guidelines
+
+:version: 2024-08-08
+
+Thank you for submitting your data to the CCHDO!
+While we still accept submissions in any format, we *strongly encourage* data submitters to follow these guidelines.
+Submissions following these guidelines will be prioritized for processing.
+This document provides a summary of our guidance; an in-depth manual with more information can be found [here][in_depth].
+If you have any questions, especially if you are a first time submitter, please don’t hesitate to reach out to the CCHDO at [[email protected]][cchdo_email].
+
+## Data Submission
+**All submissions** should follow these guidelines:
+
+* All parameters within the data file should be found using our [parameter table][parameter_table]
+  * The parameter name must match exactly as it appears in the parameter table
+  * If your parameter can not be found here:
+    * Send [[email protected]][cchdo_email] the parameter(s) you’d like added with a corresponding methods papers
+* A quality flag for each measured parameter
+  * We recommend WOCE quality flags. For more information on WOCE quality flags, please refer to our [manual][in_depth]
+     * If WOCE quality flags are not used, we accept flagging systems that are included in the following document and request that the flagging schema used is named in the submission notes: [https://odv.awi.de/fileadmin/user_upload/odv/misc/ODV_QualityFlagSets.pdf](https://odv.awi.de/fileadmin/user_upload/odv/misc/ODV_QualityFlagSets.pdf)
+
+We prefer if data are submitted in one of the following three formats.
+The CCHDO encourages submitters to choose whatever format best fits their current workflow.
+If the user does not yet have a data workflow, the .csv option is generally easiest to set up.
+
+1. **Exchange**
+
+    {style=lower-alpha}
+    1. The Exchange guidelines can be found here: [https://exchange-format.readthedocs.io/en/latest/common.html](https://exchange-format.readthedocs.io/en/latest/common.html)
+    1. Example {download}`Exchange Template <templates/Exchange_Template.csv>`
+
+        {style=lower-roman}
+        1. For a CTD file, replace ‘BOTTLE’ from the stamp with ‘CTD’
+1. **A .csv that contains the following information; in the data file, please use the parameter name in parentheses, with no variations:**
+
+    {style=lower-alpha}
+    1. If this is the first time data is submitted for a cruise:
+
+        {style=lower-roman}
+        1. Expocode (EXPOCODE)
+        1. Station Number (STNNBR)
+        1. Cast Number (CASTNO)
+        1. Sample Number (SAMPNO)
+        1. Date (DATE)
+        1. Time (TIME)
+        1. Latitude (LATITUDE)
+        1. Longitude (LONGITUDE)
+        1. CTD pressure (CTDPRS)
+
+    1. If this is a data update:
+
+        {style=lower-roman}
+        1. Station Number (STNNBR)
+        1. Cast Number (CASTNO)
+        1. Sample Number (SAMPNO)
+
+    1. Example CSV [Template][csv_template]
+1. **NetCDF**
+
+    {style=lower-alpha}
+    1. We recommend following the guidelines from NCEI - [https://www.ncei.noaa.gov/data/oceans/ncei/formats/netcdf/v2.0/index.html](https://www.ncei.noaa.gov/data/oceans/ncei/formats/netcdf/v2.0/index.html).
+       Specifically, we recommend the profile template found on the NCEI page.
+    1. Use netCDF names and attributes as listed in our [parameter table][parameter_table]
+
+        {style=lower-roman}
+        1. The same parameters required in the .csv format (Expocode, station, cast, sample, etc.) are required in this format
+
+    1. We recommend details to be in the attributes rather than highly descriptive/assumptive variable names
+
+## Cruise Report Submission
+Every cruise should have a corresponding cruise report that conveys to data users the information needed to understand the context and content of the reported data.
+PDF and .docx (Microsoft Word) formats are recommended.
+An abridged recommendation on content is provided below, but a comprehensive outline is available in our full [manual][in_depth] (Appendix A):
+
+* Linked table of contents
+* Highlights section including general cruise information such as start and end dates, ports of call, expocode, etc.
+* Cruise summary
+    * A general summary of the cruise, its main goals, number of stations completed including detailed information about each station and parameters sampled, floats and drifters deployed, moorings deployed or recovered, etc.
+* Table of all parameters sampled and the contact information for their respective PIs
+    * Name and/or persistent unique identifier ([ORCID](https://orcid.org/))
+    * Institution
+    * Measurement/s responsible for
+    * Contact information (email preferred)
+* A section for every measured parameter (underway and hydrographic measurements) that includes:
+    * Methods
+        * Instrumentation (including manufacturer and model), chemicals used, calibration information, referenced protocols, etc.
+    * At-sea sampling notes
+    * Data analysis
+    * Relevant figures
+
+[cchdo_email]: mailto:[email protected]
+[parameter_table]: https://exchange-format.readthedocs.io/en/latest/parameters.html
+[in_depth]: submission_detailed
+[csv_template]: broken_link_fix_me_2