Re: [CF-metadata] [cf-convention/cf-conventions] Clarification of newline usage (Issue #347)

2022-01-10 Thread Dave Allured
I agree with the original rationale of CF section 2.6.2, embed newline 
characters into long strings to break them into lines, for readability whenever 
possible.

Now there is a complication.  **Full netcdf-4** format offers two different 
string data types; **character** and **string**.  I think with introduction of 
the formal **string** data type, **ncdump** was changed for **both** data 
types, so that visual line breaks would be used **only to separate elements of 
an array of strings**.  I think the new intent was that if you want to display 
multiple lines, you are supposed to use an **array of strings**, rather than 
newline delimiters.

The traditional **character** data type supports only a 1-dimensional array of 
single characters.  Therefore the **original** intent of **ncdump** was to 
provide use of newlines to embed visual line breaks.

The result was a developer's choice to switch the display style based on the 
file format type.  At this time there is not much to be done to change that.

This dichotomy creates some challenges for standards, and for conversions 
between the two data types.  Note that writing formal **string** data type with 
embedded newlines is still perfectly legal according to basic netcdf-4 rules.  
I have not looked up how CF handles this.

I advise not making any reading code that depends specifically on one or the 
other of these two newline strategies.  It would be reasonable to have code 
that knows how to digest both strategies in a smart way, so that the 
application does the right thing and gets an equivalent result for both cases.

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Re: [CF-metadata] [cf-convention/cf-conventions] Clarification of newline usage (Issue #347)

2022-01-10 Thread Leon
@Dave-Allured I see, thanks. I'll stop worrying about it in that case. Perhaps 
this could be mentioned in the spec somewhere as a caveat or something. 
Otherwise this can probably be closed.

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Re: [CF-metadata] [cf-convention/cf-conventions] Clarification of newline usage (Issue #347)

2022-01-10 Thread Dave Allured
@adigitoleo, you are simply seeing an inconsistency in **ncdump**.   Recent 
version of this utility are not consistent for displaying embedded newlines in 
attributes.  This varies with the type of the internal file format.  Notice 
that true newline characters are displayed with the escape sequence "**\n**" 
inside quotes, in all cases.  However, **netcdf-3** and **netcdf4-classic** 
formats also add the extra visual line break.  From **ncdump -hs**:

:A = "line 1\n",
"line 2" ;
:_Format = "netCDF-4 classic model" ;

Whereas **full netcdf-4** format does not include the extra visual break:

:A = "line 1\nline 2" ;
:_Format = "netCDF-4" ;

The first style is traditional and was ubiquitous for several years, until 
support for string data type evolved in one of the early netcdf-4 library 
versions.   I believe that the CF readability policy was conceived early, and 
was based only on the traditional netcdf-3 behavior.

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Re: [CF-metadata] [cf-convention/cf-conventions] Clarification of newline usage (Issue #347)

2022-01-10 Thread Leon
Thanks, I guess I need to find out what `str_get_nl` is doing.

Comment about `\r\n` was inaccurate, I was using the wrong dataset. It doesn't 
work in the same way as `\n`, i.e. the symbols appear in the output but the 
line is not split. 

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Re: [CF-metadata] [cf-convention/cf-conventions] Clarification of newline usage (Issue #347)

2022-01-10 Thread Seth McGinnis
BR is just a variable, defined on the first line as the output of `str_get_nl()`

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Re: [CF-metadata] [cf-convention/cf-conventions] Clarification of newline usage (Issue #347)

2022-01-10 Thread Leon
I should clarify: when I use `'\r\n'`, I see only the first line. So the 
newline is perhaps being embedded, but there is no `'\n'` at the end and the 
other lines disappear.

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Re: [CF-metadata] [cf-convention/cf-conventions] Clarification of newline usage (Issue #347)

2022-01-10 Thread Leon
> It's noteworthy that ncdump renders an embedded newline as '\n' followed by 
> an actual newline.

Thank you for the clarification.

>  when I'm adding embedded newline characters to long strings in NCL, I just 
> add a newline, not an escape sequence

Interesting. I tried a few different ways of embedding the newline in Julia but 
they haven't worked so far. It looks like NCAR uses [CRLF for newlines][1], but 
even Julia's `'\r\n'` doesn't seem to work. I can use raw strings:

```
s = """foo
bar"""
```

but Julia always puts `'\n'` at the line endings. I was as yet unable to find 
the actual definition of that `BR` symbol in the NCAR sources, if anyone could 
point me to where the string ops are defined I could take a look, although I'll 
be going in blind with C/fortran.

Alternatively I could check the ncdump sources for the line splitting logic...

[1]: 
https://urldefense.us/v3/__https://github.com/likev/ncl/blob/49a124bbfc0247a6a8768e9c5084c18fc2207d1e/ncl_ncarg_src/ni/src/ncl/editline.c*L72__;Iw!!G2kpM7uM-TzIFchu!kNlI_g1QCIsZLT83JLXNCGj1Amo4ECQJLC6O4xeDvuNlseZ6k6EKmL5vb2oPPwALaCEyEtfQPew$
 


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Re: [CF-metadata] [cf-convention/cf-conventions] Clarification of newline usage (Issue #347)

2022-01-10 Thread Seth McGinnis
It's noteworthy that ncdump renders an embedded newline as '\n' followed by an 
actual newline.  I'm not sure how this relates to the way that Julia works, but 
when I'm adding embedded newline characters to long strings in NCL, I just add 
a newline, not an escape sequence.  So I write code like this:

```
BR = str_get_nl()
parents = "Parent files had the following history attributes:"+BR
parents = parents + "Specific humidity file "+qfile+":"+BR
parents = parents + finq@history+BR
...
fout@history_of_parent_files = parents
```

and the string that I'm assigning to the netcdf attribute has embedded newline 
characters, not \n escapes. Then when I print it out with ncdump -h, it looks 
like this:

``` :history_of_parent_files = "Parent files had the following history 
attributes:\n",
"Specific humidity file 
huss.rcp85.GFDL-ESM2M.WRF.day.NAM-22i.mbcn-Daymet.nc:\n",
"Sat Sep 25 22:32:30 MDT 2021: 
huss.rcp85.GFDL-ESM2M.WRF.day.NAM-22i.raw.nc bias-corrected using MBCn with 
Daymet obs\n",
```

I've never worked with the netcdf library directly, so unfortunately I can't 
offer any advice on that front, but maybe this will at least help narrow down 
the nature of the problem.

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Re: [CF-metadata] [cf-convention/cf-conventions] Delete unnecessary `Conventions` attribute in two examples (Issue #349)

2022-01-10 Thread David Hassell
I support this as well.

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Re: [CF-metadata] [cf-convention/cf-conventions] Delete unnecessary `Conventions` attribute in two examples (Issue #349)

2022-01-10 Thread taylor13
I support this proposal too (for the same reasons).

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Re: [CF-metadata] [cf-convention/cf-conventions] Single source version (PR #344)

2022-01-10 Thread Klaus Zimmermann
I don't think that's necessary. Let's just check that everything works as 
expected. If it doesn't, we'll update the artifacts post-hoc.

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Re: [CF-metadata] [cf-convention/cf-conventions] Delete unnecessary `Conventions` attribute in two examples (Issue #349)

2022-01-10 Thread Daniel Lee
@JonathanGregory I support this proposal, examples are most illustrative when 
they contain the minimal material to demonstrate what they're about. In that 
context the `Conventions` attribute is a distraction requiring additional 
maintenance.

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Re: [CF-metadata] [cf-convention/cf-conventions] Single source version (PR #344)

2022-01-10 Thread Daniel Lee
Would it be possible to make and destroy a test release? Or is that over the 
top?

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Re: [CF-metadata] [cf-convention/cf-conventions] Single-source the version number (Issue #343)

2022-01-10 Thread Klaus Zimmermann
Thanks, @JonathanGregory, your points make sense to me. Let's take that 
discussion in the other issue and move forward here with the corrected 
attributes in place.

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Re: [CF-metadata] [cf-convention/cf-conventions] DOIs for CF Convention releases? (#127)

2022-01-10 Thread Klaus Zimmermann
This looks to be moving in the right direction, thanks @castelao.

I am still a bit unclear on which provider should be chosen and how that choice 
should be made.
Zenodo is well-known and documented on 
https://urldefense.us/v3/__https://zenodo.org__;!!G2kpM7uM-TzIFchu!gtjhTDFpghkx-zdOIDRktMh8LdwYP3-NMkfzdytjVenxjvGqSjcSlI9ok433q2FcEReMFD1X6U4$
 .
@castelao, could you point to similar documentation for the UCAR system?

Regardless, I think the most pressing outstanding issue is 
cf-convention/cf-convention.github.io#182, i.e. the license.

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Re: [CF-metadata] [cf-convention/cf-conventions] Provision of netCDF files for the netCDF header examples shown in the Conventions? (Issue #348)

2022-01-10 Thread Mark Hedley
i think that there are some practical aspects to this request that could be 
explored, which might make it feasible to deliver over time

* netCDF enables the building of netCDF files from partial CDL, in particular 
array payloads not specified in the CDL are encoded as missing data

this would enable valid netCDF files to be encoded as CDL in the source tree, 
as plain text files, with any unnecessary array data left blank

such CDL files can be encoded into netCDF using the `ncgen` tool, enabling them 
to be used as example files

asciidoc's `include` directive enables partial inclusion of lines from another 
plain text file
https://urldefense.us/v3/__https://docs.asciidoctor.org/asciidoc/latest/directives/include/__;!!G2kpM7uM-TzIFchu!ikxGe72QWrOk7UsU90BG16YOvbIvouGbUFCKZGdbC3g1EbV7t52v4p4BY4-bSUE5I8eDWtuatm0$
 

These facets could enable the construction of an example file management 
process where:

1. an example CDL plain text file is stored in the cf-conventions source tree
2. the relevant snippets of that file are then used to populate the precise 
section of the conventions document that is required (delivering like for like 
comparison with current doc)
3. an automated action builds the CDL into NC as a pre-commit Pull Request test 
- assuring validity of CDL
4. an automated action builds the CDL into NC then validates with respect to CF 
conventions as a pre-commit Pull Request - assuring CF compliance

this work flow could fit quite neatly with the management process in place on 
this repository

if this is of interest, then we could try to prepare an example, with work 
flow, for consideration

i think that each example in the conventions doc would require some analysis to 
produce a valid CF CDL full file to subset to maintain content integrity.  So, 
we could investigate the work flow first with one example, then consider an 
ongoing activity to update (editorially) example snippets of CDL through the 
conventions document over time

hth marqh


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Re: [CF-metadata] [cf-convention/cf-conventions] Single source version (PR #344)

2022-01-10 Thread Klaus Zimmermann
Thanks, @erget. Before we merge, we should address the point raised by @ethanrd 
in #343, namely the name of the second attribute.

Also, there is one caveat: The automatic "final" tagging is hard to test 
because the real conditions only show up at the release, so at least for the 
first release we should be ready for it to fail and have an eye on that.

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Re: [CF-metadata] [cf-convention/cf-conventions] Provision of netCDF files for the netCDF header examples shown in the Conventions? (Issue #348)

2022-01-10 Thread Mathew Biddle
Both of these examples are using CF-1.6 with ACDD and other added flair:

- [NOAA's IOOS 
examples](https://urldefense.us/v3/__https://ioos.github.io/ioos-metadata/gold-standard-examples.html__;!!G2kpM7uM-TzIFchu!knTm4Sd37VELE94CuV_q_uASr48lfy6VXL4wnUD-gWiPhVX5MlLCIw2YNKTUIdKI27Fn5P1TtLc$
 )
- [NOAA's NCEI 
examples](https://urldefense.us/v3/__https://www.ncei.noaa.gov/data/oceans/ncei/formats/netcdf/v2.0/index.html*templatesexamples__;Iw!!G2kpM7uM-TzIFchu!knTm4Sd37VELE94CuV_q_uASr48lfy6VXL4wnUD-gWiPhVX5MlLCIw2YNKTUIdKI27FnFAXhMVQ$
 )

I'm sure other groups have examples too.

It would be nice if there was an authoritative source from the CF community to 
reference.

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Re: [CF-metadata] [cf-convention/cf-conventions] Single-source the version number (Issue #343)

2022-01-10 Thread JonathanGregory
Dear @zklaus 

I don't think there are any "full examples" in the document. (This [new 
issue](https://urldefense.us/v3/__https://github.com/cf-convention/cf-conventions/issues/348__;!!G2kpM7uM-TzIFchu!lZI1e-2iPbokQ-LIbAFuEADT9eEzUL6k3p_RYXQdo1Ee5Nx1UkSEuM8EXIqqHr3JsxfhxSZhQl8$
 ) is relevant to this.) That is probably because full examples are not what we 
need to illustrate particular points. I will propose the deletion of the 
`Conventions` attribute in this sole example as a separate issue.

Best wishes

Jonathan

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Re: [CF-metadata] [cf-convention/cf-conventions] Provision of netCDF files for the netCDF header examples shown in the Conventions? (Issue #348)

2022-01-10 Thread JonathanGregory
Dear @atmodatcode 

Thanks for your proposal. In fact the [rules for changing the 
conventions](https://urldefense.us/v3/__http://cfconventions.org/rules.html__;!!G2kpM7uM-TzIFchu!gylT2XXC8WSaHPC0A1ZMshzVxtz2GadZcG5Fz59sWJO_IdgIryZzsIaHo6OzakimUdXLFw9fPks$
 ) require a test file to be produced for each change, but that rule has never 
been followed, and no test files have ever been presented. As far as I know, 
the examples in the document exist only "on paper", and no netCDF files have 
been produced. Your request for the example files is reasonable and our rules 
anticipate it, but unfortunately we haven't got any to give you!

I suppose that one obstacle to producing files when changes are proposed is 
that the proposal typically affects only one feature, whereas an example file 
needs a lot more contents that aren't relevant to the change. A strict 
requirement to create such a file might delay or prevent changes being 
implemented, because of the extra work.

In any case, that wouldn't address the request for files to illustrate the 
_existing_ conventions. It would be useful to know what people think about 
whether and how such files could be provided.

Best wishes

Jonathan


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Re: [CF-metadata] [cf-convention/cf-conventions] Cutting version 1.10 (Issue #345)

2022-01-10 Thread Lars Bärring
I am just quietly following all the good ideas and solutions that you github 
experts are coming up with. Many thanks for this! 

While we are at it, here is another thought:

In the revision history I think that it would it be meaningful to have 
"subheadings" for each version of the conventions document together with its 
release data. The reason for this is that we are now and then discussing that 
in a file adhering to CF-1.X there might be a metadata construct that is 
defined/superseded/invalidated in a more recent version of the conventions, and 
that this is not a problem as it is known in which version a certain construct 
is introduced. E.g. something like 

> 
> * **Version 1.0, 28 October, 2003**
>   Initial release.
> * **Version 1.1, 17 January, 2008**
> 14 June 2004: 
> Added the section called “Lambert azimuthal equal area”.  the section called 
> "Polar Stereographic" : Added latitude_of_projection_origin map parameter.
> 1 July 2004: 
>  1/ Section 5.7, "Scalar Coordinate Variables" : Added note that use of 
> scalar coordinate variables inhibits interoperability with COARDS conforming 
> applications. 
>  2/ Example 5.13, "Multiple forecasts from a single analysis" : Added 
> positive attribute to the scalar coordinate p500 to make it unambiguous that 
> the pressure is a vertical coordinate value.
> ... ...
> 17 January 2008: 
>  1/ Preface : Changed text to refer to rules of CF governance, and 
> provisional status. 
>  2/ Chapter 4, Coordinate Types , Chapter 5, Coordinate Systems and Domain : 
> Made changes regarding use of the axis attribute to identify horizontal 
> coordinate variables. 
> ~~3/ Changed document version to 1.1.~~
> * **Version 1.2, 4 May, 2008**
> 4 May 2008: 
>  1/ Section 5.6, "Horizontal Coordinate Reference Systems, Grid Mappings, and 
> Projections", Appendix F, Grid Mappings : Additions and revisions to CF grid 
> mapping attributes to support the specification of coordinate reference 
> system properties (Trac ticket #18).
>  2/ Table 3.1, "Supported Units" : Corrected Prefix for Factor "1e-2" from 
> "deci" to "centi". (Trac ticket #25).
>  ~~3/ Changed document version to 1.2.~~

and so on, but of course properly formatted. This might take some manual work, 
which should not delay releasing 1.10 before if need be.


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[CF-metadata] [cf-convention/cf-conventions] Provision of netCDF files for the netCDF header examples shown in the Conventions? (Issue #348)

2022-01-10 Thread atmodatcode
# Title
Requesting access to the netCDF files that are shown as netCDF header examples 
in the Conventions document
# Moderator
@user
# Moderator Status Review [last updated: -MM-DD]
Brief comment on current status, update periodically
# Requirement Summary
When creating CF-compliant netCDF files, users frequently not only need an idea 
how the netCDF header should look like, but also how the data variables need to 
be stored.  So, a GitHub folder with some small sample netCDF files would be 
extremely beneficial.  
# Technical Proposal Summary
Brief proposal overview
# Benefits
Users trying to create CF-compliant netCDF files will have good netCDF example 
files for guidance. 
# Status Quo
Discussion of the current state CF and other standards.
# Associated pull request
Link to associated pull request, if present.
# Detailed Proposal
As a regular reader and user of the CF Conventions, I frequently need example 
netCDF files that demonstrate the implementation of specific CF Convention 
aspects. As of now, the CF Conventions shows example netCDF headers, but to my 
knowledge, the corresponding CF-compliant netCDF files are not provided. With 
CF-compliant, I mean netCDF files that pass state-of-the-art CF-checkers such 
as IOOS Compliance Checker. 
Also for workshops that cover aspects of the CF conventions, the availability 
of sample netCDF files that relate to the examples shown in the CF conventions 
document would be beneficial. Using them, users can e.g. try to read them in, 
modify them and check if they are still CF compliant. 
I would very much appreciate if a folder with sample netCDF files could be made 
accessible. 
Thanks a lot. 



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