Update documentation

docs/src/site/_data/sidebars/netcdfJavaTutorial_sidebar.yml

@@ -159,6 +159,10 @@ entries:
               url: /arraystructures_ref.html
               output: web, pdf
 
+            - title: CDM Section Specification
+              url: /section_specification_ref.html
+              output: web, pdf
+
             - title: CDM Calendar Date Handling
               url: /cdm_calendar_date_time_ref.html
               output: web, pdf

docs/src/site/pages/netcdfJava/SectionSpecification.md

@@ -0,0 +1,61 @@
+---
+title: Section Specification
+last_updated: 2026-06-23
+sidebar: netcdfJavaTutorial_sidebar
+toc: false
+permalink: section_specification_ref.html
+---
+## CDM Section Specification
+
+### Syntax
+
+Array sections can be specified with Fortran 90 array section syntax, using zero-based indexing. For example:
+
+`/group1/group2/varName(12:22,0:100:2,:,17)`
+
+specifies an array section for a four-dimensional variable:
+
+1. `12:22` includes all the elements from 12 to 22 inclusive
+1. `0:100:2` includes the elements from 0 to 100 inclusive, with a stride of 2
+1. `:` includes all the elements
+1. `17` includes just the 18th element.
+
+For structures, you can specify nested selectors, e.g. `record(12).wind(1:20,:,3)` does a selection on the `wind` member variable of the `record` structure at index 12.
+If you don’t specify a section, it means read the entire variable, e.g. `record.wind` means all the data in all the wind variables in all the record structures.
+
+Formally:
+
+```
+sectionSpec := selector | selector '.' selector
+selector := varName ['(' sectionSpec ')']
+varName := STRING
+sectionSpec := dim | dim ',' sectionSpec
+dim := ':' | slice | start ':' end | start ':' end ':' stride
+
+
+slice := INTEGER
+start := INTEGER
+stride := INTEGER
+end := INTEGER
+STRING := String with escaped chars = '.', '/', '(', and ')'
+```
+
+where:
+
+* Nonterminals are in lower case, terminals are in upper case, and literals are in single quotes.
+* Optional components are enclosed between square braces `[` and `]`.
+
+TBD:
+
+* escape mechanism is currently %xx , mostly following opendap
+* not sure if any other chars need to be escaped.
+
+### Restrictions
+
+A Sequence is a one-dimensional Structure with a variable length, it cannot be subsetted.
+
+A variable long name must be used, that is with its group names: `/group1/group2/varName`
+
+### Use
+
+`public Array NetcdfFile.readSection(String variableSection);`

docs/src/site/pages/netcdfJava/developer/CdmUtilityPrograms.md

@@ -7,7 +7,14 @@ permalink: cdm_utility_programs.html
 ---
 
 Below are useful command-line utilities that can be called from the CDM library.
-The easiest way to use these is to grab the latest netcdfAll.jar file.
+One way to use these tools is to grab the latest netcdfAll.jar or toolsUI.jar file from the [Unidata downloads page](https://downloads.unidata.ucar.edu/netcdf-java/){:target="_blank"} or the [netCDF-Java GitHub releases page](https://github.com/Unidata/netcdf-java/releases){:target="_blank"}.
+However, a super handy [community-led effort](https://github.com/conda-forge/netcdf-java-feedstock){:target="_blank"} makes JAR management and a set of convenient wrapper scripts (`.sh` and `.bat`) available through `conda-forge`:
+
+```bash
+conda install -c conda-forge netcdf-java
+```
+
+## Utilities
 
 * [ncdump](#ncdump): prints the textual representation of a dataset to standard output
 * [nccopy](#nccopy): copies a CDM dataset to a netCDF-3 (default) or netCDF-4 file
@@ -17,7 +24,6 @@ The easiest way to use these is to grab the latest netcdfAll.jar file.
 * [CFPointWriter](#cfpointwriter): copies a CDM point feature dataset to CF/NetCDF format
 * [GribCdmIndex](#gribcdmindex): write GRIB Collection Indexes
 * [FeatureScan](#featurescan): scans a directory to find CDM datasets and determines their FeatureTypes
-* [NetcdfDataset](#netcdfdataset): copies a NetcdfFile object, or parts of one, to a netcdf-3 or netcdf-4 disk file
 * [ToolsUI](#toolsui): Netcdf Tools user interface
 
 ## ncdump
@@ -42,6 +48,7 @@ where:
 * `-v varName1;varName2;..`: show data for these variables, use variable’s full names (including groups if present)
 * `-v varName(0:1,:,12)`: show data for a section of this variable only, using FORTRAN 90 section specification
 
+The conda wrapper script is named `ncj-ncdump`.
 
 ## nccopy
 
@@ -88,6 +95,8 @@ java -Xmx1g -classpath netcdfAll-<version>.jar ucar.nc2.write.Nccopy [options]
        Default: false
 ~~~
 
+The conda wrapper script is named `ncj-nccopy`.
+
 ## nccompare
 
 Compares two [CDM files](file_types.html) for semantic equivalence.
@@ -103,6 +112,8 @@ where
 * `file1`: first file to compare
 * `file2`: second file to compare
 
+The conda wrapper script is named `ncj-nccompare`.
+
 ## BufrSplitter
 
 Copies a BUFR file\'s messages into separate output files, depending on message type.
@@ -116,6 +127,8 @@ where
 * `--fileSpec`: file to split
 * `--dirOut`: output directory of split operation
 
+The conda wrapper script is named `ncj-bufrsplitter`.
+
 ## CFPointWriter
 
 Copies a CDM point feature dataset to CF/NetCDF format.
@@ -150,6 +163,8 @@ java -Xmx1g -classpath netcdfAll-<version>.jar ucar.nc2.ft.point.writer.CFPointW
        Default: false
 ~~~
 
+The conda wrapper script is named `ncj-cfpointwriter`.
+
 ## GribCdmIndex
 
 Write GRIB Collection Indexes from an XML file containing a [GRIB `<featureCollection>`](grib_feature_collections_ref.html) XML element.
@@ -175,11 +190,13 @@ java -Xmx1g -classpath netcdfAll-<version>.jar ucar.nc2.grib.collection.GribCdmI
 
 Note that the output file is placed in the root directory of the collection, as specified by the [Collection Specification string](https://docs.unidata.ucar.edu/tds/current/userguide/collection_spec_string_ref.html){:target="_blank"} of the GRIB [`<featureCollection>`](grib_feature_collections_ref.html).
 
+The conda wrapper script is named `ncj-gribcdmindex`.
+
 ## FeatureScan
 
 Scans all the files in a directory to see if they are [CDM files](file_types.html) and can be identified as a particular feature type.
 
-~~~basj
+~~~bash
 java -Xmx1g -classpath netcdfAll-<version>.jar ucar.nc2.ft.scan.FeatureScan directory [-subdirs]
 ~~~
 
@@ -188,6 +205,8 @@ where
 * `directory`: scan this directory
 * `-subdirs`: recurse into subdirectories
 
+The conda wrapper script is named `ncj-featurescan`.
+
 ## CatalogCrawler
 
 Crawl a catalog, optionally open datasets to look for problems.
@@ -260,13 +279,12 @@ count fail = 3
 count failException = 0
 ~~~
 
-## NetcdfDataset
-
-Use [nccopy](#nccopy) instead.
+The conda wrapper script is named `ncj-catalogcrawler`.
 
 ## ToolsUI
 
 ~~~bash
-java -Xmx8g -jar netcdfAll-<version>.jar 
+java -Xmx8g -jar toolsUI-<version>.jar
 ~~~
 
+The conda wrapper script is named `ncj-toolsui`.

docs/src/site/pages/netcdfJava_tutorial/cdmdatasets/readingcdm.md

@@ -54,6 +54,7 @@ Note that you can edit the `Variable`'s ranges (`T(0:30:10, 1, 0:3)` in this exa
 These are expressed with Fortran 90 array section syntax, using zero-based indexing.
 For example, `varName( 12:22 , 0:100:2, :, 17)` specifies an array section for a four dimensional variable.
 The first dimension includes all the elements from 12 to 22 inclusive, the second dimension includes the elements from 0 to 100 inclusive with a stride of 2, the third includes all the elements in that dimension, and the fourth includes just the 18th element.
+The [CDM section specification](section_specification_ref.html) describes the section string syntax in more detail.
 
 The following code to dump data from your program is equivalent to the above ToolsUI actions:
 
@@ -98,20 +99,22 @@ Or suppose you want to loop over all time steps, and make it general to handle a
 In this case, we call reduce(0), to reduce dimension 0, which we know has length one, but leave the other two dimensions alone.
 
 Note that `varShape` holds the total number of elements that can be read from the variable; `origin` is the starting index, and `size` is the number of elements to read.
-This is different from the Fortran 90 array syntax, which uses the starting and ending array indices (inclusive):
+This is different from the section (Fortran 90) array syntax, which uses the starting and ending array indices (inclusive):
 
 {% capture rmd %}
 {% includecodeblock netcdf-java&docs/src/test/java/examples/cdmdatasets/ReadingCdmTutorial.java&readSubset %}
 {% endcapture %}
 {{ rmd | markdownify }}
 
-If you want strided access, you can use the Fortran 90 string routine:
+If you want strided access, you can use the section string method:
 
 {% capture rmd %}
 {% includecodeblock netcdf-java&docs/src/test/java/examples/cdmdatasets/ReadingCdmTutorial.java&readByStride %}
 {% endcapture %}
 {{ rmd | markdownify }}
 
+The [CDM section specification](section_specification_ref.html) describes the section string syntax in more detail.
+
 #### Reading with Range Objects
 
 For general programing, use the read method that takes a `List` of `ucar.ma2.Range` objects. 

grib/src/test/java/ucar/nc2/grib/grib2/TestPds41.java

@@ -15,7 +15,8 @@
 import org.junit.runners.JUnit4;
 
 /**
- * Test data from Meteo Swiss CH2 https://data.geo.admin.ch/browser/#/collections/ch.meteoschweiz.ogd-forecasting-icon-ch2?.language=en
+ * Test data from Meteo Swiss CH2
+ * https://data.geo.admin.ch/browser/#/collections/ch.meteoschweiz.ogd-forecasting-icon-ch2?.language=en
  * Pollen Grasses Data (POACsnc parameter) was used to create a .gbx9 file for testing.
  * <p>
  * PDS (Secton 4) output from ecCodes grib_dump at the end of the file, uses as a basis for