Merge branch 'dev' of https://github.com/USGS-Astrogeology/ISIS3 into bundle_lidar

!isis/src/docsys/Object/build

!isis/src/docsys/Application/build

# Unignore msi2isis label files in data area as input files require these

!isis/tests/data/near/msi2isis/*.lbl

!isis/tests/data/near/msicamera/*.cub

# Ignore vs code

.vscode

    {

      "name": "Barrett, Janet"

    },

    {

      "name": "Bauck, Kirsten"

    },

    {

      "name": "Bauers, Joni"

    },

      "affiliation": "University of California, Los Angeles",

      "name": "Mehlman, Bob"

    },

    {

      "affiliation": "Arizona State University",

      "name": "Michaud, Cordell"

    },

    {

      "name": "Milazzo, Moses"

    },

# ISIS Project public API

The public API is considered to be all the interfaces that the ISIS

project provides to the community from which the ISIS user base can

build more complex tools. This API therefore includes code-level

structures accessible via software calls to libraries, but also

more user-facing structures like command-line programs and graphical

user interface (GUI) programs. Any "interface" via which a user can

reasonably interact with components of the ISIS project should be

considered part of the "ISIS Project public API" for the purposes

of [Semantic Versioning](https://semver.org).

Examples are provided below, but are not meant to be exhaustive or

complete. The above philosophy should guide our thinking in what

the public API is.  The above API definition should be used with Semantic

Versioning policies to determine when and how the ISIS version

number changes. A FAQ and some examples can be found on the [Semantic

Versioning website](https://semver.org/).

## General Guidance

The public API consists of the following.

**Code-level structures**: Public function, member, and class names,

argument signatures, and their return signatures.  Where "public"

is defined as those elements that are typically provided for use external

to a library or module, dependent on the language.

Some examples are:

- C++ public structures are those that can be access by including

  the distributed header files for libraries.

- Python public structures are those that do not begin with an underbar

  ("_"), as described in PEP 8.

**User-facing command-line and GUI programs**: program name, argument

list, argument defaults, configuration or preference names and their

defaults, and for those programs with structured output files, the

structure of those output files are analogous to the return signatures

of code-level structures.

This guidance may be more straightforward to understand and apply

for code-level structures which have more formalized argument and

return signatures.  User-facing command-line and GUI programs should

include verbose information in their documentation that describes what

a user can expect as far as the structure of the output.

## More Specific Examples

Adding new arguments to code level structures does not violate the

existing public API as long as they provide a default value. For

example changing a function *doThing(int a, double b)* to *doThing(int

a, double b, double c=1.0)* does not violate the existing API for

the *doThing* function as code that calls the *doThing* function will

still compile without modification.

Adding new optional arguments or arguments with default values to

command line programs does not violate the existing public API. For

example, adding a new argument called "check" that has a default

value of "false" to a command line program does not violate the

program's public API as scripts and commands that were valid

previously are still valid after the addition.

### Unstructured text files

For anything of an inherently unstructured file-type, like .txt;

there is no guarantee of its contents; just that it will exist.

For example, no guarantee of the contents of the bundleout.txt files

generated by jigsaw is expected. They are purely human-readable

output and not designed to be parsed programmatically. So sections

can be added, removed, spacings on tables can be changed, etc.

### CSV output files

Column names and data types are part of the API.

For example, a program that writes out a CSV should clearly describe

the output columns which include the fieldname, data type, and

whether non-data-type values can be present (e.g. a column of

floating point numbers named "minimum" that could contain the string

"NULL" instead of a floating point value).

New columns can be added (feature), but if a column's characteristics are 

changed or removed, that's a breaking change.

### PVL files

Object, group, and keyword names are a part of the API.

For example, the "minimum" keyword will exist in the "statistics"

group. This also applies to the PVL labels in Cube files.

New aggregates or keywords can be added (feature), but if any are changed

or removed, that's a breaking change.  PVL text does have data types, and

changing something from `MIN = 5` to `MIN = "5"` is changing the data type

of the keyword MIN from an integer to a string.

-->

## [Unreleased]

- Added check to determine if poles were a valid projection point in ImagePolygon when generating footprint for a map projected image. [#4390](https://github.com/USGS-Astrogeology/ISIS3/issues/4390)

- Updated the LRO photometry application Lronacpho, to use by default the current 2019 photometric model (LROC_Empirical). The model's coefficients are found in the PVL file that exists in the LRO data/mission/calibration directory. If the old parameter file is provided, the old algorithm(2014) will be used. This functionality is desired for calculation comparisons. Issue: [#4512](https://github.com/USGS-Astrogeology/ISIS3/issues/4512), PR: [#4519](https://github.com/USGS-Astrogeology/ISIS3/pull/4519)

- Added a new application, framestitch, for stitching even and odd push frame images back together prior to processing in other applications. [4924](https://github.com/USGS-Astrogeology/ISIS3/issues/4924)

- Added changes to lronaccal to use time-dependent dark files for dark correction and use of specific dark files for images with exp code of zero. Also added GTests for lronaccal and refactored code to make callable. Added 3 truth cubes to testing directory.  PR[#4520](https://github.com/USGS-Astrogeology/ISIS3/pull/4520)

### Changed

- Updated the LRO calibration application Lrowaccal to add a units label to the RadiometricType keyword of the Radiometry group in the output cube label if the RadiometricType parameter is Radiance. No functionality is changed if the RadiometricType parameter is IOF. Lrowaccal has also been refactored to be callable for testing purposes. Issue: [#4939](https://github.com/USGS-Astrogeology/ISIS3/issues/4939), PR: [#4940](https://github.com/USGS-Astrogeology/ISIS3/pull/4940)

### Added

- Improved functionality of msi2isis and MsiCamera model to support new Eros dataset, including support for Gaskell's SUMSPICE files that adjust timing, pointing and spacecraft position ephemeris. [#4886](https://github.com/USGS-Astrogeology/ISIS3/issues/4886)

- Re-added and refactored the LRO photometry application lrowacphomap to be callable for testing purposes. Issue: [#4960](https://github.com/USGS-Astrogeology/ISIS3/issues/4960), PR: [#4961](https://github.com/USGS-Astrogeology/ISIS3/pull/4961)

### Deprecated

### Fixed

- Modified cnetcheck noLatLonCheck logic to correctly exclude ignored measures. [#4649](https://github.com/USGS-Astrogeology/ISIS3/issues/4649)

- Added check to determine if poles were a valid projection point in ImagePolygon when generating footprint for a map projected image. [#4390](https://github.com/USGS-Astrogeology/ISIS3/issues/4390)

- Fixed the Mars Express HRSC SRC camera and serial number to use the StartTime instead of the StartClockCount  [#4803](https://github.com/USGS-Astrogeology/ISIS3/issues/4803)

- Fixed algorithm for applying rolling shutter jitter. Matches implementation in USGSCSM.

- Fixed isis2std incorrectly outputing signed 16 bit tiff files. [#4897](https://github.com/USGS-Astrogeology/ISIS3/issues/4897)

- Fixed CNetCombinePt logging functionality such that only merged points are included in the log. [#4973](https://github.com/USGS-Astrogeology/ISIS3/issues/4973)

## [7.0.0] - 2022-02-11

- Changed the internal logic of ObliqueDataResolution() to use LocalEmission angle rather than Emission angle.

This will cause differences in output; new values will be more accurate because they use DEM rather than

ellipsoid. The cost to compute the local emissoin will increase by approximately x1.5. [#3600](https://github.com/USGS-Astrogeology/ISIS3/issues/3600)

- Changed website layout to better surface relevant documents.

[#4839](https://github.com/USGS-Astrogeology/ISIS3/pull/4839)

[#4847](https://github.com/USGS-Astrogeology/ISIS3/pull/4847)

[#4851](https://github.com/USGS-Astrogeology/ISIS3/pull/4851)

[#4852](https://github.com/USGS-Astrogeology/ISIS3/pull/4852)

[#4856](https://github.com/USGS-Astrogeology/ISIS3/pull/4856)

[#4865](https://github.com/USGS-Astrogeology/ISIS3/pull/4865)

[#4859](https://github.com/USGS-Astrogeology/ISIS3/pull/4859)

[#4872](https://github.com/USGS-Astrogeology/ISIS3/pull/4872)

[#4871](https://github.com/USGS-Astrogeology/ISIS3/pull/4871)

### Added

- Added the USECAMSTATSTBL option to caminfo. This allows caminfo to extract existing

- Added import templates for isisimport, Cassini ISS, Cassini Vims, Kaguya TC Kaguya MI, Dawn FC, Dawn VIR, LROC NAC, LO HRC, MGS MOC, MER MI, MRO CTX, Rosetta Osiris, Viking VIS [#4606](https://github.com/USGS-Astrogeology/ISIS3/issues/4606)

- Added export templates for isisexport, LROC NAC EDR [#4606](https://github.com/USGS-Astrogeology/ISIS3/issues/4606)

- Added optional JSON data output parameter, DATA, for debugging template engine failures [#4606](https://github.com/USGS-Astrogeology/ISIS3/issues/4606)

- Added new documentatin for contributing code.

[#4859](https://github.com/USGS-Astrogeology/ISIS3/pull/4859)

[#4871](https://github.com/USGS-Astrogeology/ISIS3/pull/4871)

- Added versioning to website documentation.

[#4852](https://github.com/USGS-Astrogeology/ISIS3/pull/4852)

[#4872](https://github.com/USGS-Astrogeology/ISIS3/pull/4872)

### Deprecated

- Deprecated edrget as discussed in [#3313](https://github.com/USGS-Astrogeology/ISIS3/issues/3313).

- Fixed a bug where jigsaw would raise an error when solving for framing camera pointing in observation mode. [#4686](https://github.com/USGS-Astrogeology/ISIS3/issues/4686)

- Fixed slow runs of automos when the priority was BAND. [#4793](https://github.com/USGS-Astrogeology/ISIS3/pull/4793)

- Fixed qview crashing when attempting to load image DNs. [4818](https://github.com/USGS-Astrogeology/ISIS3/issues/4818)

- Fixed qnet crashing when entering an invalid image name in the measure selection box. [#4581](https://github.com/USGS-Astrogeology/ISIS3/issues/4581)

- Modified cnetcheck noLatLonCheck logic to correctly exclude ignored measures. [#4649](https://github.com/USGS-Astrogeology/ISIS3/issues/4649)

- Fixed bug where the original label was not attached to stereo HRSC images on import [#4816](https://github.com/USGS-Astrogeology/ISIS3/issues/4816)

## [6.0.0] - 2021-08-27

- Fixed issue where serial numbers for Kaguya TC and MI image could not be generated. [4235](https://github.com/USGS-Astrogeology/ISIS3/issues/4235)

- Fixed hardcoded file naming in the hijitter app dealing with output from pipeline. [#4372](https://github.com/USGS-Astrogeology/ISIS3/pull/4372)

- Fixed "About Qview" to point to website documentation. [4333](https://github.com/USGS-Astrogeology/ISIS3/issues/4333)

- Fixed bug where the time bias was not being added to the ephemeris times in ckwriter. [4129](https://github.com/USGS-Astrogeology/ISIS3/issues/4129)

### Changed

    ```bash

    #Create a new conda environment to install ISIS in

    conda create -n isis python=3.6

    conda create -n isis

    #Activate the environment

    #Depending on your version of Anaconda use one of the following:

    #Anaconda 3.4 and up:

    conda activate isis

    #Prior to Anaconda 3.4:

    source activate isis

    #Add the following channels to the environment

    conda config --env --add channels conda-forge

    conda config --env --add channels usgs-astrogeology

1. The environment is now ready to download ISIS and its dependencies:

    ```bash

    conda install -c usgs-astrogeology isis=6.0.0

    ```

    If you would like to work with our latest ISIS version 3, rather than updating

    to ISIS 4, instead run:

    ```bash

    conda install -c usgs-astrogeology isis=3.10.0

    conda install -c usgs-astrogeology isis=7.0.0

    ```

1. Finally, setup the environment variables: