Merge branch 'docs_test' into 'main'

[codespell]

skip = *.po,*.ts,*.js,*.map,*.css,*.bsp,*.cub,*.tsc,*.tf,*.ti

stages:

  - build

  - test

  - deploy

"Build MkDocs":

  image: "python:3"

  stage: build

  only:

    - main

  before_script:

    - pip install -r requirements.txt

  script: 

    paths:

      - site/

"Spell Check Docs":

  image: "python:3"

  stage: test

  before_script:

    - pip install codespell

  script: 

    - codespell site/

"Link Check Docs":

  image: "python:3"

  stage: test

  before_script:

    - pip install linkchecker

  script: 

    - linkchecker site/index.html --ignore-url asc-public-docs/site/docs/software/

"Grammar Check Docs":

  image: "node:latest"

  stage: test

  before_script:

    -  npm i gramma -g

  script: 

    - git diff --name-only origin/main | grep -e .md -e .MD | sed 's/^/"/;s/$/"/' | xargs -t -L1 gramma check -p || true 

  allow_failure: 

    exit_codes:

      - 1

"Sync with S3":

  image: "python:3"

  stage: deploy

{

  "api_url": "https://api.languagetool.org/v2/check",

  "api_key": "",

  "dictionary": [  

  ],

  "language": "en-US",

  "rules": {

    "casing": true,

    "colloquialisms": true,

    "compounding": true,

    "confused_words": true,

    "false_friends": true,

    "gender_neutrality": true,

    "grammar": true,

    "misc": true,

    "punctuation": true,

    "redundancy": true,

    "regionalisms": true,

    "repetitions": true,

    "semantics": true,

    "style": false,

    "typography": false,

    "typos": false

  }

}

 No newline at end of file

    */

    class ImportMapTemplateWorkOrder : public WorkOrder {....

```

Sometimes, classes are declared inside the header files for other classes.  This happens a lot in the $ISISROOT/src/qisis/objs directory where internal XmlHandler classes are defined to handle object serialization.

Sometimes, classes are declared inside the header files for other classes.  This happens a lot in the $ISISROOT/src/qisis/objs directory, where internal XmlHandler classes are defined to handle object serialization.

These classes need to be documented as well (as in this example from the ImageList header file):

```C++

For the rest of this document, we will use `appname` as the name of the application that is being worked on. Simple example at https://github.com/DOI-USGS/ISIS3/tree/dev/isis/src/base/apps/crop 

1. In the `appname` folder create two new files, `appname.cpp` and `appname.h`. These files are where the application logic will live.

1. In the `appname` folder, create two new files, `appname.cpp` and `appname.h`. These files are where the application logic will live.

1. In `appname.h` and `appname.cpp` create a new function in the `Isis` namespace with the following signature `void appname(UserInterface &ui)`. If the application has a `from` cube, add a second function with the input cube as the first argument `void appname(Cube incube, UserInterface &ui)`. 

1. Copy the contents of the existing `IsisMain` function curretly located in `main.cpp` into the new `void appname(Cube incube, UserInterface &ui)` function. (if the app doesn't take any file parameters (i.e., network, text, cube list...) copy the contents into` void appname(UserInterface &ui)`). If there is no input cube, but there are other input files, add them as input parameters similar to how the input cube was done, see spiceinit and cnetcheck tests for examples).  

1. Copy the contents of the existing `IsisMain` function currently located in `main.cpp` into the new `void appname(Cube incube, UserInterface &ui)` function. (if the app doesn't take any file parameters (i.e., network, text, cube list...) copy the contents into` void appname(UserInterface &ui)`). If there is no input cube, but there are other input files, add them as input parameters similar to how the input cube was done, see spiceinit and cnetcheck tests for examples.  

1. Modify `void appname(UserInterface &ui)` to open the input cube, usually "from", and/or other files and call the second function `void appname(Cube incube, UserInterface &ui)` 

1. Copy any helper functions or global variables from `main.cpp` into `appname.cpp`. So as to not pollute the `Isis` namespace and avoid redefining symbols

1. Copy any helper functions or global variables from `main.cpp` into `appname.cpp`. This is to not pollute the `Isis` namespace and avoid redefining symbols

1. Prototype any helper functions at the top of `appname.cpp` and define them at the bottom of `appname.cpp`. Do not define them in `appname.h`. 

1. Put all of the required includes in `appname.cpp` and `appname.h`.

1. Put all the required includes in `appname.cpp` and `appname.h`.

1. Remove the call to get the UserInterface from `appname.cpp`; it usually looks like `UserInterface &ui = Application::GetUserInterface();`.

1. In `main.ccp`, add the following

```

??? Warning "If your application uses `Application::Log()`"

     Due to how the Application singleton works, calling `Application::Log()` outside of an actual ISIS application currently causes a segmentation fault. To avoid this, modify the new `appname` function to return a Pvl that contains all of the PvlGroups that need to be logged instead of calling `Application::Log()`. Then, change your `main.cpp` to

     Due to how the Application singleton works, calling `Application::Log()` outside an ISIS application currently causes a segmentation fault. To avoid this, modify the new `appname` function to return a Pvl that contains all the PvlGroups that need to be logged instead of calling `Application::Log()`. Then, change your `main.cpp` to

     ```C++

     #include "Isis.h"

### Separating parameter parsing

The first step is to separate the UserInterface parsing from the program logic.

All of the UserInterface parsing should be done in the `appname(UserInterface &ui)` function. Then, all of the actual program logic should be moved into another function also called `appname`. The signature for this function can be quite complex and intricate. Several tips for defining the `appname` function signature are in the next sections, but there is not perfect way to do this for every application.

All the UserInterface parsing should be done in the `appname(UserInterface &ui)` function. Then, all the program logic should be moved into another function also called `appname`. The signature for this function can be quite complex and intricate. Several tips for defining the `appname` function signature are in the next sections, but there is no perfect way to do this for every application.

Once the `appname` function is defined, the `appname(UserInterface &ui)` function simply needs to call it with the appropriate parameters once it has parsed the UserInterface.

Most ISIS3 applications were designed to read their inputs from files and then output their results to the command line and/or files. Unfortunately, gtest is very poorly setup to test against files and the command line. To work around this, it is necessary to remove as much file and command line output from the new `appname` functions as possible. Here are some examples of how outputs can be separated from the application logic:

1. Anything that would be logged to the terminal should be simply returned via the log pointer. This way, it can be programmatically validated in gtest. This in fact already needs to be done because of [issues](#if-your-application-uses-applicationlog) with `Application::Log()`.

1. No input filenames should be passed as arguments. All files required by the program should be opened and converted into in-memory objects and then passed to the function. This will help eliminate the need for test data files in many applications. **Make sure that for Cubes the appropriate CubeAttributeInput and CubeAttributeOutput values are set!**

1. No input filenames should be passed as arguments. All files required by the program should be opened and converted into in-memory objects and then passed to the function. This will help eliminate the need for test data files in many applications. **Make sure that for cubes, the appropriate CubeAttributeInput and CubeAttributeOutput values are set!**

### Process, helper functions, and global variables

Many ISIS3 applications make sure of the Process class and its sub-classes. While these classes make file I/O easier, they also tightly couple it to the application logic! Some of them can take objects like cubes instead of filenames, but not all of them. They may need to be refactored to use objects instead of filenames. For now, where-ever possible use objects, but it is acceptable to use filenames if an object cannot be used.

Many ISIS3 applications make sure of the `Process` class and its subclasses. While these classes make file I/O easier, they also tightly couple it to the application logic! Some of them can take objects like cubes instead of filenames, but not all of them. They may need to be refactored to use objects instead of filenames. For now, where-ever possible use objects, but it is acceptable to use filenames if an object cannot be used.

Many of the Process sub-classes use process functions to operate on cubes. These helper functions will need to be pushed into the ISIS3 library. There is a chance that there will be symbol conflicts due to multiple applications using functions with the same name. In this case, the function can simply have its name modified. This is also a natural point at which application logic can be segmented and tested separately.

Many of the Process subclasses use process functions to operate on cubes. These helper functions will need to be pushed into the ISIS3 library. There is a chance that there will be symbol conflicts due to multiple applications using functions with the same name. In this case, the function can simply have its name modified. This is also a natural point at which application logic can be segmented and tested separately.

Because of how the Process sub-classes use process functions, many older ISIS3 applications use global variables to pass additional parameters to helper functions. This can cause serious issues because applications are no longer self-contained executables. To help with this, ProcessByBrick and ProcessByLine have been modified to use a [lambda function with captures](https://en.cppreference.com/w/cpp/language/lambda#Lambda_capture) as the process function. All of the previously global variables can now be defined in the `appname` function and then captured in the lambda function.

Because of how the Process subclasses use process functions, many older ISIS3 applications use global variables to pass additional parameters to helper functions. This can cause serious issues because applications are no longer self-contained executables. To help with this, ProcessByBrick and ProcessByLine have been modified to use a [lambda function with captures](https://en.cppreference.com/w/cpp/language/lambda#Lambda_capture) as the process function. All the previously global variables can now be defined in the `appname` function and then captured in the lambda function.

For example, here's an app called checkerboard which generates an artificial cube with a checkerboard pattern. It requires access to the variable `size` to work but `ProcessByLine.StartProcess` only supports functions `Buffer` objects as input. Therefore, the app uses a global variable in order for the checkerboard function to have `size` in it's scope:

For example, here's an app called checkerboard which generates an artificial cube with a checkerboard pattern. It requires access to the variable `size` to work, but `ProcessByLine.StartProcess` only supports functions `Buffer` objects as input. Therefore, the app uses a global variable in order for the checkerboard function to have `size` in its scope:

```C++

// original foo.cpp

#include "Isis.h"

}

```

can be refactored using a lambdas which captures the size variable: 

can be refactored using a lambda which captures the size variable: 

```C++

// callable foo.cpp

### For an Application

1. Create a new file `FunctionalTestAppname.cpp` in `isis/tests/`. For example, the tests the application `isisimport` should be in `FunctionalTestIsisImport.cpp`.

1. Add you tests to this file

1. Delete the tests and all of the test directories  

1. Add your tests to this file

1. Delete the tests and all the test directories  

Note: If your tests require the use of ISIS's Null value, you will need to include SpecialPixel.h

Be sure to choose a substring of the exception message that will uniquely identify it, but only use parts of the string identified in the actual code. Anything like `**USER ERROR**` or `in IsisAml.cpp at 1613` that are added based on user preference settings should not be included in the substring. The IException and Preferences classes test that these are properly added onto the error messages.

Normally, if the error message does not contain the substring, gtest will only output the the expression evaluated to false. To make the failure message more helpful, we add `<< e.toString().toStdString()` which outputs the full error message if the test fails.

Normally, if the error message does not contain the substring, gtest will only output the expression evaluated to false. To make the failure message more helpful, add `<< e.toString().toStdString()` which outputs the full error message if the test fails.

### Testing floating point numbers

Comparison between floating point numbers is a common problem in both writing and testing software. Carefully choosing test data can help avoid comparisons that are likely to cause problems. Whenever possible, use test data such that output values can be exactly stored in a double-precision floating point number (c++ double). For example, if a function takes its input and divides it by 116, a good test input would be 232 because 232/116 = 2 which can be stored exactly in a double. On the other hand, 1 would be a poor test input because 1/116 cannot be precisely stored in a double. If a comparison between numbers that cannot be stored precisely is required, gtest provides [Special Assertions](https://github.com/google/googletest/blob/main/docs/reference/assertions.md#floating-point) to make the comparisons more tolerant to different rounding.

In order to conform to our test case naming conventions, all test fixtures need to be named `ClassName_FixtureName`. For example, a fixture that sets up a BundleSettings object in a not-default state for the BundleSettings unit test could be called `BundleSettings_NotDefault`.

### Test parameterization

If the same process needs to be run with several different inputs, it can be easily automated via [value-parameterized tests](https://github.com/google/googletest/blob/main/docs/advanced.md#value-parameterized-tests). In order to maintain test naming conventions, when you call the `INSTANTIATE_TEST_CASE_P` macro make sure the first parameter is. `ClassName`. For example

If the same process needs to be run with several different inputs, it can be easily automated via [value-parameterized tests](https://github.com/google/googletest/blob/main/docs/advanced.md#value-parameterized-tests). In order to maintain test naming conventions, when you call the `INSTANTIATE_TEST_CASE_P` macro, make sure the first parameter is. `ClassName`. For example

```

INSTANTIATE_TEST_CASE_P(

      ::testing::Values(BundleSettings::Sigma0, BundleSettings::ParameterCorrections));

```

will ensure that the tests start with `BundleSettings`.

This will ensure that the tests start with `BundleSettings`.