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Expand Up @@ -113,7 +113,7 @@ bash <(curl https://raw.githubusercontent.com/DOI-USGS/ISIS3/refs/heads/dev/isis
./install_isis.sh --force-mamba -m $HOME/miniforge/ -l main -v 8.3.0 -n auto -p $HOME/isisdata --download-base --prefix $HOME/isis_installs/
```

## After install consideratrions
## After-Install Considerations

### ISIS DATA

Expand Down Expand Up @@ -159,13 +159,13 @@ On activation, the environment will automatically set ISISROOT, ISISDATA, and PA
# Install Manually Via Miniforge
Comment thread
jrcain-usgs marked this conversation as resolved.
### Prerequisites

??? "Mamba/Miniforge"
??? "Miniforge"

If you don't have mamba yet, download and install it. We recommend getting mamba through [MiniForge](https://github.com/mamba-forge/miniforge?tab=readme-ov-file#miniforge).
If you don't have conda yet, download and install it. We recommend getting conda through [MiniForge](https://github.com/conda-forge/miniforge).

```sh
# Via Miniforge:
curl -L -O "https://github.com/mamba-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh
```

Expand Down Expand Up @@ -386,7 +386,7 @@ If ISIS was already installed with mamba, you can update it with:

## Uninstalling ISIS

To uninstall ISIS, deactivate the ISIS mamba Environment, and then remove it. If you want to uninstall mamba as well, see your mamba installation's website ([Miniforge](https://github.com/mamba-forge/miniforge?tab=readme-ov-file#uninstallation) if you installed mamba with the above instructions).
To uninstall ISIS, deactivate the ISIS mamba Environment, and then remove it. If you want to uninstall mamba as well, see your mamba installation's website ([Miniforge](https://github.com/conda-forge/miniforge?tab=readme-ov-file#uninstall) if you installed mamba with the above instructions).

```sh
mamba deactivate
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Expand Up @@ -4,9 +4,9 @@

Follow these tutorials to set up your local ISIS environment before you get started:

1. [Getting Started With GitHub](https://astrogeology.usgs.gov/docs/how-to-guides/isis-developer-guides/developing-isis3-with-cmake/#getting-started-with-github)
2. [Anaconda and ISIS3 Dependencies](https://astrogeology.usgs.gov/docs/how-to-guides/isis-developer-guides/developing-isis3-with-cmake/#anaconda-and-isis3-dependencies)
3. [Building ISIS3](https://astrogeology.usgs.gov/docs/how-to-guides/isis-developer-guides/developing-isis3-with-cmake/#building-isis3)
1. [Fork and Clone from GitHub](../../how-to-guides/isis-developer-guides/developing-isis3-with-cmake.md/#fork-and-clone-from-github)
2. [Setup Conda Build Env and Dependencies](../../how-to-guides/isis-developer-guides/developing-isis3-with-cmake.md/#build-environment--dependencies)
3. [Building ISIS](../../how-to-guides/isis-developer-guides/developing-isis3-with-cmake.md/#building-isis)

## 2. Converting Apps and Tests

Expand All @@ -18,9 +18,9 @@ find isis/src/*/apps/ -regex '.*/tsts' | sed 's:[^/]*$::'

Apps that need to be refactored only have *app-name.xml* and *main.cpp*, other than the *Makefile* and other possible folders (like `assets` and `tsts`). Take a look at the [bandtrim](https://github.com/DOI-USGS/ISIS3/tree/dev/isis/src/base/apps/bandtrim) app for example. In comparison, apps that have been updated to fit the gtest suite will have *app-name.xml*, *app-name.cpp*, *app-name.h*, and *main.cpp*, like the [campt](https://github.com/DOI-USGS/ISIS3/tree/dev/isis/src/base/apps/campt) app.
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Similar to the last comment, all changes look good. But bandtrim has been converted to a callable app. We might want to pick another example. An option would be to point to bandtrim before it was converted. See here:
https://github.com/DOI-USGS/ISIS3/tree/a28654ac754852f188be4c9710d001172ba459ac/isis/src/base/apps/bandtrim


After finding a suitable app to refactor, follow the steps in [Refactoring ISIS3 Applications](https://astrogeology.usgs.gov/docs/how-to-guides/isis-developer-guides/writing-isis-tests-with-ctest-and-gtest/#refactoring-isis3-applications) in your selected app.
After finding a suitable app to refactor, follow the steps in [Refactoring ISIS3 Applications](../../how-to-guides/isis-developer-guides/writing-isis-tests-with-ctest-and-gtest.md/#refactoring-isis-applications) in your selected app.

To write a new test suite with gtest, follow the steps in [Creating a new test suite](https://astrogeology.usgs.gov/docs/how-to-guides/isis-developer-guides/writing-isis-tests-with-ctest-and-gtest/#creating-a-new-test-suite).
To write a new test suite with gtest, follow the steps in [Creating a new test suite](../../how-to-guides/isis-developer-guides/writing-isis-tests-with-ctest-and-gtest.md/#creating-a-new-test-suite).

A great way to get a grasp on the converting process is by looking at previous examples so here are some PRs:

Expand All @@ -29,13 +29,13 @@ A great way to get a grasp on the converting process is by looking at previous e

## 3. Run Tests

Check out [Running Tests](https://astrogeology.usgs.gov/docs/how-to-guides/isis-developer-guides/developing-isis3-with-cmake/#running-tests) to get an idea on how to run your tests.
Check out [Running Tests](../../how-to-guides/isis-developer-guides/developing-isis3-with-cmake.md/#running-tests) to get an idea on how to run your tests.

As an example, let's look at the [`skypt` test suite](https://github.com/DOI-USGS/ISIS3/blob/dev/isis/tests/FunctionalTestsSkypt.cpp). You can run the all of `skypt`'s tests with `ctest -R skypt`. Let's say you want to test only the first test case in *FunctionalTestsSkypt.cpp*, run `ctest -R FunctionalTestSkyptDefault`.

## 4. Run Coverage Checks and Static Checks

Check out [Running Tests](https://astrogeology.usgs.gov/docs/how-to-guides/isis-developer-guides/developing-isis3-with-cmake/#checking-test-coverage) to see how coverage and static checks work.
Check out [Running Tests](../../how-to-guides/isis-developer-guides/developing-isis3-with-cmake.md/#checking-test-coverage) to see how coverage and static checks work.

If you run a partial test, just look at how coverage changed for the specific class or application you updated.

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