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Replace mamba with conda
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@roomrys
roomrys committed Jun 24, 2024
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4 changes: 2 additions & 2 deletions .conda/README.md
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Expand Up @@ -3,7 +3,7 @@ This folder defines the conda package build for Linux and Windows. There are run
To build, first go to the base repo directory and install the build environment:

```
mamba env create -f environment_build.yml -n sleap_build && conda activate sleap_build
conda env create -f environment_build.yml -n sleap_build && conda activate sleap_build
```

And finally, run the build command pointing to this directory:
Expand All @@ -15,7 +15,7 @@ conda build .conda --output-folder build -c conda-forge -c nvidia -c https://con
To install the local package:

```
mamba create -n sleap_0 -c conda-forge -c nvidia -c ./build -c https://conda.anaconda.org/sleap/ -c anaconda sleap=x.x.x
conda create -n sleap_0 -c conda-forge -c nvidia -c ./build -c https://conda.anaconda.org/sleap/ -c anaconda sleap=x.x.x
```

replacing x.x.x with the version of SLEAP that you just built.
50 changes: 25 additions & 25 deletions docs/installation.md
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Expand Up @@ -8,7 +8,7 @@ SLEAP can be installed as a Python package on Windows, Linux, and Mac OS.
```bash
mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a1
conda create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a1
```
Expand All @@ -23,7 +23,7 @@ SLEAP can be installed as a Python package on Windows, Linux, and Mac OS.
```{group-tab} Mac OS
```bash
mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a1
conda create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a1
```
```{note}
Expand Down Expand Up @@ -57,7 +57,7 @@ conda config --set solver libmamba
```
```{warning}
Any subsequent `mamba` commands in the docs will need to be replaced with `conda` if you choose to use your existing Anaconda installation.
Any subsequent `conda` commands in the docs will need to be replaced with `mamba` if you have [Mamba](https://mamba.readthedocs.io/en/latest/) installed instead of Anaconda or Miniconda.
```
````
Expand Down Expand Up @@ -111,7 +111,7 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag
```bash
mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a1
conda create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a1
```
Expand All @@ -126,7 +126,7 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag
```{group-tab} Mac OS
```bash
mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a1
conda create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a1
```
```{note}
Expand Down Expand Up @@ -170,15 +170,15 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag
```{group-tab} NVIDIA GPU

```bash
mamba env create -f environment.yml -n sleap
conda env create -f environment.yml -n sleap
```

```

```{group-tab} CPU or other GPU

```bash
mamba env create -f environment_no_cuda.yml -n sleap
conda env create -f environment_no_cuda.yml -n sleap
```
```
Expand All @@ -190,7 +190,7 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag
```{group-tab} Mac OS

```bash
mamba env create -f environment_mac.yml -n sleap
conda env create -f environment_mac.yml -n sleap
```
```

Expand Down Expand Up @@ -232,15 +232,15 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag


```bash
mamba create --name sleap pip python=3.7.12 cudatoolkit=11.3 cudnn=8.2
conda create --name sleap pip python=3.7.12 cudatoolkit=11.3 cudnn=8.2
```

```

```{group-tab} CPU or other GPU

```bash
mamba create --name sleap pip python=3.7.12
conda create --name sleap pip python=3.7.12
```

Expand All @@ -251,7 +251,7 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag
2. Then activate the environment to isolate the `pip install` from other environments on your computer:

```bash
mamba activate sleap
conda activate sleap
```

```{warning}
Expand All @@ -266,11 +266,11 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag

```{note}
The pypi distributed package of SLEAP ships with the following extras:
- **pypi**: For installation without an mamba environment file. All dependencies come from PyPI.
- **pypi**: For installation without an conda environment file. All dependencies come from PyPI.
- **jupyter**: This installs all *pypi* and jupyter lab dependencies.
- **dev**: This installs all *jupyter* dependencies and developement tools for testing and building docs.
- **conda_jupyter**: For installation using a mamba environment file included in the source code. Most dependencies are listed as conda packages in the environment file and only a few come from PyPI to allow jupyter lab support.
- **conda_dev**: For installation using [a mamba environment](https://github.com/search?q=repo%3Atalmolab%2Fsleap+path%3Aenvironment*.yml&type=code) with a few PyPI dependencies for development tools.
- **conda_jupyter**: For installation using a conda environment file included in the source code. Most dependencies are listed as conda packages in the environment file and only a few come from PyPI to allow jupyter lab support.
- **conda_dev**: For installation using [a conda environment](https://github.com/search?q=repo%3Atalmolab%2Fsleap+path%3Aenvironment*.yml&type=code) with a few PyPI dependencies for development tools.
```
```
Expand All @@ -289,16 +289,16 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag

## Testing that things are working

If you installed using `mamba`, first activate the `sleap` environment by opening a terminal and typing:
If you installed using `conda`, first activate the `sleap` environment by opening a terminal and typing:

```bash
mamba activate sleap
conda activate sleap
```

````{hint}
Not sure what `mamba` environments you already installed? You can get a list of the environments on your system with:
Not sure what `conda` environments you already installed? You can get a list of the environments on your system with:
```
mamba env list
conda env list
```
````

Expand Down Expand Up @@ -331,7 +331,7 @@ python -c "import sleap; sleap.versions()"

### GPU support

Assuming you installed using either of the `mamba`-based methods on Windows or Linux, SLEAP should automatically have GPU support enabled.
Assuming you installed using either of the `conda`-based methods on Windows or Linux, SLEAP should automatically have GPU support enabled.

To check, verify that SLEAP can detect the GPUs on your system:

Expand Down Expand Up @@ -392,7 +392,7 @@ file: No such file or directory
then activate the environment:
```bash
mamba activate sleap
conda activate sleap
```
and run the commands:
Expand Down Expand Up @@ -421,13 +421,13 @@ We **strongly recommend** installing SLEAP in a fresh environment when updating.
To uninstall an existing environment named `sleap`:

```bash
mamba env remove -n sleap
conda env remove -n sleap
```

````{hint}
Not sure what `mamba` environments you already installed? You can get a list of the environments on your system with:
Not sure what `conda` environments you already installed? You can get a list of the environments on your system with:
```bash
mamba env list
conda env list
```
````

Expand All @@ -443,10 +443,10 @@ If you get any errors or the GUI fails to launch, try running the diagnostics to
sleap-diagnostic
```

If you were not able to get SLEAP installed, activate the mamba environment it is in and generate a list of the package versions installed:
If you were not able to get SLEAP installed, activate the conda environment it is in and generate a list of the package versions installed:

```bash
mamba list
conda list
```

Then, [open a new Issue](https://github.com/talmolab/sleap/issues) providing the versions from either command above, as well as any errors you saw in the console during the installation. Or [start a discussion](https://github.com/talmolab/sleap/discussions) to get help from the community.

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