diff --git a/README.md b/README.md index 03ead78..4cffe6f 100644 --- a/README.md +++ b/README.md @@ -10,27 +10,26 @@ Check the full documentation : [https://teamncmc.github.io/cuisto](https://teamn Steps 1-3 below need to be performed only once. If Anaconda or conda is already installed, skip steps 1-2 and use the Anaconda prompt instead. 1. Install [Miniforge](https://conda-forge.org/download/), as user, add conda to PATH and make it the default interpreter. 2. Open a terminal (PowerShell in Windows). run : `conda init` and restart the terminal. -3. Create a virtual environment named "hq" with Python 3.12: +3. Create a virtual environment named "cuisto-env" with Python 3.12 : + ```bash + conda create -n cuisto-env python=3.12 ``` - conda create -n hq python=3.12 +4. Activate the environment : + ```bash + conda activate cuisto-env + ```bash +5. Install `cuisto` : ``` -4. Activate the environment: - ``` - conda activate hq - ``` -5. Download the latest release from [here](https://github.com/TeamNCMC/cuisto/releases/latest) (choose "Source code (zip)) and unzip it on your computer. -6. Browse to the repository from the terminal and install the `cuisto` package: - ``` - cd /path/to/the/unzipped/folder - pip install . + pip install cuisto ``` +6. (Optional) Download the latest release from [here](https://github.com/TeamNCMC/cuisto/releases/latest) (choose "Source code (zip)) and unzip it on your computer. You can copy the `scripts/` folder to get access to the QuPath and Python scripts. You can check the notebooks in `docs/demo_notebooks` as well ! -The `cuisto` will be then available in Python from anywhere as long as the `hq` conda environment is activated. You can get started by looking and using the [Jupyter notebooks](#using-notebooks). +The `cuisto` will be then available in Python from anywhere as long as the `cuisto-env` conda environment is activated. You can get started by looking and using the [Jupyter notebooks](#using-notebooks). For more complete installation instructions, see the [documentation](https://teamncmc.github.io/cuisto/main-getting-started.html#slow-start). ## Using notebooks -Some Jupyter notebooks are available in the "docs/demo_notebooks" folder. You can open them in an IDE (such as [vscode](https://code.visualstudio.com/), select the "hq" environment as kernel in the top right) or in the Jupyter web interface (`jupyter notebook` in the terminal, with the "hq" environment activated). +Some Jupyter notebooks are available in the "docs/demo_notebooks" folder. You can open them in an IDE (such as [vscode](https://code.visualstudio.com/), select the "cuisto-env" environment as kernel in the top right) or in the Jupyter web interface (`jupyter notebook` in the terminal, with the "cuisto-env" environment activated). ## Brain structures You can generate brain structures outlines coordinates in three projections (coronal, sagittal, top-view) with the script in scripts/atlas/generate_atlas_outline.py. They are used to overlay brain regions outlines in 2D projection density maps. It might take a while so you can also grab a copy of those files here: diff --git a/docs/main-getting-started.md b/docs/main-getting-started.md index 89bad33..86c923c 100644 --- a/docs/main-getting-started.md +++ b/docs/main-getting-started.md @@ -10,14 +10,15 @@ conda create -c conda-forge -n cuisto-env python=3.12 ``` conda activate cuisto-env ``` -4. [Download](https://github.com/TeamNCMC/cuisto/releases/latest) the latest release .zip, unzip it and install it with pip, from inside the `cuisto-xxx` folder : +4. Install `cuisto` ``` -pip install . +pip install cuisto ``` -If you want to build the doc : +If you want to build the doc locally : ``` -pip install .[doc] +pip install cuisto[doc] ``` +5. Check the [Examples section](https://teamncmc.github.io/cuisto/main-using-notebooks.html) ! ## Slow start !!! tip @@ -73,8 +74,7 @@ The following commands should be run from a terminal (PowerShell). Remember that ``` conda create -c conda-forge -n cuisto-env python=3.12 ``` - 2. Get a copy of the `cuisto` Source code .zip package, from the [Releases](https://github.com/TeamNCMC/cuisto/releases/latest) page. - 3. We need to install it *inside* the `cuisto-env` environment we just created. First, you need to *activate* the `cuisto-env` environment : + 2. We need to install it *inside* the `cuisto-env` environment we just created. First, you need to *activate* the `cuisto-env` environment : ```bash conda activate cuisto-env ``` @@ -83,27 +83,15 @@ The following commands should be run from a terminal (PowerShell). Remember that (cuisto-env) PS C:\Users\myname> ``` This means that Python packages will now be installed in the `cuisto-env` environment and won't conflict with other toolboxes you might be using. - Then, we use `pip` to install `cuisto`. `pip` was installed with Python, and will scan the `cuisto` folder, specifically the "pyproject.toml" file that lists all the required dependencies. To do so, you can either : - + - ```bash - pip install /path/to/cuisto - ``` - + Change directory from the terminal : - ``` - cd /path/to/cuisto - ``` - Then install the package, "." denotes "here" : - ``` - pip install . - ``` - + Use the file explorer to get to the `cuisto` folder, use ++shift+right-button++ to "Open PowerShell window here" and run : - ``` - pip install . - ``` + 3. Then, we use `pip` to install `cuisto`. `pip` was installed with Python, and will fetch the latest release from PyPI. + ```bash + pip install cuisto + ``` + 4. Get a copy of the `cuisto` Source code .zip package, from the [Releases](https://github.com/TeamNCMC/cuisto/releases/latest) page, to have access to all the utility scripts in the `scripts/` folder. `cuisto` is now installed inside the `cuisto-env` environment and will be available in Python from that environment ! !!! tip - You will need to perform step 3. each time you want to update the package. + You can run `pip install cuisto --upgrade` from the `cuisto-env` environment to update the package. -If you already have registered data and cells in QuPath, you can export Annotations and Detections as TSV files and head to the [Example](main-using-notebooks.md) section. \ No newline at end of file +If you already have registered data and cells in QuPath, you can export Annotations and Detections as TSV files and head to the [Example](main-using-notebooks.md) section. Otherwise, check out the Guides section on the left panel. \ No newline at end of file