Add napari placeholder, improve installation instructions

CAREamics · Oct 22, 2024 · e548d2d · e548d2d
1 parent 88e4ca6
commit e548d2d
Show file tree

Hide file tree

Showing 10 changed files with 150 additions and 15 deletions.
diff --git a/docs/guides/dev_resources/CI.md b/docs/guides/dev_resources/CI.md
diff --git a/docs/guides/dev_resources/tooling.md b/docs/guides/dev_resources/tooling.md
diff --git a/docs/guides/index.md b/docs/guides/index.md
@@ -60,6 +60,51 @@ We also provide a command-line interface and developer resources!
                     </a>    
                 </div>
                 <!-- New row -->
+                <div class="responsive-grid">
+                    <!-- Installation -->
+                    <a class="card-wrapper" href="napari_plugin">
+                        <div class="card"> 
+                            <div class="card-body">
+                                <div class="logo">
+                                    <span class="twemoji">
+                                        --8<--  "device-desktop.svg"
+                                    </span>
+                                </div>
+                                <div class="card-content">
+                                    <h5>napari plugin</h5>
+                                    <p>
+                                        A UI interface for CAREamics in the popular
+                                        napari image viewer, allowing training, 
+                                        predicting and saving models on your 
+                                        own data.
+                                    </p>
+                                </div>
+                            </div>
+                        </div>
+                    </a>
+                    <!-- Installation -->
+                    <a class="card-wrapper" href="tutorials">
+                        <div class="card"> 
+                            <div class="card-body">
+                                <div class="logo">
+                                    <span class="twemoji">
+                                        --8<--  "repo.svg"
+                                    </span>
+                                </div>
+                                <div class="card-content">
+                                    <h5>Tutorials</h5>
+                                    <p>
+                                        Thematic tutorials on various ways to use
+                                        and apply CAREamics algorithms, from data
+                                        inspection to using CAREamics in other
+                                        tools.
+                                    </p>
+                                </div>
+                            </div>
+                        </div>
+                    </a>    
+                </div>
+                <!-- New row -->
                 <div class="responsive-grid">
                     <!-- Installation -->
                     <a class="card-wrapper" href="cli">
@@ -86,14 +131,15 @@ We also provide a command-line interface and developer resources!
                             <div class="card-body">
                                 <div class="logo">
                                     <span class="twemoji">
-                                        --8<--  "repo.svg"
+                                        --8<--  "law.svg"
                                     </span>
                                 </div>
                                 <div class="card-content">
                                     <h5>Developer resources</h5>
                                     <p>
-                                        More insights on how CAREamics is organized and how
-                                        to tweak it to your needs.
+                                        More details on how the documentation is set up,
+                                        and guidelines for modifying and contributing to
+                                        CAREamics.
                                     </p>
                                 </div>
                             </div>

diff --git a/docs/guides/napari_plugin/index.md b/docs/guides/napari_plugin/index.md
@@ -0,0 +1,5 @@
+# napari plugin
+
+
+!!! warning "Work in progress"
+    These pages are still under construction.
diff --git a/docs/guides/tutorials/index.md b/docs/guides/tutorials/index.md
@@ -0,0 +1,5 @@
+# Tutorials
+
+
+!!! warning "Work in progress"
+    These pages are still under construction.
diff --git a/docs/installation.md b/docs/installation.md
@@ -6,20 +6,24 @@ description: Installation instructions
 # Installation
 
 CAREamics is a deep-learning library and we therefore recommend having GPU support as
-training the algorithms on the CPU can be very slow. MacOS users can also benefit from
-GPU-acceleration if they have the new chip generations (M1, M2, etc.).
+training the algorithms on the CPU can be very slow. 
 
-Support is provided directly from PyTorch, and is still experimental for macOS.
+We currently do not provide support for macOS silicon (M1, M2, etc.) for accelerated 
+training, but we will in the near future investigate how to install and train 
+CAREamics on silicon-arm.
 
 
-
-## Step-by-step
-
 We recommend using [mamba (miniforge)](https://github.com/conda-forge/miniforge#download) 
 to install all packages in a virtual environment. As an alternative, you can use
 [conda 
-(miniconda)](https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html). 
+(miniconda)](https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html)
+with the same commands (replacing `mamba` by `conda`). 
+
+
+## CAREamics library step-by-step
 
+This section install CAREamics for use in your own library or tool, via jupyter notebook
+or as scripts. For the napari plugin, refer to the next section.
 
 === "Linux and Windows"
     1. Open the terminal and type `mamba` to verify that mamba is available.
@@ -75,10 +79,10 @@ to install all packages in a virtual environment. As an alternative, you can use
         As an example, our test machine requires:
 
         ``` bash
-        mamba install pytorch::pytorch torchvision torchaudio -c pytorch
+        mamba install pytorch::pytorch torchvision -c pytorch
         ```
 
-        :warning: Note that accelerated-training is only available on macOS silicon.
+        :warning: Note that we currently do not support silicon arm accelerated training.
 
     4. Install CAREamics. We have several extra options (`dev`, `examples`, `wandb`
         and `tensorboard`). If you wish to run the [example notebooks](https://github.com/CAREamics/careamics-examples),
@@ -105,8 +109,75 @@ Here is a list of the extra dependencies:
 - `tensorboard`: Dependencies to use [TensorBoard](https://pytorch.org/tutorials/recipes/recipes/tensorboard_with_pytorch.html) as a logger.
 - `dev`: Dependencies required to run all the tooling necessary to develop with CAREamics.
 
-## Quickstart
+### Quickstart
 
 Once you have [installed CAREamics](installation.md), the easiest way to get started
 is to look at the [applications](applications/index.md) for full examples and the 
-[guides](guides/index.md) for in-depth tweaking.
+[guides](guides/index.md) for in-depth tweaking.
+
+
+## CAREamics napari plugin
+For the napari plugin, refer to the next section.
+
+=== "Linux and Windows"
+    1. Open the terminal and type `mamba` to verify that mamba is available.
+    2. Create a new environment:
+
+        ``` bash
+        mamba create -n careamics python=3.10
+        mamba activate careamics
+        ```
+
+    3. Install PyTorch following the [official 
+        instructions](https://pytorch.org/get-started/locally/)
+
+        As an example, our test machine requires:
+
+        ``` bash
+        mamba install pytorch torchvision pytorch-cuda=11.8 -c pytorch -c nvidia
+        ```
+
+    4. Verify that the GPU is available:
+        
+        ``` bash
+        python -c "import torch; print([torch.cuda.get_device_properties(i) for i in range(torch.cuda.device_count())])"
+        ```
+
+        This should show a list of available GPUs. If the list is empty, then you
+        will need to change the `pytorch` and `pytorch-cuda` versions to match your
+        hardware (linux and windows).
+
+    5. Install CAREamics napari plugin and napari:
+
+        ``` bash
+        pip install careamics-napari "napari[all]"
+        ```
+
+    These instructions were tested on a linux virtual machine (RedHat 8.6) with a 
+    NVIDIA A40-8Q GPU.
+
+=== "macOS"
+    1. Open the terminal and type `mamba` to verify that mamba is available.
+    2. Create a new environment:
+
+        ``` bash
+        mamba create -n careamics python=3.10
+        mamba activate careamics
+        ```
+
+    3. Install PyTorch following the [official 
+        instructions](https://pytorch.org/get-started/locally/)
+
+        As an example, our test machine requires:
+
+        ``` bash
+        mamba install pytorch::pytorch torchvision -c pytorch
+        ```
+
+        :warning: Note that we currently do not support silicon arm accelerated training.
+
+    4. Install CAREamics napari plugin and napari:
+
+        ``` bash
+        pip install careamics-napari "napari[all]"
+        ```
diff --git a/docs/overrides/.icons/octicons/device-desktop.svg b/docs/overrides/.icons/octicons/device-desktop.svg
diff --git a/docs/overrides/.icons/octicons/law.svg b/docs/overrides/.icons/octicons/law.svg
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -30,6 +30,10 @@ nav:
               - guides/careamist_api/usage/prediction.md
               - guides/careamist_api/usage/model_export.md
           - FAQ: guides/careamist_api/faq.md
+      - napari plugins:
+          - guides/napari_plugin/index.md
+      - Tutorials:
+          - guides/turotials/index.md
       - Lightning API:
           - guides/lightning_api/index.md
           - guides/lightning_api/lightning_module.md

diff --git a/scripts/git_repositories.txt b/scripts/git_repositories.txt
@@ -1,2 +1,3 @@
 https://github.com/CAREamics/careamics
-https://github.com/CAREamics/careamics-portfolio
+https://github.com/CAREamics/careamics-portfolio
+https://github.com/CAREamics/careamics-napari