From c0059f872a9e8e23b3cffa59d58ee7ecc0831748 Mon Sep 17 00:00:00 2001
From: roomrys <38435167+roomrys@users.noreply.github.com>
Date: Tue, 19 Jul 2022 12:50:22 -0700
Subject: [PATCH] Update installation and labeling docs and no cuda yml

---
 .github/workflows/website.yml                 |  2 +-
 docs/installation.md                          | 22 ++++++++++--
 ...sted-labeling.rst => assisted-labeling.md} | 35 +++++++++++--------
 environment_no_cuda.yml                       | 16 +++++----
 4 files changed, 50 insertions(+), 25 deletions(-)
 rename docs/tutorials/{assisted-labeling.rst => assisted-labeling.md} (74%)

diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml
index ea8e5ba56..7a0a67ec6 100644
--- a/.github/workflows/website.yml
+++ b/.github/workflows/website.yml
@@ -8,7 +8,7 @@ on:
       # 'main' triggers updates to 'sleap.ai', 'develop' to 'sleap.ai/develop'
       - main
       - develop
-      - david/add-CLI-to-render-videos
+      - liezl/docs-update
     paths:
       - "docs/**"
       - "README.rst"
diff --git a/docs/installation.md b/docs/installation.md
index 623e4f109..6bf7011b2 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -77,20 +77,36 @@ conda create -y -n sleap -c sleap -c nvidia -c conda-forge sleap=1.2.4
 
 ### `conda` from source
 
-1. First, clone the repository:
+1. First, ensure git is installed:
+
+   ```bash
+   git --version
+   ```
+
+   If 'git' is not recognized, then [install git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git).
+
+2. Then, clone the repository:
 
    ```bash
    git clone https://github.com/talmolab/sleap && cd sleap
    ```
 
-2. Then, install from the environment file:
+3. Finally, install from the environment file:
+
    ```bash
    conda env create -f environment.yml -n sleap
    ```
+
+   If you do not have a NVIDIA GPU, then you should use the no CUDA environment file:
+
+   ```bash
+   conda env create -f environment_no_cuda.yml -n sleap
+   ```
+
    This works on **Windows**, **Linux** and **Mac OS X** (pre-M1). This is the **recommended method for development**.
 
 ```{note}
-- This install SLEAP in development mode, which means that edits to the source code will be applied the next time you run SLEAP.
+- This installs SLEAP in development mode, which means that edits to the source code will be applied the next time you run SLEAP.
 - Change the `-n sleap` in the command to create an environment with a different name (e.g., `-n sleap_develop`).
 ```
 
diff --git a/docs/tutorials/assisted-labeling.rst b/docs/tutorials/assisted-labeling.md
similarity index 74%
rename from docs/tutorials/assisted-labeling.rst
rename to docs/tutorials/assisted-labeling.md
index 611d23109..f044b5500 100644
--- a/docs/tutorials/assisted-labeling.rst
+++ b/docs/tutorials/assisted-labeling.md
@@ -1,16 +1,21 @@
-.. _assisted-labeling:
+---
+substitutions:
+  imagefix: |-
+    ```{image} ../_static/fixing-predictions.gif
+    ```
+---
 
-Prediction-assisted labeling
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+(assisted-labeling)=
 
-*Prediction-assisted labeling* has two main goals. First, it speeds up the labeling
+# Prediction-assisted labeling
+
+_Prediction-assisted labeling_ has two main goals. First, it speeds up the labeling
 process as it is faster to correct a predicted instance which is mostly
 correct than it is to add a new instance from scratch. Second, it
 provides feedback about where your model does well and where it does
 poorly, and this should give you a better idea of which frames will be
 most useful to label.
 
-
 The GUI doesn’t yet give you a way to monitor the progress during inference,
 although it will alert you if an error occurs during inference.
 
@@ -18,8 +23,7 @@ When inference finishes, you’ll be told how many instances were
 predicted. Suggested frames with predicted instances will be marked in
 red on the seekbar.
 
-Reviewing and fixing predictions
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# Reviewing and fixing predictions
 
 After you’ve successfully trained models and predicted some instances,
 you’ll get a message that inference has finished.
@@ -28,24 +32,27 @@ that you manually labeled will be marked with a thicker black line. (For
 "suggested" frames, manually labeled frames will have a dark blue line and
 predicted frames will have a lighter blue.)
 
-Predicted instances will *not* be used for future model training unless you
+Predicted instances will _not_ be used for future model training unless you
 correct the predictions in the GUI.
 
-|imagefix|
+{{ imagefix }}
 
 Predicted instances in the frame are displayed in grey with yellow
 nodes. To edit a prediction, you’ll need to replace it with an editable
 instance. **Double-click** the predicted instance and it will be converted into a regular instance.
 
+:::{note}
+All node labels on the regular instance will be colored red.
+After moving nodes, the node labels will colored green. This is just a visual indicator
+to keep track of which nodes have been moved from the original prediction.
+:::
+
 You can now edit the instance as before. Once you’ve added and/or
 corrected more instances, you can repeat the process:
 train a new model, predict on more frames, correct those predictions,
 and so on. You’ll want to regularly generate new frame suggestions,
 since active learning will return predictions for just these frames.
 
-After you have accurate frame-by-frame prediction, you’re ready to predict for entire video clips and to track animal identities. We use a variety of heuristic algorithms for tracking identities across time (see :ref:`tracking-method-details` for more details). SLEAP also includes a graphical proof-reading tool for quickly assessing the accuracy of tracking and correcting problems.
-
-
-Continue to :ref:`proofreading-tutorial`.
+After you have accurate frame-by-frame prediction, you’re ready to predict for entire video clips and to track animal identities. We use a variety of heuristic algorithms for tracking identities across time (see {ref}`tracking-method-details` for more details). SLEAP also includes a graphical proof-reading tool for quickly assessing the accuracy of tracking and correcting problems.
 
-.. |imagefix| image:: ../_static/fixing-predictions.gif
\ No newline at end of file
+Continue to {ref}`proofreading-tutorial`.
diff --git a/environment_no_cuda.yml b/environment_no_cuda.yml
index 8e213d314..04c740dcb 100644
--- a/environment_no_cuda.yml
+++ b/environment_no_cuda.yml
@@ -2,19 +2,21 @@ name: sleap
 
 dependencies:
   - python=3.7
-  # - conda-forge::numpy>=1.19.5,<=1.21.5
-  # - sleap::tensorflow>=2.6.3,<=2.7.1
-  # - conda-forge::pyside2>=5.13.2,<=5.14.1
-  # - conda-forge::h5py>=3.1.0,<=3.6.0
-  # - conda-forge::scipy>=1.4.1,<=1.7.3
+  - conda-forge::numpy>=1.19.5,<=1.21.5
+  # - conda-forge::tensorflow>=2.6.3,<=2.7.1
+  - conda-forge::pyside2>=5.13.2,<=5.14.1
+  - conda-forge::h5py=3.1.0
+  - conda-forge::scipy>=1.4.1,<=1.7.3
   - pillow=8.4.0
   - shapely=1.7.1
-  # - conda-forge::pandas
+  - conda-forge::pandas
   - ffmpeg
   # - cudatoolkit=11.3.1
   # - cudnn=8.2.1
   # - nvidia::cuda-nvcc=11.3
+  # - sleap::tensorflow=2.7.0
+  # - sleap::pyside2=5.14.1
   - conda-forge::pip<=22.0.3
   - pip:
-      - "."
+      - "--editable=."
       - "--requirement=./dev_requirements.txt"