Merge branch 'develop' into liezl/handle-no-frame-selection-for-trail…

…-overlay

.github/ISSUE_TEMPLATE/bug_report.md

@@ -28,7 +28,7 @@ Please include information about how you installed.
 - OS:
 <!-- [e.g. ubuntu 20.04, macOS 11.0] -->
 - Version(s):
-<!-- e.g. [SLEAP v1.4.1a1, python 3.8] --->
+<!-- e.g. [SLEAP v1.4.1a2, python 3.8] --->
 - SLEAP installation method (listed [here](https://sleap.ai/installation.html#)):
   - [ ] [Conda from package](https://sleap.ai/installation.html#conda-package)
   - [ ] [Conda from source](https://sleap.ai/installation.html#conda-from-source)

docs/conf.py

@@ -28,15 +28,15 @@
 copyright = f"2019–{date.today().year}, Talmo Lab"
 
 # The short X.Y version
-version = "1.4.1a1"
+version = "1.4.1a2"
 
 # Get the sleap version
 # with open("../sleap/version.py") as f:
 #     version_file = f.read()
 #     version = re.search("\d.+(?=['\"])", version_file).group(0)
 
 # Release should be the full branch name
-release = "v1.4.1a1"
+release = "v1.4.1a2"
 
 html_title = f"SLEAP ({release})"
 html_short_title = "SLEAP"
@@ -85,6 +85,7 @@
 pygments_style = "sphinx"
 pygments_dark_style = "monokai"
 
+
 # Autosummary linkcode resolution
 # https://www.sphinx-doc.org/en/master/usage/extensions/linkcode.html
 def linkcode_resolve(domain, info):

docs/guides/gui.md

@@ -60,7 +60,7 @@ Note that many of the menu command have keyboard shortcuts which can be configur
 
 "**Edge Style**" controls whether edges are drawn as thin lines or as wedges which indicate the {ref}`orientation` of the instance (as well as the direction of the part affinity field which would be used to predict the connection between nodes when using a "bottom-up" approach).
 
-"**Trail Length**" allows you to show a trail of where each instance was located in prior frames (the length of the trail is the number of prior frames). This can be useful when proofreading predictions since it can help you detect swaps in the identities of animals across frames.
+"**Trail Length**" allows you to show a trail of where each instance was located in prior frames (the length of the trail is the number of prior frames). This can be useful when proofreading predictions since it can help you detect swaps in the identities of animals across frames. By default, you can only select trail lengths of up to 250 frames. You can use a custom trail length by modifying the default length in the `preferences.yaml` file. However, using trail lengths longer than about 500 frames can result in significant lag.
 
 "**Fit Instances to View**" allows you to toggle whether the view is auto-zoomed to the instances in each frame. This can be useful when proofreading predictions.
 

docs/installation.md

@@ -137,13 +137,13 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag
 **Windows** and **Linux**
 
 ```bash
-mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a1
+mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a2
 ```
 
 **Mac OS X** and **Apple Silicon**
 
 ```bash
-mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a1
+mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a2
 ```
 
 **This is the recommended installation method**.
@@ -232,7 +232,7 @@ Although you do not need Mambaforge installed to perform a `pip install`, we rec
 3. Finally, we can perform the `pip install`:
 
    ```bash
-   pip install sleap[pypi]==1.4.1a1
+   pip install sleap[pypi]==1.4.1a2
    ```
 
    This works on **any OS except Apple silicon** and on **Google Colab**.

sleap/gui/app.py

@@ -151,6 +151,7 @@ def __init__(
         self.state["edge style"] = prefs["edge style"]
         self.state["fit"] = False
         self.state["color predicted"] = prefs["color predicted"]
+        self.state["trail_length"] = prefs["trail length"]
         self.state["trail_shade"] = prefs["trail shade"]
         self.state["marker size"] = prefs["marker size"]
         self.state["propagate track labels"] = prefs["propagate track labels"]
@@ -221,6 +222,7 @@ def closeEvent(self, event):
         prefs["edge style"] = self.state["edge style"]
         prefs["propagate track labels"] = self.state["propagate track labels"]
         prefs["color predicted"] = self.state["color predicted"]
+        prefs["trail length"] = self.state["trail_length"]
         prefs["trail shade"] = self.state["trail_shade"]
         prefs["share usage data"] = self.state["share usage data"]
 
@@ -1025,6 +1027,7 @@ def _load_overlays(self):
             labels=self.labels,
             player=self.player,
             trail_shade=self.state["trail_shade"],
+            trail_length=self.state["trail_length"],
         )
         self.overlays["instance"] = InstanceOverlay(
             labels=self.labels, player=self.player, state=self.state

sleap/gui/overlays/tracks.py

@@ -47,7 +47,9 @@ def __attrs_post_init__(self):
 
     @classmethod
     def get_length_options(cls):
-        return (0, 10, 50, 100, 250)
+        if prefs["trail length"] != 0:
+            return (0, 10, 50, 100, 250, 500, prefs["trail length"])
+        return (0, 10, 50, 100, 250, 500)
 
     @classmethod
     def get_shade_options(cls):

sleap/prefs.py

@@ -45,6 +45,10 @@ def load_(self):
             self._prefs = util.get_config_yaml(self._filename)
             if not hasattr(self._prefs, "get"):
                 self._prefs = self._defaults
+            else:
+                self._prefs["trail length"] = self._prefs.get(
+                    "trail length", self._defaults["trail length"]
+                )
         except FileNotFoundError:
             self._prefs = self._defaults
 

sleap/version.py

@@ -11,8 +11,7 @@
 Must be a semver string, "aN" should be appended for alpha releases.
 """
 
-
-__version__ = "1.4.1a1"
+__version__ = "1.4.1a2"
 
 
 def versions():