docs updates, widget thread fix

.napari/DESCRIPTION.md

@@ -93,4 +93,4 @@ yt-napari provides plugins to help load data from [yt](https://yt-project.org/)
 
 ![](https://raw.githubusercontent.com/data-exp-lab/yt-napari/main/docs/_static/nb_iso_galaxy_T_rho.png)
 
-See the [full documentation](https://yt-napari.readthedocs.io) for more details.
+See the [full documentation](https://yt-napari.readthedocs.io/en/stable/) for more details.

HISTORY.md

@@ -1,7 +1,10 @@
 ## v0.2.0
 
+This release includes some non-backwards compatible changes to the schema. Old
+json files will need to be updated to use with yt-napari >= v0.2.0
+
 ### New Features
-* new widget: yt-napari timeseries slicer
+* timeseries loading: a new widget, yt-napari timeseries slicer, is available from the napari gui and json files can also specify timeseries selections. Additionally, there is a new `yt_napari.timeseries` module for jupyter notebook interaction.
 
 ### Breaking changes
 

README.md

@@ -98,6 +98,8 @@ nbscreenshot(viewer)
 
 `yt_scene.add_to_viewer` accepts any of the keyword arguments allowed by `viewer.add_image`. See the full documentation ([yt-napari.readthedocs.io]) for more examples, including additional helper methods for linking layer appearance.
 
+Additionally, with `yt_napari`>= v0.2.0, you can use the `yt_napari.timeseries` module to help sample and load in selections from across datasets.
+
 ### loading a selection from a yt dataset interactively
 
 `yt-napari` provides two ways to sample a yt dataset and load in an image layer into a Napari viewer: the yt Reader plugin and json file specification.
@@ -110,23 +112,30 @@ To use the yt Reader plugin, click on `Plugins -> yt-napari: yt Reader`. From th
 
 You can add multiple selections and load them all at once or adjust values and click "Load" again.
 
+#### using the yt Time Series Reader plugin
+
+To use the yt Time Series Reader plugin, click on  `Plugins -> yt-napari: yt Time Series Reader`. Specify your file matching: use `file_pattern` to enter glob expressions or use `file_list` to enter a list of specific files.
+Then add a slice or region to sample for each matched dataset file (note: be careful of memory here!):
+
+![Loading timeseries selections from the napari viewer](./assets/images/readme_ex_004_gui_timeseries.gif)
+
 #### using a json file and schema
 
 `yt-napari` also provides the ability to load json that contain specifications for loading a file. Properly formatted files can be loaded from the napari GUI as you would load any image file (`File->Open`). The json file describes the selection process for a dataset as described by a json-schema. The following json file results in similar layers as the above examples:
 
 
 ```json
 {"$schema": "https://raw.githubusercontent.com/data-exp-lab/yt-napari/main/src/yt_napari/schemas/yt-napari_0.0.1.json",
- "data": [{"filename": "IsolatedGalaxy/galaxy0030/galaxy0030",
-           "selections": {"regions": [{
-                            "fields": [{"field_name": "Temperature", "field_type": "enzo", "take_log": true},
-                                       {"field_name": "Density", "field_type": "enzo", "take_log": true}],
-                            "left_edge": [460.0, 460.0, 460.0],
-                            "right_edge": [560.0, 560.0, 560.0],
-                            "resolution": [600, 600, 600]
-                          }]},
-           "edge_units": "kpc"
-         }]
+ "datasets": [{"filename": "IsolatedGalaxy/galaxy0030/galaxy0030",
+               "selections": {"regions": [{
+                                "fields": [{"field_name": "Temperature", "field_type": "enzo", "take_log": true},
+                                           {"field_name": "Density", "field_type": "enzo", "take_log": true}],
+                                "left_edge": [460.0, 460.0, 460.0],
+                                "right_edge": [560.0, 560.0, 560.0],
+                                "resolution": [600, 600, 600]
+                              }]},
+               "edge_units": "kpc"
+             }]
 }
 ```
 

docs/quickstart.rst

@@ -61,13 +61,13 @@ loading a json file from the napari gui
 .. code-block:: json
 
     {"$schema": "https://yt-napari.readthedocs.io/en/latest/_static/yt-napari_latest.json",
-     "data": [{"filename": "IsolatedGalaxy/galaxy0030/galaxy0030",
-               "selections": {"regions": [{
-                                "fields": [{"field_name": "Temperature", "field_type": "enzo", "take_log": true},
-                                           {"field_name": "Density", "field_type": "enzo", "take_log": true}],
-                                "left_edge": {"value": [460.0, 460.0, 460.0], "unit": "kpc"},
-                                "right_edge": {"value": [560.0, 560.0, 560.0], "unit": "kpc"},
-                                "resolution": [600, 600, 600]
+     "datasets": [{"filename": "IsolatedGalaxy/galaxy0030/galaxy0030",
+                   "selections": {"regions": [{
+                                  "fields": [{"field_name": "Temperature", "field_type": "enzo", "take_log": true},
+                                             {"field_name": "Density", "field_type": "enzo", "take_log": true}],
+                                 "left_edge": {"value": [460.0, 460.0, 460.0], "unit": "kpc"},
+                                 "right_edge": {"value": [560.0, 560.0, 560.0], "unit": "kpc"},
+                                 "resolution": [600, 600, 600]
                               }]}
              }]
     }
@@ -95,6 +95,16 @@ The use the yt Reader plugin, from a Napari viewer, select "Plugins -> yt-napari
 The reader plugin does its best to align new selections of data with existing yt-napari image layers and should be able to properly align selections from different yt datasets (please submit a bug report if it fails!).
 
 
+The yt-napari yt Time Series Reader:
+####################################
+
+This reader will apply a spatial selection to a set of files, similar to working with a yt `DataSeries` object. You specify
+the spatial selections and a list of files or file pattern to match. Note that while the operation is in a non-blocking
+thread, if your simulation data is large it may take a few minutes to load in your selections. Also note that 3D region
+selections can easily exceed available memory if you're not careful... for improving load times and working with
+bigger-than-memory arrays, you can instead use the jupyter notebook interface for napari with the `yt_napari.timeseries`
+module of helper functions to distribute the timestep selections using dask. See the example notebooks for usage.
+
 .. _configfile:
 
 Configuring yt-napari

src/yt_napari/_widget_reader.py

@@ -284,6 +284,6 @@ def process_timeseries_layers(self, layer_list):
 
 
 @thread_worker(progress=True)
-def time_series_load(model, worker_id):
+def time_series_load(model):
     _, layer_list = _model_ingestor._process_validated_model(model)
-    return layer_list, worker_id
+    return layer_list