Fix for plugins (#1282)

* update for importlib

* correct spec function

* give full path for importlib

* fix dependencies

* update docs

README.md

@@ -19,7 +19,7 @@ Phy provides two GUIs:
 
 
 ## What's new
-
+* [5 June 2024] phy 2.0 beta 6, bug fixes, install work, fixing some deprecations
 * [7 Sep 2021] Release of phy 2.0 beta 5, with some install and bug fixes
 * [7 Feb 2020] Release of phy 2.0 beta 1, with many new views, new features, various improvements and bug fixes...
 
@@ -44,7 +44,7 @@ Run the following commands in a terminal:
 1. Create a new conda environment with the conda dependencies:
 
     ```
-    conda create -n phy2 -y cython dask h5py joblib matplotlib numpy pillow pip pyopengl pyqt pyqtwebengine pytest python qtconsole requests responses scikit-learn scipy traitlets
+    conda create -n phy2 -y python=3.11 cython dask h5py joblib matplotlib numpy pillow pip pyopengl pyqt pyqtwebengine pytest python qtconsole requests responses scikit-learn scipy traitlets
     ```
 
 2. Activate the new conda environment with `conda activate phy2`
@@ -60,6 +60,9 @@ cd path/to/my/spikesorting/output
 phy template-gui params.py
 ```
 
+6. If there are problems with this method we also have an `environment.yml` file which allows for
+automatic install of the necessary packages. Give that a try.
+
 
 ### Dealing with the error `ModuleNotFoundError: No module named 'PyQt5.QtWebEngineWidget`
 

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python
+  - python=3.11
   - pip
   - git
   - numpy

phy/__init__.py

@@ -28,7 +28,7 @@
 
 __author__ = 'Cyrille Rossant'
 __email__ = 'cyrille.rossant at gmail.com'
-__version__ = '2.0b5'
+__version__ = '2.0b6'
 __version_git__ = __version__ + _git_version()
 
 

phy/utils/plugin.py

@@ -14,6 +14,7 @@
 import importlib
 import logging
 import os
+import sys
 from pathlib import Path
 
 from phylib.utils._misc import _fullname
@@ -97,20 +98,20 @@ def discover_plugins(dirs):
     """
     # Scan all subdirectories recursively.
     for path in _iter_plugin_files(dirs):
-        subdir = path.parent
         modname = path.stem
         if modname in ('phy_config', 'phycontrib_loader'):
             continue
-        file, path, descr = importlib.util.find_spec(modname, [subdir])
-        if file:
+        spec = importlib.util.spec_from_file_location(modname, path)
+        if spec is not None:
             # Loading the module registers the plugin in
             # IPluginRegistry.
             try:
-                mod = importlib.load_module(modname, file, path, descr)  # noqa
+                mod = importlib.util.module_from_spec(spec)  # noqa
+                sys.modules[modname] = mod
+                spec.loader.exec_module(mod)
             except Exception as e:  # pragma: no cover
                 logger.exception(e)
-            finally:
-                file.close()
+
     return IPluginRegistry.plugins
 
 

requirements.txt

@@ -8,7 +8,7 @@ dask
 cython
 pillow
 colorcet
-pyopengl
+pyopengl==3.1.6
 requests
 qtconsole
 tqdm