Update install instructions

MANIFEST.in

@@ -1,5 +1,7 @@
 include LICENSE
 include README.md
+include requirements.txt
+include requirements-dev.txt
 
 recursive-include tests *
 recursive-include phy/electrode/probes *.prb

Makefile

@@ -28,10 +28,10 @@ test-full: test test-apps
 	coverage report --omit */phy/plot/gloo/*
 
 doc:
-	python tools/api.py && python tools/extract_shortcuts.py && python tools/plugins_doc.py
+	python3 tools/api.py && python tools/extract_shortcuts.py && python tools/plugins_doc.py
 
 build:
-	python setup.py sdist --formats=zip
+	python3 setup.py sdist --formats=zip
 
 upload:
-	python setup.py sdist --formats=zip upload
+	twine upload dist/*

README.md

@@ -20,6 +20,7 @@ Phy provides two GUIs:
 
 ## What's new
 
+* [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...
 
 
@@ -33,15 +34,13 @@ Phy provides two GUIs:
 
 Phy requires a recent GPU and an SSD for storing your data (the GUI may be slow if the data is on an HDD).
 
-1. Install the latest version of [Anaconda 64-bit with Python 3](https://www.anaconda.com/distribution/#download-section).
+1. You need a recent Python distribution.
 
 2. Open a terminal and type:
 
 ```bash
-conda create -n phy2 python=3.7 pip numpy matplotlib scipy scikit-learn h5py pyqt cython pillow -y
-conda activate phy2
 pip install phy --pre --upgrade
-# Only if you plan to use the Kwik GUI:
+# If you plan to use the Kwik GUI, type the following without the leading hash # character:
 # pip install klusta klustakwik2
 ```
 
@@ -52,14 +51,41 @@ cd path/to/my/spikesorting/output
 phy template-gui params.py
 ```
 
+### Dependencies
+
+For your information, here are the Python dependencies of phy  (as found in `requirements.txt`):
+
+```
+phylib
+mtscomp
+numpy
+matplotlib
+scipy
+h5py
+dask
+cython
+pillow
+colorcet
+pyopengl
+requests
+qtconsole
+tqdm
+joblib
+click
+mkdocs
+PyQtWebEngine
+```
+
+
+
 ### Dealing with the error `ModuleNotFoundError: No module named 'PyQt5.QtWebEngineWidget`
 
 In some environments, you might get an error message related to QtWebEngineWidget. Run the command `pip install PyQtWebEngine` and try launching phy again. This command should not run if the error message doesn't appear, as it could break the PyQt5 installation.
 
 
 ### Upgrading from phy 1 to phy 2
 
-* Do not install phy 1 and phy 2 in the same conda environment.
+* Do not install phy 1 and phy 2 in the same Python environment.
 * It is recommended to delete `~/.phy/*GUI/state.json` when upgrading.
 
 
@@ -97,7 +123,7 @@ template_gui("params.py")
 
 ## Credits
 
-**phy** is developed and maintained by [Cyrille Rossant](http://cyrille.rossant.net).
+**phy** is developed and maintained by [Cyrille Rossant](https://cyrille.rossant.net).
 
 * [International Brain Laboratory](https://internationalbrainlab.org)
 * [Cortex Lab (UCL)](https://www.ucl.ac.uk/cortexlab/) ([Kenneth Harris](https://www.ucl.ac.uk/biosciences/people/harris-kenneth) and [Matteo Carandini](https://www.carandinilab.net/)).

phy/__init__.py

@@ -28,7 +28,7 @@
 
 __author__ = 'Cyrille Rossant'
 __email__ = 'cyrille.rossant at gmail.com'
-__version__ = '2.0b2.dev'
+__version__ = '2.0b5'
 __version_git__ = __version__ + _git_version()
 
 

requirements.txt

@@ -15,3 +15,4 @@ tqdm
 joblib
 click
 mkdocs
+PyQtWebEngine

setup.py

@@ -38,10 +38,10 @@ def _package_tree(pkgroot):
     version = re.search(r"__version__ = '([^']+)'", f.read()).group(1)
 
 
-with open('requirements.txt') as f:
+filename = op.join(curdir, 'requirements.txt')
+with open(filename, 'r') as f:
     require = [x.strip() for x in f.readlines() if not x.startswith('git+')]
 
-
 # Only add PyQt5 dependency if it is not already installed in the conda environment.
 try:
     import PyQt5