instllation using uv

installation_tips/README.md

@@ -1,36 +1,53 @@
 ## Installation tips
 
-If you are not (yet) an expert in Python installations (conda vs pip, mananging environements, etc.),
-here we propose a simple recipe to install `spikeinterface` and several sorters inside an anaconda
-environment for windows/mac users.
+If you are not (yet) an expert in Python installations, a main difficulty is choosing the installation procedure.
+The main ideas you need to know before starting:
+ * python itself can be distributed and installed many many ways.
+ * python itself do not contain so many features for scientifique computing you need to install "packages".
+   Numpy, scipy, matplotlib, spikeinterface, ... are python packages that have a complicated dependency graph between then. "uv"
+ * installing package  can be distributed and installed several ways (pip, conda, uv, mamba, ...)
+ * installing many packages at once is challenging (because of the depenency graph) so you need to do it in an "isolated environement"
+   to not destroy any previous installation. You need to see an "environement" as a sub installtion in dedicated folder.
+
+Choosing the installator + a environement manager + a package installer is a nightmare for beginners.
+The main options are:
+  * use "anaconda" that do everything. The most popular but bad idea because : ultra slow and agressive licensing (not free anymore)
+  * use python from the system or python.org + venv + pip : good idea for linux users.
+  * use "uv" : a new, fast and simple. We recommand this for beginners on evry os.
+
+Here we propose a steps by step recipe for beginers based on "uv".
+We used to propose here a solution based on anaconda. It is kept here for a while but we do not recommand it anymore.
+
 
 This environment will install:
  * spikeinterface full option
  * spikeinterface-gui
- * phy
- * tridesclous
+ * kilosort4
 
 Kilosort, Ironclust and HDSort are MATLAB based and need to be installed from source.
 
 ### Quick installation
 
-Steps:
+1. On macOS and Linux. Open a terminal and do
+   `$ curl -LsSf https://astral.sh/uv/install.sh | sh`
+1. On windows. Open a powershell and do
+   `powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"`
+2. exit session and log again.
+3. Download with right click + save this file corresponding in "Documents" folder:
+    * [`requirements_stable.txt`](https://raw.githubusercontent.com/SpikeInterface/spikeinterface/main/installation_tips/requirements_stable.txt)
+4. open terminal or powershell
+5. `uv venv si_env --python 3.11`
+6. `source `source si_env/bin/activate` (you should have `(si_env)` in your terminal)
+7. `uv pip install -r Documents/requirements_stable.txt`
 
-1. Download anaconda individual edition [here](https://www.anaconda.com/download)
-2. Run the installer. Check the box “Add anaconda3 to my Path environment variable”. It makes life easier for beginners.
-3. Download with right click + save the file corresponding to your OS, and put it in "Documents" folder
-    * [`full_spikeinterface_environment_windows.yml`](https://raw.githubusercontent.com/SpikeInterface/spikeinterface/main/installation_tips/full_spikeinterface_environment_windows.yml)
-    * [`full_spikeinterface_environment_mac.yml`](https://raw.githubusercontent.com/SpikeInterface/spikeinterface/main/installation_tips/full_spikeinterface_environment_mac.yml)
-4. Then open the "Anaconda Command Prompt" (if Windows, search in your applications) or the Terminal (for Mac users)
-5. If not in the "Documents" folder type `cd Documents`
-6. Then run this depending on your OS:
-    * `conda env create --file full_spikeinterface_environment_windows.yml`
-    * `conda env create --file full_spikeinterface_environment_mac.yml`
 
+More detail on [uv here](https://github.com/astral-sh/uv).
 
-Done! Before running a spikeinterface script you will need to "select" this "environment" with `conda activate si_env`.
+## Installing before release
 
-Note for **linux** users : this conda recipe should work but we recommend strongly to use **pip + virtualenv**.
+Some tools in the spikeinteface ecosystem are getting regular bug fixes (spikeinterface, spikeinterface-gui, probeinterface, python-neo, sortingview).
+We are making releases 2 to 4 times a year. In between releases if you want to install from source you can use the `requirements_rolling.txt` file to create the environment. This will install the packages of the ecosystem from source.
+This is a good way to test if patch fix your issue.
 
 
 ### Check the installation
@@ -62,6 +79,28 @@ This script tests the following:
   * opening the spikeinterface-gui
   * exporting to Phy
 
+### Legacy installation using anaconda (not recomanded)
+
+Steps:
+
+1. Download anaconda individual edition [here](https://www.anaconda.com/download)
+2. Run the installer. Check the box “Add anaconda3 to my Path environment variable”. It makes life easier for beginners.
+3. Download with right click + save the file corresponding to your OS, and put it in "Documents" folder
+    * [`full_spikeinterface_environment_windows.yml`](https://raw.githubusercontent.com/SpikeInterface/spikeinterface/main/installation_tips/full_spikeinterface_environment_windows.yml)
+    * [`full_spikeinterface_environment_mac.yml`](https://raw.githubusercontent.com/SpikeInterface/spikeinterface/main/installation_tips/full_spikeinterface_environment_mac.yml)
+4. Then open the "Anaconda Command Prompt" (if Windows, search in your applications) or the Terminal (for Mac users)
+5. If not in the "Documents" folder type `cd Documents`
+6. Then run this depending on your OS:
+    * `conda env create --file full_spikeinterface_environment_windows.yml`
+    * `conda env create --file full_spikeinterface_environment_mac.yml`
+
+
+Done! Before running a spikeinterface script you will need to "select" this "environment" with `conda activate si_env`.
+
+Note for **linux** users : this conda recipe should work but we recommend strongly to use **pip + virtualenv**.
+
+
+
 
 ## Installing before release
 

installation_tips/check_your_install.py

@@ -4,6 +4,9 @@
 import shutil
 import argparse
 
+
+job_kwargs = dict(n_jobs=-1, progress_bar=True, chunk_duration="1s")
+
 def check_import_si():
     import spikeinterface as si
 
@@ -13,15 +16,20 @@ def check_import_si_full():
 
 def _create_recording():
     import spikeinterface.full as si
-    rec, sorting = si.toy_example(num_segments=1, duration=200, seed=1, num_channels=16, num_columns=2)
-    rec.save(folder='./toy_example_recording')
+    rec, sorting = si.generate_ground_truth_recording(
+        durations=[200.],
+        sampling_frequency=30_000.,
+        num_channels=16,
+        num_units=10,
+        seed=2205
+    )
+    rec.save(folder='./toy_example_recording', **job_kwargs)
 
 
 def _run_one_sorter_and_analyzer(sorter_name):
-    job_kwargs = dict(n_jobs=-1, progress_bar=True, chunk_duration="1s")
     import spikeinterface.full as si
     recording = si.load_extractor('./toy_example_recording')
-    sorting = si.run_sorter(sorter_name, recording, output_folder=f'./sorter_with_{sorter_name}', verbose=False)
+    sorting = si.run_sorter(sorter_name, recording, folder=f'./sorter_with_{sorter_name}', verbose=False)
 
     sorting_analyzer = si.create_sorting_analyzer(sorting, recording,
                                                 format="binary_folder", folder=f"./analyzer_with_{sorter_name}",
@@ -36,12 +44,12 @@ def _run_one_sorter_and_analyzer(sorter_name):
     sorting_analyzer.compute("quality_metrics", metric_names=["snr", "firing_rate"])
 
 
-def run_tridesclous():
-    _run_one_sorter_and_analyzer('tridesclous')
-
 def run_tridesclous2():
     _run_one_sorter_and_analyzer('tridesclous2')
 
+def run_kilosort4():
+    _run_one_sorter_and_analyzer('kilosort4')
+
 
 
 def open_sigui():
@@ -75,10 +83,10 @@ def _clean():
     # clean
     folders = [
         "./toy_example_recording",
-        "./sorter_with_tridesclous",
-        "./analyzer_with_tridesclous",
         "./sorter_with_tridesclous2",
         "./analyzer_with_tridesclous2",
+        "./sorter_with_kilosort4",
+        "./analyzer_with_kilosort4",
         "./phy_example"
     ]
     for folder in folders:
@@ -100,8 +108,8 @@ def _clean():
     steps = [
         ('Import spikeinterface', check_import_si),
         ('Import spikeinterface.full', check_import_si_full),
-        ('Run tridesclous', run_tridesclous),
         ('Run tridesclous2', run_tridesclous2),
+        ('Run kilosort4', run_kilosort4),
         ]
 
     # backwards logic because default is True for end-user

installation_tips/requirements_rolling.txt

@@ -0,0 +1,16 @@
+numpy<2
+jupyterlab
+PySide6<6.8
+numba
+zarr
+hdbscan
+pyqtgraph
+ipywidgets
+ipympl
+ephyviewer
+https://github.com/NeuralEnsemble/python-neo/archive/master.zip
+https://github.com/SpikeInterface/probeinterface/archive/main.zip
+https://github.com/SpikeInterface/spikeinterface/archive/main.zip[full,widgets]
+https://github.com/SpikeInterface/spikeinterface-gui/archive/main.zip
+https://github.com/magland/sortingview/archive/main.zip
+kilosort

installation_tips/requirements_stable.txt

@@ -0,0 +1,13 @@
+numpy<2
+jupyterlab
+PySide6<6.8
+numba
+zarr
+hdbscan
+pyqtgraph
+ipywidgets
+ipympl
+ephyviewer
+spikeinterface[full,widgets]
+spikeinterface-gui
+kilosort