Merge pull request #364 from alejoe91/update-get-probe

Improve interaction with probeinterface-library

Author: alejoe91

.github/workflows/full_tests.yml

@@ -31,4 +31,8 @@ jobs:
         pip install .[test]
     - name: Pytest
       run: |
-        pytest -v
+        pytest -m "not library" -v
+    - name: Pytest library tests
+      if: ${{ matrix.os == 'ubuntu-latest' }}
+      run: |
+        pytest -m library -v

doc/library.rst

@@ -1,27 +1,58 @@
 Probeinterface public library
 =============================
 
-Probeinterface also handles a collection of probe descriptions on the
-`GitHub platform <https://github.com/SpikeInterface/probeinterface_library>`_
+Probeinterface also handles a collection of probe descriptions in the
+`ProbeInterface library <https://github.com/SpikeInterface/probeinterface_library>`_
 
-The python module has a simple function to download and cache locally by using `get_probe(...)` ::
+The python module has a simple function to download and cache locally by using ``get_probe(...)``:
+
+
+.. code-block:: python
 
     from probeinterface import get_probe
-    probe = get_probe(manufacturer='neuronexus',
-                probe_name='A1x32-Poly3-10mm-50-177')
+    probe = get_probe(
+        manufacturer='neuronexus',
+        probe_name='A1x32-Poly3-10mm-50-177'
+    )
+
+
+Once a probe is downloaded, it is cached locally for future use.
+
+There are several helper functions to explore the library:
+
+.. code-block:: python
+
+    from probeinterface.library import (
+        list_manufacturers,
+        list_probes_by_manufacturer,
+        list_all_probes
+    )
+
+    # List all manufacturers
+    manufacturers = list_manufacturers()
+
+    # List all probes for a given manufacturer
+    probes = list_probes_by_manufacturer('neuronexus')
+
+    # List all probes in the library
+    all_probes = list_all_probes()
+
+    # Cache all probes locally
+    cache_full_library()
+
 
+Each function has an optional ``tag`` argument to specify a git tag/branch/commit to get a specific version of the library.
 
-We expect to build rapidly commonly used probes in this public repository.
 
-How to contribute
------------------
+How to contribute to the library
+--------------------------------
 
-TODO: explain with more details
+Each probe in the library is represented by a JSON file and an image.
+To contribute a new probe to the library, follow these steps:
 
-  1. Generate the JSON file with probeinterface (or directly
-      with another language)
+  1. Generate the JSON file with probeinterface (or directly with another language)
   2. Generate an image of the probe with the `plot_probe` function in probeinterface
   3. Clone the `probeinterface_library repo <https://github.com/SpikeInterface/probeinterface_library>`_
-  4. Put the JSON file and image into the correct folder or make a new folder (following the format of the repo)
+  4. Put the JSON file and image into the correct folder: ``probeinterface_library/<manufacturer>/<model_name>/```
   5. Push to one of your branches with a git client
   6. Make a pull request to the main repo

pyproject.toml

@@ -18,6 +18,7 @@ classifiers = [
 dependencies = [
     "numpy",
     "packaging",
+    "requests"
 ]
 
 [project.urls]
@@ -57,6 +58,11 @@ docs = [
     "pandas",
 ]
 
+[tool.pytest.ini_options]
+markers = [
+    "library",
+]
+
 [tool.coverage.run]
 omit = [
     "tests/*",

src/probeinterface/__init__.py

@@ -39,5 +39,13 @@
     generate_multi_columns_probe,
     generate_multi_shank,
 )
-from .library import get_probe
+from .library import (
+    get_probe,
+    list_manufacturers,
+    list_probes_by_manufacturer,
+    list_all_probes,
+    get_tags_in_library,
+    cache_full_library,
+    clear_cache,
+)
 from .wiring import get_available_pathways