Merge branch 'main' into icarosadero-patch-1

Author: MMathisLab

.pre-commit-config.yaml

@@ -20,3 +20,7 @@ repos:
       - id: isort
         additional_dependencies:
           - pyproject.toml
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.280
+    hooks:
+      - id: ruff

cebra/datasets/monkey_reaching.py

@@ -77,8 +77,12 @@ def _load_data(
             "Could not import the nlb_tools package required for data loading "
             "the raw reaching datasets in NWB format. "
             "If required, you can install the dataset by running "
-            "pip install nlb_tools or installing cebra with the [datasets] "
-            "dependencies: pip install 'cebra[datasets]'")
+            "pip install nlb_tools."
+            # NOTE(stes): Install nlb_tools manually for now, also see
+            # note in setup.cfg
+            # or installing cebra with the [datasets] "
+            #"dependencies: pip install 'cebra[datasets]'")
+        )
 
     def _get_info(trial_info, data):
         passive = []

cebra/integrations/plotly.py

@@ -45,7 +45,7 @@ def _convert_cmap2colorscale(cmap: str, pl_entries: int = 11, rdigits: int = 2):
     """
     scale = np.linspace(0, 1, pl_entries)
     colors = (cmap(scale)[:, :3] * 255).astype(np.uint8)
-    pl_colorscale = [[round(s, rdigits), f"rgb{tuple(color)}"]
+    pl_colorscale = [[float(round(s, rdigits)), f"rgb{tuple(color.tolist())}"]
                      for s, color in zip(scale, colors)]
     return pl_colorscale
 

docs/source/conf.py

@@ -104,7 +104,7 @@ def get_years(start_year=2021):
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
-    "torch": ("https://pytorch.org/docs/master/", None),
+    "torch": ("https://pytorch.org/docs/stable/", None),
     "sklearn": ("https://scikit-learn.org/stable", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),

pyproject.toml

@@ -527,3 +527,56 @@ overgeneral-exceptions=[
     'Exception',
     'BaseException',
 ]
+
+[tool.ruff]
+# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
+select = ["E", "F"]
+ignore = []
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "EM", "ERA", "EXE", "FBT", "ICN", "INP", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PTH", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "TRY", "UP", "YTT"]
+unfixable = []
+
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+]
+
+# Same as Black.
+line-length = 160
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+# Assume Python 3.10.
+target-version = "py310"
+
+ignore-init-module-imports = true
+
+[tool.ruff.mccabe]
+# Unlike Flake8, default to a complexity level of 10.
+max-complexity = 10
+
+[tool.ruff.per-file-ignores]
+# ignore import issues in __init__ files
+"__init__.py" = ["E402", "F403", "F405", "F401"]

setup.cfg

@@ -31,6 +31,7 @@ where =
 python_requires = >=3.9
 install_requires =
     joblib
+    numpy<2.0.0
     literate-dataclasses
     scikit-learn
     scipy
@@ -44,7 +45,13 @@ datasets =
     # cebra.datasets.allen
     h5py
     pandas
-    nlb_tools
+    # NOTE(stes): nlb_tools currently pins pandas to <1.3.4, see here:
+    # https://github.com/neurallatents/nlb_tools/blob/1ddc15f45b56388ff093d1396b7b87b36fa32a68/requirements.txt#L1
+    # Since this is a fairly old pandas version, it causes additional version
+    # conflicts with other packages. Removing nlb_tools as a required dependency for now.
+    # The only part this package is needed is in cebra/datasets/monkey_reaching.py, where
+    # we added a warning message to tell the user how to manually install it.
+    #nlb_tools
     # additional data loading dependencies
     hdf5storage # for creating .mat files in new format
     openpyxl # for excel file format loading