Merge pull request #16 from mancusolab/develop

The most updated version SuSiE PCA

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^(docs/conf.py|tests/testdata/.*)'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.4.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -17,26 +17,20 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
-- repo: https://github.com/pycqa/isort
-  rev: 5.10.1
-  hooks:
-  - id: isort
-
 - repo: https://github.com/psf/black
-  rev: 21.11b1
+  rev: 23.3.0
   hooks:
   - id: black
     language_version: python3
     additional_dependencies: ['click==8.0.4']
 
-- repo: https://github.com/PyCQA/flake8
-  rev: 4.0.1
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: 'v0.0.277'
   hooks:
-  - id: flake8
-  ## You can add flake8 plugins via `additional_dependencies`:
-  #  additional_dependencies: [flake8-bugbear]
+    - id: ruff
+      args: [--fix]
 
-- repo: https://github.com/pre-commit/mirrors-mypy
-  rev: 'v0.971'  # Use the sha / tag you want to point at
-  hooks:
-  - id: mypy
+#- repo: https://github.com/pre-commit/mirrors-mypy
+#  rev: 'v1.4.1'  # Use the sha / tag you want to point at
+#  hooks:
+#  - id: mypy

docs/conf.py

@@ -8,9 +8,9 @@
 # serve to show the default.
 
 import os
-import shutil
 import sys
 
+
 # -- Path setup --------------------------------------------------------------
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -132,9 +132,14 @@
 ]
 
 object_description_options = [
-    ("py.*", dict(include_in_toc=False,
-                  include_fields_in_toc=False,
-                  wrap_signatures_with_css=True)),
+    (
+        "py.*",
+        dict(
+            include_in_toc=False,
+            include_fields_in_toc=False,
+            wrap_signatures_with_css=True,
+        ),
+    ),
     ("py.class", dict(include_in_toc=True)),
     ("py.function", dict(include_in_toc=True)),
 ]
@@ -278,22 +283,28 @@
 
 # -- Post process ------------------------------------------------------------
 import collections
+
+
 def remove_namedtuple_attrib_docstring(app, what, name, obj, skip, options):
     if type(obj) is collections._tuplegetter:
         return True
     return skip
 
-def autodoc_process_signature(app, what, name, obj, options, signature, return_annotation):
+
+def autodoc_process_signature(
+    app, what, name, obj, options, signature, return_annotation
+):
     signature = modify_type_hints(signature)
     return_annotation = modify_type_hints(return_annotation)
     return signature, return_annotation
 
+
 def modify_type_hints(signature):
     if signature:
         signature = signature.replace("jnp", "~jax.numpy")
     return signature
 
 
 def setup(app):
-    app.connect('autodoc-skip-member', remove_namedtuple_attrib_docstring)
+    app.connect("autodoc-skip-member", remove_namedtuple_attrib_docstring)
     app.connect("autodoc-process-signature", autodoc_process_signature)

examples/spca_simulation.py

@@ -2,18 +2,19 @@
 # -*- coding: utf-8 -*-
 import argparse as ap
 import sys
+
 from csv import writer
 from time import time
 
 import numpy as np
 import procrustes
+
 from sklearn.decomposition import SparsePCA
 
 import susiepca
 
 
 def mySparsePCA(X, n_components, seed):
-
     spca = SparsePCA(n_components=n_components, random_state=seed)
     spca_z = spca.fit_transform(X)
     spca_weights = spca.components_

examples/susie_pca_simulation.py

@@ -2,11 +2,13 @@
 # -*- coding: utf-8 -*-
 import argparse as ap
 import sys
+
 from csv import writer
 from time import time
 
 import numpy as np
 import procrustes
+
 from jax.config import config
 
 import susiepca as sp

ruff.toml

@@ -0,0 +1,17 @@
+line-length = 120
+select = ["E", "F", "I001"]
+ignore = ["E402", "E721", "E731", "E741", "F722", "F811"]
+ignore-init-module-imports = true
+
+[isort]
+combine-as-imports = true
+lines-after-imports = 2
+lines-between-types = 1
+known-local-folder = ["src"]
+known-first-party = ["susiepca"]
+section-order = ["future", "standard-library", "third-party", "jax-ecosystem", "first-party", "local-folder"]
+extra-standard-library = ["typing_extensions"]
+order-by-type = false
+
+[isort.sections]
+jax-ecosystem = ["equinox", "jax", "jaxtyping", "lineax", "optax"]

setup.cfg

@@ -81,18 +81,6 @@ testpaths = tests
 no_vcs = 1
 formats = bdist_wheel
 
-[flake8]
-# Some sane defaults for the code style checker flake8
-max_line_length = 88
-extend_ignore = E203, W503
-# ^  Black-compatible
-#    E203 and W503 have edge cases handled by black
-exclude =
-    .tox
-    build
-    dist
-    .eggs
-    docs/conf.py
 
 [pyscaffold]
 # PyScaffold's parameters when the project was created.

setup.py

@@ -8,6 +8,7 @@
 """
 from setuptools import setup
 
+
 if __name__ == "__main__":
     try:
         setup(use_scm_version={"version_scheme": "no-guess-dev"})

susiepca/__init__.py

@@ -1,5 +1,6 @@
 from importlib.metadata import PackageNotFoundError, version  # pragma: no cover
 
+
 # flat api; unfortunate but can work with autodoc
 """
 from infer import *
@@ -9,9 +10,10 @@
 from utils import *
 from io import *
 """
-from susiepca import infer, io, metrics, sim, utils
+from susiepca import infer, infer_design_matrix, io, metrics, sim, utils
+
 
-__all__ = ["infer", "metrics", "sim", "utils", "io"]
+__all__ = ["common", "infer", "infer_design_matrix", "metrics", "sim", "utils", "io"]
 
 try:
     # Change here if project is renamed and does not equal the package name