diff --git a/.flake8 b/.flake8
index 994815d8870e9822617c4578efdce0e121988c60..2534a45ee555bb5ebefd37210d19399634c7a4ee 100644
--- a/.flake8
+++ b/.flake8
@@ -1,4 +1,3 @@
[flake8]
-max-line-length = 88
-select = B,C,E,F,W,T4,B9,B950
-ignore = E501, W503, E203
+max-line-length = 80
+ignore = E501,W503,E302,E402,E203
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index aca55f5bf7de1b774b9932355b11661586c55a70..1515754e0bef52e755e793e05c3400ecf532c4c7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,20 +2,20 @@
# See https://pre-commit.com/hooks.html for more hooks
repos:
- repo: https://github.com/timothycrosley/isort
- rev: 5.8.0
+ rev: 5.9.3
hooks:
- - id: isort
- args: [--sl, --line-length, "88"]
+ - id: isort
+ args: [--settings-path, "pyproject.toml"]
- repo: https://github.com/psf/black
- rev: 20.8b1
+ rev: 21.7b0
hooks:
- id: black
- repo: https://gitlab.com/pycqa/flake8
- rev: 3.9.0
+ rev: 3.9.2
hooks:
- id: flake8
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v3.4.0
+ rev: v4.0.1
hooks:
- id: check-ast
- id: check-case-conflict
@@ -23,21 +23,5 @@ repos:
- id: end-of-file-fixer
- id: debug-statements
- id: check-added-large-files
- - repo: local
- hooks:
- - id: sphinx-build
- name: sphinx build
- entry: python -m sphinx.cmd.build
- args: [-a, -E, -W, doc, sphinx]
- language: system
- files: ^doc/
- types: [file]
- pass_filenames: false
- - id: sphinx-doctest
- name: sphinx doctest
- entry: python -m sphinx.cmd.build
- args: [-a, -E, -b, doctest, doc, sphinx]
- language: system
- files: ^doc/
- types: [file]
- pass_filenames: false
+ - id: check-yaml
+ exclude: .*/meta.yaml
diff --git a/bob/bio/gmm/algorithm/GMM.py b/bob/bio/gmm/algorithm/GMM.py
index 9f39171fde81725cebd02e7f0494defef2818ce2..48db4e569e4d98b590bb0553d3da550f4b1f7d2f 100644
--- a/bob/bio/gmm/algorithm/GMM.py
+++ b/bob/bio/gmm/algorithm/GMM.py
@@ -13,8 +13,7 @@ This adds the notions of models, probes, enrollment, and scores to GMM.
import copy
import logging
-from typing import Callable
-from typing import Union
+from typing import Callable, Union
import dask.array as da
import numpy as np
@@ -23,10 +22,7 @@ from h5py import File as HDF5File
from sklearn.base import BaseEstimator
from bob.bio.base.pipelines.vanilla_biometrics import BioAlgorithm
-from bob.learn.em import GMMMachine
-from bob.learn.em import GMMStats
-from bob.learn.em import KMeansMachine
-from bob.learn.em import linear_scoring
+from bob.learn.em import GMMMachine, GMMStats, KMeansMachine, linear_scoring
logger = logging.getLogger(__name__)
@@ -153,7 +149,9 @@ class GMM(BioAlgorithm, BaseEstimator):
or feature.ndim != 2
or feature.dtype != np.float64
):
- raise ValueError(f"The given feature is not appropriate: \n{feature}")
+ raise ValueError(
+ f"The given feature is not appropriate: \n{feature}"
+ )
if self.ubm is not None and feature.shape[1] != self.ubm.shape[1]:
raise ValueError(
"The given feature is expected to have %d elements, but it has %d"
@@ -165,7 +163,11 @@ class GMM(BioAlgorithm, BaseEstimator):
# Saves the UBM to file
logger.debug("Saving model to file '%s'", ubm_file)
- hdf5 = ubm_file if isinstance(ubm_file, HDF5File) else HDF5File(ubm_file, "w")
+ hdf5 = (
+ ubm_file
+ if isinstance(ubm_file, HDF5File)
+ else HDF5File(ubm_file, "w")
+ )
self.ubm.save(hdf5)
def load_model(self, ubm_file):
@@ -199,7 +201,10 @@ class GMM(BioAlgorithm, BaseEstimator):
for feature in data:
self._check_feature(feature)
- data = np.vstack(data)
+ # if input is a list (or SampleBatch) of 2 dimensional arrays, stack them
+ if data[0].ndim == 2:
+ data = np.vstack(data)
+
# Use the array to train a GMM and return it
logger.info("Enrolling with %d feature vectors", data.shape[0])
@@ -270,7 +275,9 @@ class GMM(BioAlgorithm, BaseEstimator):
The probe data to compare to the models.
"""
- stats = self.project(probe) if not isinstance(probe, GMMStats) else probe
+ stats = (
+ self.project(probe) if not isinstance(probe, GMMStats) else probe
+ )
return self.scoring_function(
models_means=biometric_references,
ubm=self.ubm,
@@ -284,9 +291,13 @@ class GMM(BioAlgorithm, BaseEstimator):
if isinstance(array, da.Array):
array = array.persist()
- logger.debug("UBM with %d feature vectors", len(array))
+ # if input is a list (or SampleBatch) of 2 dimensional arrays, stack them
+ if array[0].ndim == 2:
+ array = np.vstack(array)
- logger.debug(f"Creating UBM machine with {self.number_of_gaussians} gaussians")
+ logger.debug(
+ f"Creating UBM machine with {self.number_of_gaussians} gaussians and {len(array)} samples"
+ )
self.ubm = GMMMachine(
n_gaussians=self.number_of_gaussians,
diff --git a/bob/bio/gmm/test/test_gmm.py b/bob/bio/gmm/test/test_gmm.py
index 2cfd519af824e6c77e5620f22edf94af67e67531..2ecde26fa8421750e82e4fbfc0728cbe7b8032b1 100644
--- a/bob/bio/gmm/test/test_gmm.py
+++ b/bob/bio/gmm/test/test_gmm.py
@@ -27,8 +27,7 @@ import bob.bio.gmm
from bob.bio.base.test import utils
from bob.bio.gmm.algorithm import GMM
-from bob.learn.em import GMMMachine
-from bob.learn.em import GMMStats
+from bob.learn.em import GMMMachine, GMMStats
logger = logging.getLogger(__name__)
@@ -44,7 +43,8 @@ def test_class():
)
assert isinstance(gmm1, GMM)
assert isinstance(
- gmm1, bob.bio.base.pipelines.vanilla_biometrics.abstract_classes.BioAlgorithm
+ gmm1,
+ bob.bio.base.pipelines.vanilla_biometrics.abstract_classes.BioAlgorithm,
)
assert gmm1.number_of_gaussians == 512
assert "bob_fit_supports_dask_array" in gmm1._get_tags()
@@ -117,7 +117,9 @@ def test_enroll():
)
# Create a GMM object with that UBM
gmm1 = GMM(
- number_of_gaussians=2, enroll_update_means=True, enroll_update_variances=True
+ number_of_gaussians=2,
+ enroll_update_means=True,
+ enroll_update_variances=True,
)
gmm1.ubm = ubm
# Enroll the biometric reference from random features
@@ -136,7 +138,9 @@ def test_enroll():
gmm2 = gmm1.read_biometric_reference(reference_file)
assert biometric_reference.is_similar_to(gmm2)
- with tempfile.NamedTemporaryFile(prefix="bob_", suffix="_bioref.hdf5") as fd:
+ with tempfile.NamedTemporaryFile(
+ prefix="bob_", suffix="_bioref.hdf5"
+ ) as fd:
temp_file = fd.name
gmm1.write_biometric_reference(biometric_reference, temp_file)
assert GMMMachine.from_hdf5(temp_file, ubm).is_similar_to(gmm2)
@@ -148,11 +152,15 @@ def test_score():
pkg_resources.resource_filename("bob.bio.gmm.test", "data/gmm_ubm.hdf5")
)
biometric_reference = GMMMachine.from_hdf5(
- pkg_resources.resource_filename("bob.bio.gmm.test", "data/gmm_enrolled.hdf5"),
+ pkg_resources.resource_filename(
+ "bob.bio.gmm.test", "data/gmm_enrolled.hdf5"
+ ),
ubm=gmm1.ubm,
)
probe = GMMStats.from_hdf5(
- pkg_resources.resource_filename("bob.bio.gmm.test", "data/gmm_projected.hdf5")
+ pkg_resources.resource_filename(
+ "bob.bio.gmm.test", "data/gmm_projected.hdf5"
+ )
)
probe_data = utils.random_array((20, 45), -5.0, 5.0, seed=seed_value)
diff --git a/doc/conf.py b/doc/conf.py
index 69b0f39e0d584df62d92e3ba8b9109f80c65c649..3c6efbb79fd86d617adc600058b61a150c6d7f86 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -8,8 +8,7 @@ import pkg_resources
import sphinx_rtd_theme
# For inter-documentation mapping:
-from bob.extension.utils import link_documentation
-from bob.extension.utils import load_requirements
+from bob.extension.utils import link_documentation, load_requirements
# -- General configuration -----------------------------------------------------
@@ -130,9 +129,7 @@ pygments_style = "sphinx"
# Some variables which are useful for generated material
project_variable = project.replace(".", "_")
-short_description = (
- u"Tools for running biometric recognition experiments using GMM-based approximation"
-)
+short_description = u"Tools for running biometric recognition experiments using GMM-based approximation"
owner = [u"Idiap Research Institute"]
diff --git a/pyproject.toml b/pyproject.toml
index bb5e83cb40b5871b321beb790ae14606b010e4ca..b738dc847ff9705c5769673db7415f2eb9a75f4d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,12 @@
[build-system]
-requires = ["setuptools", "wheel", "bob.extension"]
-build-backend = "setuptools.build_meta"
+ requires = ["setuptools", "wheel", "bob.extension"]
+ build-backend = "setuptools.build_meta"
+
+[tool.isort]
+ profile = "black"
+ line_length = 80
+ order_by_type = true
+ lines_between_types = 1
+
+[tool.black]
+ line-length = 80
diff --git a/setup.py b/setup.py
index 6ee603a6989b1463384e67afc0e5042afef54ef9..9b28560365ce8a4c1480f4e9542e0088f186f3cc 100644
--- a/setup.py
+++ b/setup.py
@@ -33,11 +33,9 @@
# allows you to test your package with new python dependencies w/o requiring
# administrative interventions.
-from setuptools import dist
-from setuptools import setup
+from setuptools import dist, setup
-from bob.extension.utils import find_packages
-from bob.extension.utils import load_requirements
+from bob.extension.utils import find_packages, load_requirements
dist.Distribution(dict(setup_requires=["bob.extension"]))