Clean references in documentation (#722)

* clean references in documentation

* apply ruff-format change

Author: qbarthelemy

RELEASES.md

@@ -20,6 +20,7 @@
 - Add version number to the documentation (PR #696)
 - Update doc for default regularization in `ot.unbalanced` sinkhorn solvers (Issue #691, PR #700)
 - Clean documentation for `gromov`, `lp` and `unbalanced` folders (PR #710)
+- Clean references in documentation (PR #722)
 
 ## 0.9.5
 

ot/bregman/_barycenter.py

@@ -336,6 +336,7 @@ def free_support_sinkhorn_barycenter(
     ot.bregman.sinkhorn : Entropic regularized OT solver
     ot.lp.free_support_barycenter : Barycenter solver based on Linear Programming
 
+
     .. _references-free-support-barycenter:
     References
     ----------

ot/bregman/_sinkhorn.py

@@ -129,10 +129,10 @@ def sinkhorn(
     array([[0.36552929, 0.13447071],
            [0.13447071, 0.36552929]])
 
+
     .. _references-sinkhorn:
     References
     ----------
-
     .. [2] M. Cuturi, Sinkhorn Distances : Lightspeed Computation
         of Optimal Transport, Advances in Neural Information Processing
         Systems (NIPS) 26, 2013
@@ -1460,6 +1460,7 @@ def sinkhorn_epsilon_scaling(
     array([[0.36552929, 0.13447071],
            [0.13447071, 0.36552929]])
 
+
     .. _references-sinkhorn-epsilon-scaling:
     References
     ----------

ot/da.py

@@ -132,13 +132,13 @@ def sinkhorn_lpl1_mm(
     References
     ----------
     .. [5] N. Courty; R. Flamary; D. Tuia; A. Rakotomamonjy,
-       "Optimal Transport for Domain Adaptation," in IEEE
-       Transactions on Pattern Analysis and Machine Intelligence ,
-       vol.PP, no.99, pp.1-1
+        "Optimal Transport for Domain Adaptation," in IEEE
+        Transactions on Pattern Analysis and Machine Intelligence ,
+        vol.PP, no.99, pp.1-1
 
     .. [7] Rakotomamonjy, A., Flamary, R., & Courty, N. (2015).
-       Generalized conditional gradient: analysis of convergence
-       and applications. arXiv preprint arXiv:1510.06567.
+        Generalized conditional gradient: analysis of convergence
+        and applications. arXiv preprint arXiv:1510.06567.
 
     See Also
     --------
@@ -276,12 +276,12 @@ def sinkhorn_l1l2_gl(
     References
     ----------
     .. [5] N. Courty; R. Flamary; D. Tuia; A. Rakotomamonjy,
-       "Optimal Transport for Domain Adaptation," in IEEE Transactions
-       on Pattern Analysis and Machine Intelligence , vol.PP, no.99, pp.1-1
+        "Optimal Transport for Domain Adaptation," in IEEE Transactions
+        on Pattern Analysis and Machine Intelligence , vol.PP, no.99, pp.1-1
 
     .. [7] Rakotomamonjy, A., Flamary, R., & Courty, N. (2015).
-       Generalized conditional gradient: analysis of convergence and
-       applications. arXiv preprint arXiv:1510.06567.
+        Generalized conditional gradient: analysis of convergence and
+        applications. arXiv preprint arXiv:1510.06567.
 
     See Also
     --------
@@ -423,9 +423,9 @@ def emd_laplace(
     References
     ----------
     .. [5] N. Courty; R. Flamary; D. Tuia; A. Rakotomamonjy,
-       "Optimal Transport for Domain Adaptation," in IEEE
-       Transactions on Pattern Analysis and Machine Intelligence,
-       vol.PP, no.99, pp.1-1
+        "Optimal Transport for Domain Adaptation," in IEEE
+        Transactions on Pattern Analysis and Machine Intelligence,
+        vol.PP, no.99, pp.1-1
 
     .. [30] R. Flamary, N. Courty, D. Tuia, A. Rakotomamonjy,
         "Optimal transport with Laplacian regularization: Applications to domain adaptation and shape matching,"
@@ -743,8 +743,8 @@ def transform_labels(self, ys=None):
         References
         ----------
         .. [27] Ievgen Redko, Nicolas Courty, Rémi Flamary, Devis Tuia
-           "Optimal transport for multi-source domain adaptation under target shift",
-           International Conference on Artificial Intelligence and Statistics (AISTATS), 2019.
+            "Optimal transport for multi-source domain adaptation under target shift",
+            International Conference on Artificial Intelligence and Statistics (AISTATS), 2019.
 
         """
         nx = self.nx
@@ -1073,8 +1073,8 @@ class LinearGWTransport(LinearTransport):
     References
     ----------
     .. [57] Delon, J., Desolneux, A., & Salmona, A. (2022). Gromov–Wasserstein
-            distances between Gaussian distributions. Journal of Applied Probability,
-            59(4), 1178-1198.
+        distances between Gaussian distributions. Journal of Applied Probability,
+        59(4), 1178-1198.
 
     """
 
@@ -1580,17 +1580,17 @@ class SinkhornLpl1Transport(BaseTransport):
     References
     ----------
     .. [1] N. Courty; R. Flamary; D. Tuia; A. Rakotomamonjy,
-       "Optimal Transport for Domain Adaptation," in IEEE
-       Transactions on Pattern Analysis and Machine Intelligence ,
-       vol.PP, no.99, pp.1-1
+        "Optimal Transport for Domain Adaptation," in IEEE
+        Transactions on Pattern Analysis and Machine Intelligence ,
+        vol.PP, no.99, pp.1-1
 
     .. [2] Rakotomamonjy, A., Flamary, R., & Courty, N. (2015).
-       Generalized conditional gradient: analysis of convergence
-       and applications. arXiv preprint arXiv:1510.06567.
+        Generalized conditional gradient: analysis of convergence
+        and applications. arXiv preprint arXiv:1510.06567.
 
     .. [6] Ferradans, S., Papadakis, N., Peyré, G., & Aujol, J. F. (2014).
-            Regularized discrete optimal transport. SIAM Journal on Imaging
-            Sciences, 7(3), 1853-1882.
+        Regularized discrete optimal transport. SIAM Journal on Imaging
+        Sciences, 7(3), 1853-1882.
     """
 
     def __init__(
@@ -1724,8 +1724,8 @@ class EMDLaplaceTransport(BaseTransport):
     References
     ----------
     .. [1] N. Courty; R. Flamary; D. Tuia; A. Rakotomamonjy,
-           "Optimal Transport for Domain Adaptation," in IEEE Transactions
-           on Pattern Analysis and Machine Intelligence , vol.PP, no.99, pp.1-1
+        "Optimal Transport for Domain Adaptation," in IEEE Transactions
+        on Pattern Analysis and Machine Intelligence , vol.PP, no.99, pp.1-1
 
     .. [2] R. Flamary, N. Courty, D. Tuia, A. Rakotomamonjy,
         "Optimal transport with Laplacian regularization: Applications to domain adaptation and shape matching,"
@@ -1873,13 +1873,13 @@ class SinkhornL1l2Transport(BaseTransport):
     References
     ----------
     .. [1] N. Courty; R. Flamary; D. Tuia; A. Rakotomamonjy,
-       "Optimal Transport for Domain Adaptation," in IEEE
-       Transactions on Pattern Analysis and Machine Intelligence ,
-       vol.PP, no.99, pp.1-1
+        "Optimal Transport for Domain Adaptation," in IEEE
+        Transactions on Pattern Analysis and Machine Intelligence ,
+        vol.PP, no.99, pp.1-1
 
     .. [2] Rakotomamonjy, A., Flamary, R., & Courty, N. (2015).
-       Generalized conditional gradient: analysis of convergence
-       and applications. arXiv preprint arXiv:1510.06567.
+        Generalized conditional gradient: analysis of convergence
+        and applications. arXiv preprint arXiv:1510.06567.
 
     .. [6] Ferradans, S., Papadakis, N., Peyré, G., & Aujol, J. F. (2014).
             Regularized discrete optimal transport. SIAM Journal on Imaging
@@ -2352,14 +2352,13 @@ class JCPOTTransport(BaseTransport):
     References
     ----------
     .. [1] Ievgen Redko, Nicolas Courty, Rémi Flamary, Devis Tuia
-       "Optimal transport for multi-source domain adaptation under target shift",
-       International Conference on Artificial Intelligence and Statistics (AISTATS),
-       vol. 89, p.849-858, 2019.
+        "Optimal transport for multi-source domain adaptation under target shift",
+        International Conference on Artificial Intelligence and Statistics (AISTATS),
+        vol. 89, p.849-858, 2019.
 
     .. [6] Ferradans, S., Papadakis, N., Peyré, G., & Aujol, J. F. (2014).
-            Regularized discrete optimal transport. SIAM Journal on Imaging
-            Sciences, 7(3), 1853-1882.
-
+        Regularized discrete optimal transport. SIAM Journal on Imaging
+        Sciences, 7(3), 1853-1882.
 
     """
 
@@ -2524,8 +2523,8 @@ def transform_labels(self, ys=None):
         References
         ----------
         .. [27] Ievgen Redko, Nicolas Courty, Rémi Flamary, Devis Tuia
-           "Optimal transport for multi-source domain adaptation under target shift",
-           International Conference on Artificial Intelligence and Statistics (AISTATS), 2019.
+            "Optimal transport for multi-source domain adaptation under target shift",
+            International Conference on Artificial Intelligence and Statistics (AISTATS), 2019.
         """
         nx = self.nx
 

ot/dr.py

@@ -208,7 +208,7 @@ def wda(
     References
     ----------
     .. [11] Flamary, R., Cuturi, M., Courty, N., & Rakotomamonjy, A. (2016).
-            Wasserstein Discriminant Analysis. arXiv preprint arXiv:1608.08063.
+        Wasserstein Discriminant Analysis. arXiv preprint arXiv:1608.08063.
     """  # noqa
 
     if sinkhorn_method.lower() == "sinkhorn":
@@ -348,8 +348,8 @@ def projection_robust_wasserstein(
     References
     ----------
     .. [32] Huang, M. , Ma S. & Lai L. (2021).
-            A Riemannian Block Coordinate Descent Method for Computing
-            the Projection Robust Wasserstein Distance, ICML.
+        A Riemannian Block Coordinate Descent Method for Computing
+        the Projection Robust Wasserstein Distance, ICML.
     """  # noqa
 
     # initialization
@@ -489,7 +489,7 @@ def ewca(
     References
     ----------
     .. [52] Collas, A., Vayer, T., Flamary, F., & Breloy, A. (2023).
-            Entropic Wasserstein Component Analysis.
+        Entropic Wasserstein Component Analysis.
     """  # noqa
     n, d = X.shape
     X = X - X.mean(0)

ot/gromov/_gw.py

@@ -911,7 +911,6 @@ def solve_gromov_linesearch(
 
 
     .. _references-solve-linesearch:
-
     References
     ----------
     .. [24] Vayer Titouan, Chapel Laetitia, Flamary Rémi, Tavenard Romain and Courty Nicolas
@@ -1293,6 +1292,7 @@ def fgw_barycenters(
         - :math:`(\mathbf{M}_s)_s`: all distance matrices between the feature of the barycenter and the other features :math:`(dist(\mathbf{X}, \mathbf{Y}_s))_s` shape (`N`, `ns`)
         - values used in convergence evaluation.
 
+
     .. _references-fgw-barycenters:
     References
     ----------

ot/gromov/_partial.py

@@ -611,6 +611,7 @@ def partial_fused_gromov_wasserstein(
     log : dict
         Convergence information and loss.
 
+
     .. _references-partial-gromov-wasserstein:
     References
     ----------
@@ -907,6 +908,7 @@ def partial_fused_gromov_wasserstein2(
     log : dict
         log dictionary returned only if `log` is `True`
 
+
     .. _references-partial-gromov-wasserstein2:
     References
     ----------

ot/gromov/_semirelaxed.py

@@ -474,12 +474,12 @@ def semirelaxed_fused_gromov_wasserstein(
         (ICML). 2019.
 
     .. [48] Cédric Vincent-Cuaz, Rémi Flamary, Marco Corneli, Titouan Vayer, Nicolas Courty.
-            "Semi-relaxed Gromov-Wasserstein divergence and applications on graphs"
-            International Conference on Learning Representations (ICLR), 2022.
+        "Semi-relaxed Gromov-Wasserstein divergence and applications on graphs"
+        International Conference on Learning Representations (ICLR), 2022.
 
     .. [62] H. Van Assel, C. Vincent-Cuaz, T. Vayer, R. Flamary, N. Courty.
-            "Interpolating between Clustering and Dimensionality Reduction with
-            Gromov-Wasserstein". NeurIPS 2023 Workshop OTML.
+        "Interpolating between Clustering and Dimensionality Reduction with
+        Gromov-Wasserstein". NeurIPS 2023 Workshop OTML.
     """
     arr = [M, C1, C2]
     if p is not None:
@@ -688,12 +688,12 @@ def semirelaxed_fused_gromov_wasserstein2(
         (ICML). 2019.
 
     .. [48] Cédric Vincent-Cuaz, Rémi Flamary, Marco Corneli, Titouan Vayer, Nicolas Courty.
-            "Semi-relaxed Gromov-Wasserstein divergence and applications on graphs"
-            International Conference on Learning Representations (ICLR), 2022.
+        "Semi-relaxed Gromov-Wasserstein divergence and applications on graphs"
+        International Conference on Learning Representations (ICLR), 2022.
 
     .. [62] H. Van Assel, C. Vincent-Cuaz, T. Vayer, R. Flamary, N. Courty.
-            "Interpolating between Clustering and Dimensionality Reduction with
-            Gromov-Wasserstein". NeurIPS 2023 Workshop OTML.
+        "Interpolating between Clustering and Dimensionality Reduction with
+        Gromov-Wasserstein". NeurIPS 2023 Workshop OTML.
     """
     # partial get_backend as the full one will be handled in gromov_wasserstein
     nx = get_backend(C1, C2)
@@ -1244,8 +1244,8 @@ def entropic_semirelaxed_fused_gromov_wasserstein(
     References
     ----------
     .. [48] Cédric Vincent-Cuaz, Rémi Flamary, Marco Corneli, Titouan Vayer, Nicolas Courty.
-            "Semi-relaxed Gromov-Wasserstein divergence and applications on graphs"
-            International Conference on Learning Representations (ICLR), 2022.
+        "Semi-relaxed Gromov-Wasserstein divergence and applications on graphs"
+        International Conference on Learning Representations (ICLR), 2022.
     """
     arr = [M, C1, C2]
     if p is not None:
@@ -1437,8 +1437,8 @@ def entropic_semirelaxed_fused_gromov_wasserstein2(
     References
     ----------
     .. [48] Cédric Vincent-Cuaz, Rémi Flamary, Marco Corneli, Titouan Vayer, Nicolas Courty.
-            "Semi-relaxed Gromov-Wasserstein divergence and applications on graphs"
-            International Conference on Learning Representations (ICLR), 2022.
+        "Semi-relaxed Gromov-Wasserstein divergence and applications on graphs"
+        International Conference on Learning Representations (ICLR), 2022.
     """
     T, log_srfgw = entropic_semirelaxed_fused_gromov_wasserstein(
         M,

ot/gromov/_utils.py

@@ -428,9 +428,9 @@ def init_matrix_semirelaxed(C1, C2, p, loss_fun="square_loss", nx=None):
         "Gromov-Wasserstein averaging of kernel and distance matrices."
         International Conference on Machine Learning (ICML). 2016.
 
-    .. [48]  Cédric Vincent-Cuaz, Rémi Flamary, Marco Corneli, Titouan Vayer, Nicolas Courty.
-            "Semi-relaxed Gromov-Wasserstein divergence and applications on graphs"
-            International Conference on Learning Representations (ICLR), 2022.
+    .. [48] Cédric Vincent-Cuaz, Rémi Flamary, Marco Corneli, Titouan Vayer, Nicolas Courty.
+        "Semi-relaxed Gromov-Wasserstein divergence and applications on graphs"
+        International Conference on Learning Representations (ICLR), 2022.
     """
     if nx is None:
         C1, C2, p = list_to_array(C1, C2, p)

ot/lp/_barycenter_solvers.py

@@ -227,12 +227,13 @@ def free_support_barycenter(
 
 
     .. _references-free-support-barycenter:
-
     References
     ----------
-    .. [20] Cuturi, Marco, and Arnaud Doucet. "Fast computation of Wasserstein barycenters." International Conference on Machine Learning. 2014.
+    .. [20] Cuturi, Marco, and Arnaud Doucet. "Fast computation of Wasserstein barycenters."
+        International Conference on Machine Learning. 2014.
 
-    .. [43] Álvarez-Esteban, Pedro C., et al. "A fixed-point approach to barycenters in Wasserstein space." Journal of Mathematical Analysis and Applications 441.2 (2016): 744-762.
+    .. [43] Álvarez-Esteban, Pedro C., et al. "A fixed-point approach to barycenters in Wasserstein space."
+        Journal of Mathematical Analysis and Applications 441.2 (2016): 744-762.
 
     """
 
@@ -369,9 +370,12 @@ def generalized_free_support_barycenter(
     .. _references-generalized-free-support-barycenter:
     References
     ----------
-    .. [20] Cuturi, M. and Doucet, A.. "Fast computation of Wasserstein barycenters." International Conference on Machine Learning. 2014.
+    .. [20] Cuturi, M. and Doucet, A.. "Fast computation of Wasserstein barycenters."
+        International Conference on Machine Learning. 2014.
 
-    .. [42] Delon, J., Gozlan, N., and Saint-Dizier, A.. Generalized Wasserstein barycenters between probability measures living on different subspaces. arXiv preprint arXiv:2105.09755, 2021.
+    .. [42] Delon, J., Gozlan, N., and Saint-Dizier, A.. Generalized Wasserstein barycenters
+        between probability measures living on different subspaces.
+        arXiv preprint arXiv:2105.09755, 2021.
 
     """
     nx = get_backend(*X_list, *a_list, *P_list)

ot/mapping.py

@@ -743,8 +743,8 @@ def joint_OT_mapping_kernel(
     References
     ----------
     .. [8] M. Perrot, N. Courty, R. Flamary, A. Habrard,
-       "Mapping estimation for discrete optimal transport",
-       Neural Information Processing Systems (NIPS), 2016.
+        "Mapping estimation for discrete optimal transport",
+        Neural Information Processing Systems (NIPS), 2016.
 
     See Also
     --------