[MRG] Semi-relaxed (fused) gromov-wasserstein divergence and improvements of gromov-wasserstein solvers (#431)

* maj gw/ srgw/ generic cg solver

* correct pep8 on current state

* fix bug previous tests

* fix pep8

* fix bug srGW constC in loss and gradient

* fix doc html

* fix doc html

* start updating test_optim.py

* update tests gromov and optim - plus fix gromov dependencies

* add symmetry feature to entropic gw

* add symmetry feature to entropic gw

* add exemple for sr(F)GW matchings

* small stuff

* remove (reg,M) from line-search/ complete srgw tests with backend

* remove backend repetitions / rename fG to costG/ fix innerlog to True

* fix pep8

* take comments into account / new nx parameters still to test

* factor (f)gw2 + test new backend parameters in ot.gromov + harmonize stopping criterions

* split gromov.py in ot/gromov/ + update test_gromov with helper_backend functions

* manual documentaion gromov

* remove circular autosummary

* trying stuff

* debug documentation

* alphabetic ordering of module

* merge into branch

* add note in entropic gw solvers

---------

Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>

4 files changed, 24 insertions, 16 deletions

diff --git a/docs/cache_nbrun b/docs/cache_nbrun
deleted file mode 100644
index ac49515..0000000
--- a/docs/cache_nbrun
+++ /dev/null
@@ -1 +0,0 @@
-{"plot_otda_color_images.ipynb": "128d0435c08ebcf788913e4adcd7dd00", "plot_partial_wass_and_gromov.ipynb": "82242f8390df1d04806b333b745c72cf", "plot_WDA.ipynb": "27f8de4c6d7db46497076523673eedfb", "plot_screenkhorn_1D.ipynb": "af7b8a74a1be0f16f2c3908f5a178de0", "plot_otda_laplacian.ipynb": "d92cc0e528b9277f550daaa6f9d18415", "plot_OT_L1_vs_L2.ipynb": "288230c4e679d752a511353c96c134cb", "plot_otda_semi_supervised.ipynb": "568b39ffbdf6621dd6de162df42f4f21", "plot_fgw.ipynb": "f4de8e6939ce2b1339b3badc1fef0f37", "plot_otda_d2.ipynb": "07ef3212ff3123f16c32a5670e0167f8", "plot_compute_emd.ipynb": "299f6fffcdbf48b7c3268c0136e284f8", "plot_barycenter_fgw.ipynb": "9e813d3b07b7c0c0fcc35a778ca1243f", "plot_convolutional_barycenter.ipynb": "fdd259bfcd6d5fe8001efb4345795d2f", "plot_optim_OTreg.ipynb": "bddd8e49f092873d8980d41ae4974e19", "plot_UOT_1D.ipynb": "2658d5164165941b07539dae3cb80a0f", "plot_OT_1D_smooth.ipynb": "f3e1f0e362c9a78071a40c02b85d2305", "plot_barycenter_1D.ipynb": "f6fa5bc13d9811f09792f73b4de70aa0", "plot_otda_mapping.ipynb": "1bb321763f670fc945d77cfc91471e5e", "plot_OT_1D.ipynb": "0346a8c862606d11f36d0aa087ecab0d", "plot_gromov_barycenter.ipynb": "a7999fcc236d90a0adeb8da2c6370db3", "plot_UOT_barycenter_1D.ipynb": "dd9b857a8c66d71d0124d4a2c30a51dd", "plot_otda_mapping_colors_images.ipynb": "16faae80d6ea8b37d6b1f702149a10de", "plot_stochastic.ipynb": "64f23a8dcbab9823ae92f0fd6c3aceab", "plot_otda_linear_mapping.ipynb": "82417d9141e310bf1f2c2ecdb550094b", "plot_otda_classes.ipynb": "8836a924c9b562ef397af12034fa1abb", "plot_free_support_barycenter.ipynb": "be9d0823f9d7774a289311b9f14548eb", "plot_gromov.ipynb": "de06b1dbe8de99abae51c2e0b64b485d", "plot_otda_jcpot.ipynb": "65482cbfef5c6c1e5e73998aeb5f4b10", "plot_OT_2D_samples.ipynb": "9a9496792fa4216b1059fc70abca851a", "plot_barycenter_lp_vs_entropic.ipynb": "334840b69a86898813e50a6db0f3d0de"}
\ No newline at end of file
diff --git a/docs/source/_templates/module.rst b/docs/source/_templates/module.rst
index 5ad89be..495995e 100644
--- a/docs/source/_templates/module.rst
+++ b/docs/source/_templates/module.rst
@@ -2,6 +2,7 @@
 {{ underline }}
 
 .. automodule:: {{ fullname }}
+   :members:
 
    {% block functions %}
    {% if functions %}
@@ -12,6 +13,7 @@
    {% for item in functions %}
 
    .. autofunction:: {{ item }}
+      
 
    .. include:: backreferences/{{fullname}}.{{item}}.examples
 
diff --git a/docs/source/all.rst b/docs/source/all.rst
index 60cc85c..41d8e06 100644
--- a/docs/source/all.rst
+++ b/docs/source/all.rst
@@ -13,29 +13,33 @@ API and modules
    :toctree: gen_modules/
    :template: module.rst
 
-   lp
+   
    backend
    bregman
-   smooth
-   gromov
-   optim
    da
-   dr
-   utils
    datasets
+   dr
+   factored
+   gaussian
+   gromov
+   lp
+   optim
+   partial
    plot
-   stochastic
-   unbalanced
    regpath
-   partial
    sliced
+   smooth
+   stochastic
+   unbalanced
+   utils
    weak
-   factored
-   gaussian
+   
 
-.. autosummary::
-   :toctree: ../modules/generated/
-   :template: module.rst
+Main :py:mod:`ot` functions
+--------------
 
 .. automodule:: ot
    :members:
+
+
+
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 3bec150..6e76291 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -119,7 +119,7 @@ release = __version__
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -341,6 +341,9 @@ texinfo_documents = [
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
 
+autodoc_default_options = {'autosummary': True,
+                           'autosummary_imported_members': True}
+
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {'python': ('https://docs.python.org/3', None),