Fix another rtd bug (#453)

* Fix yet another RTD bug causing code-blocks to disappear from html * Add requirement for newer version of Sphinx * Add requirement on ipython * Use python3.6 with rtd-build * Add extension for ipython-highlighting * Revert back to python3.5 on rtd-build * Modify mocked modules * Modify mocked modules list * Modify mocked modules list * Modify mocked modules list * Modify rtd conf.py * Bump python version in .readthedocs.yml * Fix RTD * Fixing rtd * Test whether mocking ordering has an effect * Test if the problem is sklearn.covariance * Test if the problem is sklearn.utils * modify mocked modules * modify mocked modules * remove sklearn.utils._testing.ignore_warnings * remove sklearn.utils._testing.ignore_warnings * Mock abc * Compile rtd with py38 * Remove unnecessary mocks * Experiment with mocks * Experiment with mocks * Experiment with mocks * Test mock instead of magicmock * Remove IPython.sphinxext.ipython_console_highlighting * Add extension sphinxext.ipython_console_highlighting * Require ipython!=8.7.0 * Test ipython3 -> python * Modify .readthedocs.yml * Modify quickstart.rst code-blocks * Pin ipython-version in requirements.txt * Fix a typo * Modify requirements-dev * Test code-block instead of code for indicating code blocks * Revert to old package-versions * Add nbsphinx into requirements * Pin docutils version * Pin docutils version * Pin pillow==5.4.1 * unpin package versions * Add nbsphinx in requirements * Require newer Sphinx * Update packages * Update packages * Update packages * Pin more versions * Remove ipython sphinx extension * Add more mocked packages * Test code vs code-block logic * Test code vs code-block logic * Test code vs code-block logic * Test code vs code-block logic * Change requirements.txt * Hail mary * Add pandoc in requirements * Modify quickstart.rst * Bring back old requirements.txt * Return to original * Add docs/requirements.txt file * Change all .. code:: to .. code-block:: * Remove quickstart.rst * Revert back to old format * Remove mocking of elfi * Remove mocking of elfi * Pin packages for docs * Remove pygments_style in conf.py * add autodoc-setup to conf.py * Hail mary v0.2 * Discard nbsphinx * remove import elfi from docs * remove import elfi from docs * Use python36 * modify requirements * Use python36 * Back to basic formulation with nbsphinx * Remove clutter from requirements.txt * Fix few bugs * Modify CHANGELOG
elfi-dev · Jan 16, 2023 · 5b5db3f · 5b5db3f
1 parent e0fbbca
commit 5b5db3f
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Showing 8 changed files with 45 additions and 14 deletions.
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -21,4 +21,4 @@ formats:
 python:
   version: 3.6
   install:
-    - requirements: requirements.txt
+    - requirements: docs/requirements.txt
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,7 @@
 Changelog
 =========
 
+- Fix readthedocs configuration
 - Update penalty to shrinkage parameter conversion in synthetic likelihood calculation
 - Update BSL pre sample methods
 - Update BslSample

diff --git a/docs/conf.py b/docs/conf.py
@@ -18,18 +18,17 @@
 # http://docs.readthedocs.io/en/latest/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
 from unittest.mock import MagicMock
 
-
 class Mock(MagicMock):
     @classmethod
     def __getattr__(cls, name):
         return MagicMock()
 
-
 on_RTD = os.environ.get('READTHEDOCS', None) == 'True'
 if on_RTD:
     MOCK_MODULES = [
         'pygtk', 'gtk', 'gobject', 'argparse', 'numpy', 'pandas', 'scipy', 'unqlite', 'dask',
         'distributed', 'distributed.client', 'graphviz', 'matplotlib', 'sobol_seq', 'GPy',
+        'GPy.kern', 'GPy.models',
         'dask.delayed', 'scipy.linalg', 'scipy.optimize', 'scipy.stats', 'scipy.spatial',
         'scipy.sparse', 'scipy.special', 'matplotlib.pyplot', 'numpy.random', 'networkx',
         'ipyparallel', 'numpy.lib', 'numpy.lib.format', 'sklearn.linear_model',
@@ -93,12 +92,12 @@ def setup(app):
     'sphinx.ext.viewcode',
     'sphinx.ext.autosummary',
     'sphinx.ext.napoleon',
-    'IPython.sphinxext.ipython_console_highlighting',
+    'nbsphinx',
+    # 'IPython.sphinxext.ipython_console_highlighting',
     # Inheritance diagrams
-    # 'sphinx.ext.graphviz',
-    # 'sphinx.ext.inheritance_diagram',
+    'sphinx.ext.graphviz',
+    'sphinx.ext.inheritance_diagram'
 ]
-
 autoclass_content = 'both'
 
 # Add any paths that contain templates here, relative to this directory.
@@ -136,7 +135,7 @@ def setup(app):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = "en"
+language = 'en'
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -150,7 +149,7 @@ def setup(app):
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ['_build', '**.ipynb_checkpoints', 'Thumbs.db', '.DS_Store']
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1,31 @@
+# Documentation
+dask[distributed]>=2.30.0
+numpy>=1.12.1
+scipy>=0.19
+matplotlib>=1.1
+GPy>=1.0.9
+networkX>=2.0
+ipyparallel>=6
+toolz>=0.8
+scikit-learn>=0.18.1
+numdifftools>=0.9
+sphinx==1.8.6
+sphinx-rtd-theme==0.4.3
+sphinxcontrib-serializinghtml==1.1.5
+sphinxcontrib-websupport==1.2.4
+urllib3==1.26.9
+Pygments==2.12.0
+readthedocs-sphinx-ext==2.1.8
+jinja2==3.0.3
+docutils==0.17.1
+ipykernel==5.5.6
+ipyparallel==8.2.1
+ipython==7.16.3
+ipython-genutils==0.2.0
+jedi==0.17.2
+MarkupSafe==2.0.1
+future==0.18.2
+pillow==5.4.1
+alabaster==0.7.12
+commonmark==0.8.0
+nbsphinx
diff --git a/docs/usage/BOLFI.rst b/docs/usage/BOLFI.rst
@@ -92,7 +92,7 @@ surface is updated after each batch (especially so if the noise is 0!).
 .. code:: ipython3
 
     bolfi = elfi.BOLFI(log_d, batch_size=1, initial_evidence=20, update_interval=10, 
-                       bounds={'t1':(-2, 2), 't2':(-1, 1)}, acq_noise_var=0.1, seed=seed)
+                       bounds={'t1':(-2, 2), 't2':(-1, 1)}, acq_noise_var=[0.1, 0.1], seed=seed)
 
 Sometimes you may have some samples readily available. You could then
 initialize the GP model with a dictionary of previous results by giving

diff --git a/docs/usage/implementing-methods.rst b/docs/usage/implementing-methods.rst
@@ -176,7 +176,7 @@ is the final complete implementation of our inference method class::
 
    import numpy as np
 
-   from elfi.methods.parameter_inference import ParameterInference
+   from elfi.methods.inference.parameter_inference import ParameterInference
    from elfi.methods.results import Sample
 
 

diff --git a/elfi/methods/inference/parameter_inference.py b/elfi/methods/inference/parameter_inference.py
@@ -57,7 +57,7 @@ def __init__(self,
 
         Parameters
         ----------
-        model : ElfiModel
+        model : elfi.ElfiModel
             Model to perform the inference with.
         output_names : list
             Names of the nodes whose outputs will be requested from the ELFI graph.
@@ -67,7 +67,7 @@ def __init__(self,
             a significant performance boost.
         seed : int, optional
             Seed for the data generation from the ElfiModel
-        pool : OutputPool, optional
+        pool : elfi.store.OutputPool, optional
             OutputPool both stores and provides precomputed values for batches.
         max_parallel_batches : int, optional
             Maximum number of batches allowed to be in computation at the same time.

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -15,4 +15,4 @@ importlib-metadata<5.0.0
 
 
 # Documentation
-Sphinx>=1.4.8
+Sphinx>=1.4.8