Lay groundwork for Netlify preview builds of the docs

docs/conf.py

@@ -1,13 +1,15 @@
 # Configuration file for the Sphinx documentation builder.
 import os
 import sys
+from pathlib import Path
 
-sys.path.insert(0, os.path.abspath(".."))
+#sys.path.insert(0, os.path.abspath(".."))
+sys.path.insert(0, str(Path('..').resolve()))
 
 # -- Project information
 
 project = "Hydrogym"
-copyright = "2024, Hydrogym Developers"
+copyright = "2025, Hydrogym Developers"
 author = "The HydroGym Developers"
 
 release = "0.1"
@@ -32,6 +34,7 @@
 autoclass_content = "both"
 html_show_sourcelink = False
 autodoc_inherit_docstrings = True
+set_type_checking_flag = True
 
 intersphinx_mapping = {
     "rtd": ("https://docs.readthedocs.io/en/stable/", None),
@@ -44,8 +47,12 @@
 autodoc_mock_imports = [
     "firedrake",
     "pyadjoint",
+    "numpy",
+    "gym",
     "ufl",
-    "mpi4py",
+    "scipy",
+    "matplotlib",
+    "mpi4py"
 ]
 
 # -- Options for HTML output
@@ -63,9 +70,7 @@
     "repository_url": "https://github.com/dynamicslab/hydrogym",
     "use_repository_button": True,  # add a 'link to repository' button
     "use_issues_button": True,  # add an 'Open an Issue' button
-    "path_to_docs":
-        ("docs"),  # used to compute the path to launch notebooks in colab
-    "prev_next_buttons_location": None,
+    "path_to_docs": ("docs"),  # used to compute the path to launch notebooks in colab
     "show_navbar_depth": 1,
 }
 

docs/installation.rst

@@ -3,8 +3,8 @@ Installing Hydrogym
 
 .. _installation:
 
-Installation
-------------
+Setup
+-----
 
 **NOTE:** We are still pre-release and several components (in particular the distributed workflow) have not been fully merged.
 
@@ -34,7 +34,7 @@ which switches the behaviour to look for a Firedrake installation inside of the
 allows for debugging on any laptop. All other dependencies are handled as usual by `pip <https://pip.pypa.io/en/stable/>`_.
 
 Firedrake (local installation)
----------
+------------------------------
 
 For a local installation Firedrake and Hydrogym must be installed independently into the same virtual environment.
 This could be done by either following the `Firedrake installation instructions <https://www.firedrakeproject.org/download.html>`_

docs/quickstart.rst

@@ -125,21 +125,3 @@ present in the cylinder and pinball flows.
 * `Sipp & Lebedev (2007) <https://www.cambridge.org/core/journals/journal-of-fluid-mechanics/article/abs/global-stability-of-base-and-mean-flows-a-general-approach-and-its-applications-to-cylinder-and-open-cavity-flows/EC31631718EB33AA5C671A8F7EAA043C>`_
 * `Sipp, et al (2010) <http://www.ladhyx.polytechnique.fr/people/meliga/pdf/AMR.pdf>`_
 * `Callaham, Brunton, Loiseau (2021) <https://www.cambridge.org/core/services/aop-cambridge-core/content/view/CC2980F9AA4AC20A7453C3056ED950C4/S0022112021009940a.pdf/on-the-role-of-nonlinear-correlations-in-reduced-order-modelling.pdf>`_
-
-Backwards-facing step
-*********************
-
-.. image:: _static/imgs/step.png
-   :width: 600
-
-The backwards-facing step is a benchmark problem used both in modeling and control and as a test of numerical methods.  The flow is constricted
-upstream and expands over a step to a straight channel downstream.  While the flow is linearly stable at moderate Reynolds numbers (Re=600 by
-default here), it is an "amplifier" flow, meaning that small disturbances are amplified over a finite time horizon before being advected out
-of the domain.  Hence, this flow configuration is forced by small-amplitude random noise upstream of the step, in the approximate region where 
-analysis shows the flow is most sensitive to disturbances.
-
-**References**
-
-* `Boujo & Gallaire (2015) <https://www.cambridge.org/core/journals/journal-of-fluid-mechanics/article/abs/sensitivity-and-openloop-control-of-stochastic-response-in-a-noise-amplifier-flow-the-backwardfacing-step/3CEEBB6AD9784D555FDA086AF81BD416>`_
-* `Beneddine, et al (2016) <https://hal.inria.fr/hal-01445633/>`_
-* `Ducimetière, et al (2022) <https://www.cambridge.org/core/journals/journal-of-fluid-mechanics/article/weak-nonlinearity-for-strong-nonnormality/ADCBEAB2B445907FF022DD5E4F79A001>`_

docs/requirements.txt

@@ -1,28 +1,28 @@
-alabaster==0.7.12
-babel==2.10.3
-certifi==2024.7.4
-charset-normalizer==2.1.0
-docutils==0.17.1
-idna==3.7
-imagesize==1.4.1
-jinja2==3.1.6
-markupsafe==2.1.1
-packaging==21.3
-pygments==2.15.0
-pyparsing==3.0.9
-pytz==2022.1
-requests==2.32.2
-snowballstemmer==2.2.0
-sphinx==5.0.2
-sphinx-rtd-theme==1.0.0
+alabaster>=0.7.12
+babel>=2.10.3
+certifi>=2024.7.4
+charset-normalizer>=2.1.0
+docutils>=0.17.1
+idna>=3.7
+imagesize>=1.4.1
+jinja2>=3.1.6
+markupsafe>=2.1.1
+packaging>=21.3
+pygments>=2.15.0
+pyparsing>=3.0.9
+pytz>=2022.1
+requests>=2.32.2
+snowballstemmer>=2.2.0
+sphinx>=5.0.2
+sphinx-rtd-theme>=1.0.0
 sphinx-book-theme
-sphinxcontrib-applehelp==1.0.2
-sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp==2.0.0
-sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.5
-urllib3==1.26.19
-sphinx-design==0.5.0
+sphinxcontrib-applehelp>=1.0.2
+sphinxcontrib-devhelp>=1.0.2
+sphinxcontrib-htmlhelp>=2.0.0
+sphinxcontrib-jsmath>=1.0.1
+sphinxcontrib-qthelp>=1.0.3
+sphinxcontrib-serializinghtml>=1.1.5
+urllib3>=1.26.19
+sphinx-design>=0.5.0
 legacy-cgi
 standard-imghdr