diff --git a/docs/conf.py b/docs/conf.py index 7300e51..d271ecf 100644 --- a/docs/conf.py +++ b/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, } diff --git a/docs/installation.rst b/docs/installation.rst index 3e80d53..e317752 100644 --- a/docs/installation.rst +++ b/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 `_. 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 `_ diff --git a/docs/quickstart.rst b/docs/quickstart.rst index d495f3e..c6544a4 100644 --- a/docs/quickstart.rst +++ b/docs/quickstart.rst @@ -125,21 +125,3 @@ present in the cylinder and pinball flows. * `Sipp & Lebedev (2007) `_ * `Sipp, et al (2010) `_ * `Callaham, Brunton, Loiseau (2021) `_ - -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) `_ -* `Beneddine, et al (2016) `_ -* `Ducimetière, et al (2022) `_ diff --git a/docs/requirements.txt b/docs/requirements.txt index 2a19365..36ea160 100644 --- a/docs/requirements.txt +++ b/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