Fix sidebar theme in new sphinx version

.gitignore

@@ -61,6 +61,8 @@ _build
 ._*
 _*
 !_custom_build/
+!docs/_templates/
+!docs/_static/
 .Spotlight-V100
 .Trashes
 ehthumbs.db

.readthedocs.yaml

@@ -22,6 +22,7 @@ sphinx:
 
 python:
   install:
-  - requirements: requirements_docs.txt
-  - method: setuptools
+  - method: pip
     path: .
+    extra_requirements:
+      - docs

docs/_static/custom.css

@@ -0,0 +1,16 @@
+/* Fix for Sphinx issue #11000: nature theme sidebar overflow with autodoc names */
+/* See: https://github.com/sphinx-doc/sphinx/issues/11000 */
+
+/* Increase sidebar width to accommodate longer names */
+div.documentwrapper div.bodywrapper {
+    margin-left: 250px;
+}
+
+div.document div.sphinxsidebar {
+    width: 250px;
+}
+
+/* Add scrollbar for overflowing content */
+div.sphinxsidebarwrapper div {
+    overflow: auto;
+}

docs/_templates/localtoc.html

@@ -0,0 +1,7 @@
+{# Custom local TOC template with depth limit #}
+{%- if display_toc %}
+  <div>
+    <h3><a href="{{ pathto(root_doc)|e }}">{{ _('Table of Contents') }}</a></h3>
+    {{ toctree(maxdepth=1, collapse=False, includehidden=True) }}
+  </div>
+{%- endif %}

docs/chemical_package_tutorial.rst

@@ -4,7 +4,7 @@ Introduction to ChemicalConstantsPackage and PropertyCorrelationsPackage
 .. contents:: :local:
 
 These two objects are designed to contain information needed by flash algorithms.
-In the first iteration of thermo, data was automatically looked up in databases and there was no way to replace that data. Thermo now keeps data and algorithms completely separate. This has also been very helpful to make unit tests that do not change their results.
+In the first iteration of Thermo, data was automatically looked up in databases and there was no way to replace that data. Thermo now keeps data and algorithms completely separate. This has also been very helpful to make unit tests that do not change their results.
 
 There are five places to configure the flash and phase infrastructure:
 

docs/conf.py

@@ -184,6 +184,9 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
+# Custom CSS files
+html_css_files = ["custom.css"]
+
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the documentation.

docs/index.rst

@@ -7,15 +7,65 @@ Thermo:  Thermodynamics and Phase Equilibrium component of Chemical Engineering
 Contents:
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 1
+   :caption: Tutorial
 
    cubic_equations_of_state
    activity_coefficients
    property_objects
    chemical_package_tutorial
    tutorial_phases_and_flash
    GibbsExcessLiquid_details
-   modules
+
+.. toctree::
+   :maxdepth: 1
+   :caption: API
+
+   thermo.activity
+   thermo.bulk
+   thermo.chemical
+   thermo.chemical_package
+   thermo.datasheet
+   thermo.electrochem
+   thermo.eos
+   thermo.eos_mix
+   thermo.eos_mix_methods
+   thermo.eos_volume
+   thermo.eos_alpha_functions
+   thermo.equilibrium
+   thermo.flash
+   thermo.functional_groups
+   thermo.heat_capacity
+   thermo.interface
+   thermo.interaction_parameters
+   thermo.law
+   thermo.nrtl
+   thermo.mixture
+   thermo.permittivity
+   thermo.phases
+   thermo.phase_change
+   thermo.property_package
+   thermo.phase_identification
+   thermo.regular_solution
+   thermo.stream
+   thermo.thermal_conductivity
+   thermo.unifac
+   thermo.units
+   thermo.utils
+   thermo.vapor_pressure
+   thermo.viscosity
+   thermo.volume
+   thermo.wilson
+   thermo.uniquac
+   thermo.group_contribution.joback
+   thermo.group_contribution.fedors
+   thermo.group_contribution.wilson_jasperson
+   thermo.group_contribution.bondi
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Additional Resources
+
    examples
 
 

pyproject.toml

@@ -347,7 +347,7 @@ max-complexity = 10
 "docs/**/*.ipynb" = ["S101", "F403", "F405", "PT011", "B017", "TRY002"]
 
 [tool.pytest.ini_options]
-addopts = "--doctest-glob='*.rst' --ignore='setup.py' --ignore='chemical_compare.py' --doctest-modules"
+addopts = "--doctest-glob='*.rst'"
 norecursedirs = [".cache", ".git", "htmlcov", "notebooks", "dist", "build", "*.egg-info", ".tox", "surfaces", "prof", "benchmarks", "dev", "_build", "_custom_build", "__pycache__"]
 doctest_optionflags = ["NORMALIZE_WHITESPACE"]
 markers = [

tests/test_numba.py

@@ -36,14 +36,14 @@
 try:
     import numba
     import numba.core
+    if numba is not None:
+        import chemicals.numba
+
+        import thermo.numba
 except:
     numba = None
 import numpy as np
 
-if numba is not None:
-    import chemicals.numba
-
-    import thermo.numba
 
 jit_disabled = os.environ.get('NUMBA_DISABLE_JIT') == '1'
 

thermo/eos.py

@@ -1303,7 +1303,7 @@ def set_from_PT(self, Vs, only_l=False, only_g=False):
             self.phase = "l/g"
         else:
             # Even in the case of three real roots, it is still the min/max that make sense
-            print([self.T, self.P, b, self.delta, self.epsilon, self.a_alpha, "coordinates of failure"])
+            # print([self.T, self.P, b, self.delta, self.epsilon, self.a_alpha, "coordinates of failure"])
             if self.multicomponent:
                 extra = f", zs is {self.zs}"
             else:

thermo/eos_volume.py

@@ -860,6 +860,7 @@ def volume_solutions_halley(T, P, b, delta, epsilon, a_alpha):
     # the value of the second term plus P is equal to P.
     if a_alpha/(b*(b + delta) + epsilon) + P == P:
         return (b + R*T/P, 0.0, 0.0)
+
     # Run this first, before the low P criteria
     if a_alpha > 1e4:
         V_possible = high_alpha_one_root(T, P, b, delta, epsilon, a_alpha)