Fix docs

Author: ale94mleon

.conda_create_env/environment.yml

@@ -1,4 +1,4 @@
-name: bindflow
+name: bindflow-docs
 channels:
   - conda-forge
 dependencies:

docs/conf.py

@@ -124,6 +124,15 @@
     "https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.9.0/languages/yaml.min.js",
 ]
 
+
+# -- Mock heavy or optional dependencies to avoid import errors --
+
+autodoc_mock_imports = [
+    "pandas",
+    "toff",
+    "parmed"
+]
+
 intersphinx_mapping = {'Python': ('https://docs.python.org/3/', None),
                        'numpy': ('https://numpy.org/doc/stable/', None),
                        'rdkit': ('https://www.rdkit.org/docs/', None),

docs/source/guides/performance/index.md

@@ -54,7 +54,7 @@ Plugging into Eq. {eq}`fep_estimation`:
 - {math}`T_E=` average time (in hours) to complete the production equilibration simulation
 - {math}`T_S=` average time (in hours) to complete the sample simulation
 
-This formula provides a lower bound for the execution time. In practice, you should account for an additional ± 0.2 days to accommodate for the remaining tasks, scheduling overheads and runtime variations. Nevertheless, this estimation is usually reliable, as the total time is dominated by the FEP complex simulations. The value of {math}`T_E` and {math}`T_S` can be determined either from preliminary test runs or by monitoring ongoing simulations
+This formula provides a lower bound for the execution time. In practice, you should account for an additional ± 0.2 days to accommodate for the remaining tasks, scheduling overheads and runtime variations. Nevertheless, this estimation is usually reliable, as the total time is dominated by the production MD steps. The value of {math}`T_E` and {math}`T_S` can be determined either from preliminary test runs or by monitoring ongoing simulations
 
 ````{dropdown} Example Calculation
 :color: info

docs/source/installation.md

@@ -18,7 +18,7 @@ We would like to work in a more relaxed environment, but we have encountered cha
 
   <div>
     <strong>Features:</strong><br>
-    <label><input type="checkbox" data-feature="mmpbsa"> MM(P/G)BSA capabilities</label>
+    <label><input type="checkbox" data-feature="mmpbsa"> MM(PB/GB)SA capabilities</label>
     <label><input type="checkbox" data-feature="espaloma"> Espaloma force field</label>
   </div>
 
@@ -159,7 +159,7 @@ If `GROMACS >= 2023`, BindFlow throws a clean error at the very beginning of the
 
 ## Documentation dependencies
 
-This project has an [Sphinx](https://www.sphinx-doc.org/en/master/) documentation that can be built and accessed locally.
+This online [Sphinx](https://www.sphinx-doc.org/en/master/) documentation can also be built and accessed locally.
 
 ````{admonition} requirements_doc.txt
 :class: tip

docs/source/modules/data.md

@@ -1,3 +1,3 @@
 # Data
 
-This is sub-packege for testing.
+This is sub-package for testing.

docs/source/modules/mdp.md

@@ -4,4 +4,4 @@
 .. automodule:: bindflow.mdp.mdp
     :members:
     :special-members: __init__, __call__
-```{eval-rst}
+```

pyproject.toml

@@ -48,7 +48,6 @@ dependencies = [
     "numpy",
     "pandas",
     "mdanalysis",
-    # "TOFF >= 0.2.0",
     "pyyaml",
 ]
 

requirements_docs.txt

@@ -7,5 +7,9 @@ sphinxcontrib-katex
 sphinxcontrib-mermaid
 sphinx-inline-tabs
 sphinx_copybutton
-sphinx-autobuild
-roman
+roman
+
+# 🔧 Live-reload server (pin stable versions to avoid asyncio crash)
+sphinx-autobuild==2021.3.14
+uvicorn<0.30
+watchfiles<0.20