Fixes to use latest sphinx

[rly]

• Use the latest sphinx version
• Update Makefiles
• Fix broken favicon
• Add logo.pdf for latex builds
• Avoid creating unlinked modules.rst

[codecov]

Codecov Report

Merging #1139 into dev will increase coverage by 0.34%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##              dev    #1139      +/-   ##
==========================================
+ Coverage   67.49%   67.83%   +0.34%     
==========================================
  Files          38       38              
  Lines        2301     2279      -22     
  Branches      397      397              
==========================================
- Hits         1553     1546       -7     
+ Misses        679      664      -15     
  Partials       69       69

Impacted Files	Coverage Δ
src/pynwb/validate.py	0% <ø> (ø)	⬆️
src/pynwb/retinotopy.py	100% <100%> (+5.12%)	⬆️
src/pynwb/misc.py	85.08% <100%> (+1.32%)	⬆️
src/pynwb/file.py	71.37% <100%> (+0.45%)	⬆️
src/pynwb/image.py	93.54% <100%> (+2.77%)	⬆️
src/pynwb/ophys.py	94.26% <100%> (+1.46%)	⬆️
src/pynwb/base.py	92% <100%> (+1.37%)	⬆️
src/pynwb/ecephys.py	96.07% <100%> (+1.79%)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update fedc199...b5e82c4. Read the comment docs.