119 sphinx autodocs

[zmorris248]

Overview

This PR sets up the foundation for automated documentation of our python modules using sphinx autodocs. Currently, we have the file structure for sphinx created and documentation files for a good portion of our modules created. There is a readme file that describes the structure and how to build your documentation.

There is still a lot of work to be done that will be in future PRs, including automatic generation of rst files (although there is a script that does this at a basic level - rst_autogenerate.py), and deployment and automatic updating through something like ReadTheDocs.

Implementation

• Run pip install sphinx
• Run sphinx-quickstart
• Modify the conf.py file inside the source folder to have relevant system paths and configs
• Create rst files and index files
• Run the sphinx build command (sphinx-build -b html source/ build/) that creates the html in the build folder

Testing

None

Problems Faced

Some configuration issues with the conf.py and how the paths to the python modules should be referenced

Notes

Closes #119

[github-actions[bot]]

Jest Coverage

Summary

Lines	Statements	Branches	Functions
	74.87% (438/585)	57.14% (68/119)	68.57% (120/175)

Junit Summary

Tests	Skipped	Failures	Errors	Time
35	0 :zzz:	0 :x:	0 :fire:	3.738s :stopwatch:

Coverage Report (74%)

File	% Stmts	% Branch	% Funcs	% Lines	Uncovered Line #s
All files	74.87	57.14	68.57	74.25
fixtures	100	100	100	100
kidneyStudyFixture.tsx	100	100	100	100
src/components	90.09	44.44	82.75	91.17
ErrorMessageBox.tsx	83.33	100	0	100
EventTimeline.tsx	71.42	0	0	75	79–83
Metadata.tsx	85.71	0	80	84.61	74–75
Navbar.tsx	90.47	50	100	90	150, 163
StackedChart.tsx	100	66.66	100	100	72–85
withAuthenticated.tsx	100	100	100	100
src/contexts	90	100	58.33	89.28
authContext.tsx	90	100	58.33	89.28	72, 90, 104
src/data	30.09	28.57	39.47	20
index.ts	30.09	28.57	39.47	20	17–27, 38–48, 56–66, 76–86, 98–107, 119–129, 139–148, 158–163, 175–198, 209–217, 227–232, 245–284, 300–301
src/hooks	100	100	100	100
useAuthContext.ts	100	100	100	100
src/pages	86.84	77.41	83.33	87.5
analytics.tsx	96.15	100	88.88	96	90
dashboard.tsx	100	100	100	100
index.tsx	100	100	100	100
login.tsx	83.87	88.88	85.71	83.33	52–57, 109
profile.tsx	78.57	66.66	75	83.33	63–66
signup.tsx	80.48	57.14	72.72	80	65–67, 82–83, 163–170, 194
src/pages/apikeys	73.21	54.54	64.28	71.69
index.tsx	73.21	54.54	64.28	71.69	74–77, 89, 94–99, 104–108, 195
src/pages/studies	75.23	47.22	67.74	78.12
[id].tsx	68.57	37.5	57.89	71.42	84, 93–107, 111–113, 124–125, 129, 133, 142, 218
index.tsx	88.57	66.66	83.33	90.9	69, 78, 95

[sonarcloud[bot]]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

[zmorris248]

@Ivan-E-Johnson @powersaudrey25 @mbrzus I have fixed the errors with the failing CI. I ended up removing the backend init.py file as that was the root of the error. Sphinx imports for doc creation still work without it, and now the CI's pass. Just needs a review from you guys