update: set timepoint considering full complement

[lisphilar]

Related issues

#851 and #878

What was changed

• Close [Fix] ValueError when adding phases manually to fully-complemented data #878

[sourcery-ai]

Sourcery Code Quality Report

✅  Merging this PR will increase code quality in the affected files by 0.17%.

Quality metrics	Before	After	Change
Complexity	3.33 ⭐	3.19 ⭐	-0.14 👍
Method Length	75.89 🙂	75.57 🙂	-0.32 👍
Working memory	9.17 🙂	9.20 🙂	0.03 👎
Quality	67.02% 🙂	67.19% 🙂	0.17% 👍

Other metrics	Before	After	Change
Lines	2551	2527	-24

Changed files	Quality Before	Quality After	Quality Change
covsirphy/version.py	100.00% ⭐	100.00% ⭐	0.00%
covsirphy/analysis/data_handler.py	69.77% 🙂	71.13% 🙂	1.36% 👍
covsirphy/analysis/scenario.py	67.14% 🙂	67.09% 🙂	-0.05% 👎
covsirphy/cleaning/jhu_data.py	64.31% 🙂	64.20% 🙂	-0.11% 👎

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
covsirphy/analysis/scenario.py	Scenario.add	10 🙂	225 ⛔	15 😞	39.10% 😞	Try splitting into smaller methods. Extract out complex expressions
covsirphy/analysis/scenario.py	Scenario.fit	7 ⭐	247 ⛔	13 😞	43.33% 😞	Try splitting into smaller methods. Extract out complex expressions
covsirphy/cleaning/jhu_data.py	JHUData.show_complement	9 🙂	170 😞	13 😞	46.94% 😞	Try splitting into smaller methods. Extract out complex expressions
covsirphy/analysis/data_handler.py	DataHandler.estimate_delay	2 ⭐	239 ⛔	13 😞	48.66% 😞	Try splitting into smaller methods. Extract out complex expressions
covsirphy/analysis/scenario.py	Scenario.track	4 ⭐	170 😞	14 😞	50.34% 🙂	Try splitting into smaller methods. Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

• ⭐ excellent
• 🙂 good
• 😞 poor
• ⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

---

Please see our documentation here for details on how these metrics are calculated.

We are actively working on this report - lots more documentation and extra metrics to come!

Help us improve this quality report!

[sourcery-ai]

Sourcery Code Quality Report

✅  Merging this PR will increase code quality in the affected files by 0.17%.

Quality metrics	Before	After	Change
Complexity	3.33 ⭐	3.19 ⭐	-0.14 👍
Method Length	75.89 🙂	75.57 🙂	-0.32 👍
Working memory	9.17 🙂	9.20 🙂	0.03 👎
Quality	67.02% 🙂	67.19% 🙂	0.17% 👍

Other metrics	Before	After	Change
Lines	2551	2527	-24

Changed files	Quality Before	Quality After	Quality Change
covsirphy/version.py	100.00% ⭐	100.00% ⭐	0.00%
covsirphy/analysis/data_handler.py	69.77% 🙂	71.13% 🙂	1.36% 👍
covsirphy/analysis/scenario.py	67.14% 🙂	67.09% 🙂	-0.05% 👎
covsirphy/cleaning/jhu_data.py	64.31% 🙂	64.20% 🙂	-0.11% 👎

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
covsirphy/analysis/scenario.py	Scenario.add	10 🙂	225 ⛔	15 😞	39.10% 😞	Try splitting into smaller methods. Extract out complex expressions
covsirphy/analysis/scenario.py	Scenario.fit	7 ⭐	247 ⛔	13 😞	43.33% 😞	Try splitting into smaller methods. Extract out complex expressions
covsirphy/cleaning/jhu_data.py	JHUData.show_complement	9 🙂	170 😞	13 😞	46.94% 😞	Try splitting into smaller methods. Extract out complex expressions
covsirphy/analysis/data_handler.py	DataHandler.estimate_delay	2 ⭐	239 ⛔	13 😞	48.66% 😞	Try splitting into smaller methods. Extract out complex expressions
covsirphy/analysis/scenario.py	Scenario.track	4 ⭐	170 😞	14 😞	50.34% 🙂	Try splitting into smaller methods. Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

• ⭐ excellent
• 🙂 good
• 😞 poor
• ⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

---

Please see our documentation here for details on how these metrics are calculated.

We are actively working on this report - lots more documentation and extra metrics to come!

Help us improve this quality report!

[codeclimate]

Code Climate has analyzed commit fce1da2 and detected 0 issues on this pull request.

The test coverage on the diff in this pull request is 98.6% (50% is the threshold).

This pull request will bring the total coverage in the repository to 82.5% (0.0% change).

View more on Code Climate.