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Update to 2.0.0 #20

Merged
merged 62 commits into from
May 4, 2024
Merged

Update to 2.0.0 #20

merged 62 commits into from
May 4, 2024

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chtsai0105
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@chtsai0105
Remove unused argument
759b2fe
@chtsai0105
Move more project configs to config.py and download HMM to .phyling/H…
4c0afa4 
…MM instead of user specified path.
@chtsai0105
Print already downloaded markersets when using download list; update …
3695d33 
…changelog
@chtsai0105
Use wrapper to auto adjust text length
ed27378
@chtsai0105
Functionalize the ambiguous seq substitution step and make the sequen…
8afeea4 
…ces all uppercases
@chtsai0105
Make the tree methods as a config param
60a318c
@chtsai0105
Remove the capitalization steps and simplify the Fasttree/vft functions
c024d21
@chtsai0105
Ignore W503 to align the behavior of black formatter
7696559
@chtsai0105
Use config param to determine the tree building method
1ef8fd3
@chtsai0105
Add custom error msg for missing software
6e2ff69
@chtsai0105
Implement the PhyKIT treeness/RCV for marker filtering
5c34490
@chtsai0105
Add phykit to dependency
2cc1580
@chtsai0105
Change the error type to reflect the error more correctly
4789bb6
@chtsai0105
Functionalize the tree building process to simplify the unit tests
e4c1097
@chtsai0105
Update phylotree unit tests
c5ff327
@chtsai0105
Fix the warning msg caused by -fastmath and ignore the E402 warning
2c000d7
@chtsai0105
Add partition for concatenate (not completed)
dc9281b
@chtsai0105
Add partition for concatenate
8e379f2
@chtsai0105
Add additional env yml for developer
ac2c424
@chtsai0105
Report runtime for step
1045fa2
@chtsai0105
Use custom formatter to simplify the codes and fix some of the text w…
cf2e2ce 
…rapping issue
@chtsai0105
Unify the punctuation usage of the msgs
f3a814a
@chtsai0105
Add unit tests for partition feature
956c611
@chtsai0105
Add the info for partition and treeness to module menu
d3f49f8
@chtsai0105
Update the README.md
0f26bd8
@chtsai0105
Do the seqtype check when loading from .checkpoint.pkl and cast a war…
6829b3b 
…ning when the seqtype of new inputs and checkpoint do not match
@chtsai0105
Fix the partition file model assignment
7e197e9
@chtsai0105
Create symlink for selected MSAs to tree module output directory
19c5a36
@chtsai0105
Integrate iqtree and raxml and optimize the phylotree module with che…
61fefa4 
…ckpoint feature
@chtsai0105
Update tests input files
ad8e378
chtsai0105 added 22 commits April 18, 2024 18:00
@chtsai0105
Update tests data
56b6d31
@chtsai0105
Update libphyling_test.py
00fec84
@chtsai0105
Complete the test files and corresponding changes in the script
58c0a93
@chtsai0105
Update workflows to run slow test functions
2aa616a
@chtsai0105
Update README.md; add iqtree and raxml to environment.yml
1a79057
@chtsai0105
Add future annotation and remove unused importlib_metadata
e303a58
@chtsai0105
Update github action; import future annotations in test scripts
2ac8cd4
@chtsai0105
Update python-versions.yml
cb0db8b
@chtsai0105
Test without phylotree_tree
4a398af
@chtsai0105
Fix isinstance to make it compatable with py39
08179f1
@chtsai0105
Swap generator with completed result lists in hmmsearch; add cpu coun…
c4cdfc3 
…t hint in entry script.
@chtsai0105
Update pre-commit and github workflow params for consistency
95cd9e7
@chtsai0105
Fix py39 isinstance issue.
137b6c9
@chtsai0105
Correct type annotation on _run_hmmsearch function and typo.
0ddb3a6
@chtsai0105
Remove VeryFastTree; Fix bug that hinder some of the executables to b…
e49a08a 
…e found in phylotree module.
@chtsai0105
Add more tests on pipeline.py and adjust the evalue failure boundary.
fb17be8
@chtsai0105
Add pytest-cov to detect code coverage.
9a38202
@chtsai0105
Try to fix again the py39 isinstance issue.
ad8d7d2
@chtsai0105
Codecov integration to github workflow.
19c3227
@chtsai0105
Fix CoverageWarning: No data was collected issue.
ffee6ca
@chtsai0105
Update changelog; Version pumb to 2.0.0.
d921883
@chtsai0105
Update .gitattributes
670eb59
chtsai0105
chtsai0105 commented May 4, 2024
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@chtsai0105 chtsai0105 closed this May 4, 2024
@chtsai0105 chtsai0105 reopened this May 4, 2024
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codecov bot commented May 4, 2024

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Once you merge this PR into your default branch, you're all set! Codecov will compare coverage reports and display results in all future pull requests.

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@chtsai0105 chtsai0105 merged commit 0848edc into main May 4, 2024
13 checks passed
@chtsai0105 chtsai0105 deleted the dev branch November 5, 2024 18:55
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@chtsai0105