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version 2.0.0 #78

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a2bffdd
refactor: change the entrypoint file from AmpliGone.py to __main__.py
florianzwagemaker Apr 2, 2024
af579e3
ci: update publish and release workflows
florianzwagemaker May 25, 2024
e09cb10
deps: update dependencies in setup.py and env.yml
florianzwagemaker May 25, 2024
0fe1beb
deps: update minimum required python version in setup.py
florianzwagemaker May 25, 2024
3c298b8
refactor: move program name and version to __init__.py
florianzwagemaker May 25, 2024
603058a
refactor: move logger function to its own file (log.py)
florianzwagemaker May 25, 2024
eb9e2f4
refactor: move argument parser to its own file including helpdoc form…
florianzwagemaker May 25, 2024
0af9de1
refactor: remove func.py
florianzwagemaker May 25, 2024
e84d3d1
refactor: take the application name from the __prog__ variable in set…
florianzwagemaker May 25, 2024
edf23ac
refactor: move the functionality of alignment preset from mappreset.p…
florianzwagemaker May 25, 2024
5abae9a
refactor: change the imports in fasta2bed to not be relative imports …
florianzwagemaker May 25, 2024
daed988
fix: change the table of IUPAC data to actually reference the IUPACDa…
florianzwagemaker May 25, 2024
e670d2b
refactor: change name of MakeCoordinateLists method to find_or_read_p…
florianzwagemaker May 25, 2024
5b16301
feat: add the --verbose flag and debugging log messages
florianzwagemaker May 25, 2024
f3aef53
style: formatting with isort & black
florianzwagemaker May 25, 2024
cfd25e3
deps: add pgzip to the dependency list
florianzwagemaker May 25, 2024
3620f2f
feat: add the 'virtual primer support' to link closely positioned pri…
florianzwagemaker May 25, 2024
16967e7
feat: add quiet mode, only prints WARNING and ERROR log messages
florianzwagemaker Jul 11, 2024
71b0882
refactor: add verbose mode (debugging) to standalone args of fasta2be…
florianzwagemaker Jul 11, 2024
36c4479
feat!: change fasta2bed method from fuzzyregex to semi-global alignme…
florianzwagemaker Jul 11, 2024
6d70bfa
refactor: remove the extended regex library from AmpliGone.args and u…
florianzwagemaker Jul 11, 2024
ed916b8
deps: update dependencies in env.yml
florianzwagemaker Jul 11, 2024
abe1f69
fix: proper grouping of the regex to clean cigar strings
florianzwagemaker Jul 11, 2024
d3bb8b5
fix: do not update per-thread progression when processing very low re…
florianzwagemaker Jul 22, 2024
57e74b5
fix: improve error message when too little threads are given
florianzwagemaker Aug 15, 2024
910f75a
docs: expand function docstring to better explain the edge cases
florianzwagemaker Aug 15, 2024
ce4be91
refactor: represent the primer-alignment in a percentage of matches o…
florianzwagemaker Oct 29, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/publish.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ jobs:
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: "3.8"
python-version: "3.10"

- name: Build package
run: |
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/release.yml
Original file line number Diff line number Diff line change
Expand Up @@ -57,4 +57,4 @@ jobs:

- name: Publish docs
run: |
mike deploy --config-file mkdocs.yml --push --force --update-aliases $(git tag --sort=committerdate | tail -1 | sed 's/v//') latest
mike deploy --config-file mkdocs.yml --push --update-aliases $(git tag --sort=committerdate | tail -1 | sed 's/v//') latest
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