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Bump to v1.4.2 #72

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merged 10 commits into from
Dec 1, 2024
Merged

Bump to v1.4.2 #72

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7cdf4bc
Update deps
moshi4 Dec 1, 2024
4251a6e
Fix log msg a little
moshi4 Dec 1, 2024
ed617cc
Add type ignore comment
moshi4 Dec 1, 2024
920876a
Fix to remove completely overlap alignment links
moshi4 Dec 1, 2024
7909f76
Fix log msg a little
moshi4 Dec 1, 2024
01f04d2
Update pgv-viewer demo page to latest version
moshi4 Dec 1, 2024
9db1c2a
Autoupdate pre-commit-config
moshi4 Dec 1, 2024
75caaff
Fix pre-commit-config to ignore notebook
moshi4 Dec 1, 2024
035800c
Update getting started docs for latest version
moshi4 Dec 1, 2024
ac8aa6d
Change v1.4.1 to v1.4.2
moshi4 Dec 1, 2024
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4 changes: 3 additions & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,12 @@
# See https://pre-commit.com/hooks.html for more hooks
repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.6.5
rev: v0.8.1
hooks:
- id: ruff
name: ruff lint check
types_or: [python, pyi]
args: [--fix]
- id: ruff-format
name: ruff format check
types_or: [python, pyi]
46 changes: 23 additions & 23 deletions docs/getting_started.ipynb
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15,167 changes: 2,260 additions & 12,907 deletions docs/images/pgv-viewer_demo1.html
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25,684 changes: 12,842 additions & 12,842 deletions docs/images/pgv-viewer_demo2.html
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112 changes: 55 additions & 57 deletions requirements-dev.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,9 @@
# universal: false

-e file:.
altair==5.4.1
altair==5.5.0
# via streamlit
asttokens==2.4.1
asttokens==3.0.0
# via stack-data
attrs==24.2.0
# via jsonschema
Expand All @@ -23,18 +23,18 @@ beautifulsoup4==4.12.3
# via nbconvert
biopython==1.84
# via pygenomeviz
black==24.8.0
bleach==6.1.0
black==24.10.0
bleach==6.2.0
# via nbconvert
blinker==1.8.2
blinker==1.9.0
# via streamlit
cachetools==5.5.0
# via streamlit
certifi==2024.8.30
# via requests
cfgv==3.4.0
# via pre-commit
charset-normalizer==3.3.2
charset-normalizer==3.4.0
# via requests
click==8.1.7
# via black
Expand All @@ -48,42 +48,42 @@ comm==0.2.2
# via ipykernel
contourpy==1.3.0
# via matplotlib
coverage==7.6.1
coverage==7.6.8
# via pytest-cov
cycler==0.12.1
# via matplotlib
debugpy==1.8.5
debugpy==1.8.9
# via ipykernel
decorator==5.1.1
# via ipython
defusedxml==0.7.1
# via nbconvert
distlib==0.3.8
distlib==0.3.9
# via virtualenv
exceptiongroup==1.2.2
# via ipython
# via pytest
executing==2.1.0
# via stack-data
fastjsonschema==2.20.0
fastjsonschema==2.21.0
# via nbformat
filelock==3.16.0
filelock==3.16.1
# via virtualenv
fonttools==4.53.1
fonttools==4.55.0
# via matplotlib
ghp-import==2.1.0
# via mkdocs
gitdb==4.0.11
# via gitpython
gitpython==3.1.43
# via streamlit
griffe==1.3.0
griffe==1.5.1
# via mkdocstrings-python
identify==2.6.0
identify==2.6.3
# via pre-commit
idna==3.8
idna==3.10
# via requests
importlib-metadata==8.4.0
importlib-metadata==8.5.0
# via jupyter-client
# via markdown
# via mkdocs
Expand All @@ -98,7 +98,7 @@ ipykernel==6.29.5
# via mkdocs-jupyter
ipython==8.18.1
# via ipykernel
jedi==0.19.1
jedi==0.19.2
# via ipython
jinja2==3.1.4
# via altair
Expand All @@ -110,9 +110,9 @@ jinja2==3.1.4
jsonschema==4.23.0
# via altair
# via nbformat
jsonschema-specifications==2023.12.1
jsonschema-specifications==2024.10.1
# via jsonschema
jupyter-client==8.6.2
jupyter-client==8.6.3
# via ipykernel
# via nbclient
jupyter-core==5.7.2
Expand All @@ -137,13 +137,13 @@ markdown-it-py==3.0.0
# via jupytext
# via mdit-py-plugins
# via rich
markupsafe==2.1.5
markupsafe==3.0.2
# via jinja2
# via mkdocs
# via mkdocs-autorefs
# via mkdocstrings
# via nbconvert
matplotlib==3.9.2
matplotlib==3.9.3
# via pygenomeviz
matplotlib-inline==0.1.7
# via ipykernel
Expand All @@ -167,20 +167,20 @@ mkdocs-autorefs==1.2.0
# via mkdocstrings-python
mkdocs-get-deps==0.2.0
# via mkdocs
mkdocs-jupyter==0.25.0
mkdocs-material==9.5.34
mkdocs-jupyter==0.25.1
mkdocs-material==9.5.46
# via mkdocs-jupyter
mkdocs-material-extensions==1.3.1
# via mkdocs-material
mkdocstrings==0.26.1
mkdocstrings==0.27.0
# via mkdocstrings-python
mkdocstrings-python==1.11.1
mkdocstrings-python==1.12.2
# via mkdocstrings
mypy-extensions==1.0.0
# via black
narwhals==1.6.4
narwhals==1.15.0
# via altair
nbclient==0.10.0
nbclient==0.10.1
# via nbconvert
nbconvert==7.16.4
# via mkdocs-jupyter
Expand All @@ -197,11 +197,10 @@ numpy==2.0.2
# via contourpy
# via matplotlib
# via pandas
# via pyarrow
# via pydeck
# via pygenomeviz
# via streamlit
packaging==24.1
packaging==24.2
# via altair
# via black
# via ipykernel
Expand All @@ -213,7 +212,7 @@ packaging==24.1
# via streamlit
paginate==0.5.7
# via mkdocs-material
pandas==2.2.2
pandas==2.2.3
# via streamlit
pandocfilters==1.5.1
# via nbconvert
Expand All @@ -224,29 +223,29 @@ pathspec==0.12.1
# via mkdocs
pexpect==4.9.0
# via ipython
pillow==10.4.0
pillow==11.0.0
# via matplotlib
# via streamlit
platformdirs==4.3.2
platformdirs==4.3.6
# via black
# via jupyter-core
# via mkdocs-get-deps
# via mkdocstrings
# via virtualenv
pluggy==1.5.0
# via pytest
pre-commit==3.8.0
prompt-toolkit==3.0.47
pre-commit==4.0.1
prompt-toolkit==3.0.48
# via ipython
protobuf==5.28.0
protobuf==5.29.0
# via streamlit
psutil==6.0.0
psutil==6.1.0
# via ipykernel
ptyprocess==0.7.0
# via pexpect
pure-eval==0.2.3
# via stack-data
pyarrow==17.0.0
pyarrow==18.1.0
# via streamlit
pydeck==0.9.1
# via streamlit
Expand All @@ -256,20 +255,20 @@ pygments==2.18.0
# via mkdocs-material
# via nbconvert
# via rich
pymdown-extensions==10.9
pymdown-extensions==10.12
# via mkdocs-material
# via mkdocstrings
pyparsing==3.1.4
pyparsing==3.2.0
# via matplotlib
pytest==8.3.3
# via pytest-cov
pytest-cov==5.0.0
pytest-cov==6.0.0
python-dateutil==2.9.0.post0
# via ghp-import
# via jupyter-client
# via matplotlib
# via pandas
pytz==2024.1
pytz==2024.2
# via pandas
pyyaml==6.0.2
# via jupytext
Expand All @@ -286,41 +285,39 @@ pyzmq==26.2.0
referencing==0.35.1
# via jsonschema
# via jsonschema-specifications
regex==2024.7.24
regex==2024.11.6
# via mkdocs-material
requests==2.32.3
# via mkdocs-material
# via streamlit
rich==13.8.1
rich==13.9.4
# via streamlit
rpds-py==0.20.0
rpds-py==0.21.0
# via jsonschema
# via referencing
ruff==0.6.4
ruff==0.8.1
six==1.16.0
# via asttokens
# via bleach
# via python-dateutil
smmap==5.0.1
# via gitdb
soupsieve==2.6
# via beautifulsoup4
stack-data==0.6.3
# via ipython
streamlit==1.38.0
streamlit==1.40.2
# via pygenomeviz
tenacity==8.5.0
tenacity==9.0.0
# via streamlit
tinycss2==1.3.0
tinycss2==1.4.0
# via nbconvert
toml==0.10.2
# via streamlit
tomli==2.0.1
tomli==2.2.1
# via black
# via coverage
# via jupytext
# via pytest
tornado==6.4.1
tornado==6.4.2
# via ipykernel
# via jupyter-client
# via streamlit
Expand All @@ -339,21 +336,22 @@ typing-extensions==4.12.2
# via black
# via ipython
# via mkdocstrings
# via rich
# via streamlit
tzdata==2024.1
tzdata==2024.2
# via pandas
urllib3==2.2.2
urllib3==2.2.3
# via requests
virtualenv==20.26.4
virtualenv==20.28.0
# via pre-commit
watchdog==4.0.2
watchdog==6.0.0
# via mkdocs
# via streamlit
wcwidth==0.2.13
# via prompt-toolkit
webencodings==0.5.1
# via bleach
# via tinycss2
zipp==3.20.1
zipp==3.21.0
# via importlib-metadata
# via importlib-resources
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