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Notebook test fixes #154

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merged 4 commits into from
Jul 22, 2024
Merged

Notebook test fixes #154

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0360201
Merge pull request #12 from open2c/master
efriman Jul 2, 2024
6485506
requirements, fixed lineplot mpl3.8, updated action nodes
efriman Jul 4, 2024
2624a1d
testing removing pytest cov
efriman Jul 5, 2024
ad0c588
nbval skip
efriman Jul 5, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/pythonpublish.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@ jobs:
deploy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v1
uses: actions/setup-python@v3
with:
python-version: '3.x'
- name: Install dependencies
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4 changes: 2 additions & 2 deletions .github/workflows/pythonpublish_manual.yml
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Expand Up @@ -6,9 +6,9 @@ jobs:
deploy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v1
uses: actions/setup-python@v3
with:
python-version: '3.x'
- name: Install dependencies
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4 changes: 2 additions & 2 deletions .github/workflows/tests.yml
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Expand Up @@ -18,9 +18,9 @@ jobs:
python-version: [ '3.8', '3.9', '3.10' ]

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v1
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
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2 changes: 1 addition & 1 deletion coolpuppy/coolpup.py
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Expand Up @@ -924,7 +924,7 @@ def __init__(

for region_name, region in self.view_df.iterrows():
lo, hi = self.clr.extent(region)
chroffset = self.clr.offset(region[0])
chroffset = self.clr.offset(region.iloc[0])
self.view_df_extents[region_name] = lo - chroffset, hi - chroffset

self.chroms = natsorted(
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5 changes: 5 additions & 0 deletions coolpuppy/plotpup.py
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Expand Up @@ -492,6 +492,11 @@ def plot_stripes(
colnames=colnames,
)
logger.debug(f"Plotting lineplot on top of stripes")
try:
for ax in fg.axes[0]:
ax.remove()
except:
pass
else:
fg.map(
add_heatmap,
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19,828 changes: 300 additions & 19,528 deletions docs/source/Examples/Walkthrough_API.ipynb
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1,132 changes: 699 additions & 433 deletions docs/source/Examples/Walkthrough_CLI.ipynb
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2 changes: 1 addition & 1 deletion pytest.ini
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Expand Up @@ -8,4 +8,4 @@ addopts =
filterwarnings =
ignore::PendingDeprecationWarning
testpaths =
tests
tests
5 changes: 2 additions & 3 deletions requirements.txt
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Expand Up @@ -2,15 +2,14 @@ h5py>=3.0
Cython
cooler
numpy>=1.16.5
pandas
pandas<=2.2.2
scipy
cooltools>=0.5.2
pyyaml
more_itertools
bioframe>=0.3.3
matplotlib
matplotlib<=3.8.0
seaborn
natsort
m2r2
h5sparse
multiprocessing_logging
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