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chore: pyarrow minimum to 14.0.1 #231

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merged 9 commits into from
Nov 16, 2023
Merged

chore: pyarrow minimum to 14.0.1 #231

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25fe482
chore: pyarrow minimum to 14.0.1
alsmith151 Nov 15, 2023
54fe1f7
fix(build): pyarrow 14.0.0 min
alsmith151 Nov 15, 2023
cb667a9
fix(build): removed ucsc-fetchchromsizes
alsmith151 Nov 15, 2023
766257b
fix(build): install latest pyarrow through pip
alsmith151 Nov 15, 2023
8422cb0
fix(build): bumped pydantic
alsmith151 Nov 15, 2023
573ce90
fix(deps): wrong pydantic max version
alsmith151 Nov 15, 2023
87594de
fix(build): pinned pydantic
alsmith151 Nov 15, 2023
1433f8f
chore(build): added log collection as artifact
alsmith151 Nov 16, 2023
d984e38
chore(deps): pinned ibis, pydantic,ray
alsmith151 Nov 16, 2023
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7 changes: 7 additions & 0 deletions .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,13 @@ jobs:
run: |
pip install pytest-cov pytest-lazy-fixture pytest-order pytest-xdist
pytest -vv -s --log-cli-level info --cov=./ --cov-report=xml --cores 2
- name: Archive production artifacts
uses: actions/upload-artifact@v3
with:
name: capcruncher_output_logs
path: |
capcruncher_output/logs/*
- name: Upload Coverage to Codecov
uses: codecov/codecov-action@v3
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7 changes: 3 additions & 4 deletions environment.yml
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Expand Up @@ -11,7 +11,7 @@ dependencies:
- cookiecutter<=2.1.1
- fastqc<=0.12.1
- flash<=1.2.11
- ibis-framework>=6.0.0,<=7.0.0
- ibis-framework>6.1.0,<=7.0.0
- iced<=0.5.10
- joblib<=1.2.0
- loguru
Expand All @@ -22,9 +22,9 @@ dependencies:
- pip<=22.2.2
- panel<=1.3.0
- pandera<=0.17.1
- pydantic<=2.4.2
- pydantic==2.5.0
- plotly>5.0.0,<=5.15.0
- pyarrow>8.0.0,<12.0.0
- pyarrow>=11.0.0,<15.0.0
- pybedtools<=0.9.0
- pyranges<=0.0.127
- pysam>0.19.1,<=0.22.0
Expand All @@ -41,5 +41,4 @@ dependencies:
- trim-galore<=0.6.10
- ucsc-bedgraphtobigwig
- ucsc-bedtobigbed
- ucsc-fetchchromsizes
- ujson<=5.7.0
10 changes: 4 additions & 6 deletions requirements.txt
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Expand Up @@ -5,23 +5,21 @@ cooler<=0.9.2
duckdb<=0.9.1
grpcio >= 1.54.2
h5py
ibis-framework[duckdb]
ibis-framework[duckdb]>6.1.0,<=7.0.0
loguru<=0.7.2
more-itertools
numpy<=1.23
pandas<=2.1.2
pandera<=0.17.2
pandera<=0.17.2
panel<=1.3.0
plotly>5.0.0,<=5.18.0
pyarrow>8.0.0,<15.0.0
pyarrow>11.0.0,<14.0.0
pybedtools<=0.9.0
pydantic<=2.3.0
pydantic<=2.3.0
pydantic>2.4.0,<2.5.0
pyranges<=0.0.127
pysam>0.15.0,<=0.21.0
quarto
ray<=2.8.0
ray>=2.8.0
seaborn<=0.12.2
snakemake<=7.32.4
tqdm<=4.65.0
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