Merge branch 'master' into feat-cooler-bedgraph-to-pyranges

.github/workflows/CI.yml

@@ -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

environment.yml

@@ -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
@@ -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
@@ -41,5 +41,4 @@ dependencies:
   - trim-galore<=0.6.10
   - ucsc-bedgraphtobigwig
   - ucsc-bedtobigbed
-  - ucsc-fetchchromsizes
   - ujson<=5.7.0

requirements.txt

@@ -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