From c02bd2c57bee86d38f4b91a08c3247d753c8bc5d Mon Sep 17 00:00:00 2001
From: Alastair Smith <49727900+alsmith151@users.noreply.github.com>
Date: Thu, 16 Nov 2023 14:43:22 +0000
Subject: [PATCH] chore(deps): pinned pydantic, pyarrow and ray (#231)

* chore: pyarrow minimum to 14.0.1

* fix(build): pyarrow 14.0.0 min

* fix(build): removed ucsc-fetchchromsizes

* fix(build): install latest pyarrow through pip

* fix(build): bumped pydantic

* fix(deps): wrong pydantic max version

* fix(build): pinned pydantic

* chore(build): added log collection as artifact

* chore(deps): pinned ibis, pydantic,ray
---
 .github/workflows/CI.yml |  7 +++++++
 environment.yml          |  7 +++----
 requirements.txt         | 10 ++++------
 3 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index c56c8eae..c1952bb0 100644
--- a/.github/workflows/CI.yml
+++ b/.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
diff --git a/environment.yml b/environment.yml
index 157c1fe2..18ae2240 100644
--- a/environment.yml
+++ b/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
diff --git a/requirements.txt b/requirements.txt
index 14054e24..d3323ba1 100644
--- a/requirements.txt
+++ b/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