Bump pytorch-lightning from 1.8.3.post1 to 2.3.3

.github/workflows/docs.yml

@@ -3,6 +3,8 @@ on:
   workflow_dispatch: {}
   push:
     branches: [main] # branch to trigger deployment
+permissions:
+  contents: write
 jobs:
   build:
     runs-on: ubuntu-latest

.github/workflows/test.yml

@@ -26,7 +26,7 @@ jobs:
           version: 1.8.5
       - name: Install dependencies and run tests
         run: |
-          export CI_CD=1
+          export BIH_HPC=0
           poetry install
           poetry run task coverage-test
       - name: Generate coverage badge

.gitignore

@@ -1,5 +1,7 @@
 *__pycache__
 *.pyc
+dist/
 
 data/*
 !*.gitkeep
+docs/build/

config/plugins/genetic/debug.yaml

@@ -1,6 +1,6 @@
 name: GeneticPlugin
 __init__: __init__
-src: ['all_chrs_extended_tr.fincad100', 'all_chrs_valid.fincad100', 'all_chrs_test.fincad100']
+src: ['genetic_extended_tr', 'genetic_valid', 'genetic_test']
 src_names: ['train', 'valid', 'test']
 genetic_json: 'res/ukb_genetic.json'
 ontology: 'molecular_function'

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "udm"
-version = "0.2.0"
+version = "1.0.0"
 description = "DataModule used for unified access to UKBB data across BIH projects."
 authors = [
     "Luis Herrmann <luismherrmann@gmail.com>",
@@ -48,7 +48,7 @@ scipy = {version = "^1.9.3", source = "pypi"}
 tqdm = {version = "^4.64.1", source = "pypi"}
 wandb = {version = "^0.13.6", source = "pypi"}
 zstandard = {version = "^0.19.0", source = "pypi"}
-pytorch-lightning = {version = "^1.8.3.post1", source = "pypi"}
+pytorch-lightning = {version = "^2.3.3.0", source = "pypi"}
 pytest = "^7.2.1"
 dill = "^0.3.6"
 tensorstore = "^0.1.33"