Update github actions to node v20

.github/workflows/autoblack_pull_request.yml

@@ -9,10 +9,10 @@ jobs:
   black-code:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.head_ref }}
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
       - run: pip install black

.github/workflows/docs-tests.yml

@@ -8,15 +8,15 @@ jobs:
   docs-build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: ammaraskar/sphinx-action@0.4
       with:
         docs-folder: "docs/"
 
   docs-link-check:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: ammaraskar/sphinx-action@0.4
       with:
         docs-folder: "docs/"

.github/workflows/github-actions.yml

@@ -7,8 +7,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v3
-      - uses: mamba-org/setup-micromamba@v1.4.3
+        uses: actions/checkout@v4
+      - uses: mamba-org/setup-micromamba@v1.8.0
         with:
           environment-name: deeprvat-gh-action
           environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
@@ -41,8 +41,8 @@ jobs:
     needs: DeepRVAT-Pipeline-Smoke-Tests
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v3
-      - uses: mamba-org/setup-micromamba@v1.4.3
+        uses: actions/checkout@v4
+      - uses: mamba-org/setup-micromamba@v1.8.0
         with:
           environment-name: deeprvat-gh-action
           environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
@@ -82,8 +82,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v3
-      - uses: mamba-org/setup-micromamba@v1.4.3
+        uses: actions/checkout@v4
+      - uses: mamba-org/setup-micromamba@v1.8.0
         with:
           environment-name: deeprvat-preprocess-gh-action
           environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml
@@ -115,8 +115,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v3
-      - uses: mamba-org/setup-micromamba@v1.4.3
+        uses: actions/checkout@v4
+      - uses: mamba-org/setup-micromamba@v1.8.0
         with:
           environment-name: deeprvat-preprocess-gh-action
           environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml
@@ -135,8 +135,8 @@ jobs:
     needs: DeepRVAT-Preprocessing-Pipeline-Smoke-Tests
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v3
-      - uses: mamba-org/setup-micromamba@v1.4.3
+        uses: actions/checkout@v4
+      - uses: mamba-org/setup-micromamba@v1.8.0
         with:
           environment-name: deeprvat-preprocess-gh-action
           environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml
@@ -149,7 +149,7 @@ jobs:
 
       - name: Cache Fasta file
         id: cache-fasta
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: example/preprocess/workdir/reference
           key: ${{ runner.os }}-reference-fasta
@@ -176,8 +176,8 @@ jobs:
     steps:
 
       - name: Check out repository code
-        uses: actions/checkout@v3
-      - uses: mamba-org/setup-micromamba@v1.4.3
+        uses: actions/checkout@v4
+      - uses: mamba-org/setup-micromamba@v1.8.0
         with:
           environment-name: deeprvat-preprocess-gh-action
           environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml
@@ -190,7 +190,7 @@ jobs:
 
       - name: Cache Fasta file
         id: cache-fasta
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: example/preprocess/workdir/reference
           key: ${{ runner.os }}-reference-fasta

.github/workflows/test-runner.yml

@@ -7,8 +7,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v3
-      - uses: mamba-org/setup-micromamba@v1.4.3
+        uses: actions/checkout@v4
+      - uses: mamba-org/setup-micromamba@v1.8.0
         with:
           environment-name: deeprvat-preprocess-gh-action
           environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
@@ -27,8 +27,8 @@ jobs:
     steps:
 
       - name: Check out repository code
-        uses: actions/checkout@v3
-      - uses: mamba-org/setup-micromamba@v1.4.3
+        uses: actions/checkout@v4
+      - uses: mamba-org/setup-micromamba@v1.8.0
         with:
           environment-name: deeprvat-preprocess-gh-action
           environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml

deeprvat/deeprvat/evaluate.py

@@ -162,9 +162,11 @@ def get_pvals(results, method_mapping=None, phenotype_mapping={}):
 
     if phenotype_mapping is not None:
         pvals["phenotype"] = pvals["phenotype"].apply(
-            lambda x: phenotype_mapping[x]
-            if x in phenotype_mapping
-            else " ".join(x.split("_"))
+            lambda x: (
+                phenotype_mapping[x]
+                if x in phenotype_mapping
+                else " ".join(x.split("_"))
+            )
         )
 
     return pvals

deeprvat/seed_gene_discovery/seed_gene_discovery.py

@@ -495,9 +495,9 @@ def update_config(
     if variant_type is not None:
         logger.info(f"Variant type is {variant_type}")
         if variant_type == "missense":
-            rare_threshold_config[
-                "Consequence_missense_variant"
-            ] = "Consequence_missense_variant == 1"
+            rare_threshold_config["Consequence_missense_variant"] = (
+                "Consequence_missense_variant == 1"
+            )
         elif variant_type == "plof":
             rare_threshold_config["is_plof"] = "is_plof == 1"
         elif variant_type == "all":
@@ -517,9 +517,9 @@ def update_config(
     if rare_maf is not None:
         logger.info(f"setting association testing maf to {rare_maf}")
         config["data"]["dataset_config"]["min_common_af"][maf_column] = rare_maf
-        rare_threshold_config[
-            maf_column
-        ] = f"{maf_column} < {rare_maf} and {maf_column} > 0"
+        rare_threshold_config[maf_column] = (
+            f"{maf_column} < {rare_maf} and {maf_column} > 0"
+        )
 
     logger.info(f"Rare variant thresholds: {rare_threshold_config}")
     with open(new_config_file, "w") as f: