r2dt-bio · AntonPetrov · Dec 22, 2024 · Oct 13, 2024 · Oct 13, 2024 · Oct 13, 2024
diff --git a/.github/workflows/base-image.yml b/.github/workflows/base-image.yml
@@ -35,6 +35,10 @@ jobs:
           tags: |
             type=ref,event=pr
 
+      - name: Calculate Dockerfile hash
+        id: dockerfile_hash
+        run: echo "hash=$(sha256sum base_image/Dockerfile | cut -d' ' -f1)" >> $GITHUB_OUTPUT
+
       - name: Build and push Docker image
         id: build
         uses: docker/build-push-action@v6
@@ -43,7 +47,7 @@ jobs:
           push: true
           labels: ${{ steps.docker_meta.outputs.labels }}
           tags: ${{ steps.docker_meta.outputs.tags }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
+          cache-from: type=registry,ref=rnacentral/r2dt-base:cache-${{ steps.dockerfile_hash.outputs.hash }}
+          cache-to: type=registry,ref=rnacentral/r2dt-base:cache-${{ steps.dockerfile_hash.outputs.hash }},mode=max
           file: base_image/Dockerfile
           context: base_image/
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - main
+      - develop
   pull_request:
     branches:
       - main

diff --git a/.github/workflows/parallel-base-image.yml b/.github/workflows/parallel-base-image.yml
@@ -34,13 +34,17 @@ jobs:
           username: ${{ secrets.DOCKER_USER }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
+      - name: Calculate Dockerfile hash
+        id: dockerfile_hash
+        run: echo "hash=$(sha256sum base_image/Dockerfile | cut -d' ' -f1)" >> $GITHUB_OUTPUT
+
       - name: Build ${{ matrix.stage }} stage
         uses: docker/build-push-action@v6
         with:
           platforms: ${{ matrix.platform }}
           target: ${{ matrix.stage }}
-          cache-from: type=registry,ref=rnacentral/r2dt-base:cache-${{ matrix.stage }}-${{ matrix.shorthand }}
-          cache-to: type=registry,ref=rnacentral/r2dt-base:cache-${{ matrix.stage }}-${{ matrix.shorthand }},mode=max
+          cache-from: type=registry,ref=rnacentral/r2dt-base:cache-${{ matrix.stage }}-${{ matrix.shorthand }}-${{ steps.dockerfile_hash.outputs.hash }}
+          cache-to: type=registry,ref=rnacentral/r2dt-base:cache-${{ matrix.stage }}-${{ matrix.shorthand }}-${{ steps.dockerfile_hash.outputs.hash }},mode=max
           file: base_image/Dockerfile
           context: base_image/
 
@@ -66,6 +70,10 @@ jobs:
           tags: |
             type=ref,event=pr
 
+      - name: Calculate Dockerfile hash
+        id: dockerfile_hash
+        run: echo "hash=$(sha256sum base_image/Dockerfile | cut -d' ' -f1)" >> $GITHUB_OUTPUT
+
       - name: Log in to DockerHub
         uses: docker/login-action@v3
         with:
@@ -80,22 +88,22 @@ jobs:
           labels: ${{ steps.docker_meta.outputs.labels }}
           tags: ${{ steps.docker_meta.outputs.tags }}
           cache-from: |
-            type=registry,ref=rnacentral/r2dt-base:cache-rscape-amd64
-            type=registry,ref=rnacentral/r2dt-base:cache-tRNAscan-SE-amd64
-            type=registry,ref=rnacentral/r2dt-base:cache-Bio-Easel-amd64
-            type=registry,ref=rnacentral/r2dt-base:cache-traveler-amd64
-            type=registry,ref=rnacentral/r2dt-base:cache-scripts-amd64
-            type=registry,ref=rnacentral/r2dt-base:cache-ribovore-infernal-easel-amd64
+            type=registry,ref=rnacentral/r2dt-base:cache-rscape-amd64-${{ steps.dockerfile_hash.outputs.hash }}
+            type=registry,ref=rnacentral/r2dt-base:cache-tRNAscan-SE-amd64-${{ steps.dockerfile_hash.outputs.hash }}
+            type=registry,ref=rnacentral/r2dt-base:cache-Bio-Easel-amd64-${{ steps.dockerfile_hash.outputs.hash }}
+            type=registry,ref=rnacentral/r2dt-base:cache-traveler-amd64-${{ steps.dockerfile_hash.outputs.hash }}
+            type=registry,ref=rnacentral/r2dt-base:cache-scripts-amd64-${{ steps.dockerfile_hash.outputs.hash }}
+            type=registry,ref=rnacentral/r2dt-base:cache-ribovore-infernal-easel-amd64-${{ steps.dockerfile_hash.outputs.hash }}
 
-            type=registry,ref=rnacentral/r2dt-base:cache-rscape-arm64
-            type=registry,ref=rnacentral/r2dt-base:cache-tRNAscan-SE-arm64
-            type=registry,ref=rnacentral/r2dt-base:cache-Bio-Easel-arm64
-            type=registry,ref=rnacentral/r2dt-base:cache-traveler-arm64
-            type=registry,ref=rnacentral/r2dt-base:cache-scripts-arm64
-            type=registry,ref=rnacentral/r2dt-base:cache-ribovore-infernal-easel-arm64
+            type=registry,ref=rnacentral/r2dt-base:cache-rscape-arm64-${{ steps.dockerfile_hash.outputs.hash }}
+            type=registry,ref=rnacentral/r2dt-base:cache-tRNAscan-SE-arm64-${{ steps.dockerfile_hash.outputs.hash }}
+            type=registry,ref=rnacentral/r2dt-base:cache-Bio-Easel-arm64-${{ steps.dockerfile_hash.outputs.hash }}
+            type=registry,ref=rnacentral/r2dt-base:cache-traveler-arm64-${{ steps.dockerfile_hash.outputs.hash }}
+            type=registry,ref=rnacentral/r2dt-base:cache-scripts-arm64-${{ steps.dockerfile_hash.outputs.hash }}
+            type=registry,ref=rnacentral/r2dt-base:cache-ribovore-infernal-easel-arm64-${{ steps.dockerfile_hash.outputs.hash }}
 
-            type=registry,ref=rnacentral/r2dt-base:cache-final
-          cache-to: type=registry,ref=rnacentral/r2dt-base:cache-final,mode=max
+            type=registry,ref=rnacentral/r2dt-base:cache-final-${{ steps.dockerfile_hash.outputs.hash }}
+          cache-to: type=registry,ref=rnacentral/r2dt-base:cache-final-${{ steps.dockerfile_hash.outputs.hash }},mode=max
           file: base_image/Dockerfile
           context: base_image/
           target: final-build
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-ARG BASE_IMAGE_VERSION=v2.0
+ARG BASE_IMAGE_VERSION=v2.0.1
 
 FROM rnacentral/r2dt-base:${BASE_IMAGE_VERSION}
 

diff --git a/base_image/Dockerfile b/base_image/Dockerfile
@@ -2,7 +2,7 @@
 
 ENV tRNAscan_VER=2.0.11 \
     BioEasel_COMMIT=a52f0f7f7cae879bb95489bb794c04c1a0110aa7 \
-    traveler_COMMIT=0ee67cbb9c5aaa2f98340065fd047c9a8feea53e \
+    traveler_COMMIT=8054f5bee8327bb158385893e0633d4242676f95 \
     jiffy_COMMIT=31d6c3b826d432a30620507830749cee58e15e68 \
     Rscape_VER=v2.0.4.c \
     Ribovore_COMMIT=5df943c6f2866d7979bb13c948ca9d8531076898 \
@@ -154,7 +154,7 @@
    VECPLUSDIR="$RIBOINSTALLDIR/vecscreen_plus_taxonomy" \
    RRNASENSORDIR="$RIBOINSTALLDIR/rRNA_sensor"

 ENV \
    RIBOSCRIPTSDIR="$RIBOINSTALLDIR/ribovore" \
    RIBOINFERNALDIR="$RIBOINSTALLDIR/infernal/binaries" \
    RIBOEASELDIR="$RIBOINSTALLDIR/infernal/binaries" \
@@ -165,7 +165,7 @@
    PERL5LIB="$RIBOSCRIPTSDIR":"$RIBOSEQUIPDIR":"$VECPLUSDIR":"$PERL5LIB" \
    PATH="$RIBOSCRIPTSDIR":"$RRNASENSORDIR":"$PATH"

 ENV \
    PATH="$RIBOSCRIPTSDIR":"$RRNASENSORDIR":"$PATH" \
    PATH="$RNA/traveler/bin:$RIBODIR:$RIBOEASELDIR:$RIBOINFERNALDIR:/rna/rscape/bin:/rna/jiffy-infernal-hmmer-scripts:/rna/r2dt:/rna/RNAstructure/exe:$PATH" \
    PERL5LIB="$RIBOSCRIPTSDIR:$RIBOSEQUIPDIR:$VECPLUSDIR:$BIOEASELDIR:$RIBODIR:$EPNOPTDIR:$EPNOFILEDIR:$EPNTESTDIR:$PERL5LIB:/usr/lib/tRNAscan-SE"

diff --git a/examples/bad-fasta-name.fasta b/examples/bad-fasta-name.fasta
@@ -0,0 +1,4 @@
+>DB|TEXT|MORE Some example name
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
+GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
+U
diff --git a/r2dt.py b/r2dt.py
@@ -242,6 +242,8 @@ def draw(
     if not quiet:
         rprint(shared.get_r2dt_version_header())
 
+    fasta_input = shared.sanitise_fasta(fasta_input)
+
     if is_templatefree(fasta_input):
         if not quiet:
             rprint("Detected templatefree input.")
@@ -526,6 +528,8 @@ def gtrnadb_draw(
         rprint(shared.get_r2dt_version_header())
     os.makedirs(output_folder, exist_ok=True)
 
+    fasta_input = shared.sanitise_fasta(fasta_input)
+
     if domain and isotype:
         core.visualise_trna(
             domain.upper(),
@@ -592,6 +596,9 @@ def rnasep_draw(
     if not quiet:
         rprint(shared.get_r2dt_version_header())
     os.makedirs(output_folder, exist_ok=True)
+
+    fasta_input = shared.sanitise_fasta(fasta_input)
+
     with open(
         shared.get_ribotyper_output(
             fasta_input, output_folder, config.RNASEP_CM_LIBRARY, skip_ribovore_filters
@@ -652,6 +659,9 @@ def rrna_draw(
     if not quiet:
         rprint(shared.get_r2dt_version_header())
     os.makedirs(output_folder, exist_ok=True)
+
+    fasta_input = shared.sanitise_fasta(fasta_input)
+
     with open(
         shared.get_ribotyper_output(
             fasta_input, output_folder, config.CRW_CM_LIBRARY, skip_ribovore_filters
@@ -712,6 +722,9 @@ def ribovision_draw_lsu(
     if not quiet:
         rprint(shared.get_r2dt_version_header())
     os.makedirs(output_folder, exist_ok=True)
+
+    fasta_input = shared.sanitise_fasta(fasta_input)
+
     with open(
         shared.get_ribotyper_output(
             fasta_input,
@@ -768,6 +781,9 @@ def ribovision_draw_ssu(
     if not quiet:
         rprint(shared.get_r2dt_version_header())
     os.makedirs(output_folder, exist_ok=True)
+
+    fasta_input = shared.sanitise_fasta(fasta_input)
+
     with open(
         shared.get_ribotyper_output(
             fasta_input,
@@ -853,6 +869,9 @@ def rfam_draw(
         template_type = "rscape"
     else:
         template_type = "auto"
+
+    fasta_input = shared.sanitise_fasta(fasta_input)
+
     if rfam.has_structure(rfam_acc):
         rfam.generate_2d(
             rfam_acc,
@@ -934,6 +953,9 @@ def force_draw(
     # pylint: disable=too-many-arguments, too-many-locals
     if not quiet:
         rprint(shared.get_r2dt_version_header())
+
+    fasta_input = shared.sanitise_fasta(fasta_input)
+
     model_type = lm.get_model_type(model_id)
     if not model_type:
         rprint("Error: Model not found. Please check model_id")
@@ -1029,6 +1051,8 @@ def templatefree(fasta_input, output_folder, rnartist, rscape, quiet):
     if rnartist and rscape:
         raise ValueError("Please specify only one template type")
 
+    fasta_input = shared.sanitise_fasta(fasta_input)
+
     if rnartist:
         output_folder = Path(output_folder)
         results_folder = output_folder / "results"

diff --git a/tests/examples/animate/PZ39_Dfold_3.animated.svg b/tests/examples/animate/PZ39_Dfold_3.animated.svg
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,6 +4,7 @@ on: @@
       push:
         branches:
           - main
+          - develop
       pull_request:
         branches:
           - main
@@ Expand Down @@