Release 2.0

.devcontainer/Dockerfile

@@ -0,0 +1,10 @@
+FROM mcr.microsoft.com/devcontainers/universal:2-linux
+
+RUN wget -qO - 'https://proget.makedeb.org/debian-feeds/prebuilt-mpr.pub' | gpg --dearmor | sudo tee /usr/share/keyrings/prebuilt-mpr-archive-keyring.gpg 1> /dev/null && \
+    echo "deb [arch=all,$(dpkg --print-architecture) signed-by=/usr/share/keyrings/prebuilt-mpr-archive-keyring.gpg] https://proget.makedeb.org prebuilt-mpr $(lsb_release -cs)" | sudo tee /etc/apt/sources.list.d/prebuilt-mpr.list && \
+    sudo apt-get -qq update && \
+    sudo apt-get install --no-install-recommends -qq -y \
+    imagemagick \
+    libmagickwand-dev \
+    chafa \
+    just

.devcontainer/devcontainer.json

@@ -0,0 +1,16 @@
+{
+  "name": "R2DT",
+  "build": {
+    "dockerfile": "Dockerfile"
+  },
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-vscode-remote.remote-containers",
+        "ms-azuretools.vscode-docker"
+      ]
+    }
+  }
+}

.dockerignore

@@ -9,3 +9,4 @@ docs/_*
 .vscode
 .git
 1.4/
+.venv/

.gitattributes

@@ -0,0 +1,2 @@
+# Mark PostScript files as vendored
+*.ps linguist-vendored

.github/workflows/parallel-base-image.yml

@@ -0,0 +1,101 @@
+name: Build and Push Base Docker image (parallel)
+
+on:
+  pull_request:
+    paths:
+      - 'base_image/**'
+      - '.github/workflows/parallel-base-image.yml'
+
+jobs:
+  build-stages:
+    runs-on: ${{ matrix.runner }}
+    strategy:
+      fail-fast: true
+      matrix:
+        stage: [rscape, tRNAscan-SE, Bio-Easel, traveler, scripts, ribovore-infernal-easel]
+        platform: [linux/amd64, linux/arm64]
+        include:
+          - platform: 'linux/amd64'
+            runner: 'ubuntu-latest'
+            shorthand: 'amd64'
+          - platform: 'linux/arm64'
+            runner: 'buildjet-2vcpu-ubuntu-2204-arm'
+            shorthand: 'arm64'
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USER }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Build ${{ matrix.stage }} stage
+        uses: docker/build-push-action@v5
+        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
+          file: base_image/Dockerfile
+          context: base_image/
+
+  final-build:
+    needs: build-stages
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Docker Meta
+        id: docker_meta
+        uses: docker/metadata-action@v4
+        with:
+          images: rnacentral/r2dt-base
+          flavor: latest=false
+          tags: |
+            type=ref,event=pr
+
+      - name: Log in to DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USER }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Build and push final Docker image
+        uses: docker/build-push-action@v5
+        with:
+          platforms: linux/amd64,linux/arm64
+          push: true
+          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-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-final
+          cache-to: type=registry,ref=rnacentral/r2dt-base:cache-final,mode=max
+          file: base_image/Dockerfile
+          context: base_image/
+          target: final-build

.gitignore

@@ -6,6 +6,7 @@ data/crw-bpseq/*.sto
 data/crw-bpseq/*.fasta
 data/cms/*
 data/rfam/RF*/*.seed
+data/local_data/*
 RF00177.cm
 temp.*
 output/*
@@ -19,6 +20,8 @@ tests/**/*.png
 docs/_build/*
 results/**
 1.4/**
+2.0/**
 .idea/**
 .python-version
 .venv
+all.fa*

.pre-commit-config.yaml

@@ -29,4 +29,9 @@ repos:
     rev: 5.12.0
     hooks:
     -   id: isort
+- repo: https://github.com/MarcoGorelli/auto-walrus
+  rev: 'v0.2.2'
+  hooks:
+    - id: auto-walrus
+      name: Auto-apply the walrus operator :=
 exclude: .+?\.(cm|ps|bpseq|tr|fasta|xml|svg)$

.pylintrc

@@ -5,10 +5,6 @@
 # only in one or another interpreter, leading to false positives when analysed.
 analyse-fallback-blocks=no
 
-# Clear in-memory caches upon conclusion of linting. Useful if running pylint
-# in a server-like mode.
-clear-cache-post-run=no
-
 # Load and enable all available extensions. Use --list-extensions to see a list
 # all available extensions.
 #enable-all-extensions=
@@ -93,12 +89,6 @@ py-version=3.11
 # Discover python modules and packages in the file system subtree.
 recursive=yes
 
-# Add paths to the list of the source roots. Supports globbing patterns. The
-# source root is an absolute path or a path relative to the current working
-# directory used to determine a package namespace for modules located under the
-# source root.
-source-roots=.
-
 # When enabled, pylint would attempt to guess common misconfiguration and emit
 # user-friendly hints instead of false-positive error messages.
 suggestion-mode=yes
@@ -363,9 +353,6 @@ single-line-if-stmt=no
 # one.
 allow-any-import-level=
 
-# Allow explicit reexports by alias from a package __init__.
-allow-reexport-from-package=no
-
 # Allow wildcard imports from modules that define __all__.
 allow-wildcard-with-all=no
 

Dockerfile

@@ -1,4 +1,6 @@
-FROM rnacentral/r2dt-base:pr-123
+ARG BASE_IMAGE_VERSION=v2.0
+
+FROM rnacentral/r2dt-base:${BASE_IMAGE_VERSION}
 
 # Create venv
 ENV VENV=$RNA/venv

Readme.md

@@ -1,10 +1,10 @@
 # R2DT
 
-**Version 1.4 (2023)**
+**Version 2.0 (2024)**
 
 **[See the R2DT documentation](https://r2dt.readthedocs.io/)**
 
-The [R2DT software](https://github.com/RNAcentral/R2DT) automatically generates [RNA secondary structure](https://en.wikipedia.org/wiki/Nucleic_acid_secondary_structure) diagrams in consistent, reproducible and recongnisable layouts using a library of templates representing a wide range of RNAs.
+The [R2DT software](https://github.com/r2dt-bio/R2DT) automatically generates [RNA secondary structure](https://en.wikipedia.org/wiki/Nucleic_acid_secondary_structure) diagrams in consistent, reproducible and recongnisable layouts using a library of templates representing a wide range of RNAs.
 
 ## Examples
 
@@ -20,6 +20,8 @@ R2DT can be used in a number of ways:
 * [API](https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=r2dt) powered by EMBL-EBI Web Services
 * As a command line tool with [Docker](https://www.docker.com), [Singularity](https://sylabs.io/docs/#singularity), or in a bare metal installation
 
+You can also [![open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/RNAcentral/R2DT)
+
 ## Citation
 
 If you use R2DT in your work, please consider citing the following paper:

base_image/Dockerfile

@@ -1,13 +1,14 @@
-FROM gcc:13 as build
+FROM gcc:13 AS build
 
 ENV tRNAscan_VER=2.0.11 \
-    BioEasel_COMMIT=e7fae0ab43fc47058183b71ff498ee0d0d2de6a7 \
+    BioEasel_COMMIT=a52f0f7f7cae879bb95489bb794c04c1a0110aa7 \
     traveler_COMMIT=0ee67cbb9c5aaa2f98340065fd047c9a8feea53e \
     jiffy_COMMIT=31d6c3b826d432a30620507830749cee58e15e68 \
-    Rscape_VER=v2.0.2.d \
-    Ribovore_VER=1.0.5 \
+    Rscape_VER=v2.0.4.c \
+    Ribovore_COMMIT=5df943c6f2866d7979bb13c948ca9d8531076898 \
     BioEasel_VER=0.11 \
-    INFERNAL_VER=1.1.5
+    INFERNAL_VER=1.1.5 \
+    RNArtist_VER=0.4.6
 
 
 FROM build AS rscape
@@ -20,7 +21,7 @@ RUN  cp /usr/share/automake-1.16/config.guess /rscape/lib/R2R/R2R-current/config
       mkdir -p /rna/rscape && cd rscape && ./configure --prefix=/rna/rscape -q && make -j 2 && make install
 
 
-FROM build AS tRNAscan-SE
+FROM build AS trnascan-se
 
 # Install tRNAScan-SE
 RUN \
@@ -29,7 +30,7 @@ RUN \
     cd tRNAscan-SE-${tRNAscan_VER} && ./configure -q --prefix=/install/ && make && make install
 
 
-FROM build AS Bio-Easel
+FROM build AS bio-easel
 
 # Install Bio-Easel
 RUN \
@@ -68,16 +69,27 @@ RUN \
     chmod +x *.pl && mkdir -p /install/ && cp *.pl /install/
 
 
-FROM build as ribovore-infernal-easel
+FROM build AS ribovore-infernal-easel
 
-# Install Ribovore, Infernal, and easel
+# Install Ribovore
 RUN \
     mkdir -p /install/ && \
     cd /install/ && \
-    wget --no-verbose -O - "https://raw.githubusercontent.com/ncbi/ribovore/ribovore-${Ribovore_VER}/install.sh" | bash -s -- "rt-linux" && \
-    rm -Rf /install/ribovore/models /install/ribovore/testfiles
+    git clone https://github.com/ncbi/ribovore && \
+    cd ribovore && \
+    git checkout ${Ribovore_COMMIT} && \
+    rm -Rf .git models testfiles taxonomy
 
-# Overwrite Infernal binaries installed by Ribovore by compiling Infernal from source
+# Install Sequip (Ribovore dependency)
+RUN \
+    cd /install/ && \
+    sequip_version=ribovore-1.0.5 && \
+    wget -O sequip-${sequip_version}.zip https://github.com/nawrockie/sequip/archive/${sequip_version}.zip && \
+    unzip sequip-${sequip_version}.zip && \
+    mv sequip-${sequip_version} sequip && \
+    rm sequip-${sequip_version}.zip
+
+# Install Infernal
 RUN \
     wget -q "http://eddylab.org/infernal/infernal-${INFERNAL_VER}.tar.gz" && \
     tar xzf "infernal-${INFERNAL_VER}.tar.gz" && \
@@ -88,20 +100,29 @@ RUN \
     make install && \
     cd easel && \
     make install && \
+    mkdir -p /install/infernal/binaries && \
     mv /infernal/bin/* /install/infernal/binaries/
 
+FROM build AS rnartist
+
+# Install RNArtist
+RUN \
+    wget -q -O rnartist.jar https://github.com/fjossinet/RNArtistCore/releases/download/${RNArtist_VER}-SNAPSHOT/rnartistcore-${RNArtist_VER}-SNAPSHOT-jar-with-dependencies.jar
 
-FROM debian:bookworm-slim as final-build
+FROM debian:bookworm-slim AS final-build
 
 ENV \
     RNA=/rna
 
 RUN \
     apt-get -qq update && apt-get install -qq -y --no-install-recommends  \
+    ncbi-blast+ \
+    openjdk-17-jre-headless \
     python3  \
     python3-pip  \
     python3-venv  \
     python3-cairo  \
+    chafa \
     procps \
     perl &&  \
     rm -rf /var/lib/{apt,lpkg,cache,log}
@@ -129,7 +150,7 @@ ENV \
     RIBOSCRIPTSDIR="$RIBOINSTALLDIR/ribovore" \
     RIBOINFERNALDIR="$RIBOINSTALLDIR/infernal/binaries" \
     RIBOSEQUIPDIR="$RIBOINSTALLDIR/sequip" \
-    RIBOBLASTDIR="$RIBOINSTALLDIR/ncbi-blast/bin" \
+    RIBOBLASTDIR="/usr/bin" \
     VECPLUSDIR="$RIBOINSTALLDIR/vecscreen_plus_taxonomy" \
     RRNASENSORDIR="$RIBOINSTALLDIR/rRNA_sensor"
 
@@ -138,30 +159,30 @@ ENV \
     RIBOINFERNALDIR="$RIBOINSTALLDIR/infernal/binaries" \
     RIBOEASELDIR="$RIBOINSTALLDIR/infernal/binaries" \
     RIBOSEQUIPDIR="$RIBOINSTALLDIR/sequip" \
-    RIBOBLASTDIR="$RIBOINSTALLDIR/ncbi-blast/bin" \
     RIBOTIMEDIR=/usr/bin \
     RRNASENSORDIR="$RIBOINSTALLDIR/rRNA_sensor" \
     VECPLUSDIR="$RIBOINSTALLDIR/vecscreen_plus_taxonomy" \
     PERL5LIB="$RIBOSCRIPTSDIR":"$RIBOSEQUIPDIR":"$VECPLUSDIR":"$PERL5LIB" \
-    PATH="$RIBOSCRIPTSDIR":"$RIBOBLASTDIR":"$RRNASENSORDIR":"$PATH"
+    PATH="$RIBOSCRIPTSDIR":"$RRNASENSORDIR":"$PATH"
 
 ENV \
-    PATH="$RIBOSCRIPTSDIR":"$RIBOBLASTDIR":"$RRNASENSORDIR":"$PATH" \
+    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"
 
 COPY --from=rscape /rna/rscape/ ${RNA}/rscape
 
-COPY --from=tRNAscan-SE /install/ /usr
+COPY --from=trnascan-se /install/ /usr
 RUN sed -i -e 's|/install/bin|/usr/bin|' -e 's|/install/lib|/usr/lib|' /usr/bin/tRNAscan-SE.conf
 
-COPY --from=Bio-Easel /install/usr/* /usr
-COPY --from=Bio-Easel /install/Bio-Easel $RNA/Bio-Easel
-COPY --from=Bio-Easel /usr/local/share/perl/5.36.0/ /usr/share/perl/5.36/
+COPY --from=bio-easel /install/usr/* /usr
+COPY --from=bio-easel /install/Bio-Easel $RNA/Bio-Easel
+COPY --from=bio-easel /usr/local/share/perl/5.36.0/ /usr/share/perl/5.36/
 
 COPY --from=scripts /install/ ${RNA}/jiffy-infernal-hmmer-scripts/
 
 COPY --from=ribovore-infernal-easel /install/ ${RNA}/ribovore
+COPY --from=rnartist /rnartist.jar /usr/local/bin/
 
 COPY --from=traveler /install/traveler /usr/local/bin/traveler
 COPY --from=traveler /install/utils/* ${RNA}/traveler/utils/