Release 2.2

.dockerignore

@@ -1,5 +1,4 @@
 temp
-data/cms
 data/crw-cms.tar.gz
 data/crw-pdf
 docs/_*
@@ -8,6 +7,7 @@ docs/_*
 .github
 .vscode
 .git
-1.4/
-2.0/
 .venv/
+tests/results
+tests/html
+data/local_data/*/

.github/workflows/main.yml

@@ -5,28 +5,17 @@ on:
     branches:
       - main
       - develop
+    tags:
+      - 'v*'  # Push events to tags matching v*, i.e. v1.0, v20.15.10
   pull_request:
     branches:
       - main
       - develop
 
-
 permissions:
   pull-requests: write
 
 jobs:
-  initial-notification:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Initial notification
-        uses: rtCamp/action-slack-notify@v2
-        env:
-          SLACK_MESSAGE: 'Creating image in Docker Hub'
-          SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}
-          MSG_MINIMAL: true
-
   create-docker-tag:
     runs-on: ubuntu-latest
     steps:
@@ -92,16 +81,3 @@ jobs:
             ${{ steps.docker_meta.outputs.labels }}
             ```
           edit-mode: replace
-
-  final-notification:
-    runs-on: ubuntu-latest
-    needs: create-docker-tag
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Final notification
-        uses: rtCamp/action-slack-notify@v2
-        env:
-          SLACK_MESSAGE: 'New image created in Docker Hub'
-          SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}
-          MSG_MINIMAL: true

.gitignore

@@ -19,8 +19,11 @@ tests/**/*.png
 *.code-workspace
 docs/_build/*
 results/**
-1.4/**
-2.0/**
 .idea/**
 .python-version
 .venv
+data/rfam/cms/all.cm
+data/rfam/cms/all.cm.*
+data/rfam/cms/*.ssi
+data/crw/all.cm
+data/crw/*.ssi

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v5.0.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
@@ -11,11 +11,11 @@ repos:
     -   id: check-json
     -   id: mixed-line-ending
 -   repo: https://github.com/ambv/black
-    rev: 22.10.0
+    rev: 25.1.0
     hooks:
     -   id: black
 -   repo: https://github.com/PyCQA/pylint
-    rev: v2.15.6
+    rev: v3.3.6
     hooks:
     -   id: pylint
         args:
@@ -26,11 +26,11 @@ repos:
                 docs/conf.py
             )$
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 6.0.1
     hooks:
     -   id: isort
 - repo: https://github.com/MarcoGorelli/auto-walrus
-  rev: 'v0.2.2'
+  rev: '0.3.4'
   hooks:
     - id: auto-walrus
       name: Auto-apply the walrus operator :=

Dockerfile

@@ -1,7 +1,20 @@
-ARG BASE_IMAGE_VERSION=v2.1
+ARG BASE_IMAGE_VERSION=v2.2
 
 FROM rnacentral/r2dt-base:${BASE_IMAGE_VERSION}
 
+WORKDIR /rna/r2dt
+
+# Set up the Rfam and CRW data directories
+ADD data/rfam/cms/all.cm.tar.gz data/rfam/cms/
+RUN \
+    rm -f data/rfam/cms/all.cm.ssi && \
+    cmfetch --index data/rfam/cms/all.cm
+
+ADD data/crw/all.cm.tar.gz data/crw/
+RUN \
+    rm -f data/crw/all.cm.ssi && \
+    cmfetch --index data/crw/all.cm
+
 # Create venv
 ENV VENV=$RNA/venv
 ENV PATH="$VENV/bin:$PATH"
@@ -10,6 +23,4 @@ RUN python3 -m venv $VENV && pip3 install --upgrade pip
 ADD requirements.txt /tmp/requirements.txt
 RUN pip3 install -r /tmp/requirements.txt --no-cache-dir
 
-WORKDIR /rna/r2dt
-
 ADD . /rna/r2dt

Readme.md

@@ -1,6 +1,8 @@
 # R2DT
 
-**Version 2.1 (2025)**
+[![RTD badge](https://readthedocs.org/projects/r2dt/badge/?version=latest)](https://r2dt.readthedocs.io/en/latest/?badge=latest)
+[![GitHub release](https://img.shields.io/github/release/rnacentral/r2dt.svg)](https://github.com/r2dt-bio/r2dt/releases/)
+[![Citation Badge](https://api.juleskreuer.eu/citation-badge.php?doi=10.1038/s41467-021-23555-5)](https://www.nature.com/articles/s41467-021-23555-5)
 
 🚀 **[Read the R2DT documentation](https://r2dt.readthedocs.io/)** | 📄 [Latest paper](https://academic.oup.com/nar/article/53/4/gkaf032/8005627).
 

base_image/Dockerfile

@@ -5,11 +5,11 @@
     traveler_COMMIT=78c1cd63dcf40be83d97d07b8eb9eb6a9dc63f7f \
     jiffy_COMMIT=31d6c3b826d432a30620507830749cee58e15e68 \
     Rscape_VER=v2.0.4.c \
-    Ribovore_COMMIT=5df943c6f2866d7979bb13c948ca9d8531076898 \
+    Ribovore_COMMIT=50786b64c7f503a5a4481121a6cbd7592c7eee60 \
     BioEasel_VER=0.11 \
     INFERNAL_VER=1.1.5 \
-    RNArtist_VER=0.4.6
-
+    RNArtist_VER=0.4.6 \
+    RNAView_COMMIT=2f74eccc47c86acdf0627004e6243454978cd4c1
 
 FROM build AS rscape
 
@@ -109,6 +109,25 @@
 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 build AS rnaview
+
+# Install RNAview
+RUN \
+    git clone https://github.com/rcsb/RNAView && \
+    cd RNAView && \
+    git checkout ${RNAView_COMMIT} && \
+    make && \
+    mkdir -p /install/rnaview && \
+    cp -r ./* /install/rnaview/
+
+FROM build AS s5cmd
+
+# Install s5cmd, required for AWS S3
+RUN \
+    wget -q https://github.com/peak/s5cmd/releases/download/v2.3.0/s5cmd_2.3.0_Linux-64bit.tar.gz \
+    && tar -xzf s5cmd_2.3.0_Linux-64bit.tar.gz \
+    && mv s5cmd /usr/local/bin/
+
 FROM debian:bookworm-slim AS final-build
 
 ENV \
@@ -118,6 +137,7 @@
     apt-get -qq update && apt-get install -qq -y --no-install-recommends  \
     ncbi-blast+ \
     openjdk-17-jre-headless \
+    awscli \
     python3  \
     python3-pip  \
     python3-venv  \
@@ -154,7 +174,7 @@
     VECPLUSDIR="$RIBOINSTALLDIR/vecscreen_plus_taxonomy" \
     RRNASENSORDIR="$RIBOINSTALLDIR/rRNA_sensor"
 
 ENV \
     RIBOSCRIPTSDIR="$RIBOINSTALLDIR/ribovore" \
     RIBOINFERNALDIR="$RIBOINSTALLDIR/infernal/binaries" \
     RIBOEASELDIR="$RIBOINSTALLDIR/infernal/binaries" \
@@ -165,11 +185,22 @@
     PERL5LIB="$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"
 
+
+
+    ENV \
+    RNAVIEW="${RNA}/rnaview" \
+    PATH="${RNA}/rnaview/bin:${PATH}"
+
+
+COPY --from=rnaview /install/ ${RNA}/
+
 COPY --from=rscape /rna/rscape/ ${RNA}/rscape
 
 COPY --from=trnascan-se /install/ /usr
@@ -183,6 +214,7 @@
 
 COPY --from=ribovore-infernal-easel /install/ ${RNA}/ribovore
 COPY --from=rnartist /rnartist.jar /usr/local/bin/
+COPY --from=s5cmd /usr/local/bin/s5cmd /usr/local/bin/s5cmd
 
 COPY --from=traveler /install/traveler /usr/local/bin/traveler
 COPY --from=traveler /install/utils/* ${RNA}/traveler/utils/