Merge pull request #148 from r2dt-bio/develop

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/base-image.yml

@@ -37,7 +37,7 @@ jobs:
 
       - name: Build and push Docker image
         id: build
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           platforms: linux/amd64,linux/arm64
           push: true

.github/workflows/main.yml

@@ -9,6 +9,10 @@ on:
       - main
       - develop
 
+
+permissions:
+  pull-requests: write
+
 jobs:
   initial-notification:
     runs-on: ubuntu-latest
@@ -53,7 +57,7 @@ jobs:
             type=semver,pattern={{major}}.{{minor}}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           platforms: linux/amd64,linux/arm64
           push: true
@@ -63,7 +67,7 @@ jobs:
           tags: ${{ steps.docker_meta.outputs.tags }}
 
       - name: Find comment for image tags
-        uses: peter-evans/find-comment@v2
+        uses: peter-evans/find-comment@v3
         if: github.event_name == 'pull_request'
         id: fc
         with:
@@ -72,7 +76,7 @@ jobs:
           body-includes: Docker image tag(s) pushed
 
       - name: Create or update comment for image tags
-        uses: peter-evans/create-or-update-comment@v2
+        uses: peter-evans/create-or-update-comment@v4
         if: github.event_name == 'pull_request'
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}

.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@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
+          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@v6
+        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 +20,7 @@ tests/**/*.png
 docs/_build/*
 results/**
 1.4/**
+2.0/**
 .idea/**
 .python-version
 .venv

.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: