Merge branch 'main' into resclust-ouput2

.github/dependabot.yml

@@ -8,4 +8,4 @@ updates:
   - package-ecosystem: "pip" # See documentation for possible values
     directory: "/" # Location of package manifests
     schedule:
-      interval: "weekly"
+      interval: "monthly"

.github/workflows/ci.yml

@@ -25,13 +25,17 @@ jobs:
 
       - run: poetry install --no-interaction --no-root
 
-      - uses: trunk-io/trunk-action@v1
-        with:
-          check-mode: all
+      - name: Check types
+        run: poetry run mypy src/ --ignore-missing-imports --explicit-package-bases --disallow-incomplete-defs # --check-untyped-defs
+
+      - name: Run sanity check on the API endpoints
+        run: poetry run pytest -m sanity -vvv
+
+      - name: Run unit tests
+        run: poetry run pytest -m "not (sanity or integration)" --cov=./ --cov-report=xml -v
 
-      - name: Test
-        run: |
-          poetry run pytest --cov=./ --cov-report=xml -v
+      - name: Run integration tests
+        run: poetry run pytest -m integration
 
       - name: Run codacy-coverage-reporter
         uses: codacy/codacy-coverage-reporter-action@v1

.github/workflows/docker-publish.yml

@@ -0,0 +1,47 @@
+name: build and publish image
+
+on:
+  push:
+    # run only against tags
+    tags:
+      - "*"
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/pypi-publish.yml

@@ -0,0 +1,30 @@
+name: publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  pypi_release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - uses: snok/install-poetry@v1
+        with:
+          version: 1.3.2
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      - run: poetry install
+
+      - run: poetry run pytest
+
+      - run: poetry config pypi-token.pypi "${{ secrets.PYPI_API_KEY }}"
+
+      - name: Publish package
+        run: poetry publish --build

.trunk/.gitignore

@@ -2,6 +2,8 @@
 *logs
 *actions
 *notifications
+*tools
 plugins
 user_trunk.yaml
 user.yaml
+tmp

.trunk/configs/.hadolint.yaml

@@ -0,0 +1,4 @@
+# Following source doesn't work in most setups
+ignored:
+  - SC1090
+  - SC1091

.trunk/configs/.isort.cfg

@@ -0,0 +1,2 @@
+[settings]
+profile=black

.trunk/configs/.markdownlint.yaml

@@ -1,10 +1,2 @@
-# Autoformatter friendly markdownlint config (all formatting rules disabled)
-default: true
-blank_lines: false
-bullet: false
-html: false
-indentation: false
-line_length: false
-spaces: false
-url: false
-whitespace: false
+# Prettier friendly markdownlint config (all formatting rules disabled)
+extends: markdownlint/style/prettier

.trunk/configs/.yamllint.yaml

@@ -0,0 +1,7 @@
+rules:
+  quoted-strings:
+    required: only-when-needed
+    extra-allowed: ["{|}"]
+  key-duplicates: {}
+  octal-values:
+    forbid-implicit-octal: true

.trunk/configs/ruff.toml

@@ -0,0 +1,5 @@
+# Generic, formatter-friendly config.
+select = ["B", "D3", "E", "F"]
+
+# Never enforce `E501` (line length violations). This should be handled by formatters.
+ignore = ["E501"]

.trunk/trunk.yaml

@@ -1,31 +1,42 @@
+# This file controls the behavior of Trunk: https://docs.trunk.io/cli
+# To learn more about the format of this file, see https://docs.trunk.io/reference/trunk-yaml
 version: 0.1
 cli:
-  version: 1.4.1
+  version: 1.21.0
+# Trunk provides extensibility via plugins. (https://docs.trunk.io/plugins)
 plugins:
   sources:
     - id: trunk
-      ref: v0.0.9
+      ref: v1.4.5
       uri: https://github.com/trunk-io/plugins
-lint:
-  enabled:
-    - [email protected]
-    - [email protected]
-    - [email protected]
-    - [email protected]
-    - git-diff-check
-    - [email protected]
-    - [email protected]
-    - [email protected]
-    - [email protected]
-    - [email protected]
-    - [email protected]
-  disabled:
-    - isort
+# Many linters and tools depend on runtimes - configure them here. (https://docs.trunk.io/runtimes)
 runtimes:
   enabled:
-    - go@1.18.3
+    - go@1.21.0
     - [email protected]
     - [email protected]
+# This is the section where you manage your linters. (https://docs.trunk.io/check/configuration)
+lint:
+  enabled:
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - git-diff-check
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
 actions:
   enabled:
     - trunk-announce

CITATION.cff

@@ -0,0 +1,29 @@
+# YAML 1.2
+# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
+cff-version: 1.0.3
+message: If you use this software, please cite it using these metadata.
+# FIXME title as repository name might not be the best name, please make human readable
+title: 'haddocking/arctic3d: v0.5.1'
+doi: 10.5281/zenodo.10839520
+# FIXME splitting of full names is error prone, please check if given/family name are correct
+authors:
+- given-names: Marco
+  family-names: Giulini
+  affiliation: Utrecht University
+- given-names: Rodrigo
+  family-names: Honorato
+  name-particle: Vargas
+  affiliation: '@UtrechtUniversity'
+- given-names: Aldo
+  family-names: van den Nieuwendijk
+  affiliation:
+- given-names: Alexandre
+  family-names: Bonvin
+  affiliation: '@UtrechtUniversity'
+- given-names: Anton
+  family-names: Bushuiev
+  affiliation: Czech Technical University in Prague
+version: 0.5.1
+date-released: 2024-03-19
+repository-code: https://github.com/haddocking/arctic3d
+license: cc-by-4.0

CONTRIBUTING.md

@@ -1,7 +1,5 @@
 # Developing ARCTIC-3D
 
-This section is still work in progress
-
 ## Installation
 
 We use `poetry` to manage the dependencies and the virtual environment, so it makes things easier if you need to install it first; check the [official documentation](https://python-poetry.org/docs/#installation) for more details.

Dockerfile

@@ -0,0 +1,6 @@
+FROM python:3.10
+WORKDIR /opt/software
+COPY . .
+RUN pip install .
+WORKDIR /data
+ENTRYPOINT [ "arctic3d" ]

README.md

@@ -1,17 +1,29 @@
 # ARCTIC-3D
 
+![PyPI - License](https://img.shields.io/pypi/l/arctic3d)
+![PyPI - Status](https://img.shields.io/pypi/status/arctic3d)
+![PyPI - Version](https://img.shields.io/pypi/v/arctic3d)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/arctic3d)
+
 [![ci](https://github.com/haddocking/arctic3d/actions/workflows/ci.yml/badge.svg)](https://github.com/haddocking/arctic3d/actions/workflows/ci.yml)
 [![Codacy Badge](https://app.codacy.com/project/badge/Coverage/dc788367452c47928e30f2f1f481d7e4)](https://www.codacy.com/gh/haddocking/arctic3d/dashboard?utm_source=github.com&utm_medium=referral&utm_content=haddocking/arctic3d&utm_campaign=Badge_Coverage)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/dc788367452c47928e30f2f1f481d7e4)](https://www.codacy.com/gh/haddocking/arctic3d/dashboard?utm_source=github.com&utm_medium=referral&utm_content=haddocking/arctic3d&utm_campaign=Badge_Grade)
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10839520.svg)](https://doi.org/10.5281/zenodo.10839520)
 [![SQAaaS badge shields.io](https://img.shields.io/badge/sqaaas%20software-bronze-e6ae77)](https://api.eu.badgr.io/public/assertions/oAuS52pQTWaC90qMk97hlA "SQAaaS bronze badge achieved")
-[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B%20%20%E2%97%8B%20%20%E2%97%8F-orange)](https://fair-software.eu)
+[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
+
 
 [![SQAaaS badge](https://github.com/EOSC-synergy/SQAaaS/raw/master/badges/badges_150x116/badge_software_bronze.png)](https://api.eu.badgr.io/public/assertions/oAuS52pQTWaC90qMk97hlA "SQAaaS bronze badge achieved")
 
-<img src="docs/imgs/arctic3d.png" width="450">
+<img src="https://raw.githubusercontent.com/haddocking/arctic3d/main/docs/imgs/arctic3d.png" width="450">
 
 **A**utomatic **R**etrieval and **C**lus**T**ering of **I**nterfaces in Complexes from **3D** structural information
 
+## WEB SERVER
+
+ARCTIC-3D is available at this webserver https://wenmr.science.uu.nl/arctic3d/
+
 ## ARCTIC-3D: all you want to know about protein-specific interfaces
 
 ARCTIC-3D is a software for data-mining and clustering of protein interface information. It allows you to retrieve all the existing interface information for your desired protein from the PDBE graph database (https://www.ebi.ac.uk/pdbe/pdbe-kb/), grouping similar interfaces in interacting surfaces.
@@ -28,6 +40,15 @@ Check [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 
 ### With `conda`
 
+Clone the repository on your computer and navigate to it
+
+```bash
+git clone [email protected]:haddocking/arctic3d.git
+cd arctic3d
+```
+
+Here you can create the arctic3d environment:
+
 ```bash
 conda create -n arctic3d python=3.10
 conda activate arctic3d
@@ -41,7 +62,11 @@ arctic3d -h
 bash install_blast_deps.sh
 ```
 
-And put `blastp` in your `$PATH`.
+And put `blastp` in your `$PATH` by adding the following line to your `.bashrc` or `.bash_profile` file:
+
+```bash
+export PATH="PATH_TO_YOUR_ARCTIC3D_INSTALLATION/src/ncbi-blast-2.15.0+/bin:$PATH"
+```
 
 ## Example usage
 
@@ -59,3 +84,9 @@ sphinx-build -E docs ./arctic3d-docs
 ```
 
 Then you can open the file `arctic3d-docs/index.html`, which contains all the necessary documentation.
+
+## Citing us
+
+If you used ARCTIC-3D in your work please cite the following publication:
+
+**Marco Giulini, Rodrigo V. Honorato, Jesús L. Rivera, and Alexandre MJJ Bonvin**: "ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information." Communications Biology 7, no. 1 (2024): 49. (www.nature.com/articles/s42003-023-05718-w)

install_blast_deps.sh

@@ -1,27 +1,38 @@
 #!/bin/bash
 CWD="$(pwd)"
+echo "Current working directory: ${CWD}"
 DB_DIR=${CWD}/db
+# if DB_DIR does not exist, create it
+if [ ! -d "$DB_DIR" ]; then
+	mkdir -p "$DB_DIR"
+fi
 SRC_DIR=${CWD}/src
 OS=$(uname -s)
-
+echo "Operating System: ${OS}"
 echo "Downloading BLAST+ executables and swissprot database..."
 
 #======================================================================#
 echo "Downloading BLAST+..."
 cd "${SRC_DIR}" || exit
 
-if [ "${OS}" == "Darwin" ]; then
+# if the OS is Darwin or Mac OS X, download the Mac OS X version of BLAST+
+# if the OS is Linux, download the Linux version of BLAST+
+if [ "${OS}" == "Darwin" ] || [ "${OS}" == "Mac OS X" ]; then
 	# Do something under Mac OS X platform
-	BLAST_URL="https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.13.0+-x64-macosx.tar.gz"
+	echo "Downloading BLAST+ for Mac OS X..."
+	BLAST_URL="https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.15.0/ncbi-blast-2.15.0+-x64-macosx.tar.gz"
 elif [ "${OS}" == "Linux" ]; then
 	# Do something under GNU/Linux platform
-	BLAST_URL="https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.13.0+-x64-linux.tar.gz"
+	echo "Downloading BLAST+ for Linux..."
+	BLAST_URL="https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.15.0/ncbi-blast-2.15.0+-x64-linux.tar.gz"
 fi
 
+echo "Downloading BLAST+ from ${BLAST_URL}..."
 wget "$BLAST_URL" >/dev/null 2>&1
+echo "BLAST downloaded in ${SRC_DIR}"
 
-tar -xzf ncbi-blast-2.13.0+-x64-*.tar.gz
-rm ncbi-blast-2.13.0+-x64-*.tar.gz
+tar -xzf ncbi-blast-2.15.0+-x64-*.tar.gz
+rm ncbi-blast-2.15.0+-x64-*.tar.gz
 #======================================================================#
 echo "Downloading SwissProt DB..."
 cd "$DB_DIR" || exit