ci: implement ruff

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,29 +1,29 @@
 ---
 name: Bug report
 about: Create a report to help us improve
-title: 'Bug: <please fill here>'
-labels: 'bug'
-assignees: ''
-
+title: "Bug: <please fill here>"
+labels: "bug"
+assignees: ""
 ---
 
 **Describe the bug**
 A clear and concise description of what the bug is.
 
 **Environment:**
+
 - OS system:
 - Version:
-- Branch commit ID: 
+- Branch commit ID:
 - Inputs:
 
 **To Reproduce**
 Steps/commands/screenshots to reproduce the behaviour:
- 
- 1.  
- 
- 2.
- 
- 3. 
+
+1.
+
+2.
+
+3.
 
 **Expected Results**
 A clear and concise description of what you expected to happen.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,10 +1,9 @@
 ---
 name: Feature request
 about: Suggest an idea for this project
-title: 'Add/edit'
-labels: 'feature'
-assignees: ''
-
+title: "Add/edit"
+labels: "feature"
+assignees: ""
 ---
 
 **Is your feature request related to a problem? Please describe.**
@@ -20,7 +19,8 @@ A clear and concise description of any alternative solutions or features you've
 Add any other context or screenshots about the feature request here.
 
 **Checks for the developer**
-After having implemented the request, please remember to: 
+After having implemented the request, please remember to:
+
 - [ ] Add all the necessary tests. Make sure that the parameter functionality is well tested, from all points of views.
 - [ ] Add the proper documentation to the source code (docstrings).
 - [ ] Add the proper documentation to the readme. Examples about how using the new feature should be clear and easy to follow.

.github/actions/install-python-and-package/action.yml

@@ -3,7 +3,6 @@ name: "Install Python and deeprank2"
 description: "Installs Python, updates pip and installs deeprank2 together with its dependencies."
 
 inputs:
-
   python-version:
     required: false
     description: "The Python version to use. Specify major and minor version, e.g. '3.10'."
@@ -15,14 +14,13 @@ inputs:
     default: "test"
 
 runs:
-
   using: "composite"
 
   steps:
     - name: Cancel Previous Runs and Set up Python
       uses: styfle/cancel-workflow-action@0.4.0
       with:
-          access_token: ${{ github.token }}
+        access_token: ${{ github.token }}
     - uses: actions/checkout@v3
     - name: Setup conda
       uses: s-weigand/setup-conda@v1
@@ -43,7 +41,7 @@ runs:
         CMAKE_INSTALL_PREFIX: .local
       if: runner.os == 'Linux'
       run: |
-        # Install dependencies not handled by setuptools 
+        # Install dependencies not handled by setuptools
         ## DSSP
         sudo apt-get install -y dssp
         ## MSMS
@@ -59,7 +57,7 @@ runs:
         CMAKE_INSTALL_PREFIX: .local
       if: runner.os == 'macOS'
       run: |
-        # Install dependencies not handled by setuptools 
+        # Install dependencies not handled by setuptools
         ## DSSP
         git clone https://github.com/PDB-REDO/libcifpp.git --recurse-submodules
         cd libcifpp

.github/workflows/build.yml

@@ -36,8 +36,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest']
-        python-version: ['3.10', '3.11']
+        os: ["ubuntu-latest"]
+        python-version: ["3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/cffconvert.yml

@@ -16,4 +16,4 @@ jobs:
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/cffconvert-github-action@2.0.0
         with:
-          args: "--validate"
+          args: "--validate"

.github/workflows/coveralls.yml

@@ -37,7 +37,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ['3.10']
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/draft-pdf.yml

@@ -23,4 +23,4 @@ jobs:
           # This is the output path where Pandoc will write the compiled
           # PDF. Note, this should be the same directory as the input
           # paper.md
-          path: paper/paper.pdf
+          path: paper/paper.pdf

.github/workflows/fair-software.yml

@@ -5,7 +5,7 @@ on:
     branches:
       - main
   pull_request:
-      types: [opened, synchronize, reopened, ready_for_review]
+    types: [opened, synchronize, reopened, ready_for_review]
 
 jobs:
   verify:

.github/workflows/linting.yml

@@ -37,13 +37,13 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ['3.10']
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v3
       - uses: ./.github/actions/install-python-and-package
         with:
           python-version: ${{ matrix.python-version }}
           extras-require: test
-      - name: Check style against standards using prospector
-        run: prospector --die-on-tool-error
+      - name: Check style against standards using ruff
+        run: ruff .

.github/workflows/markdown-link-check.yml

@@ -3,7 +3,7 @@ name: markdown-link-check
 on:
   push:
     branches:
-    - main
+      - main
     paths:
       # filetypes
       - "**.md"
@@ -25,7 +25,7 @@ jobs:
     name: Check markdown links
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: gaurav-nelson/github-action-markdown-link-check@v1
-      with:
-        config-file: '.github/workflows/markdown-link-check.yml'
+      - uses: actions/checkout@v3
+      - uses: gaurav-nelson/github-action-markdown-link-check@v1
+        with:
+          config-file: ".github/workflows/markdown-link-check.yml"

.github/workflows/release.yml

@@ -14,8 +14,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest']
-        python-version: ['3.10']
+        os: ["ubuntu-latest"]
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/stale_issue_pr.yml

@@ -21,4 +21,4 @@ jobs:
           days-before-pr-close: -1
           stale-pr-message: "This PR is stale because it has been open for 14 days with no activity."
           close-pr-message: "This PR was closed because it has been inactive for 7 days since being marked as stale."
-          exempt-issue-labels: 'blocked'
+          exempt-issue-labels: "blocked"

.readthedocs.yaml

@@ -12,4 +12,4 @@ sphinx:
 # Explicitly set the version of Python and its requirements
 python:
   install:
-    - requirements: docs/requirements.txt
+    - requirements: docs/requirements.txt

.vscode/settings.json

@@ -1,15 +1,23 @@
 {
-    "[python]": {
-        "editor.codeActionsOnSave": {
-            "source.organizeImports": true
-        },
-        "files.trimTrailingWhitespace": true,
+  // Python
+  "[python]": {
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+      "source.fixAll": "explicit"
     },
+    "editor.defaultFormatter": "charliermarsh.ruff"
+  },
+  "autoDocstring.docstringFormat": "google",
 
-    "python.linting.prospectorEnabled": true,
-    "notebook.lineNumbers": "on",
+  // Notebooks
+  "notebook.lineNumbers": "on",
+  "notebook.formatOnSave.enabled": true,
+  "notebook.codeActionsOnSave": {
+    "notebook.source.fixAll": "explicit"
+  },
+  "notebook.diff.ignoreMetadata": true,
 
-    "[*.yml]": {
-        "files.trimTrailingWhitespace": true,
-    },
+  // Format all files on save
+  "editor.formatOnSave": true,
+  "editor.defaultFormatter": "esbenp.prettier-vscode"
 }