Repo-wide cleaning and linting (#25)

* add trunk linter

* lint clis

* update pyproject.toml

* linting

.devcontainer/devcontainer.json

@@ -19,4 +19,4 @@
       ]
     }
   }
-}
+}

.github/workflows/test.yml

@@ -3,7 +3,6 @@ name: ci
 on:
   push:
 
-
 jobs:
   test:
     runs-on: ubuntu-latest

.trunk/.gitignore

@@ -0,0 +1,9 @@
+*out
+*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

@@ -0,0 +1,2 @@
+# Prettier friendly markdownlint config (all formatting rules disabled)
+extends: markdownlint/style/prettier

.trunk/configs/.shellcheckrc

@@ -0,0 +1,7 @@
+enable=all
+source-path=SCRIPTDIR
+disable=SC2154
+
+# If you're having issues with shellcheck following source, disable the errors via:
+# disable=SC1090
+# disable=SC1091

.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/configs/svgo.config.js

@@ -0,0 +1,14 @@
+module.exports = {
+  plugins: [
+    {
+      name: "preset-default",
+      params: {
+        overrides: {
+          removeViewBox: false, // https://github.com/svg/svgo/issues/1128
+          sortAttrs: true,
+          removeOffCanvasPaths: true,
+        },
+      },
+    },
+  ],
+};

.trunk/trunk.yaml

@@ -0,0 +1,45 @@
+# 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: 1.21.0
+# Trunk provides extensibility via plugins. (https://docs.trunk.io/plugins)
+plugins:
+  sources:
+    - id: trunk
+      ref: v1.4.5
+      uri: https://github.com/trunk-io/plugins
+# Many linters and tools depend on runtimes - configure them here. (https://docs.trunk.io/runtimes)
+runtimes:
+  enabled:
+    - go@1.21.0
+    - node@18.12.1
+    - python@3.10.8
+# This is the section where you manage your linters. (https://docs.trunk.io/check/configuration)
+lint:
+  enabled:
+    - actionlint@1.6.27
+    - bandit@1.7.8
+    - black@24.4.0
+    - checkov@3.2.73
+    - git-diff-check
+    - hadolint@2.12.0
+    - isort@5.13.2
+    - markdownlint@0.39.0
+    - oxipng@9.1.0
+    - prettier@3.2.5
+    - ruff@0.4.1
+    - shellcheck@0.10.0
+    - shfmt@3.6.0
+    - svgo@3.2.0
+    - taplo@0.8.1
+    - terrascan@1.19.1
+    - trivy@0.50.1
+    - trufflehog@3.71.0
+    - yamllint@1.35.1
+actions:
+  enabled:
+    - trunk-announce
+    - trunk-check-pre-push
+    - trunk-fmt-pre-commit
+    - trunk-upgrade-available

INSTALLATION.md

@@ -19,9 +19,9 @@ To install Whiscy, follow these steps:
 
 - Clone the repository:
 
-    ```bash
-    git clone https://github.com/haddocking/whiscy && cd whiscy
-    ```
+  ```bash
+  git clone https://github.com/haddocking/whiscy && cd whiscy
+  ```
 
 - Install the scripts
 
@@ -33,23 +33,23 @@ To install Whiscy, follow these steps:
 
 - Check the installation
 
-    ```text
-    $ whiscy -h
-    usage: whiscy [-h] [-o output_file] [--version]
-                  surface_list conversion_table alignment_file distance_file
-
-    positional arguments:
-      surface_list          Surface list
-      conversion_table      Conversion table
-      alignment_file        Alignment file
-      distance_file         Distance file
-
-    options:
-      -h, --help            show this help message and exit
-      -o output_file, --output output_file
-                            If set, output prediction to this file
-      --version             show program's version number and exit
-    ```
+  ```text
+  $ whiscy -h
+  usage: whiscy [-h] [-o output_file] [--version]
+                surface_list conversion_table alignment_file distance_file
+
+  positional arguments:
+    surface_list          Surface list
+    conversion_table      Conversion table
+    alignment_file        Alignment file
+    distance_file         Distance file
+
+  options:
+    -h, --help            show this help message and exit
+    -o output_file, --output output_file
+                          If set, output prediction to this file
+    --version             show program's version number and exit
+  ```
 
 ### Troubleshooting
 

USAGE.md

@@ -10,9 +10,9 @@ Below we will give an example of how to use WHISCY to predict the binding site o
 
 Download the PDB file of the protein 1PPE from the [RCSB PDB](https://www.rcsb.org/structure/1PPE) website.
 
-  ```bash
-  wget https://files.rcsb.org/download/1PPE.pdb
-  ```
+```bash
+wget https://files.rcsb.org/download/1PPE.pdb
+```
 
 ### Setup the prediction
 
@@ -32,26 +32,26 @@ $ whiscy_setup 1PPE.pdb E
   2024-04-22 11:44:44,046 cli_setup:319 INFO - Protdist calculated
   2024-04-22 11:44:44,054 cli_setup:326 INFO - Conversion table file generated
   2024-04-22 11:44:44,054 cli_setup:328 INFO - Whiscy setup finished
-  ```
+```
 
 This script will generate a set of files needed for the prediction step with `whiscy`. Here it is a list of the generated files in our 1PPE complex.
 
 > Follow the links to see a set of pre-generated files for the 1PPE protein.
 
-| File name                                 |    Explanation                                                 |
-| ----------------------------------------- |----------------------------------------------------------------|
-| [1ppe.hssp](example/1ppe.hssp)           | Multiple sequence alignment download from the HSSP database     |
-| [1ppe.hssp.bz2](example/1ppe.hssp.bz2)   | HSSP MSA file compressed                                        |
-| [1ppe.pdb](example/1ppe.pdb)             | PDB file download from the Protein Data Bank                    |
-| [1ppe_E.pdb](example/1ppe_E.pdb)         | 1ppe.pdb parsed to select only the given `chain_id`             |
-| [1ppe_E.rsa](example/1ppe_E.rsa)         | SASA output of `freesasa` in `NACCESS` format of `1ppe_E.pdb` file|
-| [1ppe_E.fasta](example/1ppe_E.fasta)     | Sequence of 1ppe_E.pdb. Alternative residues have been removed  |
-| [1ppe_E.phylseq](example/1ppe_E.phylseq) | MSA file translated from HSSP to PHYLIP format                  |
-| [1ppe_E.conv](example/1ppe_E.conv)       | PDB residue numeration to FASTA sequence numeration             |
-| [1ppe_E.out](example/1ppe_E.out)         | Output of the `protdist` software on 1ppe_E.pdb                 |
-| [1ppe_E.sur](example/1ppe_E.sur)         | >15 % surface residue list according to `sa_pred_cutoff` cutoff |
-| [1ppe_E.suract](example/1ppe_E.suract)   | >40 % surface residue list according to `sa_act_cutoff` cutoff  |
-| [1ppe_E.lac](example/1ppe_E.lac)         | 0-15 % accessible residue list                                  |
+| File name                                | Explanation                                                        |
+| ---------------------------------------- | ------------------------------------------------------------------ |
+| [1ppe.hssp](example/1ppe.hssp)           | Multiple sequence alignment download from the HSSP database        |
+| [1ppe.hssp.bz2](example/1ppe.hssp.bz2)   | HSSP MSA file compressed                                           |
+| [1ppe.pdb](example/1ppe.pdb)             | PDB file download from the Protein Data Bank                       |
+| [1ppe_E.pdb](example/1ppe_E.pdb)         | 1ppe.pdb parsed to select only the given `chain_id`                |
+| [1ppe_E.rsa](example/1ppe_E.rsa)         | SASA output of `freesasa` in `NACCESS` format of `1ppe_E.pdb` file |
+| [1ppe_E.fasta](example/1ppe_E.fasta)     | Sequence of 1ppe_E.pdb. Alternative residues have been removed     |
+| [1ppe_E.phylseq](example/1ppe_E.phylseq) | MSA file translated from HSSP to PHYLIP format                     |
+| [1ppe_E.conv](example/1ppe_E.conv)       | PDB residue numeration to FASTA sequence numeration                |
+| [1ppe_E.out](example/1ppe_E.out)         | Output of the `protdist` software on 1ppe_E.pdb                    |
+| [1ppe_E.sur](example/1ppe_E.sur)         | >15 % surface residue list according to `sa_pred_cutoff` cutoff    |
+| [1ppe_E.suract](example/1ppe_E.suract)   | >40 % surface residue list according to `sa_act_cutoff` cutoff     |
+| [1ppe_E.lac](example/1ppe_E.lac)         | 0-15 % accessible residue list                                     |
 
 ### Make the interface prediction
 

pyproject.toml

@@ -1,9 +1,17 @@
 [tool.poetry]
 name = "whiscy"
-version = "1.1.3"
-description = "WHISCY is a software program that predicts protein-protein interfaces using conservation and structural information by calculating prediction scores for each surface residue based on sequence alignment."
+version = "1.2.0"
+description = "WHISCY is a software that predicts protein-protein interfaces using conservation and structural information by calculating prediction scores for each surface residue based on sequence alignment."
 authors = ["Bonvin Lab <bonvinlab.support@uu.nl>"]
 readme = "README.md"
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "License :: OSI Approved :: Apache Software License",
+  "Operating System :: Unix",
+  "Programming Language :: Python :: 3.11",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Intended Audience :: Science/Research",
+]
 
 [tool.poetry.dependencies]
 python = "^3.11"

src/whiscy/cli_bfactor.py

@@ -1,12 +1,5 @@
-#!/usr/bin/env python3
-
-"""Adds the WHISCY scoring prediction to the B-factor column of a given PDB"""
-
-__version__ = 1.0
-
 import argparse
 import os
-import sys
 
 STANDARD_TYPES = {
     "ALA": "A",
@@ -65,9 +58,6 @@ def main():
         action="store_true",
         default=False,
     )
-    parser.add_argument(
-        "--version", action="version", version="%(prog)s {}".format(__version__)
-    )
     args = parser.parse_args()
 
     input_pdb_file_name = args.input_pdb_file

src/whiscy/cli_consadjust.py

@@ -1,10 +1,4 @@
-#!/usr/bin/env python3
-
-__version__ = 1.0
-
 import argparse
-
-# Logging
 import logging
 import math
 import os
@@ -13,12 +7,12 @@
 
 import numpy as np
 
+from whiscy.modules import PARAM_PATH
 from whiscy.modules.whiscy_data import (
     load_cons_file,
     load_residue_weights,
     load_z_table,
 )
-from whiscy.modules import PARAM_PATH
 
 logger = logging.getLogger("consadjust")
 logger.setLevel(logging.INFO)
@@ -45,9 +39,6 @@ def main():
         dest="output_file",
         metavar="output_file",
     )
-    parser.add_argument(
-        "--version", action="version", version="%(prog)s {}".format(__version__)
-    )
     args = parser.parse_args()
 
     if not os.path.exists(args.cons_file):
@@ -93,7 +84,7 @@ def main():
             neg = True
 
         index = np.argmax(z_values < currz)
-        upperz = z_values[index]
+        z_values[index]
 
         if index >= 24999:
             pscore = 0.5

src/whiscy/cli_haddock.py

@@ -1,16 +1,12 @@
-#!/usr/bin/env python3
-
-"""Calculates the active/passive residues for HADDOCK
+"""
+Calculates the active/passive residues for HADDOCK
 
 - Active residues: >=0.18 (WHISCY score)
 - Passive residues: radius of 6.5A of active residues
 """
 
-__version__ = 1.0
-
 import argparse
 import os
-import sys
 
 import Bio.PDB
 
@@ -64,9 +60,6 @@ def main():
     parser.add_argument(
         "whiscy_scores_file", help="WHISCY scores file", metavar="whiscy_scores_file"
     )
-    parser.add_argument(
-        "--version", action="version", version="%(prog)s {}".format(__version__)
-    )
     args = parser.parse_args()
 
     input_pdb_file_name = args.input_pdb_file
@@ -104,7 +97,7 @@ def main():
         neighbors.remove(active)
         for passive in neighbors:
             res_id = "{}{}".format(
-                STANDARD_TYPES[passive.get_resname()], passive.get_id()[1]
+                STANDARD_TYPES[passive.get_resname()], passive.get_id()[1]  # type: ignore
             )
             passive_residue_ids.append(res_id)
 

src/whiscy/cli_parasmooth.py

@@ -1,10 +1,4 @@
-#!/usr/bin/env python3
-
-__version__ = 1.0
-
 import argparse
-
-# Logging
 import logging
 import math
 import os
@@ -134,9 +128,6 @@ def main():
         dest="output_file",
         metavar="output_file",
     )
-    parser.add_argument(
-        "--version", action="version", version="%(prog)s {}".format(__version__)
-    )
     args = parser.parse_args()
 
     logger.info("Reading input files")