Merge branch 'master' into develop

CI now archives build and tests if CLI works

.devcontainer/devcontainer.json

@@ -0,0 +1,22 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+	"name": "Python 3",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye"
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "pip3 install --user -r requirements.txt",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.gitignore

@@ -1,5 +1,21 @@
-# Created by https://www.toptal.com/developers/gitignore/api/python,visualstudiocode
-# Edit at https://www.toptal.com/developers/gitignore?templates=python,visualstudiocode
+# File created using '.gitignore Generator' for Visual Studio Code: https://bit.ly/vscode-gig
+# Created by https://www.toptal.com/developers/gitignore/api/visualstudiocode,linux,python
+# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode,linux,python
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
 
 ### Python ###
 # Byte-compiled / optimized / DLL files
@@ -192,4 +208,7 @@ pyrightconfig.json
 .history
 .ionide
 
-# End of https://www.toptal.com/developers/gitignore/api/python,visualstudiocode
+# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode,linux,python
+
+# Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
+

.vscode/launch.json

@@ -8,11 +8,12 @@
             "name": "Run Fasta Filter",
             "type": "python",
             "request": "launch",
-            "program": "fasta_filter.py",
+            "module": "filterfasta.cli",
             "args": [
                 "reference_standards.fas",
                 "reference_standards_filtered.fas",
-                "-c", "rt"
+                "-c",
+                "rt"
             ],
             "console": "integratedTerminal",
             "justMyCode": true

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "python.formatting.provider": "black"
+}

Jenkinsfile

@@ -0,0 +1,42 @@
+pipeline {
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'pip'
+            inheritFrom 'pip'
+        }
+    }
+    stages {
+        stage("install") {
+            steps {
+                sh 'pip install -r requirements.txt'
+            }
+        }
+        stage("build") {
+            steps {
+                sh "python -m build"
+            }
+        }
+        stage("test") {
+            steps {
+                sh "pip install dist/*.whl"
+                sh "filterfasta -h"
+            }
+        }
+        stage("archive") {
+            steps {
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
+            }
+        }
+        stage("publish") {
+            when {
+                branch '**/master'
+            }
+            steps {
+                withCredentials([usernamePassword(credentialsId: '4d6f64be-d26d-4f95-8de3-b6a9b0beb311', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
+                    sh returnStdout: true, script: "python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --non-interactive --disable-progress-bar --verbose dist/*"
+                }
+            }
+        }
+    }
+}

environment.yml

@@ -0,0 +1,10 @@
+name: filterfasta
+channels:
+  - conda-forge
+dependencies:
+  - build=0.7
+  - pytest=7
+  - twine=4
+  - biopython=1.81
+  - python=3.11
+prefix: ./env

fasta_filter.py

@@ -1,65 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-from Bio import SeqIO
-import argparse
-
-
-def main(args):
-    kept_records = []
-    for s_record in SeqIO.parse(args.input, "fasta"):
-        if args.property != "all" and not (
-                    args.contains in getattr(s_record, args.property)
-                ):
-            kept_records.append(s_record)
-        elif args.property == "all" and not (
-            args.contains in s_record.id
-            or args.contains in s_record.name
-                or args.contains in s_record.description):
-            kept_records.append(s_record)
-    SeqIO.write(
-        kept_records,
-        os.path.abspath(args.output),
-        "fasta"
-    )
-
-
-if __name__ == "__main__":
-    argparser = argparse.ArgumentParser(
-        "Removes sequences where id contains certain string.")
-    argparser.add_argument(
-        "input",
-        type=str,
-        metavar="i",
-        help="The input fasta file."
-    )
-
-    argparser.add_argument(
-        "output",
-        type=str,
-        metavar="o",
-        help="The output file path."
-    )
-
-    argparser.add_argument(
-        "-c",
-        "--contains",
-        type=str,
-        default=None,
-        required=False,
-        help="The string to search for."
-    )
-
-    argparser.add_argument(
-        "-p",
-        "--property",
-        type=str,
-        default="all",
-        required=False,
-        help="""
-        The part of the fasta file to look through. Valid options are: id,
-        name, description, or all.
-        """
-    )
-
-    main(argparser.parse_args())

filterfasta/cli.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+
+import os
+from Bio import SeqIO
+import argparse
+
+
+def filter(input: str, a_property: str, contains: str):
+    kept_records = []
+    for s_record in SeqIO.parse(input, "fasta"):
+        if a_property != "all" and not (contains in getattr(s_record, a_property)):
+            kept_records.append(s_record)
+        elif a_property == "all" and not (
+            contains in s_record.id
+            or contains in s_record.name
+            or contains in s_record.description
+        ):
+            kept_records.append(s_record)
+    return kept_records
+
+
+def write_to_fasta(kept_records, output: str):
+    SeqIO.write(kept_records, os.path.abspath(output), "fasta")
+
+
+def run(args):
+    kept = filter(args.input, args.property, args.contains)
+    write_to_fasta(kept, args.output)
+
+
+def main():
+    argparser = argparse.ArgumentParser(
+        "Removes sequences where id contains certain string."
+    )
+    argparser.add_argument("input", type=str, metavar="i", help="The input fasta file.")
+
+    argparser.add_argument(
+        "output", type=str, metavar="o", help="The output file path."
+    )
+
+    argparser.add_argument(
+        "-c",
+        "--contains",
+        type=str,
+        default=None,
+        required=False,
+        help="The string to search for.",
+    )
+
+    argparser.add_argument(
+        "-p",
+        "--property",
+        type=str,
+        default="all",
+        required=False,
+        help="""
+        The part of the fasta file to look through. Valid options are: 'id',
+        'name', 'description', or 'all'.
+        """,
+    )
+    args = argparser.parse_args()
+    run(args)
+
+
+if __name__ == "__main__":
+    main()

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = ["setuptools", "wheel"]

requirements.txt

@@ -1 +1,5 @@
 Bio==1.5.6
+build
+pytest
+twine
+biopython==1.81

setup.cfg

@@ -0,0 +1,10 @@
+[metadata]
+name = filterfasta
+version = 0.0.3
+
+[options]
+packages = filterfasta
+
+[options.entry_points]
+console_scripts =
+    filterfasta = filterfasta.cli:main

setup.py

@@ -0,0 +1,3 @@
+from setuptools import setup
+
+setup()

tox.ini

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 88
+extend-ignore = E203