Initial commit, copied from autoBIGS.engine-bioconda

.devcontainer/Dockerfile

@@ -0,0 +1,16 @@
+FROM mcr.microsoft.com/devcontainers/miniconda:1-3
+
+# Copy environment.yml (if found) to a temp location so we update the environment. Also
+# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
+COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
+RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \
+    && rm -rf /tmp/conda-tmp
+
+# [Optional] Uncomment to install a different version of Python than the default
+# RUN conda install -y python=3.6 \
+#     && pip install --no-cache-dir pipx \
+#     && pipx reinstall-all
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>

.devcontainer/devcontainer.json

@@ -0,0 +1,24 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/miniconda
+{
+	"name": "Miniconda (Python 3)",
+	"build": { 
+		"context": "..",
+		"dockerfile": "Dockerfile"
+	}
+
+	// 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": "python --version",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.devcontainer/noop.txt

@@ -0,0 +1,3 @@
+This file is copied into the container along with environment.yml* from the
+parent folder. This is done to prevent the Dockerfile COPY instruction from 
+failing if no environment.yml is found.

.vscode/launch.json

@@ -0,0 +1,19 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        
+        {
+            "name": "Python Debugger: Current File with Arguments",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "args": [
+                "${command:pickArgs}"
+            ]
+        }
+    ]
+}

Jenkinsfile

@@ -0,0 +1,53 @@
+pipeline {
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'miniforge3'
+            inheritFrom 'miniforge'
+        }
+    }
+    stages {
+        stage("prepare") {
+            parallel {
+                stage("recipes repo") {
+                    steps {
+                        sh 'git clone https://github.com/Syph-and-VPD-Lab/bioconda-recipes.git'
+                        dir('bioconda-recipes') {
+                            sh 'git pull'
+                            sh 'git pull origin update-autobigs-cli'
+                            sh 'git checkout update-autobigs-cli'
+                        }
+                    }
+                }
+                stage("conda") {
+                    steps {
+                        sh 'conda env update -n base --file environment.yml'
+                    }
+                }
+            }
+        }
+        stage("generate recipe") {
+            steps {
+                sh 'grayskull pypi autobigs.cli --maintainers "Harrison Deng"'
+                sh 'python scripts/adapt_names.py autobigs.cli'
+            }
+        }
+        stage("build") {
+            steps {
+                sh 'conda build autobigs-cli'
+            }
+        }
+        stage("commit") {
+            environment {
+                TOKEN = credentials('github.com')
+            }
+            steps {
+                dir('bioconda-recipes') {
+                    sh 'cp -r ../autobigs-cli/* recipes/autobigs-cli/.'
+                    sh 'git commit -a -m "Automatically updated autobigs-cli bioconda recipe to $(python ../scripts/package_latest_version.py autoBIGS.cli)."'
+                    sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/bioconda-recipes.git update-autobigs-cli'
+                }
+            }
+        }
+    }
+}

autobigs-cli/meta.yaml

@@ -0,0 +1,50 @@
+{% set name = "autoBIGS.cli" %}
+{% set version = "0.4.2" %}
+
+package:
+  name: {{ name|lower|replace(".", "-") }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/autobigs_cli-{{ version }}.tar.gz
+  sha256: fc7bf6c604974796f5c8aae52fd9ab9924f5490f4f207a26be803217aae30c82
+
+build:
+  entry_points:
+    - autoBIGS = autobigs.cli.program:run
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage( name|lower|replace(".", "-"), max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.12
+    - setuptools >=64
+    - setuptools-scm >=8
+    - pip
+  run:
+    - python >=3.12
+    - autobigs-engine
+
+test:
+  imports:
+    - autobigs
+  commands:
+    - pip check
+    - autoBIGS --help
+    - autoBIGS info -h
+    - autoBIGS st -h
+  requires:
+    - pip
+
+about:
+  home: https://github.com/RealYHD/autoBIGS.cli
+  summary: A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases.
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - Harrison Deng

autobigs-engine/meta.yaml

@@ -0,0 +1,44 @@
+{% set name = "autobigs.engine" %}
+{% set version = "0.11.0" %}
+
+package:
+  name: {{ name|lower|replace(".", "-") }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/autobigs_engine-{{ version }}.tar.gz
+  sha256: d479b0bce5fcf2c3eb2e666b780b55d0c8a2c03293c9200db9eeac74e869f47b
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+
+requirements:
+  host:
+    - python >=3.12
+    - setuptools >=64
+    - setuptools-scm >=8
+    - pip
+  run:
+    - python >=3.12
+    - biopython ==1.85
+    - aiohttp ==3.11.*
+
+test:
+  imports:
+    - autobigs
+  commands:
+    - pip check
+  requires:
+    - pip
+
+about:
+  summary: A library to rapidly fetch fetch MLST profiles given sequences for various diseases.
+  dev_url: https://github.com/RealYHD/autoBIGS.engine
+  license: GPL-3.0
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - RealYHD

environment.yml

@@ -0,0 +1,10 @@
+name: base
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-build
+  - grayskull
+  - bioconda-utils
+  - python=3.10
+  - git

scripts/adapt_names.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python3
+
+import argparse
+from os import fdopen, path
+import os
+import re
+import shutil
+from sys import argv
+import tempfile
+
+def update_naming_scheme(recipe_path):
+    original_recipe = path.abspath(recipe_path)
+    original_meta = path.join(original_recipe, "meta.yaml")    
+    new_fd, new_file_path = tempfile.mkstemp()
+    with fdopen(new_fd, "w") as new_file_handle:
+        with open(original_meta, "r") as original_file_handle:
+            for line in original_file_handle:
+                matches = re.finditer(r"\{\{\s*name\|lower()\s+\}\}", line)
+                modified_line = line
+                for match in matches:
+                    modified_line = modified_line[:match.start(1)] + r'|replace(".", "-")' + modified_line[match.end(1):]
+                new_file_handle.write(modified_line)
+    shutil.move(new_file_path, original_meta)
+    new_recipe_name = path.join(
+                    path.dirname(original_recipe),
+                    path.basename(original_recipe).replace(".", "-").lower())
+    shutil.rmtree(new_recipe_name, ignore_errors=True)
+    os.replace(original_recipe, 
+                new_recipe_name)
+
+if __name__ == "__main__":
+    update_naming_scheme(argv[1])

scripts/package_latest_version.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python3
+
+import sys
+import requests
+import json
+try:
+    from packaging.version import parse
+except ImportError:
+    from pip._vendor.packaging.version import parse
+
+
+URL_PATTERN = 'https://pypi.python.org/pypi/{package}/json'
+
+
+def get_version(package, url_pattern=URL_PATTERN):
+    """Return version of package on pypi.python.org using json."""
+    req = requests.get(url_pattern.format(package=package))
+    version = parse('0')
+    if req.status_code == requests.codes.ok:
+        j = json.loads(req.text.encode(req.encoding or "utf-8"))
+        releases = j.get('releases', [])
+        for release in releases:
+            ver = parse(release)
+            if not ver.is_prerelease:
+                version = max(version, ver)
+    return version
+
+
+if __name__ == '__main__':
+    print(get_version(sys.argv[1]), end="")