Removed submodule

.gitignore

@@ -175,4 +175,5 @@ pyrightconfig.json
 
 # End of https://www.toptal.com/developers/gitignore/api/python
 
-autobigs-engine/*
+autobigs-engine/*
+bioconda-recipes/*

.vscode/launch.json

@@ -4,7 +4,13 @@
     // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
     "version": "0.2.0",
     "configurations": [
-        
+        {
+            "name": "Python Debugger: Current File",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal"
+        },
         {
             "name": "Python Debugger: Current File with Arguments",
             "type": "debugpy",

Jenkinsfile

@@ -6,21 +6,28 @@ pipeline {
             inheritFrom 'miniforge'
         }
     }
+    environment {
+        TOOL_VER = """${sh(
+                returnStdout: true,
+                script: 'python pypi_latest_ver.py autoBIGS.engine'
+            )}"""
+    }
     stages {
         stage("prepare") {
             parallel {
                 stage("recipes repo") {
                     steps {
-                        sh 'git clone https://github.com/Syph-and-VPD-Lab/bioconda-recipes.git'
-                        dir('bioconda-recipes') {
-                            sh 'git pull'
-                            sh 'git pull origin update-autobigs-engine'
-                            sh 'git checkout update-autobigs-engine'
+                        sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main'
+                        sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main/auto-updated-bioconda-recipes'
+                        sh 'git clone https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git'
+                        dir('auto-updated-bioconda-recipes') {
+                            sh 'git checkout -b update-autobigs-engine-${TOOL_VER}'
                         }
                     }
                 }
                 stage("conda") {
                     steps {
+                        sh 'conda config --add channels bioconda'
                         sh 'conda env update -n base --file environment.yml'
                     }
                 }
@@ -28,24 +35,31 @@ pipeline {
         }
         stage("generate recipe") {
             steps {
-                sh 'grayskull pypi autobigs.engine --maintainers "Harrison Deng"'
-                sh 'python scripts/adapt_names.py autobigs.engine'
+                sh 'grayskull pypi autoBIGS.engine --maintainers "Harrison Deng"'
+                sh 'python patch_recipe.py'
+                sh 'cp -r autobigs-engine/* auto-updated-bioconda-recipes/recipes/autobigs-engine/.'
             }
         }
         stage("build") {
             steps {
-                sh 'conda build autobigs-engine'
+                sh 'conda build auto-updated-bioconda-recipes/recipes/autobigs-engine --output-folder ./conda-bld'
             }
         }
-        stage("commit") {
+        stage('lint') {
+            steps {
+                dir('auto-updated-bioconda-recipes') {
+                    sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
+                }
+            }
+        }
+        stage('commit') {
             environment {
                 TOKEN = credentials('github.com')
             }
             steps {
-                dir('bioconda-recipes') {
-                    sh 'cp -r ../autobigs-engine/* recipes/autobigs-engine/.'
-                    sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../scripts/package_latest_version.py autoBIGS.engine)."'
-                    sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/bioconda-recipes.git update-autobigs-engine'
+                dir('auto-updated-bioconda-recipes') {
+                    sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to ${TOOL_VER}."'
+                    sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine-${TOOL_VER}'
                 }
             }
         }

autobigs-cli/meta.yaml

@@ -1,50 +0,0 @@
-{% 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

environment.yml

@@ -5,4 +5,8 @@ channels:
 dependencies:
   - conda-build
   - grayskull
-  - git
+  - git
+  - bioconda-utils
+  - python=3.10.*
+  - curl
+  - conda-verify

patch_recipe.py

@@ -0,0 +1,103 @@
+#!/usr/bin/env python3
+
+import argparse
+from os import fdopen, path
+import os
+import re
+import shutil
+from sys import argv
+import tempfile
+
+INDENTATION = "  "
+GRAYSKULL_OUTPUT_PATH = "autoBIGS.engine"
+RUN_EXPORTED_VALUE = r'{{ pin_subpackage( name|lower|replace(".", "-"), max_pin="x.x") }}'
+LICENSE_SUFFIX = "-or-later"
+HOME_PAGE = "https://github.com/Syph-and-VPD-Lab/autoBIGS.engine"
+
+def _calc_indentation(line: str):
+    return len(re.findall(INDENTATION, line.split(line.strip())[0])) if line != "\n" else 0
+
+def read_grayskull_output():
+    original_recipe = path.abspath(GRAYSKULL_OUTPUT_PATH)
+    original_meta = path.join(original_recipe, "meta.yaml")
+    meta_file = open(original_meta)
+    lines = meta_file.readlines()
+    meta_file.close()
+    return lines
+
+def update_naming_scheme(lines):
+    modified_lines = []
+    for line in lines:
+        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):]
+        modified_lines.append(modified_line)
+    return modified_lines
+
+def inject_run_exports(lines: list[str]):
+    package_indent = False
+    modified_lines = []
+    for line in lines:
+        indentation_count = _calc_indentation(line)
+        if line == "build:\n" and indentation_count == 0:
+            package_indent = True
+            modified_lines.append(line)
+        elif package_indent and indentation_count == 0:
+            modified_lines.append(INDENTATION*1 + "run_exports:\n")
+            modified_lines.append(INDENTATION*2 + "- " + RUN_EXPORTED_VALUE + "\n")
+            package_indent = False
+        else:
+            modified_lines.append(line)
+    return modified_lines
+
+def suffix_license(lines: list[str]):
+    about_indent = False
+    modified_lines = []
+    for line in lines:
+        indentation_count = _calc_indentation(line)
+        if line == "about:\n" and indentation_count == 0:
+            about_indent = True
+            modified_lines.append(line)
+        elif about_indent and indentation_count == 1 and line.lstrip().startswith("license:"):
+            modified_lines.append(line.rstrip() + LICENSE_SUFFIX  + "\n")
+            about_indent = False
+        else:
+            modified_lines.append(line)
+    return modified_lines
+
+def inject_home_page(lines: list[str]):
+    about_indent = False
+    modified_lines = []
+    for line in lines:
+        indentation_count = _calc_indentation(line)
+        if line == "about:\n" and indentation_count == 0:
+            about_indent = True
+            modified_lines.append(line)
+        elif about_indent and indentation_count == 0:
+            modified_lines.append(INDENTATION + "home: " + HOME_PAGE + "\n")
+            about_indent = False
+        else:
+            modified_lines.append(line)
+    return modified_lines
+
+def write_to_original(lines: list[str]):
+    original_recipe = path.abspath(GRAYSKULL_OUTPUT_PATH)
+    original_meta = path.join(original_recipe, "meta.yaml")
+    with open(original_meta, "w") as file:
+        file.writelines(lines)
+
+def rename_recipe_dir():
+    new_recipe_name = path.abspath(path.join(GRAYSKULL_OUTPUT_PATH.replace(".", "-").lower()))
+    shutil.rmtree(new_recipe_name, ignore_errors=True)
+    os.replace(path.abspath(GRAYSKULL_OUTPUT_PATH), new_recipe_name)
+
+if __name__ == "__main__":
+    original_grayskull_out = read_grayskull_output()
+    modified_recipe_meta = None
+    modified_recipe_meta = update_naming_scheme(original_grayskull_out)
+    modified_recipe_meta = inject_run_exports(modified_recipe_meta)
+    modified_recipe_meta = suffix_license(modified_recipe_meta)
+    modified_recipe_meta = inject_home_page(modified_recipe_meta)
+    write_to_original(modified_recipe_meta)
+    rename_recipe_dir()

pypi_latest_ver.py

@@ -8,6 +8,7 @@ try:
 except ImportError:
     from pip._vendor.packaging.version import parse
 
+# Courtesy of https://stackoverflow.com/questions/28774852/pypi-api-how-to-get-stable-package-version
 
 URL_PATTERN = 'https://pypi.python.org/pypi/{package}/json'
 

scripts/adapt_names.py

@@ -1,32 +0,0 @@
-#!/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])