Re-organizing repositories by splitting this into two

.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 +1,54 @@
+pipeline {
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'miniforge3'
+            inheritFrom 'miniforge'
+        }
+    }
+    stages {
+        stage("prepare") {
+            parallel {
+                stage("recipes repo") {
+                    steps {
+                        sh 'git clone https://github.com/RealYHD/bioconda-recipes.git'
+                        dir('bioconda-recipes') {
+                            sh 'git pull'
+                            sh 'git pull origin update-autobigs-engine'
+                            sh 'git pull origin update-autobigs-engine'
+                        }
+                    }
+                }
+                stage("conda") {
+                    steps {
+                        sh 'conda env update -n base --file environment.yml'
+                    }
+                }
+            }
+        }
+        stage("update recipes") {
+            parallel {
+                stage("autoBIGS.cli") {
+                    steps {
+                        sh 'grayskull pypi autobigs.cli --maintainers "Harrison Deng"'
+                        sh 'python scripts/adapt_names.py autobigs.cli'
+                    }
+                }
+                stage("autoBIGS.engine") {
+                    steps {
+                        sh 'grayskull pypi autobigs.cli --maintainers "Harrison Deng"'
+                        sh 'python scripts/adapt_names.py autobigs.engine'
+                    }
+                }
+            }
+            stage("overwrite") {
+                steps {
+                    dir('bioconda-recipes') {
+                        sh 'checkout '
+                        sh 'cp autobigs-engine/* '
+                    }
+                }
+            }
+        }
+    }
+}

autobigs-engine/meta.yaml

@@ -1,4 +1,4 @@
-{% set name = "autoBIGS.engine" %}
+{% set name = "autobigs.engine" %}
 {% set version = "0.11.0" %}
 
 package:
@@ -13,8 +13,6 @@ build:
   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:
@@ -24,8 +22,8 @@ requirements:
     - pip
   run:
     - python >=3.12
-    - biopython
-    - aiohttp
+    - biopython ==1.85
+    - aiohttp ==3.11.*
 
 test:
   imports:
@@ -36,11 +34,11 @@ test:
     - pip
 
 about:
-  home: https://github.com/RealYHD/autoBIGS.engine
   summary: A library to rapidly fetch fetch MLST profiles given sequences for various diseases.
-  license: GPL-3.0-or-later
+  dev_url: https://github.com/RealYHD/autoBIGS.engine
+  license: GPL-3.0
   license_file: LICENSE
 
 extra:
   recipe-maintainers:
-    - Harrison Deng
+    - 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 +1,30 @@
+import argparse
+from os import fdopen, path
+import os
+import re
+import shutil
+from sys import argv
+import tempfile
+
+def main():
+    original_recipe = path.abspath(argv[1])
+    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__":
+    main()