.devcontainer/Dockerfile

@@ -1,11 +0,0 @@
-FROM mcr.microsoft.com/devcontainers/anaconda: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 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

@@ -1,11 +1,9 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
-// README at: https://github.com/devcontainers/templates/tree/main/src/anaconda
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
 {
-	"name": "Anaconda (Python 3)",
+	"name": "Python 3",
-	"build": { 
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
-		"context": "..",
+	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
-		"dockerfile": "Dockerfile"
-	}
 
 	// Features to add to the dev container. More info: https://containers.dev/features.
 	// "features": {},
@@ -14,7 +12,14 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	// "postCreateCommand": "python --version",
+	"postCreateCommand": "pip3 install --user -r requirements.txt",
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"mechatroner.rainbow-csv"
+			]
+		}
+	}
 
 	// Configure tool-specific properties.
 	// "customizations": {},

.devcontainer/noop.txt

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

.gitignore

@@ -1,6 +1,6 @@
 # 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
+# Created by https://www.toptal.com/developers/gitignore/api/visualstudiocode,svelte,python,linux,node
-# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode,linux,python
+# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode,svelte,python,linux,node
 
 ### Linux ###
 *~
@@ -17,6 +17,146 @@
 # .nfs files are created when an open file is removed but is still being accessed
 .nfs*
 
+### Node ###
+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+lerna-debug.log*
+.pnpm-debug.log*
+
+# Diagnostic reports (https://nodejs.org/api/report.html)
+report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+*.lcov
+
+# nyc test coverage
+.nyc_output
+
+# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (https://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# Snowpack dependency directory (https://snowpack.dev/)
+web_modules/
+
+# TypeScript cache
+*.tsbuildinfo
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Optional stylelint cache
+.stylelintcache
+
+# Microbundle cache
+.rpt2_cache/
+.rts2_cache_cjs/
+.rts2_cache_es/
+.rts2_cache_umd/
+
+# Optional REPL history
+.node_repl_history
+
+# Output of 'npm pack'
+*.tgz
+
+# Yarn Integrity file
+.yarn-integrity
+
+# dotenv environment variable files
+.env
+.env.development.local
+.env.test.local
+.env.production.local
+.env.local
+
+# parcel-bundler cache (https://parceljs.org/)
+.cache
+.parcel-cache
+
+# Next.js build output
+.next
+out
+
+# Nuxt.js build / generate output
+.nuxt
+dist
+
+# Gatsby files
+.cache/
+# Comment in the public line in if your project uses Gatsby and not Next.js
+# https://nextjs.org/blog/next-9-1#public-directory-support
+# public
+
+# vuepress build output
+.vuepress/dist
+
+# vuepress v2.x temp and cache directory
+.temp
+
+# Docusaurus cache and generated files
+.docusaurus
+
+# Serverless directories
+.serverless/
+
+# FuseBox cache
+.fusebox/
+
+# DynamoDB Local files
+.dynamodb/
+
+# TernJS port file
+.tern-port
+
+# Stores VSCode versions used for testing VSCode extensions
+.vscode-test
+
+# yarn v2
+.yarn/cache
+.yarn/unplugged
+.yarn/build-state.yml
+.yarn/install-state.gz
+.pnp.*
+
+### Node Patch ###
+# Serverless Webpack directories
+.webpack/
+
+# Optional stylelint cache
+
+# SvelteKit build / generate output
+.svelte-kit
+
 ### Python ###
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -62,7 +202,6 @@ htmlcov/
 .nox/
 .coverage
 .coverage.*
-.cache
 nosetests.xml
 coverage.xml
 *.cover
@@ -76,7 +215,6 @@ cover/
 *.pot
 
 # Django stuff:
-*.log
 local_settings.py
 db.sqlite3
 db.sqlite3-journal
@@ -140,7 +278,6 @@ celerybeat.pid
 *.sage.py
 
 # Environments
-.env
 .venv
 env/
 venv/
@@ -189,6 +326,13 @@ poetry.toml
 # LSP config files
 pyrightconfig.json
 
+### Svelte ###
+# gitignore template for the SvelteKit, frontend web component framework
+# website: https://kit.svelte.dev/
+
+.svelte-kit/
+package
+
 ### VisualStudioCode ###
 .vscode/*
 !.vscode/settings.json
@@ -208,8 +352,9 @@ pyrightconfig.json
 .history
 .ionide
 
-# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode,linux,python
+# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode,svelte,python,linux,node
 
 # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
 
-conda-bld
+output
+*.private.*

.vscode/extensions.json

@@ -1,5 +0,0 @@
-{
-    "recommendations": [
-        "piotrpalarz.vscode-gitignore-generator"
-    ]
-}

Jenkinsfile

@@ -2,14 +2,14 @@ pipeline {
     agent {
         kubernetes {
             cloud 'rsys-devel'
-            defaultContainer 'miniforge3'
+            defaultContainer 'pip'
-            inheritFrom 'miniforge'
+            inheritFrom 'pip'
         }
     }
     stages {
         stage("install") {
             steps {
-                sh 'conda env update -n base -f environment.yml'
+                sh 'python -m pip install -r requirements.txt'
             }
         }
         stage("unit tests") {
@@ -22,14 +22,11 @@ pipeline {
         stage("build") {
             steps {
                 sh "python -m build"
-                sh "grayskull pypi dist/*.tar.gz --maintainers 'Harrison Deng'"
-                sh "python scripts/patch_recipe.py"
-                sh 'conda build autobigs-engine -c bioconda --output-folder conda-bld --verify'
             }
         }
         stage("archive") {
             steps {
-                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl, conda-bld/**/*.conda, autobigs-engine/*.yaml', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
             }
         }
         stage("publish") {
@@ -39,8 +36,7 @@ pipeline {
                         CREDS = credentials('username-password-rs-git')
                     }
                     steps {
-                        sh 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
+                        sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
-                        sh 'curl --user ${CREDS_USR}:${CREDS_PSW} --upload-file conda-bld/**/*.conda https://git.reslate.systems/api/packages/${CREDS_USR}/conda/$(basename conda-bld/**/*.conda)'
                     }
                 }
                 stage ("pypi.org") {

autobigs-engine/meta.yaml

@@ -1,44 +0,0 @@
-{% set name = "autoBIGS.engine" %}
-{% set version = "0.12.1.dev1+gb8cebb8.d20250221" %}
-
-package:
-  name: {{ name|lower|replace(".", "-") }}
-  version: {{ version }}
-
-source:
-  url: file:///workspaces/autoBIGS.engine/dist/autobigs_engine-0.12.1.dev1%2Bgb8cebb8.d20250221.tar.gz
-  sha256: c86441b94f935cfa414ff28ca4c026a070e0fb15988ea3bb7d1a942859a09b16
-
-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:
-    - 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.
-  license: GPL-3.0-or-later
-  license_file: LICENSE
-  home: https://github.com/Syph-and-VPD-Lab/autoBIGS.engine
-extra:
-  recipe-maintainers:
-    - Harrison Deng

environment.yml

@@ -1,16 +0,0 @@
-name: ci
-channels:
-  - bioconda
-  - conda-forge
-dependencies:
-  - aiohttp==3.11.*
-  - biopython==1.85
-  - pytest
-  - pytest-asyncio
-  - python-build
-  - conda-build
-  - twine==6.0.1
-  - setuptools_scm
-  - pytest-cov
-  - grayskull
-  - curl

requirements.txt

@@ -0,0 +1,8 @@
+aiohttp[speedups]==3.11.*
+biopython==1.85
+pytest
+pytest-asyncio
+build
+twine
+setuptools_scm
+pytest-cov

scripts/patch_recipe.py

@@ -1,103 +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
-
-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()