Reapply "Began preparing for conda deployment"

This reverts commit 3bbef9ac3e0ca58f6f5f62a1e9bd1d8ae02fd75c.

.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

@@ -1,9 +1,11 @@
 // 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
+// README at: https://github.com/devcontainers/templates/tree/main/src/miniconda
 {
-	"name": "Python 3",
+	"name": "Miniconda (Python 3)",
-	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"build": { 
-	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
+		"context": "..",
+		"dockerfile": "Dockerfile"
+	},
 
 	// Features to add to the dev container. More info: https://containers.dev/features.
 	// "features": {},
@@ -12,18 +14,18 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip3 install --user -r requirements.txt",
+	// "postCreateCommand": "python --version",
+
+	// Configure tool-specific properties.
 	"customizations": {
 		"vscode": {
 			"extensions": [
-				"mechatroner.rainbow-csv"
+				"mechatroner.rainbow-csv",
+				"piotrpalarz.vscode-gitignore-generator"
 			]
 		}
 	}
 
-	// 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.

.gitignore

@@ -357,4 +357,5 @@ package
 # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
 
 output
-*.private.*
+*.private.*
+conda-bld

.vscode/extensions.json

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

Jenkinsfile

@@ -2,49 +2,55 @@ pipeline {
     agent {
         kubernetes {
             cloud 'rsys-devel'
-            defaultContainer 'pip'
+            defaultContainer 'miniforge3'
-            inheritFrom 'pip'
+            inheritFrom 'miniforge'
         }
     }
     stages {
         stage("install") {
             steps {
-                sh 'python -m pip install -r requirements.txt'
+                sh 'conda env update -n base -f environment.yml'
             }
         }
         stage("unit tests") {
             steps {
-                sh returnStatus: true, script: "python -m pytest --junitxml=test_results.xml --cov=src --cov-report xml:coverage.xml"
+                sh returnStatus: true, script: "pytest --junitxml=test_results.xml --cov=src --cov-report xml:coverage.xml"
                 xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results.xml', stopProcessingIfError: true)]
                 recordCoverage(tools: [[parser: 'COBERTURA', pattern: 'coverage.xml']])
             }
         }
         stage("build") {
+            environment {
+                GIT_AUTHOR_NAME = "Harrison Deng"
+                GIT_AUTHOR_EMAIL = "yunyangdeng@outlook.com"
+            }
             steps {
                 sh "python -m build"
+                sh "conda-build automlst.engine --output-folder conda-bld"
             }
         }
         stage("archive") {
             steps {
-                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl conda-bld/**/*.conda', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
             }
         }
         stage("publish") {
             parallel {
-                stage ("git.reslate.systems") {
+                stage ("internal") {
                     environment {
-                        CREDS = credentials('username-password-rs-git')
+                        TOKEN = credentials('git.reslate.systems')
                     }
                     steps {
-                        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 returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
                     }
                 }
-                stage ("pypi.org") {
+                stage ("external") {
                     when {
                         tag '*.*'
                     }
                     environment {
-                        TOKEN = credentials('pypi.org')
+                        PYPI_TOKEN = credentials('pypi.org')
+                        CONDA_TOKEN = credentials('anaconda.org')
                     }
                     steps {
                         sh returnStatus: true, script: 'python -m twine upload -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'

automlst.engine/meta.yaml

@@ -0,0 +1,43 @@
+{% set name = "automlst.engine" %}
+{% set version = "0.5.2.dev2+gde36956" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: file:///workspaces/automlst.engine/dist/automlst_engine-0.5.2.dev2%2Bgde36956.tar.gz
+  sha256: 2dee4910744f063b7ec5c923bbf369c23151c82cc59b8b99da19e162414ba61d
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+
+requirements:
+  host:
+    - python >=3.11
+    - setuptools >=64
+    - setuptools-scm >=8
+    - pip
+  run:
+    - python >=3.11
+    - biopython
+    - aiohttp
+
+test:
+  imports:
+    - automlst
+  commands:
+    - pip check
+  requires:
+    - pip
+
+about:
+  summary: A library to rapidly fetch fetch MLST profiles given sequences for various diseases.
+  license: GPL-3.0
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - RealYHD

environment.yml

@@ -0,0 +1,14 @@
+name: base
+channels:
+  - conda-forge
+dependencies:
+- aiohttp[speedups]
+- biopython
+- pytest
+- pytest-asyncio
+- python-build
+- twine
+- setuptools_scm
+- pytest-cov
+- grayskull
+- conda-build

pyproject.toml

@@ -6,7 +6,12 @@ build-backend = "setuptools.build_meta"
 name = "automlst.engine"
 dynamic = ["version"]
 readme = "README.md"
-
+authors = [
+  {name = "Harrison Deng"},
+]
+maintainers = [
+  {name = "Harrison Deng"},
+]
 dependencies = [
     "biopython",
     "aiohttp[speedups]",

requirements.txt

@@ -1,8 +0,0 @@
-aiohttp[speedups]
-biopython
-pytest
-pytest-asyncio
-build
-twine
-setuptools_scm
-pytest-cov