Revert "Reapply "Began preparing for conda deployment""

This reverts commit ade2f3b84572b4356d404da2dbcd1d7266f10205.

.devcontainer/Dockerfile

@@ -1,16 +0,0 @@
-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

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

@@ -1,3 +0,0 @@
-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

@@ -358,4 +358,3 @@ package
 
 output
 *.private.*
-conda-bld

.vscode/extensions.json

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

Jenkinsfile

@@ -2,42 +2,36 @@ pipeline {
     agent {
         kubernetes {
             cloud 'rsys-devel'
-            defaultContainer 'miniforge3'
-            inheritFrom 'miniforge'
+            defaultContainer 'pip'
+            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") {
             steps {
-                sh returnStatus: true, script: "pytest --junitxml=test_results.xml --cov=src --cov-report xml:coverage.xml"
+                sh returnStatus: true, script: "python -m 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 "grayskull pypi dist/*.tar.gz"
-                sh "conda-build autobigsst.engine --output-folder conda-bld"
             }
         }
         stage("archive") {
             steps {
-                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl conda-bld/**/*.conda', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
             }
         }
         stage("publish") {
             parallel {
-                stage ("internal") {
+                stage ("git.reslate.systems") {
                     environment {
                         CREDS = credentials('username-password-rs-git')
                     }
@@ -45,12 +39,12 @@ pipeline {
                         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/*'
                     }
                 }
-                stage ("external") {
+                stage ("pypi.org") {
                     when {
                         tag '*.*'
                     }
                     environment {
-                        PYPI_TOKEN = credentials('pypi.org')
+                        TOKEN = credentials('pypi.org')
                     }
                     steps {
                         sh returnStatus: true, script: 'python -m twine upload -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'

environment.yml

@@ -1,17 +0,0 @@
-name: base
-channels:
-  - conda-forge
-dependencies:
-- aiohttp[speedups]
-- biopython
-- pytest
-- pytest-asyncio
-- python-build
-- twine
-- setuptools_scm
-- pytest-cov
-- grayskull
-- conda-build
-- anaconda-client
-- conda-utils
-- bioconda-build

pyproject.toml

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

requirements.txt

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