Updated publication credentials

.devcontainer/devcontainer.json

@@ -0,0 +1,22 @@
+// 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
+{
+	"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": {},
+
+	// 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": "pip3 install --user -r requirements.txt",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.gitignore

@@ -213,5 +213,5 @@ pyrightconfig.json
 # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
 
 output
-!docs
-docs/build
+!docs/source/
+docs/source/autodoc

Jenkinsfile

@@ -1,15 +1,21 @@
 pipeline {
-    agent any
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'pip'
+            inheritFrom 'pip'
+        }
+    }
+
     stages {
         stage("install") {
             steps {
-                sh 'mamba env update --file environment.yml || mamba env create --force --file environment.yml'
-                sh 'echo "mamba activate bmlsa" >> ~/.bashrc'
+                sh 'pip install -r requirements.txt'
             }
         }
         stage("unit tests") {
             steps {
-                sh "python -m pytest --junitxml=test_results.xml"
+                sh returnStatus: true, script: "python -m pytest --junitxml=test_results.xml"
                 xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results.xml', stopProcessingIfError: true)]
             }
         }
@@ -18,11 +24,13 @@ pipeline {
                 sh 'rm -rf ./dist/*'
                 sh 'rm -rf ./docs/build/*'
                 sh "python -m build"
-                sh 'sphinx-apidoc -o docs/source/ src/bmlsa --force'
-                sh 'make -C docs html'
+                container('sphinx') {
+                    sh 'sphinx-apidoc -o docs/source/autodoc/bmlsa src/bmlsa --force'
+                    sh 'sphinx-build -M html ./docs/source ./docs/build'
                     publishHTML([allowMissing: false, alwaysLinkToLastBuild: false, keepAll: false, reportDir: 'docs/build/html', reportFiles: 'index.html', reportName: 'Documentation', reportTitles: ''])
                 }
             }
+        }
         stage("test installation") {
             steps {
                 sh "pip install dist/*.whl --force-reinstall"
@@ -40,7 +48,7 @@ pipeline {
                 branch '**/master'
             }
             steps {
-                withCredentials([usernamePassword(credentialsId: 'rs-git-package-registry-ydeng', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
+                withCredentials([usernamePassword(credentialsId: '4d6f64be-d26d-4f95-8de3-b6a9b0beb311', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
                     sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --non-interactive --disable-progress-bar --verbose dist/*'
                 }
             }

README.md

@@ -2,7 +2,7 @@
 
 # BMLSA
 
-A Basic multi local sequence alignment tool using the Biopython implementation of the Smith-Waterman alignment algorithm.
+A Basic multi local sequence alignment tool using the Biopython implementation of the Smith-Waterman alignment algorithm. May be used as a python library, or as a full command line interface.
 
 ## Features
 
@@ -13,6 +13,21 @@ A Basic multi local sequence alignment tool using the Biopython implementation o
  - Automatically align with all sequences in reference FASTA
  - All produced output is human readable!
 
+ ## Install via `pip`
+
+Just run `pip install --index-url https://git.reslate.systems/api/packages/ydeng/pypi/simple/ bmlsa` in a console that is capable of running `pip`!
+
+## CLI Demo from Git Repo
+
+Resources have been provided in this package for CI purposes, but you may use them to try out the program yourself!
+
+1. Install the program
+2. clone this repository
+3. Change into the cloned repository directory
+4. Run `bmlsa -I id -S sequence -B BLASTp tests/resources/SARS_CoV-2_genes.csv tests/resources/NC_045512_coding.fasta ./output/`
+
+The results will show up in a `output` folder (which will be generated if it doesn't exist). Use `bmlsa -h` to see what each part of the above command does!
+
 ## More Information
 
 For all live downloadable artifacts, build statuses, unit test results, and documentation, check out the continuous integration page for the [master branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/master/) ([development branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/develop/)).

docs/source/bmlsa.rst

@@ -1,53 +0,0 @@
-bmlsa package
-=============
-
-Submodules
-----------
-
-bmlsa.aligner module
---------------------
-
-.. automodule:: bmlsa.aligner
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-bmlsa.cli module
-----------------
-
-.. automodule:: bmlsa.cli
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-bmlsa.datatypes module
-----------------------
-
-.. automodule:: bmlsa.datatypes
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-bmlsa.exceptions module
------------------------
-
-.. automodule:: bmlsa.exceptions
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-bmlsa.io module
----------------
-
-.. automodule:: bmlsa.io
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: bmlsa
-   :members:
-   :undoc-members:
-   :show-inheritance:

docs/source/conf.py

@@ -3,7 +3,7 @@ import sys
 
 # Configure system path
 
-sys.path.insert(0, os.path.abspath("../src/"))
+sys.path.insert(0, os.path.abspath("../../src/"))
 
 # Configuration file for the Sphinx documentation builder.
 #

docs/source/index.rst

@@ -7,10 +7,11 @@ Welcome to BMLSA's documentation!
 =================================
 
 .. toctree::
+   :glob:
    :maxdepth: 2
    :caption: Contents:
    
-   modules
+   autodoc/**/modules
 
 
 Indices and tables

docs/source/modules.rst

@@ -1,7 +0,0 @@
-bmlsa
-=====
-
-.. toctree::
-   :maxdepth: 4
-
-   bmlsa

environment.yml

@@ -9,3 +9,4 @@ dependencies:
   - python-build=0.10.0
   - setuptools=67.6
   - sphinx=6.2
+prefix: ./env

requirements.txt

@@ -0,0 +1,6 @@
+biopython==1.81
+pytest
+hypothesis
+twine
+build
+setuptools