Merge pull request #5 from BIONF/dev

Refactoring & new web app

Author: aromberg

.github/workflows/pylint.yml

@@ -0,0 +1,13 @@
+name: pylint
+on: [push]
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Pylint Code Linter
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+          pip install pylint
+          pylint --fail-under=9.0 src/xspect

.github/workflows/pypi.yml

@@ -0,0 +1,61 @@
+name: Publish to PyPI
+
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+
+  upload_testpypi:
+    needs: [release-build]
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published' && github.event.release.prerelease
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  upload_pypi:
+    needs: [release-build]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published' && !github.event.release.prerelease
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -174,4 +174,8 @@ saved_options.txt
 
 files/
 out.gv
-out.png
+out.png
+
+xspect-data/
+
+.devcontainer/

README.md

@@ -1,7 +1,11 @@
 # XspecT - Acinetobacter Species Assignment Tool
-<img src="/src/xspect/static/Logo.png" height="50%" width="50%">
+![Test](https://github.com/bionf/xspect2/actions/workflows/test.yml/badge.svg)
+[![linting: pylint](https://img.shields.io/badge/linting-pylint-yellowgreen)](https://github.com/pylint-dev/pylint)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+<img src="/src/docs/img/logo.png" height="50%" width="50%">
 <!-- start intro -->
-XspecT is a Python-based tool to taxonomically classify sequence-reads (or assembled genomes) on the species and/or sub-type level using [Bloom Filters](https://en.wikipedia.org/wiki/Bloom_filter) and a [Support Vector Machine](https://en.wikipedia.org/wiki/Support-vector_machine). It also identifies existing [blaOxa-genes](https://en.wikipedia.org/wiki/Beta-lactamase#OXA_beta-lactamases_(class_D)) and provides a list of relevant research papers for further information.
+XspecT is a Python-based tool to taxonomically classify sequence-reads (or assembled genomes) on the species and/or sub-type level using [Bloom Filters] and a [Support Vector Machine]. It also identifies existing [blaOxa-genes] and provides a list of relevant research papers for further information.
 <br/><br/>
 
 XspecT utilizes the uniqueness of kmers and compares extracted kmers from the input-data to a reference database. Bloom Filter ensure a fast lookup in this process. For a final prediction the results are classified using a Support Vector Machine. 
@@ -11,6 +15,10 @@ Local extensions of the reference database are supported.
 <br/>
 
 The tool is available as a web-based application and a smaller command line interface.
+
+[Bloom Filters]: https://en.wikipedia.org/wiki/Bloom_filter
+[Support Vector Machine]: https://en.wikipedia.org/wiki/Support-vector_machine
+[blaOxa-genes]: https://en.wikipedia.org/wiki/Beta-lactamase#OXA_beta-lactamases_(class_D)
 <!-- end intro -->
 
 <!-- start quickstart -->
@@ -19,11 +27,7 @@ To install Xspect, please download the lastest 64 bit Python version and install
 ```
 pip install xspect
 ```
-If you would like to train filters yourself, you need to install Jellyfish, which is used to count distinct k-meres in the assemblies. It can be installed using bioconda:
-```
-conda install -c bioconda jellyfish
-```
-On Apple Silicon, it is possible that this command installs an incorrect Jellyfish package. Please refer to the official [Jellyfish project](https://github.com/gmarcais/Jellyfish) for installation guidance.
+Please note that Apple Silicon is currently not supported.
 
 ## Usage
 ### Get the Bloomfilters
@@ -37,23 +41,19 @@ xspect train you-ncbi-genus-name
 ```
 
 ### How to run the web app
-Run the following command lines in a console, a browser window will open automatically after the application is fully loaded.
+To run the web app, install and run [XspecT Web](https://github.com/aromberg/xspect-web). Additionally, run XspecT in API mode:
 ```
-xspect web
+xspect api
 ```
 
 ### How to use the XspecT command line interface
 Run xspect with the configuration you want to run it with as arguments.
 ```
 xspect classify your-genus path/to/your/input-set
 ```
-For further instructions on how to use the command line interface, execute:
+For further instructions on how to use the command line interface, please refer to the [documentation] or execute:
 ```
 xspect --help
 ```
-<!-- end quickstart -->
-
-## Input Data
-XspecT is able to use either raw sequence-reads (FASTQ-format .fq/.fastq) or already assembled genomes (FASTA-format .fasta/.fna). Using sequence-reads saves up the assembly process but high-quality reads with a low error-rate are needed (e.g. Illumina-reads).
-
-The amount of reads that will be used has to be set by the user when using sequence-reads. The minimum amount is 5000 reads for species classification and 500 reads for sub-type classification. The maximum number of reads is limited by the browser and is usually around ~8 million reads. Using more reads will lead to a increased runtime (xsec./1mio reads).
+[documentation]: https://bionf.github.io/XspecT2/cli.html
+<!-- end quickstart -->