Implemented changes described in comments in the previous PR

.github/workflows/python_lint.yml

@@ -0,0 +1,35 @@
+name: python_lint
+
+on:
+  push:
+    paths:
+      - '**.py'
+  pull_request:
+    paths:
+      - '**.py'
+
+jobs:
+  flake8_py3:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.9.x
+          architecture: x64
+      - name: Checkout PyTorch
+        uses: actions/checkout@master
+      - name: Install flake8
+        run: pip install flake8
+      - name: Run flake8
+        run: flake8 --ignore E501,W503,E203,W605
+
+  black_lint:
+    runs-on: ubuntu-latest
+    steps:
+        - name: Setup
+          uses: actions/checkout@v2
+        - name: Install black in jupyter
+          run: pip install black[jupyter]
+        - name: Check code lints with Black
+          uses: psf/black@stable

.github/workflows/tests.yml

@@ -1,38 +1,31 @@
 name: tests ci
-# This workflow runs the pipeline with the minimal test dataset to check that it completes any errors
+# This workflow runs the pipeline with the minimal test dataset to check 
+# is completed without any errors
 on:
-  push:
-    branches: [develop]
-  pull_request_target:
-    branches: [develop]
-  release:
-    types: [published]
+    pull_request:
+    push:
 
 jobs:
-  push_dockerhub:
-    name: Push new Docker image to Docker Hub (dev)
+  test_analyze_schema:
     runs-on: ubuntu-latest
-    # Only run for the official repo, for releases and merged PRs
-    if: ${{ github.repository == 'BU-ISCIII/taranis' }}
-    env:
-      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
-      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASSWORD }}
+
     steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-      - name: Build new docker image
-        run: docker build --no-cache . -t buisciii/taranis:dev
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: taranis_env
+          environment-file: environment.yml
 
-      - name: Push Docker image to DockerHub (develop)
-        run: |
-          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-          docker push buisciii/taranis:dev
-  run-tests:
-    name: Run tests
-    needs: push_dockerhub
-    runs-on: ubuntu-latest
-    steps:
-      - name: Run pipeline with test data
+      - name: Verify Conda environment
+        run: conda env list
+
+      - name: Activate env and install taranis
         run: |
-            docker run buisciii/taranis:dev bash -c /opt/taranis/test/test.sh
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate taranis_env
+          poetry install
+          taranis analyze-schema -i  test/MLST_listeria -o analyze_schema_test  --cpus 1 --output-allele-annot --remove-no-cds --remove-duplicated --remove-subset
+

.gitignore

@@ -29,6 +29,7 @@ wheels/
 .installed.cfg
 *.egg
 MANIFEST
+poetry.lock
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

environment.yml

@@ -1,18 +1,15 @@
-name: taranis
+name: taranis_env
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - conda-forge::python>=3.6
-  - conda-forge::biopython==1.72
-  - conda-forge::pandas==1.2.4
-  - conda-forge::openpyxl==3.0.7
-  - conda-forge::plotly==5.0.0
-  - conda-forge::numpy==1.20.3
-  - conda-forge::rich==13.7.0
-  - conda-forge::python-kaleido
+  - python=3.10
+  - conda-forge::poetry=1.7.1
   - bioconda::prokka>=1.14
   - bioconda::blast>=2.9
   - bioconda::mash>=2
   - bioconda::prodigal=2.6.3
+  - pip
+  - pip :
+      -  -r requirements.txt

pyproject.toml

@@ -0,0 +1,18 @@
+[tool.poetry]
+name = "taranis"
+version = "3.0.0"
+description = "Tools for gene-by-gene allele calling analysis"
+readme = "README.md"
+authors = ["Sara Monzon <[email protected]>"]
+license = "GNU-3.0"
+
+[tool.poetry.dependencies]
+python = "^3.10"
+
+[tool.poetry.scripts]
+taranis = "taranis.__main__:run_taranis"
+
+
+[tool.setuptools.packages.find]
+exclude = ["img", "virtualenv"]
+

requirements.txt

@@ -1,5 +1,8 @@
+biopython
+rich
 click
 questionary
 bio
 scikit-learn
-plotly
+plotly
+kaleido

taranis/__init__.py

@@ -1,3 +1,3 @@
 import pkg_resources
 
-__version__ = pkg_resources.get_distribution("taranis").version
+__version__ = pkg_resources.get_distribution("taranis").version