Merge branch 'main' of https://github.com/tahiri-lab/aPhyloGeo

.github/workflows/pypi-publish.yml

@@ -1,39 +1,31 @@
-# This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
-
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
-
-name: Upload Python Package
+name: Publish to Pypi
 
 on:
   release:
     types: [published]
-
-permissions:
-  contents: read
+  workflow_dispatch:
 
 jobs:
-  deploy:
-
-    runs-on: ubuntu-latest
-
+  publish:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.11]
+        poetry-version: [1.6.1]
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build
-    - name: Build package
-      run: python -m build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Run image
+        uses: abatilo/[email protected]
+        with:
+          poetry-version: ${{ matrix.poetry-version }}
+      - name: Publish
+        env:
+          PYPI_TOKEN: ${{ secrets.PYPI_API_KEY }}
+        run: |
+          poetry config pypi-token.pypi $PYPI_TOKEN
+          poetry publish --build

aphylogeo/main.py

@@ -1,5 +1,5 @@
 import pandas as pd
-from aphylogeo.alignement import AlignSequences, Alignment
+from aphylogeo.alignement import AlignSequences
 
 from aphylogeo.params import Params
 from aphylogeo import utils
@@ -24,9 +24,9 @@
     sequenceFile = utils.loadSequenceFile(Params().reference_gene_file)
     seq_alignment = AlignSequences(sequenceFile).align()
     # Phylo.write(tree1, "data/tree1.nwk", "newick")
-    seq_alignment.save_to_json("./debug/sequences_aligned.json")
+    # seq_alignment.save_to_json("./debug/sequences_aligned.json")
 
-    loaded_seq_alignment = Alignment.load_from_json("./debug/sequences_aligned.json")
+    # loaded_seq_alignment = Alignment.load_from_json("./debug/sequences_aligned.json")
 
     geneticTrees = utils.geneticPipeline(seq_alignment.msa)
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "aphylogeo"
-version = "0.2.2"
+version = "0.3.2"
 description = "A phylogenetic and geographic analysis tool"
 authors = ["'Tahiri Lab'"]
 license = "MIT"
@@ -16,7 +16,7 @@ pyyaml = "^6.0.1"
 pytest = "^7.4.2"
 numpy = "^1.26.0"
 cython = "^3.0.2"
-pymuscle5 = {git = "https://github.com/althonos/pymuscle5"}
+#pymuscle5 = {git = "https://github.com/althonos/pymuscle5"}
 robinson-foulds = "^1.2"
 ete3 = "^3.1.3"
 dendropy = "^4.6.1"