testing new pyproject.toml file

.github/workflows/tests.yml

@@ -6,7 +6,7 @@ on:
     push:
 
 jobs:
-  create-conda-env:
+  test_analyze_schema:
     runs-on: ubuntu-latest
 
     steps:
@@ -26,6 +26,8 @@ jobs:
         run: |
           source $CONDA/etc/profile.d/conda.sh
           conda activate taranis_env
+      - name: testung analyze schema
+        run:
           pip install .
           taranis analyze-schema -i  test/MLST_listeria -o analyze_schema_test  --cpus 1
 

environment.yml

@@ -5,6 +5,7 @@ channels:
   - defaults
 dependencies:
   - python=3.10
+  - conda-forge::poetry=1.7.1
   - bioconda::prokka>=1.14
   - bioconda::blast>=2.9
   - bioconda::mash>=2

pyproject.toml

@@ -1,27 +1,18 @@
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-[project]
+[tool.poetry]
 name = "taranis"
 version = "3.0.0"
-dynamic = ["dependencies"]
-requires-python = ">=3.10"
-
-authors = [
-    {name = "Sara Monzon", email = "[email protected]"},
-    {name = "Luis Chapado", email = "[email protected]"},
-]
-maintainers = [
-    {name = "Luis Chapado", email = "[email protected]"}
-]
 description = "Tools for gene-by-gene allele calling analysis"
 readme = "README.md"
-license = {file = "LICENSE"}
+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.dynamic]
-dependencies = {file = ["requirements.txt"]}
 
 [tool.setuptools.packages.find]
-exclude = ["img", "virtualenv"]
+exclude = ["img", "virtualenv"]
+