diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d04729d..9a8095c 100644 --- a/.github/workflows/tests.yml +++ b/.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 \ No newline at end of file diff --git a/environment.yml b/environment.yml index f4e5e64..a2ef128 100644 --- a/environment.yml +++ b/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 diff --git a/pyproject.toml b/pyproject.toml index 0c1156b..2389545 100644 --- a/pyproject.toml +++ b/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 = "smonzon@isciii.es"}, - {name = "Luis Chapado", email = "lchapado@externos.isciii.es"}, -] -maintainers = [ - {name = "Luis Chapado", email = "lchapado@externos.isciii.es"} -] description = "Tools for gene-by-gene allele calling analysis" readme = "README.md" -license = {file = "LICENSE"} +authors = ["Sara Monzon "] +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"] \ No newline at end of file +exclude = ["img", "virtualenv"] +