Switch from setup.py to pyproject.toml and poetry

.github/workflows/main.yml

@@ -33,16 +33,15 @@ jobs:
     - name: Install dependencies
       run: |
         pip install coveralls pytest-cov
-        pip install -r requirements_dev.txt
 
     - name: install package itself
       run: |
-         pip install .
-         pip install sequana_fastqc
+         pip install poetry
+         poetry install
 
     - name: testing
       run: |
-        pytest --cov-report term --cov=sequana_pipetools
+        poetry run pytest --cov-report term --cov=sequana_pipetools
     - name: coveralls
       run: |
         echo $COVERALLS_REPO_TOKEN

.gitignore

@@ -24,7 +24,7 @@ doc/_build
 *.egg-info/
 .installed.cfg
 *.egg
-
+poetry.lock
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

README.rst

@@ -253,6 +253,7 @@ Changelog
 ========= ======================================================================
 Version   Description
 ========= ======================================================================
+0.13.0    * switch to pyproject and fixes #64
 0.12.5    * automatically populater 'wrappers' in PipelineManager' based on the 
             config entry 'sequana_wrappers'.
 0.12.4    * handles sequana pipeline with underscores (e.g. pacbio_qc)

pyproject.toml

@@ -0,0 +1,61 @@
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+
+#maintainer ?#maintainer email
+[tool.poetry]
+name = "sequana_pipetools"
+version = "0.13.0"
+description = "A set of tools to help building or using Sequana pipelines"
+authors = ["Sequana Team"]
+license = "BSD-3"
+repository = "https://github.com/sequana/sequana_pipetools"
+readme = "README.rst"
+keywords = ["snakemake", "sequana", "pipelines"]
+classifiers = [
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Education",
+        "Intended Audience :: End Users/Desktop",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "Operating System :: OS Independent",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.10",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Scientific/Engineering :: Information Analysis",
+]
+packages = [
+    { include = "sequana_pipetools" }
+]
+
+[tool.poetry.dependencies]
+python = ">=3.8"
+deprecated = ">=1.2.13"
+easydev = ">=0.12.1"
+parse = ">=1.19.0"
+"ruamel.yaml" = ">=0.17.32"
+packaging = ">=23.1"
+pykwalify = ">=1.8"
+importlib_resources = ">=5.4.0"
+pyyaml = ">=1.3"
+aiohttp = ">=3.8.4"
+tqdm = ">=4.65"
+charset-normalizer = "^2"
+
+
+[tool.poetry.scripts]
+sequana_completion = "sequana_pipetools.scripts.completion:main"
+sequana_slurm_status = "sequana_pipetools.scripts.slurm:main"
+
+
+[tool.poetry.group.dev.dependencies]
+black = "^23.7.0"
+pytest = "^7.4.0"
+mock = "^5.1.0"
+pytest-mock = "^3.11.1"
+sequana-fastqc = "^1.7.1"
+pytest-cov = "^4.1.0"
+

sequana_pipetools/snaketools/file_factory.py

@@ -198,8 +198,10 @@ def _pathname(self):
         pathname = set(self.pathnames)
         if len(pathname) == 1:
             return list(pathname)[0] + os.sep
+        elif len(pathname) == 0:
+            raise ValueError(f"found no pathname; no input files found in  {self.patten} ?")
         else:
-            raise ValueError("found more than one pathname")
+            raise ValueError(f"found more than one pathname {pathname}.")
 
     pathname = property(_pathname, doc="the common relative path")
 

tests/snaketools/test_filefactory.py

@@ -22,12 +22,12 @@ def inner_test(ff):
         ff.extensions
 
     # list
-    list_files = glob.glob("*.py")
+    list_files = glob.glob("*.*")
     ff = snaketools.FileFactory(list_files)
     inner_test(ff)
 
     # glob
-    ff = snaketools.FileFactory("*py")
+    ff = snaketools.FileFactory("*.*")
     inner_test(ff)
 
     ff = snaketools.FastQFactory(test_dir + "/data/Hm2*fastq.gz", verbose=True)

tests/snaketools/test_sequana_config.py

@@ -83,13 +83,14 @@ def test_sequana_config(tmpdir):
     # test all installed pipelines saving/reading config file
     output = tmpdir.join("test.yml")
     for pipeline in snaketools.pipeline_names:
-        config_filename = Module(pipeline)._get_config()
-        cfg1 = SequanaConfig(config_filename)
-
-        cfg1.save(output)
-        cfg2 = SequanaConfig(str(output))
-        assert cfg2._yaml_code == cfg1._yaml_code
-        assert cfg1.config == cfg2.config
+        if "_fastqc" in pipeline:
+            config_filename = Module(pipeline)._get_config()
+            cfg1 = SequanaConfig(config_filename)
+
+            cfg1.save(output)
+            cfg2 = SequanaConfig(str(output))
+            assert cfg2._yaml_code == cfg1._yaml_code
+            assert cfg1.config == cfg2.config
 
     # test config with a _directory or _file  based on the fastqc pipeline
     cfg = SequanaConfig(s.config)

tests/test_manager.py

@@ -155,7 +155,7 @@ def test_copy_requirements(tmpdir):
     requirements = [
         # "phiX174.fa",
         str(tmp_require),
-        "https://raw.githubusercontent.com/sequana/sequana/master/README.rst",
+        "https://raw.githubusercontent.com/sequana/sequana/main/README.rst",
         "__init__.py",
         "setup.py",
     ]