Merge pull request sequana#24 from cokelaer/fix_from_project

Fix from project

README.rst

@@ -170,6 +170,7 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+0.7.1     * Fix the --from-project option
 0.7.0     * Set the --wrapper-prefix to point to the  sequana-wrappers github
 0.6.3     * Fix SequanaConfig file
 0.6.2     * Fix script creation to include wrapper and take new snakemake 

sequana_pipetools/sequana_manager.py

@@ -74,7 +74,8 @@ def __init__(self, options, name="undefined"):
         self.config = None
         if "from_project" in dir(options) and options.from_project:
             possible_filenames = (
-                options.from_project,  # exact config file path
+                # from project tries to find a valid config.yaml
+                #options.from_project,  # exact config file path
                 f"{options.from_project}/{config_name}",  # config file in project path
                 f"{options.from_project}/.sequana/{config_name}",  # config file in .sequana dir
             )

setup.py

@@ -3,7 +3,7 @@
 
 _MAJOR = 0
 _MINOR = 7
-_MICRO = 0
+_MICRO = 1
 version = f"{_MAJOR}.{_MINOR}.{_MICRO}"
 release = f"{_MAJOR}.{_MINOR}"
 

tests/snaketools/test_sequana_config.py

@@ -4,6 +4,8 @@
 
 from sequana_pipetools import snaketools, Module, SequanaConfig
 
+from urllib.error import URLError
+
 from .. import test_dir
 
 
@@ -121,7 +123,14 @@ def test_copy_requirements(tmpdir):
         "setup.py",
         "https://raw.githubusercontent.com/sequana/sequana/master/README.rst",
     ]
-    cfg.copy_requirements(target=str(tmpdir))
+
+    # if not internet connection, catch the URLError
+    try:
+        cfg.copy_requirements(target=str(tmpdir))
+    except URLError:
+        assert True
+    except Exception:
+        assert False
 
     # error
     cfg.config.requirements = ["dummy"]