Merge pull request #21 from qbicsoftware/release-0.3.0

Release 0.3.0

CHANGELOG.md

@@ -1,4 +1,9 @@
 
+## 0.3.0
+- Removes r channel
+- Requires bioconda and conda-forge as manadatory channels
+- Template has been adjusted to pass linting
+
 ## 0.1.1: Hotfix
 - Fix failing PyPi deployment
 

rmageddon/lint.py

@@ -82,7 +82,10 @@ def check_files_exist(self):
                 self.passed.append((1, 'Dir {} found.'.format(files)))
 
         if os.path.isfile(self.pf('environment.yml')):
-            with open(self.pf('environment.yml'), 'r') as fh:
+            self.load_environment_config()
+
+    def load_environment_config(self):
+        with open(self.pf('environment.yml'), 'r') as fh:
                 yaml = YAML()
                 self.conda_config = yaml.load(fh)
 
@@ -184,13 +187,14 @@ def check_conda_environment(self):
         # Define the mandatory conda channels (min. requirement)
         mand_channel_settings = [
             'defaults',
-            'r'
+            'conda-forge',
+            'bioconda'
         ]
-
+        
         # Check that the mandatory conda env declarations are there
-        for declaration in mand_conda_settings:
-            if not self.conda_config.get(declaration):
-                self.failed.append((3, f"The conda env declaration \'{declaration}\' is missing."))
+        for setting in mand_conda_settings:
+            if not self.conda_config.get(setting):
+                self.failed.append((3, f"The conda environment setting \'{setting}\' is missing."))
                 return
 
         # Check the name regex
@@ -202,10 +206,9 @@ def check_conda_environment(self):
             Make sure, it follows the guidelines."))
             return
 
-        # Check that channels 'default' and 'r' are present
+        # Find missing channels
         missing_channels = list([ch for ch in mand_channel_settings
                                  if not ch in self.conda_config.get('channels')])
-
         for ch in missing_channels:
             self.failed.append((3, f"Channel {ch} was not defined."))
             return

setup.py

@@ -3,7 +3,7 @@
 from setuptools import setup, find_packages
 import sys
 
-version = '0.2.2'
+version = '0.3.0'
 
 with open('README.md') as f:
     readme = f.read()

tests/lint_examples/awesome_working_example/environment.yml

@@ -1,7 +1,7 @@
 name: qtest000_1_ranalysis_123
 channels:
   - bioconda
-  - r
+  - conda-forge
   - defaults
 dependencies:
   - r-base=3.4.3

tests/lint_examples/bad_example/environment.yml

@@ -1,4 +1,4 @@
-name: qbicsoftware-dd-ranalyses-1.0
+name: qtest000_1_ranalysis_123
 channels:
   - bioconda
   - r

tests/lint_examples/minimal_working_example/environment.yml

@@ -1,7 +1,7 @@
 name: qtest000_1_ranalysis
 channels:
   - bioconda
-  - r
+  - conda-forge
   - defaults
 dependencies:
   - r-base=3.4.3

tests/test_lint.py

@@ -103,6 +103,15 @@ def test_rpackage_empty_warn(self):
         expectations = {"failed": 1, "warned": 0, "passed": 0}
         self.assess_lint_status(lint_obj, **expectations)
 
+    def test_semantic_version_container_fail(self):
+        """ If the container version does not follow the sematic versioning
+        style-guide, the linting should fail."""
+        lint_obj = lint.RContainerLint(PATH_BAD_EXAMPLE)
+        lint_obj.load_environment_config()
+        lint_obj.check_conda_environment()
+        expectations = {"failed": 1, "warned": 0, "passed": 0}
+        self.assess_lint_status(lint_obj, **expectations)
+
     def test_rpackage_pass(self):
         """ Check if the rpackages.txt is formatted correctly """
         lint_obj = lint.RContainerLint(PATH_MINIMAL_WORKING_EXAMPLE)

{{cookiecutter.project_code}}/environment.yml

@@ -1,7 +1,7 @@
 name: {{ cookiecutter.project_code }}000_{{ cookiecutter.project_label }}_ranalysis{{ cookiecutter.container_version }}
 channels:
+  - conda-forge
   - bioconda
-  - r
   - defaults
 dependencies:
   - r-base={{ cookiecutter.r_version  }}