Merge pull request nf-core#33 from ewels/master

New lint test for Dockerfile that builds from conda

nf_core/lint.py

@@ -29,6 +29,7 @@ def __init__(self, pipeline_dir):
         self.files = []
         self.config = {}
         self.pipeline_name = None
+        self.dockerfile = []
         self.conda_config = {}
         self.passed = []
         self.warned = []
@@ -67,7 +68,8 @@ def lint_pipeline(self, release=False):
             'check_nextflow_config',
             'check_ci_config',
             'check_readme',
-            'check_conda_env_yaml'
+            'check_conda_env_yaml',
+            'check_conda_dockerfile'
         ]
         if release:
             self.releaseMode = True
@@ -150,6 +152,7 @@ def check_docker(self):
         # Implicitely also checks if empty.
         if 'FROM ' in content:
             self.passed.append((2, "Dockerfile check passed"))
+            self.dockerfile = content.splitlines()
             return
 
         self.failed.append((2, "Dockerfile check failed"))
@@ -445,6 +448,36 @@ def check_conda_env_yaml(self, api_timeout=10):
                     else:
                         self.failed.append((8, "Could not find Conda dependency using the Anaconda API: {}".format(dep)))
 
+    def check_conda_dockerfile(self):
+        """ Check that the Docker build file looks right, if working with conda
+
+        Make sure that a name is given and is consistent with the pipeline name
+        Check that depedency versions are pinned
+        Warn if dependency versions are not the latest available """
+
+        if 'environment.yml' not in self.files or len(self.dockerfile) == 0:
+            return
+
+        expected_strings = [
+            'FROM continuumio/miniconda',
+            'ENV PATH /opt/conda/envs/{}/bin:$PATH'.format(self.conda_config['name']),
+            'COPY environment.yml /',
+            'RUN conda update -n base conda && \\',
+            '    conda env create -f /environment.yml && \\',
+            '    conda clean -a'
+        ]
+        found_strings = [False for x in expected_strings]
+        for l in self.dockerfile:
+            for idx, s in enumerate(expected_strings):
+                if l == s:
+                    found_strings[idx] = True
+        if all(found_strings):
+            self.passed.append((9, "Found all expected strings in Dockerfile"))
+        else:
+            for idx, s in enumerate(expected_strings):
+                if not found_strings[idx]:
+                    self.failed.append((9, "Could not find Dockerfile string: {}".format(s)))
+
     def print_results(self):
         # Print results
         rl = "\n  Using --release mode linting tests" if self.releaseMode else ''

tests/lint_examples/minimal_working_example/Dockerfile

@@ -1 +1,10 @@
-FROM busybox
+FROM continuumio/miniconda
+MAINTAINER Phil Ewels <[email protected]>
+LABEL authors="[email protected]" \
+    description="Docker image containing all requirements for the nf-core tools pipeline"
+
+COPY environment.yml /
+RUN conda update -n base conda && \
+    conda env create -f /environment.yml && \
+    conda clean -a
+ENV PATH /opt/conda/envs/nfcore-tools/bin:$PATH

tests/test_lint.py

@@ -36,7 +36,7 @@ def pf(wd, path):
     pf(WD, 'lint_examples/license_incomplete_example')]
 
 # The maximum sum of passed tests currently possible
-MAX_PASS_CHECKS = 52
+MAX_PASS_CHECKS = 53
 # The additional tests passed for releases
 ADD_PASS_RELEASE = 1
 
@@ -283,3 +283,31 @@ def test_conda_env_skip(self):
         lint_obj.check_conda_env_yaml()
         expectations = {"failed": 0, "warned": 0, "passed": 0}
         self.assess_lint_status(lint_obj, **expectations)
+
+    def test_conda_dockerfile_pass(self):
+        """ Tests the conda Dockerfile test works with a working example """
+        lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
+        lint_obj.files = ['environment.yml']
+        with open(os.path.join(PATH_WORKING_EXAMPLE, 'Dockerfile'), 'r') as fh:
+            lint_obj.dockerfile = fh.read().splitlines()
+        lint_obj.conda_config['name'] = 'nfcore-tools'
+        lint_obj.check_conda_dockerfile()
+        expectations = {"failed": 0, "warned": 0, "passed": 1}
+        self.assess_lint_status(lint_obj, **expectations)
+
+    def test_conda_dockerfile_fail(self):
+        """ Tests the conda Dockerfile test fails with a bad example """
+        lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
+        lint_obj.files = ['environment.yml']
+        lint_obj.conda_config['name'] = 'nfcore-tools'
+        lint_obj.dockerfile = ['fubar']
+        lint_obj.check_conda_dockerfile()
+        expectations = {"failed": 6, "warned": 0, "passed": 0}
+        self.assess_lint_status(lint_obj, **expectations)
+
+    def test_conda_dockerfile_skip(self):
+        """ Tests the conda Dockerfile test is skipped when not needed """
+        lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
+        lint_obj.check_conda_dockerfile()
+        expectations = {"failed": 0, "warned": 0, "passed": 0}
+        self.assess_lint_status(lint_obj, **expectations)