Lint

Author: mboudet

github-ci/src/biocontainersci/ci.py

@@ -13,6 +13,7 @@
 from biocontainersci.utils import send_github_pr_comment, send_status, BiocontainersCIException
 from biocontainersci.biotools import Biotools
 
+
 class CI:
     '''
     Class to manage build/check of containers
@@ -43,13 +44,13 @@ def local_name(self, f):
             return None
         return self.config['registry']['url'] + '/biocontainers/' + f['container'] + ':' + f['tag']
 
-    def run_test(self, f:dict, test: str):
+    def run_test(self, f: dict, test: str):
         '''
         Execute a test against container
         '''
         logging.info("[ci][test] run test: " + test)
         base_container_name = self.name(f)
-        volumes={}
+        volumes = {}
         volumes[self.workdir()] = {'bind': '/biocontainers', 'mode': 'ro'}
         logs = self.docker_client.containers.run(
             base_container_name,
@@ -94,7 +95,6 @@ def docker_logs(self, build_logs):
                 for line in chunk['stream'].splitlines():
                     logging.info(line)
 
-
     def docker_push(self, repo, auth_config=None):
         '''
         Push to registry
@@ -140,7 +140,6 @@ def biotools(self, f, labels):
         )
         '''
 
-
     def anchore(self, f):
         '''
         Add image to anchore security scan
@@ -189,26 +188,27 @@ def singularity(self, f):
             logging.exception('[ci][singularity] convert failed: ' + str(e))
             raise BiocontainersCIException('singularity conversion failed')
 
-
         if self.config['dry']:
             logging.info('[ci][singularity] dry mode, do not push image')
             return
         try:
-            s3_client = boto3.client(service_name="s3", region_name=self.config['s3']['region'],
-                            endpoint_url=self.config['s3']['endpoint'],
-                            verify=False,
-                            aws_access_key_id = self.config['s3']['access_key'],
-                            aws_secret_access_key=self.config['s3']['secret_access_key'])
-            s3_client.upload_file(sing_image, self.config['s3']['bucket'], 'SingImgsRepo/'+f['container'] + '/' + f['tag'] + '/' + f['container'] + '_' + f['tag'] + '.sif')
-        except Exception as e:
+            s3_client = boto3.client(
+                service_name="s3",
+                region_name=self.config['s3']['region'],
+                endpoint_url=self.config['s3']['endpoint'],
+                verify=False,
+                aws_access_key_id=self.config['s3']['access_key'],
+                aws_secret_access_key=self.config['s3']['secret_access_key'])
+
+            s3_client.upload_file(sing_image, self.config['s3']['bucket'], 'SingImgsRepo/' + f['container'] + '/' + f['tag'] + '/' + f['container'] + '_' + f['tag'] + '.sif')
+        except Exception:
             os.unlink(sing_image)
             raise BiocontainersCIException('singularity s3 upload failed')
         # need to be root...
         os.unlink(sing_image)
-        #s3 = boto3.resource('s3')
-        #data = open('/tmp/singimage', 'rb')
-        #s3.Bucket(self.config['s3']['bucket']).put_object(Key='SingImgsRepo/'+f['container'] + '/' + f['tag'] + '/' + f['container'] + '_' + f['tag'] + '.img', Body=data)
-
+        # s3 = boto3.resource('s3')
+        # data = open('/tmp/singimage', 'rb')
+        # s3.Bucket(self.config['s3']['bucket']).put_object(Key='SingImgsRepo/'+f['container'] + '/' + f['tag'] + '/' + f['container'] + '_' + f['tag'] + '.img', Body=data)
 
     def workdir(self):
         return os.environ.get('GITHUB_WORKSPACE', os.getcwd())
@@ -227,12 +227,12 @@ def workflow(self, f):
         # check for dockerfile
         with open(os.path.join(self.workdir(), f['container'], f['version'], 'Dockerfile'), 'r') as d:
             lines = d.readlines()
-            for l in lines:
-                if '.aws' in l:
+            for line in lines:
+                if '.aws' in line:
                     logging.error('[ci] private biocontainers-ci directory access in dockerfile forbiden')
                     send_github_pr_comment(self.config, 'Forbiden access to biocontainers-ci private files in Dockerfile')
                     raise BiocontainersCIException('private biocontainers-ci directory access in dockerfile forbiden')
-                if 'etc/biocontainers-ci' in l:
+                if 'etc/biocontainers-ci' in line:
                     logging.error('[ci] private biocontainers-ci directory access in dockerfile forbiden')
                     send_github_pr_comment(self.config, 'Forbiden access to biocontainers-ci directory in Dockerfile')
                     raise BiocontainersCIException('private biocontainers-ci directory access in dockerfile forbiden')
@@ -312,7 +312,7 @@ def workflow(self, f):
         except Exception as e:
             logging.exception('[ci][workflow] error: ' + str(e))
             status = False
-        
+
         try:
             self.docker_client.images.remove(image=self.name(f), force=True)
         except Exception:
@@ -332,25 +332,23 @@ def workflow(self, f):
         logging.info('Docker containers prune')
         self.docker_client.containers.prune()
         return status
-        
-
 
     '''
     Check labels in docker image
     '''
-    def check_labels(self, f:dict, labels:dict):
+    def check_labels(self, f: dict, labels: dict):
         label_errors = []
         software = 'unknown'
         if 'software' not in labels or not labels['software']:
             label_errors.append('software label not present')
             status = False
         else:
-            software =  labels['software']
-            #labels['software'].strip()
-            pattern=re.compile("^([a-z0-9_-])+$")
+            software = labels['software']
+            # labels['software'].strip()
+            pattern = re.compile("^([a-z0-9_-])+$")
             if pattern.match(labels['software']) is None:
                 logging.warning('[ci][labels] ' + software + " has invalid name, using directory name")
-                software =  f['container']
+                software = f['container']
                 labels['container'] = f['container']
 
         if 'base_image' not in labels or not labels['base_image']:
@@ -419,7 +417,7 @@ def check_labels(self, f:dict, labels:dict):
             else:
                 bio = requests.get('https://bio.tools/api/tool/' + str(software) + '/?format=json')
                 if bio.status_code != 404:
-                    send_github_pr_comment(self.config, 'Found a biotools entry matching the software name (https://bio.tools/' + labels['software']+ '), if this is the same software, please add the extra.identifiers.biotools label to your Dockerfile')
+                    send_github_pr_comment(self.config, 'Found a biotools entry matching the software name (https://bio.tools/' + labels['software'] + '), if this is the same software, please add the extra.identifiers.biotools label to your Dockerfile')
                 else:
                     send_github_pr_comment(self.config, 'No biotools label defined, please check if tool is not already defined in biotools (https://bio.tools) and add extra.identifiers.biotools label if it exists. If it is not defined, you can ignore this comment.')
 
@@ -434,7 +432,7 @@ def check_labels(self, f:dict, labels:dict):
                     logging.info("biotools entry is ok")
 
             # Check if exists in conda
-            conda_url = 'https://bioconda.github.io/recipes/' + labels['software']+'/README.html'
+            conda_url = 'https://bioconda.github.io/recipes/' + labels['software'] + '/README.html'
             conda = requests.get(conda_url)
             if conda.status_code == 200:
                 send_github_pr_comment(self.config, 'Found an existing bioconda package for this software (' + conda_url + '), is this the same, then you should update the recipe in bioconda to avoid duplicates.')