Updating biopython

README.md

@@ -17,7 +17,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb_common.readthedocs.io/en/latest/).
 
 ### Version
-v3.5.0 2020.4
+v3.5.1 2020.4
 
 ### Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).

biobb_common/docs/source/readme.md

@@ -17,7 +17,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb_common.readthedocs.io/en/latest/).
 
 ### Version
-v3.5.0 2020.4
+v3.5.1 2020.4
 
 ### Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).

biobb_common/json_schemas/biobb_common.json

@@ -6,7 +6,7 @@
     "conda": "https://anaconda.org/bioconda/biobb_common",
     "docker": "https://quay.io/repository/biocontainers/biobb_common",
     "singularity": "https://www.singularity-hub.org/collections/2734/usage",
-    "version": "3.5.0",
+    "version": "3.5.1",
     "tools" : [
         {
             "block" : "",

biobb_common/tools/file_utils.py

@@ -59,7 +59,7 @@ def create_unique_dir(path: str = '', prefix: str = '', number_attempts: int = 1
             if out_log:
                 out_log.info(new_dir + ' Already exists')
                 out_log.info('Retrying %i times more' % (number_attempts - i))
-            new_dir = prefix + str(uuid.uuid4())
+            new_dir = prefix + str(uuid.uuid4().hex)
             if path:
                 new_dir = str(Path(path).joinpath(new_dir))
             if out_log:
@@ -434,8 +434,10 @@ def copy_to_container(container_path: str, container_volume_path: str, io_dict:
             if Path(file_path).exists():
                 shutil.copy2(file_path, unique_dir)
                 log(f'Copy: {file_path} to {unique_dir}')
-            # Default files in GMXLIB path
-            container_io_dict["in"][file_ref] = str(Path(container_volume_path).joinpath(Path(file_path).name))
+                container_io_dict["in"][file_ref] = str(Path(container_volume_path).joinpath(Path(file_path).name))
+            else:
+                # Default files in GMXLIB path like gmx_solvate -> input_solvent_gro_path (spc216.gro)
+                container_io_dict["in"][file_ref] = file_path
 
     # OUT files assign INTERNAL PATH
     for file_ref, file_path in io_dict["out"].items():
@@ -466,7 +468,7 @@ def create_cmd_line(cmd: typing.Iterable[str], container_path: str = '', host_vo
     if container_path.endswith('singularity'):
         log('Using Singularity image %s' % container_image, out_log, global_log)
         if not Path(container_image).exists():
-            log(f"{container_image} does not exist trying to pull it")
+            log(f"{container_image} does not exist trying to pull it", out_log, global_log)
             container_image_name = str(Path(container_image).with_suffix('.sif').name)
             singularity_pull_cmd = [container_path, 'pull', '--name', container_image_name, container_image]
             try:
@@ -475,10 +477,10 @@ def create_cmd_line(cmd: typing.Iterable[str], container_path: str = '', host_vo
                 if Path(container_image_name).exists():
                     container_image = container_image_name
                 else:
-                    raise
+                    raise FileNotFoundError
             except:
-                log(f"{' '.join(singularity_pull_cmd)} not found")
-                raise
+                log(f"{' '.join(singularity_pull_cmd)} not found", out_log, global_log)
+                raise FileNotFoundError
         singularity_cmd = [container_path, 'exec', '-e', '--bind', host_volume + ':' + container_volume, container_image]
         # If we are working on a mac remove -e option because is still no available
         if platform == "darwin":

biobb_common/tools/test_fixtures.py

@@ -6,6 +6,7 @@ import sys
 import shutil
 import hashlib
 import Bio.PDB
+import codecs
 from biobb_common.configuration import settings
 from biobb_common.tools import file_utils as fu
 
@@ -185,9 +186,9 @@ def compare_top_itp(file_a: str, file_b: str) -> bool:
     print("Comparing TOP/ITP:")
     print("     FILE_A: "+file_a)
     print("     FILE_B: "+file_b)
-    with open(file_a) as f_a:
+    with codecs.open(file_a, 'r', encoding='utf-8', errors='ignore') as f_a:
         next(f_a)
-        with open(file_b) as f_b:
+        with codecs.open(file_b, 'r', encoding='utf-8', errors='ignore') as f_b:
             next(f_b)
             return [line.strip() for line in f_a if not line.strip().startswith(';')] == [line.strip() for line in f_b if not line.strip().startswith(';')]
 

setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="biobb_common",
-    version="3.5.0",
+    version="3.5.1",
     author="Biobb developers",
     author_email="pau.andrio@bsc.es",
     description="Biobb_common is the base package required to use the biobb packages.",