Merge branch 'release/0.5.2'

.travis.yml

@@ -33,7 +33,7 @@ before_install:
   - conda info -a
 
 install:
-  - conda install ucsc-genepredtobed ucsc-genepredtogtf ucsc-bedtogenepred ucsc-gtftogenepred bwa minimap2 bowtie2 hisat2 gmap msgpack-python pyfaidx>=0.5.1 bucketcache norns>0.1.1 xmltodict pytest coverage pyyaml requests
+  - conda install ucsc-genepredtobed ucsc-genepredtogtf ucsc-bedtogenepred ucsc-gtftogenepred bwa minimap2 bowtie2 hisat2 gmap pyfaidx>=0.5.1 bucketcache norns>0.1.1 xmltodict pytest coverage pyyaml requests
   - python setup.py develop
   - python setup.py build
   - pip install coveralls

CHANGELOG.md

@@ -2,16 +2,28 @@
 
 Here, the changes to `genomepy` will be summarized.
 
-## Version 0.3.1
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
-* Added requests dependency
-* Removed dependency on xdg, as it didn't support OSX
-* Fixed string decoding bug
+## [Unreleased]
 
-## Version 0.3.0
+## [0.5.2] - 2018-09-11
 
-* Started CHANGELOG.
-* Genome listings are cached locally.
-* Added `-m hard` option to `install` to hard-mask sequences.
-* Added `-l` option to `install` for a custom name.
-* Added `-r` and `--match/--no-match` option to select sequences by regex.
+### Fixed
+
+- Fixed genome_dir argument to `genomepy install`
+- Fixed msgpack dependency
+- Fixed issue with `config generate` where config directory does note exist.
+
+## [0.3.1]
+
+- Added requests dependency
+- Removed dependency on xdg, as it didn't support OSX
+- Fixed string decoding bug
+
+## [0.3.0]
+
+- Started CHANGELOG.
+- Genome listings are cached locally.
+- Added `-m hard` option to `install` to hard-mask sequences.
+- Added `-l` option to `install` for a custom name.
+- Added `-r` and `--match/--no-match` option to select sequences by regex.

genomepy/__about__.py

@@ -1,3 +1,3 @@
 """Metadata"""
-__version__ = '0.5.1'
+__version__ = '0.5.2'
 __author__ = "Simon van Heeringen"

genomepy/cli.py

@@ -34,7 +34,7 @@ def search(term, provider=None):
 def install(name, provider, genome_dir, localname, mask, regex, match, annotation):
     """Install genome NAME from provider PROVIDER in directory GENOME_DIR."""
     genomepy.install_genome(
-            name, provider, genome_dir, localname=localname, mask=mask, 
+            name, provider, genome_dir=genome_dir, localname=localname, mask=mask, 
             regex=regex, invert_match=not(match), annotation=annotation)
 
 @click.command('genomes', short_help="list available genomes")

genomepy/functions.py

@@ -33,7 +33,10 @@ def manage_config(cmd, *args):
         fname = os.path.join(
                 user_config_dir("genomepy"), "{}.yaml".format("genomepy")
             )
-
+
+        if not os.path.exists(user_config_dir("genomepy")):
+            os.makedirs(user_config_dir("genomepy"))
+
         with open(fname, "w") as fout:
             with open(config.config_file) as fin:
                 fout.write(fin.read())
@@ -282,34 +285,35 @@ def __init__(self, name, genome_dir=None):
             super(Genome, self).__init__(name)
             self.name = os.path.basename(name)
         except:
-            if os.path.isdir(name):
-                genome_dir = name
+            if os.path.isdir(name) and len(glob.glob(os.path.join(name, "*.fa"))) == 1 and genome_dir is not None:
+                fname = glob.glob(os.path.join(name, "*.fa"))[0]
+                name = os.path.basename(fname)  
             else:
                 if not genome_dir:
                     genome_dir = config.get("genome_dir", None)
                 if not genome_dir:
                     raise norns.exceptions.ConfigError("Please provide or configure a genome_dir")
 
-            genome_dir = os.path.expanduser(genome_dir)
-            if not os.path.exists(genome_dir):
-                raise FileNotFoundError(
-                        "genome_dir {} does not exist".format(genome_dir)
-                        )
+                genome_dir = os.path.expanduser(genome_dir)
+                if not os.path.exists(genome_dir):
+                    raise FileNotFoundError(
+                            "genome_dir {} does not exist".format(genome_dir)
+                            )
 
-            pattern = os.path.join(genome_dir, name, "*.fa")
-            fnames = glob.glob(pattern)
-            if len(fnames) == 0:
-                raise FileNotFoundError(
-                        "no *.fa files found in genome_dir {}".format(
-                            os.path.join(genome_dir, name)
+                pattern = os.path.join(genome_dir, name, "*.fa")
+                fnames = glob.glob(pattern)
+                if len(fnames) == 0:
+                    raise FileNotFoundError(
+                            "no *.fa files found in genome_dir {}".format(
+                                os.path.join(genome_dir, name)
+                                )
                             )
-                        )
-            elif len(fnames) > 1:
-                fname = os.path.join(genome_dir, name, "{}.fa".format(name))
-                if fname not in fnames:
-                    raise Exception("More than one FASTA file found, no {}.fa!".format(name))
-            else:
-                fname = fnames[0]
+                elif len(fnames) > 1:
+                    fname = os.path.join(genome_dir, name, "{}.fa".format(name))
+                    if fname not in fnames:
+                        raise Exception("More than one FASTA file found, no {}.fa!".format(name))
+                else:
+                    fname = fnames[0]
 
             super(Genome, self).__init__(fname)
 

genomepy/provider.py

@@ -18,18 +18,20 @@
 except:
         from urllib import urlopen, urlretrieve, urlcleanup
 
-from bucketcache import Bucket,JSONBackend,MessagePackBackend
+from bucketcache import Bucket
 from pyfaidx import Fasta
 from appdirs import user_cache_dir
 
 from genomepy import exceptions
 from genomepy.utils import filter_fasta
+from genomepy.__about__ import __version__
 
+my_cache_dir = os.path.join(user_cache_dir("genomepy"), __version__)
 # Create .cache dir if it does not exist
-if not os.path.exists(user_cache_dir("genomepy")):
-    os.makedirs(user_cache_dir("genomepy"))
+if not os.path.exists(my_cache_dir):
+    os.makedirs(my_cache_dir)
 
-cached = Bucket(user_cache_dir("genomepy"), days=7, backend=MessagePackBackend)
+cached = Bucket(my_cache_dir, days=7)
 
 class ProviderBase(object):
 

setup.py

@@ -38,7 +38,6 @@
     'norns>0.1.1',
     'xmltodict',
     'bucketcache',
-    'msgpack',
     'requests',
     'appdirs',
 ]