Remove pandas dependency (#273)

* removing MemoryCache and pandas requirement

* got rid of six dependency

* got rid of two different requirements lists

* added unit test for shell

pyensembl/__init__.py

@@ -10,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .memory_cache import MemoryCache
 from .database import Database
 from .download_cache import DownloadCache
 from .ensembl_release import EnsemblRelease, cached_release
@@ -41,7 +40,6 @@
 
 __all__ = [
     "__version__",
-    "MemoryCache",
     "DownloadCache",
     "Database",
     "EnsemblRelease",

pyensembl/common.py

@@ -14,7 +14,6 @@
 
 from functools import wraps
 
-
 def dump_pickle(obj, filepath):
     with open(filepath, "wb") as f:
         # use lower protocol for compatibility between Python 2 and Python 3

pyensembl/database.py

@@ -16,7 +16,6 @@
 
 import datacache
 from typechecks import require_integer, require_string
-
 from gtfparse import read_gtf, create_missing_features
 
 from .common import memoize

pyensembl/genome.py

@@ -21,7 +21,6 @@
 
 from serializable import Serializable
 
-from .memory_cache import MemoryCache
 from .download_cache import DownloadCache
 from .database import Database
 from .exon import Exon
@@ -108,7 +107,6 @@ def __init__(
             copy_local_files_to_cache=self.copy_local_files_to_cache,
             install_string_function=self.install_string,
             cache_directory_path=cache_directory_path)
-        self.memory_cache = MemoryCache()
         self._init_lazy_fields()
 
     @property
@@ -435,8 +433,7 @@ def __hash__(self):
 
     def clear_cache(self):
         """
-        Clear any in-memory cached values and short-lived on-disk
-        materializations from MemoryCache
+        Clear any in-memory cached values
         """
         for maybe_fn in self.__dict__.values():
             # clear cache associated with all memoization decorators,

pyensembl/sequence_data.py

@@ -14,10 +14,7 @@
 from os.path import exists, abspath, split, join
 import logging
 from collections import Counter
-
-from six.moves import cPickle as pickle
-from six import string_types
-
+import pickle 
 from .common import (load_pickle, dump_pickle)
 from .fasta import parse_fasta_dictionary
 
@@ -34,7 +31,7 @@ def __init__(
             fasta_paths,
             cache_directory_path=None):
 
-        if isinstance(fasta_paths, string_types):
+        if type(fasta_paths) is str:
             fasta_paths = [fasta_paths]
 
         self.fasta_paths = [abspath(path) for path in fasta_paths]

pyensembl/version.py

@@ -1 +1 @@
-__version__ = '2.1.0'
+__version__ = '2.2.0'

requirements.txt

@@ -1,11 +1,8 @@
 typechecks>=0.0.2
-numpy>=1.7
-pandas>=0.15
 datacache>=1.1.4
 memoized-property>=1.0.2
-nose>=1.3.3
 tinytimer
-six>=1.9.0
+gtfparse>=1.3.0
+serializable
+nose>=1.3.3
 pylint>=1.4.4
-gtfparse>=1.1.0
-serializable

setup.py

@@ -41,6 +41,9 @@
     raise RuntimeError('Cannot find version information')
 
 if __name__ == '__main__':
+    with open("requirements.txt") as f:
+        requirements = [l.strip() for l in f]
+
     setup(
         name=package_name,
         version=version,
@@ -63,15 +66,7 @@
             'Programming Language :: Python',
             'Topic :: Scientific/Engineering :: Bio-Informatics',
         ],
-        install_requires=[
-            "typechecks>=0.0.2",
-            "pandas>=0.15",
-            "datacache>=1.1.4",
-            "memoized-property>=1.0.2",
-            "gtfparse>=1.1.0",
-            "serializable",
-            "tinytimer",
-        ],
+        install_requires=requirements,
         long_description=readme_markdown,
         long_description_content_type='text/markdown',
         packages=[package_name],

test/common.py

@@ -1,5 +1,3 @@
-from __future__ import absolute_import
-
 import functools
 
 from pyensembl import (

test/test_download_cache.py

@@ -1,5 +1,3 @@
-from __future__ import absolute_import
-
 from nose.tools import assert_raises, ok_
 from pyensembl.download_cache import (
     DownloadCache,

test/test_gene_objects.py

@@ -1,5 +1,3 @@
-from __future__ import absolute_import
-
 from nose.tools import eq_
 
 from .common import test_ensembl_releases

test/test_id_length.py

@@ -1,5 +1,3 @@
-from __future__ import absolute_import
-
 from .common import major_releases
 
 from nose.tools import nottest

test/test_locus.py

@@ -1,5 +1,3 @@
-from __future__ import absolute_import
-
 from pyensembl.locus import Locus
 from pyensembl.normalization import normalize_chromosome
 

test/test_missing_genome_sources.py

@@ -1,5 +1,3 @@
-from __future__ import absolute_import
-
 from pyensembl import Genome
 from nose.tools import eq_, ok_, assert_raises
 

test/test_mouse.py

@@ -1,5 +1,3 @@
-from __future__ import absolute_import
-
 from nose.tools import eq_, with_setup
 
 from .data import (