# Copyright (c) 2015. Mount Sinai School of Medicine
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from __future__ import print_function, division, absolute_import

from .memory_cache import MemoryCache
from .database import Database
from .download_cache import DownloadCache
from .ensembl_release import EnsemblRelease
from .ensembl_release_versions import MAX_ENSEMBL_RELEASE
from .exon import Exon
from .genome import Genome
from .gene import Gene
from .locus import Locus
from .search import find_nearest_locus
from .sequence_data import SequenceData
from .species import (
    find_species_by_name,
    find_species_by_reference,
    which_reference,
    check_species_object,
    normalize_reference_name,
    normalize_species_name,
)
from .transcript import Transcript

__version__ = '1.2.2'

def cached_release(release, species="human"):
    """
    Create an EnsemblRelease instance only if it's hasn't already been made,
    otherwise returns the old instance.

    Keeping this function for backwards compatibility but this functionality
    has been moving into the cached method of EnsemblRelease.
    """
    return EnsemblRelease.cached(release=release, species=species)

def genome_for_reference_name(reference_name):
    reference_name = normalize_reference_name(reference_name)
    species = find_species_by_reference(reference_name)
    (_, max_ensembl_release) = species.reference_assemblies[reference_name]
    return cached_release(release=max_ensembl_release, species=species)

ensembl_grch36 = ensembl54 = cached_release(54)  # last release for GRCh36/hg18
ensembl_grch37 = ensembl75 = cached_release(75)  # last release for GRCh37/hg19
ensembl_grch38 = cached_release(MAX_ENSEMBL_RELEASE)  # most recent for GRCh38


__all__ = [
    "MemoryCache",
    "DownloadCache",
    "Database",
    "EnsemblRelease",
    "MAX_ENSEMBL_RELEASE",
    "cached_release",
    "Gene",
    "Transcript",
    "Exon",
    "SequenceData",
    "find_nearest_locus",
    "find_species_by_name",
    "find_species_by_reference",
    "which_reference",
    "check_species_object",
    "normalize_reference_name",
    "normalize_species_name",
    "Genome",
    "Locus",
    "Exon",
    "ensembl_grch36",
    "ensembl_grch37",
    "ensembl_grch38",
]

# Copyright (c) 2015. Mount Sinai School of Medicine
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from __future__ import print_function, division, absolute_import

from .memory_cache import MemoryCache
from .database import Database
from .download_cache import DownloadCache
from .ensembl_release import EnsemblRelease
from .ensembl_release_versions import MAX_ENSEMBL_RELEASE
from .exon import Exon
from .genome import Genome
from .gene import Gene
from .locus import Locus
from .search import find_nearest_locus
from .sequence_data import SequenceData
from .species import (
    find_species_by_name,
    find_species_by_reference,
    which_reference,
    check_species_object,
    normalize_reference_name,
    normalize_species_name,
)
from .transcript import Transcript

__version__ = '1.2.3'

def cached_release(release, species="human"):
    """
    Create an EnsemblRelease instance only if it's hasn't already been made,
    otherwise returns the old instance.

    Keeping this function for backwards compatibility but this functionality
    has been moving into the cached method of EnsemblRelease.
    """
    return EnsemblRelease.cached(release=release, species=species)

def genome_for_reference_name(reference_name):
    reference_name = normalize_reference_name(reference_name)
    species = find_species_by_reference(reference_name)
    (_, max_ensembl_release) = species.reference_assemblies[reference_name]
    return cached_release(release=max_ensembl_release, species=species)

ensembl_grch36 = ensembl54 = cached_release(54)  # last release for GRCh36/hg18
ensembl_grch37 = ensembl75 = cached_release(75)  # last release for GRCh37/hg19
ensembl_grch38 = cached_release(MAX_ENSEMBL_RELEASE)  # most recent for GRCh38


__all__ = [
    "MemoryCache",
    "DownloadCache",
    "Database",
    "EnsemblRelease",
    "MAX_ENSEMBL_RELEASE",
    "cached_release",
    "Gene",
    "Transcript",
    "Exon",
    "SequenceData",
    "find_nearest_locus",
    "find_species_by_name",
    "find_species_by_reference",
    "which_reference",
    "check_species_object",
    "normalize_reference_name",
    "normalize_species_name",
    "Genome",
    "Locus",
    "Exon",
    "ensembl_grch36",
    "ensembl_grch37",
    "ensembl_grch38",
]

Update __init__.py