Make learna installable via pip

Makefile

@@ -82,6 +82,8 @@ data-rfam-learn:
 requirements:
 	./thirdparty/miniconda/make_miniconda.sh
 	conda env create -f environment.yml
+	@source activate learna && \
+	pip install .
 
 
 ################################################################################

environment.yml

@@ -17,5 +17,4 @@ dependencies:
     - tqdm
     - black
     - Distance
-    - tensorforce==0.3.3
     - dataclasses

learna/__init__.py

@@ -0,0 +1 @@
+__version__ = '0.0.1'

src/data/download_and_build_eterna.py → learna/data/download_and_build_eterna.py

@@ -9,7 +9,7 @@ def _download_dataset_from_http(url, download_path):
             unit="B",
             unit_scale=True,
             unit_divisor=1024,
-            total=int(response.headers["Content-Length"]),
+            total=int(response.headers["X-ELS-SIZE"]),
         )
         for data in tqdm(response.iter_content()):
             progress_bar.update(len(data))

src/learna/design_rna.py → learna/learna/design_rna.py

@@ -1,10 +1,10 @@
 import time
 
 import tensorflow as tf
-from ..tensorforce.runner import Runner
+from learna.tensorforce.runner import Runner
 
-from .agent import NetworkConfig, get_network, AgentConfig, get_agent_fn
-from .environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
+from learna.learna.agent import NetworkConfig, get_network, AgentConfig, get_agent_fn
+from learna.learna.environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
 
 
 def _get_episode_finished(timeout, stop_once_solved):

src/learna/environment_test.py → learna/learna/environment_test.py

@@ -1,5 +1,5 @@
 """
-    Testsuite for RNA-Design environment.
+Testsuite for RNA-Design environment.
 """
 
 import pytest
@@ -9,13 +9,8 @@
 from distance import hamming
 from itertools import product
 
-from .environment import _string_difference_indices
-from .environment import RnaDesignEnvironmentConfig
-from .environment import _encode_dot_bracket
-from .environment import _encode_pairing
-from .environment import _Target
-from .environment import _Design
-from .environment import RnaDesignEnvironment
+from learna.learna.environment import _string_difference_indices, RnaDesignEnvironmentConfig, _encode_dot_bracket, \
+    _encode_pairing, _Target, _Design, RnaDesignEnvironment
 
 from RNA import fold
 

src/learna/learn_to_design_rna.py → learna/learna/learn_to_design_rna.py

@@ -1,10 +1,10 @@
 import multiprocessing
 from pathlib import Path
 
-from .agent import NetworkConfig, get_network, AgentConfig, ppo_agent_kwargs, get_agent
-from .environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
+from learna.learna.agent import NetworkConfig, get_network, AgentConfig, ppo_agent_kwargs, get_agent
+from learna.learna.environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
 
-from ..tensorforce.threaded_runner import clone_worker_agent, ThreadedRunner
+from learna.tensorforce.threaded_runner import clone_worker_agent, ThreadedRunner
 
 
 def episode_finished(stats):

src/optimization/bohb.py → learna/optimization/bohb.py

@@ -14,8 +14,8 @@
 import hpbandster.core.result as hpres
 
 from hpbandster.optimizers import BOHB as BOHB
-from src.optimization.learna_worker import LearnaWorker
-from src.optimization.meta_learna_worker import MetaLearnaWorker
+from learna.optimization.learna_worker import LearnaWorker
+from learna.optimization.meta_learna_worker import MetaLearnaWorker
 
 
 parser = argparse.ArgumentParser(
@@ -66,7 +66,7 @@
 parser.add_argument("--mode", choices=["learna", "meta_learna"], default="learna")
 
 
-# args=parser.parse_args("--run_id test --nic_name lo --shared_directory /tmp --n_cores 4 --data_dir src/data --mode L2DesignRNA".split())
+# args=parser.parse_args("--run_id test --nic_name lo --shared_directory /tmp --n_cores 4 --data_dir learna/data --mode L2DesignRNA".split())
 args = parser.parse_args()
 
 os.makedirs(args.shared_directory, exist_ok=True)

src/optimization/bohb_worker/LEARNA.py → learna/optimization/bohb_worker/LEARNA.py

@@ -10,9 +10,9 @@
 from hpbandster.core.worker import Worker
 
 
-from src.learna.agent import NetworkConfig, get_network, AgentConfig
-from src.learna.environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
-from src.learna.design_rna import design_rna
+from learna.learna.agent import NetworkConfig, get_network, AgentConfig
+from learna.learna.environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
+from learna.learna.design_rna import design_rna
 
 
 class DesignRNAWorker(Worker):

src/optimization/bohb_worker/MetaLEARNA.py → learna/optimization/bohb_worker/MetaLEARNA.py

@@ -7,10 +7,10 @@
 import ConfigSpace as CS
 from hpbandster.core.worker import Worker
 
-from src.learna.agent import NetworkConfig, get_network, AgentConfig
-from src.learna.environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
-from src.learna.design_rna import design_rna
-from src.learna.learn_to_design_rna import learn_to_design_rna
+from learna.learna.agent import NetworkConfig, get_network, AgentConfig
+from learna.learna.environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
+from learna.learna.design_rna import design_rna
+from learna.learna.learn_to_design_rna import learn_to_design_rna
 
 
 class L2DesignRNAWorker(Worker):

src/optimization/learna_worker.py → learna/optimization/learna_worker.py

@@ -10,10 +10,10 @@
 from hpbandster.core.worker import Worker
 
 
-from src.learna.agent import NetworkConfig, get_network, AgentConfig
-from src.learna.environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
-from src.learna.design_rna import design_rna
-from src.data.parse_dot_brackets import parse_dot_brackets
+from learna.learna.agent import NetworkConfig, get_network, AgentConfig
+from learna.learna.environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
+from learna.learna.design_rna import design_rna
+from learna.data.parse_dot_brackets import parse_dot_brackets
 
 
 class LearnaWorker(Worker):

src/optimization/meta_learna_worker.py → learna/optimization/meta_learna_worker.py

@@ -7,11 +7,11 @@
 import ConfigSpace as CS
 from hpbandster.core.worker import Worker
 
-from src.learna.agent import NetworkConfig, get_network, AgentConfig
-from src.learna.environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
-from src.learna.design_rna import design_rna
-from src.learna.learn_to_design_rna import learn_to_design_rna
-from src.data.parse_dot_brackets import parse_dot_brackets
+from learna.learna.agent import NetworkConfig, get_network, AgentConfig
+from learna.learna.environment import RnaDesignEnvironment, RnaDesignEnvironmentConfig
+from learna.learna.design_rna import design_rna
+from learna.learna.learn_to_design_rna import learn_to_design_rna
+from learna.data.parse_dot_brackets import parse_dot_brackets
 
 
 class MetaLearnaWorker(Worker):

setup.py

@@ -0,0 +1,46 @@
+# -*- encoding: utf-8 -*-
+
+import setuptools
+
+def read_file(file_name):
+    with open(file_name, encoding='utf-8') as fh:
+        text = fh.read()
+    return text
+
+
+def get_version(file_name):
+    with open(file_name, 'r') as fh:
+        for line in fh.readlines():
+            if "__version__" in line:
+                return line.split()[2].replace('\'', '')
+
+setuptools.setup(
+    name='learna',
+    author_email='[email protected]',
+    description='End-to-end RNA Design using deep reinforcement learning',
+    long_description=read_file('README.md'),
+    long_description_content_type='text/markdown',
+    license='Apache-2.0',
+    url='https://github.com/automl/learna',
+    project_urls={'Source Code': 'https://github.com/automl/learna'},
+    version=get_version('learna/__init__.py'),
+    packages=setuptools.find_packages(exclude=['*.tests', '*.tests.*', 'tests.*', 'tests'],),
+    python_requires='>=3',
+    platforms=['Linux'],
+    classifiers=['Programming Language :: Python :: 3',
+                 'Programming Language :: Python :: 3.5',
+                 'Programming Language :: Python :: 3.6',
+                 'Programming Language :: Python :: 3.7',
+                 'Development Status :: 4 - Beta',
+                 'Natural Language :: English',
+                 'Environment :: Console',
+                 'Environment :: GPU',
+                 'Intended Audience :: Developers',
+                 'Intended Audience :: Education',
+                 'Intended Audience :: Science/Research',
+                 'License :: OSI Approved :: Apache Software License',
+                 'Operating System :: POSIX :: Linux',
+                 'Topic :: Scientific/Engineering',
+                 'Topic :: Scientific/Engineering :: Artificial Intelligence',
+                 'Topic :: Scientific/Engineering :: Bio-Informatics']
+)

utils/execution_scripts/LEARNA-10min.sh

@@ -2,7 +2,7 @@
 TARGET_STRUCTURE_PATH=$1
 
 source thirdparty/miniconda/miniconda/bin/activate learna
-/usr/bin/time -f"%U" python -m src.learna.design_rna \
+/usr/bin/time -f"%U" python -m learna.learna.design_rna \
   --batch_size 32 \
   --conv_channels 8 1 \
   --embedding_size 0 \

utils/execution_scripts/LEARNA-30min.sh

@@ -2,7 +2,7 @@
 TARGET_STRUCTURE_PATH=$1
 
 source thirdparty/miniconda/miniconda/bin/activate learna
-/usr/bin/time -f"%U" python -m src.learna.design_rna \
+/usr/bin/time -f"%U" python -m learna.learna.design_rna \
   --batch_size 79 \
   --conv_channels 10 3 \
   --embedding_size 0 \

utils/execution_scripts/LEARNA.sh

@@ -2,7 +2,7 @@
 TARGET_STRUCTURE_PATH=$1
 
 source thirdparty/miniconda/miniconda/bin/activate learna
-/usr/bin/time -f"%U" python -m src.learna.design_rna \
+/usr/bin/time -f"%U" python -m learna.learna.design_rna \
   --mutation_threshold 5 \
   --batch_size 126 \
   --conv_sizes 17 5 \

utils/execution_scripts/Meta-LEARNA-Adapt.sh

@@ -2,7 +2,7 @@
 TARGET_STRUCTURE_PATH=$1
 
 source thirdparty/miniconda/miniconda/bin/activate learna
-/usr/bin/time -f"%U" python -m src.learna.design_rna \
+/usr/bin/time -f"%U" python -m learna.learna.design_rna \
   --mutation_threshold 5 \
   --batch_size 123 \
   --conv_sizes 11 3 \

utils/execution_scripts/Meta-LEARNA.sh

@@ -2,7 +2,7 @@
 TARGET_STRUCTURE_PATH=$1
 
 source thirdparty/miniconda/miniconda/bin/activate learna
-/usr/bin/time -f"%U" python -m src.learna.design_rna \
+/usr/bin/time -f"%U" python -m learna.learna.design_rna \
   --mutation_threshold 5 \
   --batch_size 123 \
   --conv_sizes 11 3 \