installation improvements and version (#121)

* cleaning install & reqs

* lenient req where one can be

* consistency

* fix

* consistency again

* ok

helixer/core/scripts.py

@@ -4,7 +4,7 @@
 from pprint import pprint
 from termcolor import colored
 from abc import ABC, abstractmethod
-
+from importlib.metadata import version
 
 class ParameterParser(ABC):
     """Bundles code that parses script parameters from the command line and a config file."""
@@ -26,7 +26,7 @@ def __init__(self, config_file_path=''):
         self.data_group.add_argument('--no-multiprocess', action='store_true',
                                      help='Whether to not parallize the numerification of large sequences. Uses half the memory '
                                           'but can be much slower when many CPU cores can be utilized.')
-
+        self.parser.add_argument('--version', action='version', version='%(prog)s ' + version('helixer'))
         # Default values have to be specified - and potentially added - here
         self.defaults = {'compression': 'gzip', 'no_multiprocess': False}
 

helixer/export/exporter.py

@@ -5,7 +5,7 @@
 import sqlite3
 import datetime
 import subprocess
-import pkg_resources
+from importlib.metadata import version
 
 import geenuff
 import helixer
@@ -86,7 +86,7 @@ def _add_data_attrs(self):
                     strip().decode()
             except subprocess.CalledProcessError:
                 attrs[module.__name__ + '_commit'] = 'commit not found, version: {}'.format(
-                    pkg_resources.require(module.__name__)[0].version
+                    version(module.__name__) 
                 )
                 print('logged installed version in place of git commit for {}'.format(module.__name__))
         os.chdir(pwd)

helixer/prediction/HelixerModel.py

@@ -14,7 +14,7 @@
 import numcodecs
 import argparse
 import datetime
-import pkg_resources
+from importlib.metadata import version
 import subprocess
 import numpy as np
 import tensorflow as tf
@@ -913,8 +913,7 @@ def _print_model_info(self, model):
             commit = subprocess.check_output(cmd, stderr=subprocess.STDOUT).strip().decode()
             print(f'Current Helixer branch: {branch} ({commit})')
         except subprocess.CalledProcessError:
-            version = pkg_resources.require('helixer')[0].version
-            print(f'Current Helixer version: {version}')
+            print(f'Current Helixer version: {version("helixer")}')
 
         try:
             if os.path.isfile(self.load_model_path):

requirements.3.10.txt

@@ -0,0 +1,93 @@
+absl-py==2.1.0
+appdirs==1.4.4
+astor==0.8.1
+astunparse==1.6.3
+cachetools==5.3.3
+certifi==2024.2.2
+charset-normalizer==3.3.2
+cloudpickle==3.0.0
+colorama==0.4.6
+contextlib2==21.6.0
+contourpy==1.2.0
+cycler==0.12.1
+dill==0.3.8
+#dustdas @ git+https://github.com/gglyptodon/dustdas@d95083163eae361853ad8ef967ed30224a9695ea
+exceptiongroup==1.2.0
+filelock==3.11.0
+flatbuffers==24.3.7
+fonttools==4.50.0
+gast==0.5.4
+#geenuff @ git+https://github.com/weberlab-hhu/GeenuFF@702cbf3c2a8eba05dc2f26038a0d3aa0da8242b8
+google-auth==2.29.0
+google-auth-oauthlib==1.2.0
+google-pasta==0.2.0
+grpcio==1.62.1
+h5py==3.10.0
+#-e git+ssh://git@github-realname/weberlab-hhu/Helixer.git@887e09104cf0895f1e3937434ae75d0fc15ff21a#egg=helixer
+HTSeq==2.0.5
+idna==3.6
+iniconfig==2.0.0
+intervaltree==3.1.0
+joblib==1.3.2
+json-tricks==3.17.3
+keras==2.15.0
+keras-layer-normalization==0.16.0
+kiwisolver==1.4.5
+libclang==18.1.1
+Markdown==3.6
+MarkupSafe==2.1.5
+matplotlib==3.8.3
+ml-dtypes==0.3.2
+multiprocess==0.70.16
+nni==2.10.1
+numcodecs==0.12.1
+numpy==1.26.4
+oauthlib==3.2.2
+opt-einsum==3.3.0
+packaging==24.0
+pandas==2.2.1
+pillow==10.2.0
+pluggy==1.4.0
+prettytable==3.10.0
+protobuf==4.25.3
+psutil==5.9.8
+pyasn1==0.5.1
+pyasn1-modules==0.3.0
+pyparsing==3.1.2
+pysam==0.22.0
+pytest==8.1.1
+python-dateutil==2.9.0.post0
+PythonWebHDFS==0.2.3
+pytz==2024.1
+PyYAML==6.0.1
+requests==2.31.0
+requests-oauthlib==2.0.0
+responses==0.25.0
+rsa==4.9
+schema==0.7.5
+scikit-learn==1.4.1.post1
+scipy==1.12.0
+seaborn==0.13.2
+simplejson==3.19.2
+six==1.16.0
+sortedcontainers==2.4.0
+SQLAlchemy==1.3.22
+tensorboard==2.15.2
+tensorboard-data-server==0.7.2
+tensorflow==2.15.1
+tensorflow-addons==0.23.0
+tensorflow-estimator==2.15.0
+tensorflow-io-gcs-filesystem==0.36.0
+termcolor==2.4.0
+terminaltables==3.1.10
+threadpoolctl==3.4.0
+tomli==2.0.1
+tqdm==4.66.2
+typeguard==2.13.3
+typing_extensions==4.10.0
+tzdata==2024.1
+urllib3==2.2.1
+wcwidth==0.2.13
+websockets==12.0
+Werkzeug==3.0.1
+wrapt==1.14.1

requirements.3.8.txt

@@ -0,0 +1,96 @@
+absl-py==2.1.0
+appdirs==1.4.4
+astor==0.8.1
+astunparse==1.6.3
+cachetools==5.3.3
+certifi==2024.2.2
+charset-normalizer==3.3.2
+cloudpickle==3.0.0
+colorama==0.4.6
+contextlib2==21.6.0
+contourpy==1.1.1
+cycler==0.12.1
+dill==0.3.8
+git+https://github.com/gglyptodon/[email protected]
+exceptiongroup==1.2.0
+filelock==3.11.0
+flatbuffers==24.3.7
+fonttools==4.50.0
+gast==0.4.0
+#geenuff==0.3.0
+google-auth==2.29.0
+google-auth-oauthlib==1.0.0
+google-pasta==0.2.0
+grpcio==1.62.1
+h5py==3.10.0
+#helixer==0.3.2
+HTSeq==2.0.5
+idna==3.6
+importlib-metadata==7.1.0
+importlib-resources==6.4.0
+iniconfig==2.0.0
+intervaltree==3.1.0
+joblib==1.3.2
+json-tricks==3.17.3
+keras==2.13.1
+keras-layer-normalization==0.16.0
+kiwisolver==1.4.5
+libclang==18.1.1
+Markdown==3.6
+MarkupSafe==2.1.5
+matplotlib==3.7.5
+multiprocess==0.70.16
+nni==3.0
+numcodecs==0.12.1
+numpy==1.24.3
+nvidia-ml-py==12.535.133
+oauthlib==3.2.2
+opt-einsum==3.3.0
+packaging==24.0
+pandas==2.0.3
+pillow==10.2.0
+pluggy==1.4.0
+prettytable==3.10.0
+protobuf==4.25.3
+psutil==5.9.8
+pyasn1==0.5.1
+pyasn1-modules==0.3.0
+pyparsing==3.1.2
+pysam==0.22.0
+pytest==8.1.1
+python-dateutil==2.9.0.post0
+PythonWebHDFS==0.2.3
+pytz==2024.1
+PyYAML==6.0.1
+requests==2.31.0
+requests-oauthlib==2.0.0
+responses==0.25.0
+rsa==4.9
+schema==0.7.5
+scikit-learn==1.3.2
+scipy==1.10.1
+seaborn==0.13.2
+simplejson==3.19.2
+six==1.16.0
+sortedcontainers==2.4.0
+SQLAlchemy==1.3.22
+tensorboard==2.13.0
+tensorboard-data-server==0.7.2
+tensorflow==2.13.1
+tensorflow-addons==0.21.0
+tensorflow-estimator==2.13.0
+tensorflow-io-gcs-filesystem==0.34.0
+termcolor==2.4.0
+terminaltables==3.1.10
+threadpoolctl==3.4.0
+tomli==2.0.1
+tqdm==4.66.2
+typeguard==4.1.2
+typing-extensions==4.10.0
+tzdata==2024.1
+urllib3==2.2.1
+wcwidth==0.2.13
+websockets==12.0
+werkzeug==3.0.1
+wrapt==1.16.0
+zipp==3.18.1

setup.py

@@ -2,12 +2,27 @@
 
 setup(
    name='helixer',
-   version='0.3.2',
+   version='0.3.3',
    description='Deep Learning fun on gene structure data',
    packages=['helixer', 'helixer.core', 'helixer.prediction', 'helixer.evaluation', 'helixer.tests', 'helixer.export'],
    package_data={'helixer': ['testdata/*.fa', 'testdata/*.gff']},
-   install_requires=["geenuff @ https://github.com/weberlab-hhu/GeenuFF/archive/refs/heads/main.zip"],
-   dependency_links=["https://github.com/weberlab-hhu/GeenuFF/archive/refs/heads/main.zip#egg=geenuff"],
+   install_requires=["geenuff @ git+https://github.com/weberlab-hhu/[email protected]",
+                     "sqlalchemy==1.3.22",
+                     "tensorflow>=2.6.2",
+                     "tensorflow-addons>=0.21.0",
+                     "nni",
+                     "seaborn",
+                     "Keras<3.0.0",
+                     "keras_layer_normalization",
+                     "terminaltables",
+                     "HTSeq",
+                     "intervaltree",
+                     "numpy",
+                     "h5py",
+                     "multiprocess",
+                     "numcodecs",
+                     "appdirs",
+                    ],
    scripts=["Helixer.py", "fasta2h5.py", "geenuff2h5.py", "helixer/prediction/HybridModel.py", "scripts/fetch_helixer_models.py"],
    zip_safe=False,
 )