update to 2.2.0

.gitignore

@@ -45,6 +45,7 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *,cover
+.pytest_cache/*
 
 # Translations
 *.mo

README.md

@@ -11,18 +11,18 @@ For general information on MINE Databases, please consult [JJeffryes et al. 2015
 Documentation is hosted at https://mine-database.readthedocs.io/en/latest/. It gives more detailed descriptions and example uses of the software.
 
 ## Installation
-MINE-Database requires the use of [rdkit](https://rdkit.org/), which currently is unavailable to install on pip. Thus, we recommend you use conda to create a new environment and then install rdkit into that environment before proceeding:
+If a conda environment is desired to be used:
 
 `conda create -n mine`
 
 `conda activate mine`
 
-`conda install -c rdkit rdkit`
 
-Then, use pip (in your conda environment) to install minedatabase:
+Then, use pip (with or without conda) to install minedatabase:
 
 `pip install minedatabase`
 
+
 ## Running Pickaxe
 ### Running Pickaxe through a python file (recommended)
 An example file, [pickaxe_run_template.py](https://github.com/tyo-nu/MINE-Database/blob/master/pickaxe_run_template.py), provides a framework for running pickaxe through a python file. Feel free to download it and change it to your needs. The starting compounds, rules and cofactors, optional database information, and Pickaxe run options are specified. After running the results are stored in a specified database or written to .tsv files.

requirements.txt

@@ -1,9 +1,9 @@
 keras
-lxml
-mordred
+lxml==4.9
+mordred==1.2
 numpy
 pandas
-pymongo
+pymongo==4.3
 pytest
 pytest-cov
 python-libsbml

setup.cfg

@@ -0,0 +1,13 @@
+[options]
+python_requires = >= 3.7, <3.10
+install_requires =
+    keras
+    python-libsbml
+    lxml==4.9
+    mordred==1.2
+    pandas
+    pymongo
+    rdkit
+    scikit-learn
+[options.extras_require]
+test = pytest

setup.py

@@ -6,16 +6,16 @@
     long_description = fh.read()
 
 setup(name='minedatabase',
-      version='2.1.0',
+      version='2.2.0',
       description='Metabolic In silico Network Expansions',
       long_description=long_description,
       long_description_content_type="text/markdown",
       url='https://github.com/tyo-nu/MINE-Database',
-      author='Jonathan Strutz',
+      author='Kevin Shebek, Jonathan Strutz',
       author_email='[email protected]',
       license='MIT',
-      packages=setuptools.find_packages(),
-      install_requires=['mordred', 'pymongo', 'scikit-learn<=0.23.2', 'seaborn'],
+      packages=setuptools.find_packages(exclude=["docs", "tests"]),
+    #   install_requires=['pymongo'],#, 'rdkit', 'scikit-learn'],
       package_data={'minedatabase': ['data/*'],
                     'minedatabase.NP_Score': ['*.gz'],
                     'minedatabase.tests': ['data/*'],
@@ -28,5 +28,7 @@
           'Topic :: Scientific/Engineering :: Bio-Informatics',
           'Topic :: Scientific/Engineering :: Chemistry',
           'Programming Language :: Python :: 3.7',
+          'Programming Language :: Python :: 3.9',
+          'Programming Language :: Python :: 3.8',
       ],
       )

tests/test_unit/test_feas.py

@@ -0,0 +1,28 @@
+## TODO update this to work
+# # Running feasibility test is an issue and crashes, do it here instead
+# from minedatabase.pickaxe import Pickaxe
+# from pathlib import Path
+
+# try:
+#     error_loading = False
+#     from minedatabase.filters.feasibility import ReactionFeasibilityFilter
+# except:
+#     error_loading = True
+
+# cwd = Path(__file__).parent
+
+# data_path = cwd / "../../tests/data/test_filters"
+# pk = Pickaxe(
+#     rule_list=data_path / "test_filter_rules.tsv",
+#     coreactant_list=data_path / "metacyc_coreactants.tsv",
+#     filter_after_final_gen=True,
+#     quiet=True,
+# )
+# pk.load_compound_set(data_path / "test_filter_compounds.csv")
+# pk.load_targets(data_path / "test_filter_targets.csv")
+
+# _filter = ReactionFeasibilityFilter(use_unpredicted=False)
+# pk.filters.append(_filter)
+# pk.transform_all(generations=1)
+
+# len(pk.compounds) == 58