Updated to integrate scripts and transition over to using versioningi…

…t for version control

.gitignore

@@ -9,6 +9,8 @@ __pycache__/
 *~
 
 metapredict/tests/test_cli/output/*
+!metapredict/tests/test_cli/output/readme.txt
+
 
 # cython-specific stuff
 metapredict/backend/cython/domain_definition.c

MANIFEST.in

@@ -2,4 +2,9 @@ include LICENSE
 include MANIFEST.in
 
 graft metapredict
-global-exclude *.py[cod] __pycache__ *.so
+graft metapredict/scripts
+global-exclude *.py[cod] __pycache__ *.so
+
+#recursive-include metapredict/backend/networks *
+#recursive-exclude metapredict/backend/tests *
+

README.md

@@ -85,6 +85,11 @@ Emenecker, R. J., Griffith, D. & Holehouse, A. S. Metapredict V2: An update to m
 
 For changes see the `changelog.md` file in this directory.
 
+## Running tests
+Note that to run tests you must compile the cython code in place. We suggest doing this by running the following set of commands:
+
+pip uninstall metapredict; rm -rf build dist *.egg-info; python -m build; pip install .
+
 ## Acknowledgements
 
 PARROT, created by Dan Griffith, was used to generate the network used for metapredict. See [https://pypi.org/project/idptools-parrot/](https://pypi.org/project/idptools-parrot/) for some very cool machine learning stuff.

install_for_tests.sh

@@ -0,0 +1,16 @@
+#!/bin/zsh
+# This script cleans everything 
+
+# remove all previous build directories
+
+echo "Deleting previous build directories, if present"
+rm -rf build dist *.egg-info > /dev/null 2>&1
+
+# remove cython files
+echo "Deleting cython files, if present"
+rm metapredict/backend/cython/*so > /dev/null 2>&1
+rm metapredict/backend/cython/*c > /dev/null 2>&1
+
+echo "Building the package"
+python -m build
+python setup.py build_ext --inplace

metapredict/__init__.py

@@ -14,11 +14,8 @@
 import os
 from importlib.metadata import version, PackageNotFoundError
 
-try:
-    __version__ = version("metapredict")
-except PackageNotFoundError:
-    # package is not installed
-    pass
+# import current version
+from ._version import __version__
 
 # To crash on LIBOMP error set this to False
 IGNORE_LIBOMP_ERROR = True

metapredict/_version.py

@@ -0,0 +1 @@
+__version__ = "2.63+18.gc528e66.dirty"

scripts/metapredict-graph-disorder → metapredict/scripts/metapredict_graph_disorder.py

@@ -16,7 +16,7 @@
 from metapredict import meta
 
 
-if __name__ == "__main__":
+def main():
 
     # Parse command line arguments.
     parser = argparse.ArgumentParser(description='Generate disorder figures for all sequences in a FASTA file.')

scripts/metapredict-graph-pLDDT → metapredict/scripts/metapredict_graph_pLDDT.py

@@ -16,7 +16,7 @@
 from metapredict import meta
 
 
-if __name__ == "__main__":
+def main():
 
     # Parse command line arguments.
     parser = argparse.ArgumentParser(description='Generate Alphafold2 pLDDT score figures for all sequences in a FASTA file.')

scripts/metapredict-name → metapredict/scripts/metapredict_name.py

@@ -11,7 +11,7 @@
 from metapredict.backend.uniprot_predictions import seq_from_name
 from getSequence import getseq
 
-if __name__ == "__main__":
+def main():
 
     # Parse command line arguments.
     parser = argparse.ArgumentParser(description='Predict intrinsic disorder from a protein name.')

scripts/metapredict-predict-disorder → metapredict/scripts/metapredict_predict_disorder.py

@@ -10,7 +10,7 @@
 import metapredict as meta
 
 
-if __name__ == "__main__":
+def main():
 
     # Parse command line arguments.
     parser = argparse.ArgumentParser(description='Generate disorder scores for all sequences in a FASTA file.')

scripts/metapredict-predict-idrs → metapredict/scripts/metapredict_predict_idrs.py

@@ -8,13 +8,9 @@
 import protfasta
 
 from metapredict.meta import predict_disorder_batch
-
-
-
 import metapredict as meta
 
-
-if __name__ == "__main__":
+def main():
 
     # Parse command line arguments.
     parser = argparse.ArgumentParser(description='Predict IDRs for all sequences in a FASTA file.')

scripts/metapredict-predict-pLDDT → metapredict/scripts/metapredict_predict_pLDDT.py

@@ -6,11 +6,10 @@
 import os
 import argparse
 
-
 import metapredict as meta
 
 
-if __name__ == "__main__":
+def main():
 
     # Parse command line arguments.
     parser = argparse.ArgumentParser(description='Generate AlphaFold2 pLDDT scores for all sequences in a FASTA file.')

scripts/metapredict-quick-graph → metapredict/scripts/metapredict_quick_graph.py

@@ -8,8 +8,7 @@
 
 VALID_AA = ['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y']
 
-
-if __name__ == "__main__":
+def main():
     # Parse command line arguments.
     parser = argparse.ArgumentParser(description='Predict intrinsic disorder of amino acid sequences.')
     parser.add_argument('sequence', help='The amino acid sequence to predict disorder for.')

scripts/metapredict-quick-predict → metapredict/scripts/metapredict_quick_predict.py

@@ -6,7 +6,7 @@
 import argparse
 import metapredict as meta
 
-if __name__ == "__main__":
+def main():
     # Parse command line arguments.
     parser = argparse.ArgumentParser(description='Predict intrinsic disorder of amino acid sequences.')
     parser.add_argument('sequence', help='The amino acid sequence to predict disorder for.')

scripts/metapredict-uniprot → metapredict/scripts/metapredict_uniprot.py

@@ -9,7 +9,7 @@
 from metapredict.metapredict_exceptions import MetapredictError
 import metapredict as meta
 
-if __name__ == "__main__":
+def main():
 
     # Parse command line arguments.
     parser = argparse.ArgumentParser(description='Predict intrinsic disorder from a UniProt accession number.')

metapredict/tests/output/readme.txt

@@ -0,0 +1 @@
+This directory stores test output

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=61", "setuptools-scm>=8", "wheel", "cython", "numpy"]
+requires = ["setuptools>=61", "cython", "numpy", "versioningit~=2.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -25,28 +25,49 @@ dependencies = [
     "getSequence >= 1.6",
 ]
 
-[project.scripts]
-metapredict-graph-disorder = "scripts.metapredict_graph_disorder:main"
-metapredict-predict-disorder = "scripts.metapredict_predict_disorder:main"
-metapredict-quick-graph = "scripts.metapredict_quick_graph:main"
-metapredict-quick-predict = "scripts.metapredict_quick_predict:main"
-metapredict-uniprot = "scripts.metapredict_uniprot:main"
-metapredict-predict-idrs = "scripts.metapredict_predict_idrs:main"
-metapredict-graph-pLDDT = "scripts.metapredict_graph_pLDDT:main"
-metapredict-predict-pLDDT = "scripts.metapredict_predict_pLDDT:main"
-metapredict-name = "scripts.metapredict_name:main"
-
-[tool.coverage.run]
-omit = [
-    "*/tests/*",
+[project.optional-dependencies]
+test = [
+  "pytest>=6.1.2",
 ]
 
-[tool.yapf]
-column_limit = 119
-indent_width = 4
-use_tabs = false
 
-[tool.flake8]
-max-line-length = 119
+[project.scripts]
+metapredict-graph-disorder = "metapredict.scripts.metapredict_graph_disorder:main"
+metapredict-predict-disorder = "metapredict.scripts.metapredict_predict_disorder:main"
+metapredict-quick-graph = "metapredict.scripts.metapredict_quick_graph:main"
+metapredict-quick-predict = "metapredict.scripts.metapredict_quick_predict:main"
+metapredict-uniprot = "metapredict.scripts.metapredict_uniprot:main"
+metapredict-predict-idrs = "metapredict.scripts.metapredict_predict_idrs:main"
+metapredict-graph-pLDDT = "metapredict.scripts.metapredict_graph_pLDDT:main"
+metapredict-predict-pLDDT = "metapredict.scripts.metapredict_predict_pLDDT:main"
+metapredict-name = "metapredict.scripts.metapredict_name:main"
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+
+[tool.setuptools.packages.find]
+namespaces = true
+where = ["."]
+include = ["metapredict", "metapredict.*"]  # Discover all sub-packages under metapredict
+
+[tool.setuptools.package-data]
+metapredict = ["py.typed"]
+
+[tool.versioningit]
+default-version = "1+unknown"
+
+[tool.versioningit.format]
+distance = "{base_version}+{distance}.{vcs}{rev}"
+dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+
+[tool.versioningit.vcs]
+# The method key:
+method = "git"  # <- The method name
+# Parameters to pass to the method:
+match = ["*"]
+default-tag = "1.0.0"
 
-[tool.setuptools_scm]
+[tool.versioningit.write]
+file = "metapredict/_version.py"

setup.cfg

@@ -0,0 +1,22 @@
+# Helper file to handle all configs
+
+[coverage:run]
+# .coveragerc to control coverage.py and pytest-cov
+omit =
+    # Omit the tests
+    */tests/*
+    # Omit generated versioneer
+    metapredict/_version.py
+
+[yapf]
+# YAPF, in .style.yapf files this shows up as "[style]" header
+COLUMN_LIMIT = 119
+INDENT_WIDTH = 4
+USE_TABS = False
+
+[flake8]
+# Flake8, PyFlakes, etc
+max-line-length = 119
+
+[aliases]
+test = pytest

setup.py

@@ -2,21 +2,24 @@
 from Cython.Build import cythonize
 import os
 import numpy
-from setuptools_scm import get_version
 
 cython_file = os.path.join("metapredict", "backend", "cython", "domain_definition.pyx")
 
 extensions = [
     Extension(
         name="metapredict.backend.cython.domain_definition",
-        sources=[cython_file],
-        include_dirs=[numpy.get_include()],
-    )
-]
-
+         sources=[cython_file],
+         include_dirs=[numpy.get_include()],
+     )
+ ]
+
+
 setup(
-    ext_modules=cythonize(extensions, compiler_directives={'language_level': "3"}),
-    version=get_version(),
+    ext_modules = cythonize(extensions, compiler_directives={'language_level' : "3"}),
     packages=find_packages(),
-    include_package_data=True,
-)
+
+    # Optional include package data to ship with your package
+    # Customize MANIFEST.in if the general case does not suit your needs
+    # Comment out this line to prevent the files from being packaged with your software
+    include_package_data=True
+    )