metapredict 2.63__tar.gz → 2.65.0__tar.gz

{metapredict-2.63 → metapredict-2.65.0}/.gitignore

@@ -9,6 +9,10 @@ __pycache__/
 *~
 
 metapredict/tests/test_cli/output/*
+!metapredict/tests/test_cli/output/readme.txt
+
+metapredict/_version.py
+
 
 # cython-specific stuff
 metapredict/backend/cython/domain_definition.c

{metapredict-2.63 → metapredict-2.65.0}/.lgtm.yml

@@ -6,7 +6,4 @@ extraction:
       version: 3  # Specify Version 3
 path_classifiers:
   library:
-    - versioneer.py  # Set Versioneer.py to an external "library" (3rd party code)
     - devtools/*
-  generated:
-    - metapredict/_version.py

metapredict-2.65.0/CONTRIBUTING.md

@@ -0,0 +1,72 @@
+# Contributing to metapredict
+
+Thanks so much for considering contributing to metapredict! To contribute please consider the following guidelines.
+
+# How to contribute
+
+We welcome contributions from external contributors and this document
+describes how to merge code changes into metapredict. 
+
+## Getting Started
+
+* Make sure you have a [GitHub account](https://github.com/signup/free).
+* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub.
+* On your local machine,
+  [clone](https://help.github.com/articles/cloning-a-repository/) your fork of
+  the repository.
+
+## Making Changes
+
+* Add some really awesome code to your local fork.  It's usually a [good
+  idea](http://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/)
+  to make changes on a
+  [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
+  with the branch name relating to the feature you are going to add.
+* When you are ready for others to examine and comment on your new feature,
+  navigate to your fork of metapredict on GitHub and open a [pull
+  request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
+  after you launch a PR from one of your fork's branches, all
+  subsequent commits to that branch will be added to the open pull request
+  automatically.  Each commit added to the PR will be validated for
+  mergability, compilation and test suite compliance; the results of these tests
+  will be visible on the PR page.
+* If you're providing a new feature, you must add test cases and documentation.
+* When the code is ready to go, make sure you run the test suite using pytest.
+* When you're ready to be considered for merging, check the "Ready to go"
+  box on the PR page to let the metapredict devs know that the changes are complete.
+  The code will not be merged until this box is checked, the continuous
+  integration returns checkmarks,
+  and multiple core developers give "Approved" reviews.
+
+# Additional Resources
+
+* [General GitHub documentation](https://help.github.com/)
+* [PR best practices](http://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/)
+* [A guide to contributing to software packages](http://www.contribution-guide.org)
+* [Thinkful PR example](http://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR)
+
+
+# Guidelines for distinct typs of PRs
+
+### Small edits 
+If your contribution is a small commit (i.e., fixing a minor bug, typo etc), please:
+
+1. Fork and clone (as described above)
+2. Make changes to your local version.
+3. Ensure all tests run after changes.
+4. Submit a pull request explaining (1) What the small change is, (2) Why it was necessary and useful, and (3) how the change was implemented.
+
+### New features
+If your contribution is a larger commit (i.e., adding a new feature, changing inner code etc), it's probably worth raising an Issue first to ensure you're not duplicating effort and/or making changes that would impact the software goals. 
+
+That said, to make such a change, please consider the following steps:
+
+1. Fork and clone (as described above)
+2. Make changes on your local branch and add a new feature. 
+3. Ensure all tests run on your new feature.
+4. Write integrated tests (using PyTest) for your new feature, being especially mindful of defensive programming.
+5. Ensure your new feature is documented appropriately in the metapredict docs.
+6. Submit a pull request detailing explicitly (1) What your feature is, (2) Why it's useful, (3) how it's implemented, and (4) pointing to the documentation.
+7. Please be ready to respond to questions.
+
+Note that the Holehouse lab reserves the right to (respectfully) decline proposed features or bug fixes, although a cogent and logical explanation will be provided in such a scenario. 

metapredict-2.65.0/MANIFEST.in

@@ -0,0 +1,10 @@
+include LICENSE
+include MANIFEST.in
+
+graft metapredict
+graft metapredict/scripts
+global-exclude *.py[cod] __pycache__ *.so
+
+#recursive-include metapredict/backend/networks *
+#recursive-exclude metapredict/backend/tests *
+

metapredict-2.65.0/PKG-INFO

@@ -0,0 +1,20 @@
+Metadata-Version: 2.1
+Name: metapredict
+Version: 2.65.0
+Summary: A machine learning-based tool for predicting protein disorder.
+Author-email: Ryan Emenecker <remenecker@wustl.edu>
+License: MIT
+Requires-Python: >=3.8
+License-File: LICENSE
+Requires-Dist: cython
+Requires-Dist: torch
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: protfasta
+Requires-Dist: scipy
+Requires-Dist: urllib3
+Requires-Dist: tqdm
+Requires-Dist: alphaPredict>=1.3.0
+Requires-Dist: getSequence>=2.2.1
+Provides-Extra: test
+Requires-Dist: pytest>=6.1.2; extra == "test"

metapredict-2.63/PKG-INFO → metapredict-2.65.0/README.md

@@ -1,27 +1,5 @@
-Metadata-Version: 2.1
-Name: metapredict
-Version: 2.63
-Home-page: https://github.com/idptools/metapredict.git
-Author: Ryan Emenecker - Holehouse Lab - WUSM
-Author-email: remenecker@wustl.edu
-License: MIT
-Requires-Python: >=3.5,<3.12.0
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: cython
-Requires-Dist: torch
-Requires-Dist: numpy
-Requires-Dist: matplotlib
-Requires-Dist: protfasta
-Requires-Dist: scipy
-Requires-Dist: urllib3
-Requires-Dist: tqdm
-Requires-Dist: alphaPredict==1.0
-Requires-Dist: getSequence>=1.6
-
 # metapredict: A machine learning-based tool for predicting protein disorder.
-### Last updated November 2023
-
+### Last updated October 2024
 
 ## Current version: metapredict V2-FF (V2.6)
 The current recommended and default version of metapredict is metapredict V2-FF (version 2.6). Small increments (2.6.x) may be made as bug fixes or feature enhancements.
@@ -30,7 +8,6 @@ For context, V2-FF provides identical predictions to metapredict V2, but via `pr
 
 To quantify this yourself, run:
 
-
 	import metapredict
 	metapredict.print_performance(batch=True)
 	metapredict.print_performance(batch=False)
@@ -38,14 +15,34 @@ To quantify this yourself, run:
 To compare the number of residues-per-second metapredict V2-FF predicts in batch mode vs. non-batch mode. For CPUs this is typically a 10-20x improvement. If GPUs are available this value can be substantially higher.	
 
 ## Installation
+Metapredict is a software package written in Python. It can be installed from [PyPI](https://pypi.org/project/metapredict/) (the Python Package Index) using the tool `pip`. We always recommend managing your Python environment with conda. If these ideas are foreign to you, we recommend reading up a bit on Python package management and [conda](https://conda.io/projects/conda/en/latest/user-guide/getting-started.html) before continuing.
+
+#### TL/DR: Recommended install commands are:
+In most situations, the following two commands will ensure all the necessary dependencies are installed and work correctly:
+
+	# ensure dependencies are from the same ecosystem (conda)
+	conda install -c conda-forge -c pytorch python=3.11 numpy pytorch scipy cython matplotlib
+	
+	
+	# install from PyPI
+	pip install metapredict
 
+To check the installation has worked run:
+
+	metapredict-predict-disorder --help
+	
+from the command line; this should yield help info on the `metapredict-predict-disorder` command.
+	
+#### WARNING: Segfault when mixing `conda` and `pip` installs (March 2024)
+As of at least PyTorch 2.2.2 on macOS, there are binary incompatibilities between `pip` and `conda` versions of PyTorch and numpy. Therefore, it is essential your numpy and PyTorch installs are from the same package manager. metapredict will - by default - pull dependencies from PyPI. However, other packages installed from conda may require conda-dependent numpy installations, which can "brick" a previously-working installation.
+
+#### Extended installation info
 The current stable version of **metapredict** is available through GitHub or the Python Package Index (PyPI). 
 
 To install from PyPI, run:
 
 	pip install metapredict
 
-
 You can also install the current development version from
 
 	pip install git+https://git@github.com/idptools/metapredict
@@ -82,12 +79,17 @@ Emenecker, R. J., Griffith, D. & Holehouse, A. S. Metapredict: a fast, accurate,
 
 Note that in addition to the original paper, there's a V2 preprint; HOWEVER, we ask you only cite the original paper and describe the version being used (V1, V2 or V2-FF).
 
-Emenecker, R. J., Griffith, D. & Holehouse, A. S. Metapredict V2: An update to metapredict, a fast, accurate, and easy-to-use predictor of consensus disorder and structure. bioRxiv 2022.06.06.494887 (2022). doi:10.1101/2022.06.06.494887## Changes
+Emenecker, R. J., Griffith, D. & Holehouse, A. S. Metapredict V2: An update to metapredict, a fast, accurate, and easy-to-use predictor of consensus disorder and structure. bioRxiv 2022.06.06.494887 (2022). doi:10.1101/2022.06.06.494887
 
 ## Changes
 
 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.
@@ -99,7 +101,7 @@ We would like to thank the **DeepMind** team for developing AlphaFold and EBI/Un
 We would also like to thank the team at MobiDB for creating the database that was used to train this predictor. Check out their awesome stuff at [https://mobidb.bio.unipd.it](https://mobidb.bio.unipd.it)
 
 ## Copyright
-Copyright (c) 2020-2023, Holehouse Lab - Washington University School of Medicine
+Copyright (c) 2020-2024, Holehouse Lab - Washington University School of Medicine
 
 
 

{metapredict-2.63 → metapredict-2.65.0}/changelog.md

@@ -1,6 +1,18 @@
 ## Changelog
 This section is a log of recent changes with metapredict. My hope is that as I change things, this section can help you figure out why a change was made and if it will break any of your current workflows. The first major changes were made for the 0.56 release, so tracking will start there. Reasons are not provided for bug fixes for because the reason can assumed to be fixing the bug...
 
+#### V2.65 (October 2024)
+Changes:
+
+* Changed tag to 2.65. Yep, that's it. Necessary to get a clean build up to Pypi.
+
+#### V2.64 (October 2024)
+Changes:
+
+* Changed over to use pyproject.toml
+* Removed max Python version of 3.12
+* Changed alphaPredict to use 1.2 to get rid of Torch warning
+
 #### V2.63 (November 2023)
 Changes:
 

{metapredict-2.63 → metapredict-2.65.0}/devtools/README.md

@@ -48,10 +48,9 @@ This directory contains OS agnostic helper scripts which don't fall in any of th
    *  `git tag -a X.Y.Z [latest pushed commit] && git push --follow-tags`
 - [ ] Get the PR merged in
 
-## Versioneer Auto-version
-[Versioneer](https://github.com/warner/python-versioneer) will automatically infer what version 
-is installed by looking at the `git` tags and how many commits ahead this version is. The format follows 
-[PEP 440](https://www.python.org/dev/peps/pep-0440/) and has the regular expression of:
+## Versioning
+Versioning will be automatically identified from the `git` tags and how many commits ahead this version is. The format 
+follows [PEP 440](https://www.python.org/dev/peps/pep-0440/) and has the regular expression of:
 ```regexp
 \d+.\d+.\d+(?\+\d+-[a-z0-9]+)
 ```

{metapredict-2.63 → metapredict-2.65.0}/docs/conf.py

@@ -74,7 +74,7 @@ master_doc = 'index'
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

{metapredict-2.63 → metapredict-2.65.0}/metapredict/__init__.py

@@ -3,38 +3,32 @@
 ## A protein disorder predictor based on a BRNN (IDP-Parrot) trained on the consensus disorder values from 
 ## 8 disorder predictors from 12 proteomes.
 ##
+import sys
+import importlib.util
 
 # import user-facing functions
-from .meta import *
+from metapredict.meta import *
 from metapredict.backend.meta_predict_disorder import get_metapredict_legacy_network_version
 from metapredict.backend.metameta_hybrid_predict import get_metapredict_network_version
 
-
-
 import os
-import sys
+from importlib.metadata import version, PackageNotFoundError
 
+# import current version
+from ._version import __version__
 
 # To crash on LIBOMP error set this to False
 IGNORE_LIBOMP_ERROR = True
 
-
 # ------------------------------------------------------------
 #
-# Handle versioneer
-from ._version import get_versions
-versions = get_versions()
-__version__ = versions['version']
-__git_revision__ = versions['full-revisionid']
-del get_versions, versions
-
-
 # Handle omplib error 
 if IGNORE_LIBOMP_ERROR:
     if sys.platform == 'darwin':
         os.environ['KMP_DUPLICATE_LIB_OK']='True'
 
 
+
 # Standardized function to check performance
 def print_performance(seq_len=500, num_seqs=100, verbose=True, batch=True, legacy=False, batch_mode=None, variable_length=False):
     """
@@ -146,3 +140,4 @@ def print_metapredict_network_version():
     """
 
     return get_metapredict_network_version()
+

metapredict-2.65.0/metapredict/_version.py

@@ -0,0 +1 @@
+__version__ = "2.65.0"