Add tensor parsing util (#244)

* Add tensor parsing util * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add missing arg comma * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add backbone check util * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * linting * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add chain tensor * add test for io utils * fix loguru import * add torchtyping dependency * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix import message import * add tests for angle utils * add tests for angle utils * add tests for tensor parsing * add tests for tensor parsing * add sidechain atom groups * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add io tests * add geometry tests * add geom ad sequence mnodules * add test for inferring sequence from coordinates * add einops as an optional dependecy * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add sequence inference utils * add data testing utils * add nan util * add angle computation utils * add test for distmat reconstruction * wrap torch imports * wrap imports * wrap imports * add representation utils * wrap torch-dependent tests * add edge tensor type * update changelog * add build params * add updated angles script * add graphein package test * wrap imports * add plotting utils * push tensor utils * update centering default args * add reconstruction utils * add data objects * add PyG dep * add PyG dep * add PyG dep * add PyG dep * add PyG dep * add PyG dep * add PyG dep * add PyG dep * add pnerf * update nx to numpy array to support 3.0 * fix kabsch test * fix centering masking * remove nx.info - deprecated in nx 3.0 * rm gpickle reference - deprecated in nx 3.0 * rm gpickle reference - deprecated in nx 3.0 * fix nx 3.0 adjacency issues * fix for nx 3.0 * ignore tensor tests for minimal build * ignore tensor tests for minimal build * add additional docs * add additional testin utils * add docstrings to plot * finish sequence docstrings * add notimplemented errors and todos * finalise io * add tensor submodule to docs * add edges * update license year * add documented code * add documented code and edge funcs * add updated tests * update doc config * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add additional constants * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix test * update changelog * update readme * update docstrings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update docstrings * update docstrings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * bump license year * fix angle dims * add noising and plotting * add node id to plots * add esmfold util * add noise util * Add structural metrics (#245) * Add gdt metric * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add TMScore * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add init * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update readme Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * add dataloader * add folding utils * update readme * add docs * add tutorial notebooks * add fasta parsing util * add data updates * fix df output * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove DL-dependent notebooks from minimal install test * add watermark * rm dataloaders from test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix typo in inc_dict attr * add doc dep install to build * fix typo * remove wildcard pyyaml version * add try/except for atomic peptide bonds * update tensor tutorial --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
a-r-j · Jan 30, 2023 · 4f9563b · 4f9563b
1 parent 4634887
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diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -16,26 +16,26 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        python-version: [3.7, 3.8]
-        torch: [1.6.0, 1.7.0, 1.8.0, 1.9.0]
-        include:
-          - torch: 1.6.0
-            torchvision: 0.7.0
-          - torch: 1.7.0
-            torchvision: 0.8.1
-          - torch: 1.8.0
-            torchvision: 0.9.0
-          - torch: 1.9.0
-            torchvision: 0.10.0
-          - torch: 1.8.0
-            torchvision: 0.9.0
-            python-version: 3.9
-          - torch: 1.9.0
-            torchvision: 0.10.0
-            python-version: 3.8
-          - torch: 1.9.0
-            torchvision: 0.10.0
-            python-version: 3.9
+        python-version: [3.8, 3.9]
+        torch: [1.12.0, 1.13.0]
+        #include:
+        #  - torch: 1.6.0
+        #    torchvision: 0.7.0
+        #  - torch: 1.7.0
+        #    torchvision: 0.8.1
+        #  - torch: 1.8.0
+        #    torchvision: 0.9.0
+        #  - torch: 1.9.0
+        #    torchvision: 0.10.0
+        #  - torch: 1.8.0
+        #    torchvision: 0.9.0
+        #    python-version: 3.9
+        #  - torch: 1.9.0
+        #    torchvision: 0.10.0
+        #    python-version: 3.8
+        #  - torch: 1.9.0
+        #    torchvision: 0.10.0
+        #    python-version: 3.9
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
@@ -44,7 +44,7 @@ jobs:
         uses: s-weigand/setup-conda@v1
         with:
           python-version: ${{ matrix.python-version }}
-          conda-channels: "conda-forge, salilab"
+          conda-channels: "conda-forge, salilab, pytorch, pyg"
 
       #- name: Set up Python ${{ matrix.python-version }}
       #  uses: actions/setup-python@v2
@@ -57,7 +57,10 @@ jobs:
       - name: Install DSSP
         run: conda install -c salilab dssp
       - name: Install PyTorch
-        run: pip install torch==${{matrix.torch}}+cpu torchvision==${{matrix.torchvision}}+cpu -f https://download.pytorch.org/whl/torch_stable.html
+        run: conda install -c pytorch pytorch==${{matrix.torch}} cpuonly
+        #run: pip install torch==${{matrix.torch}}+cpu torchvision==${{matrix.torchvision}}+cpu -f https://download.pytorch.org/whl/torch_stable.html
+      - name: Install PyG
+        run: conda install -c pyg pyg
       - name: Install BLAST
         run: sudo apt install ncbi-blast+
       - name: Install Graphein
@@ -66,7 +69,9 @@ jobs:
         run: pip install -r .requirements/extras.in
       - name: Install Dev Dependencies
         run: pip install -r .requirements/dev.in
+      - name: Install doc dependencies
+        run: pip install -r .requirements/docs.in
       - name: Run unit tests and generate coverage report
         run: pytest .
       - name: Test notebook execution
-        run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb"
+        run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb"
diff --git a/.github/workflows/minimal__install.yaml b/.github/workflows/minimal__install.yaml
@@ -38,6 +38,6 @@ jobs:
       - name: Install Dev Dependencies
         run: pip install -r .requirements/dev.in
       - name: Run unit tests and generate coverage report
-        run: pytest .
+        run: pytest . --ignore-glob="tests/protein/tensor"
       - name: Test notebook execution
-        run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/higher_order_graphs.ipynb" --ignore-glob="notebooks/protein_graph_analytics.ipynb" --ignore-glob="notebooks/subgraphing_tutorial.ipynb" --ignore-glob="notebooks/splitting_a_dataset.ipynb"
+        run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/higher_order_graphs.ipynb" --ignore-glob="notebooks/protein_graph_analytics.ipynb" --ignore-glob="notebooks/subgraphing_tutorial.ipynb" --ignore-glob="notebooks/splitting_a_dataset.ipynb" --ignore-glob="notebooks/protein_tensors.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb"
diff --git a/.requirements/base.in b/.requirements/base.in
@@ -13,10 +13,11 @@ pydantic
 rich
 rich-click
 seaborn
-pyyaml>=5.1,<6.*
+pyyaml>=5.1,<6.0
 scikit-learn
 scipy
 tqdm
 typing_extensions
 wget
 xarray
+torchtyping
diff --git a/.requirements/docs.in b/.requirements/docs.in
@@ -11,3 +11,4 @@ sphinx-inline-tabs
 sphinxext-opengraph
 sphinxcontrib-gtagjs
 ipython
+watermark
diff --git a/.requirements/extras.in b/.requirements/extras.in
@@ -5,3 +5,4 @@ mpl_chord_diagram==0.3.2
 rdkit
 selfies
 smilite
+einops
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,7 +1,14 @@
-### 1.5.3 - UNRELEASED
+### 1.6.0dev - UNRELEASED
+
+#### New Features
+* [Metrics] - [#245](https://github.com/a-r-j/graphein/pull/221) Adds a selection of structural metrics relevant to protein structures.
+* [Tensor Operations] - [#244](https://github.com/a-r-j/graphein/pull/244) Adds suite of utilities for working directly with tensor-based representations of proteins (graphein.protein.tensor).
+* [Tensor Operations] - [#244](https://github.com/a-r-j/graphein/pull/244) Adds suite of utilities for working with ESMfold (graphein.protein.folding_utils).
+
 
 
 #### Improvements
+
 * [Logging] - [#221](https://github.com/a-r-j/graphein/pull/221) Adds global control of logging with `graphein.verbose(enabled=False)`.
 * [Logging] - [#242](https://github.com/a-r-j/graphein/pull/242) Adds control of protein graph construction logging. Resolves [#238](https://github.com/a-r-j/graphein/issues/238)
 
@@ -14,6 +21,18 @@
 * [Bugfix] - [#220](https://github.com/a-r-j/graphein/pull/220) Fixes edge metadata conversion to PyG. Contribution by @manonreau.
 * [Bugfix] - [#220](https://github.com/a-r-j/graphein/pull/220) Fixes centroid atom grouping & avoids unnecessary edge computation where none are found. Contribution by @manonreau.
 
+
+#### Documentation
+* [Tensor Module] - [#244](https://github.com/a-r-j/graphein/pull/244) Documents new graphein.protein.tensor module.
+* [CI] - [#244](https://github.com/a-r-j/graphein/pull/244) Updates to intersphinx maps
+
+
+#### Package
+* [CI] - [#244](https://github.com/a-r-j/graphein/pull/244) CI now runs for python 3.8, 3.9 and torch 1.12.0 and 1.13.0
+* [CI] - [#244](https://github.com/a-r-j/graphein/pull/244) Separate builds for core library and library with DL dependencies.
+* [Licence] - [#244](https://github.com/a-r-j/graphein/pull/244) Bump to 2023
+
+
 ### 1.5.2 - 19/9/2022
 
 #### Protein

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019-2022 Arian Jamasb
+Copyright (c) 2019-2023 Arian Jamasb
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -34,6 +34,7 @@ This package provides functionality for producing geometric representations of p
 
 |   |   |
 |---|---|
+| [Protein Tensor Module](http://graphein.ai/notebooks/protein_tensors.html)  |  [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/protein_tensors.ipynb)   |
 | [Constructing molecular graphs](http://graphein.ai/notebooks/molecule_tutorial.html)  |  [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/molecule_tutorial.ipynb)   |
 | [Ready-to-go Dataloaders for PyTorch Geometric](http://graphein.ai/notebooks/dataloader_tutorial.html)  |  [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/dataloader_tutorial.ipynb)   |
 | [Extracting subgraphs from protein graphs](http://graphein.ai/notebooks/subgraphing_tutorial.html)  |  [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/a-r-j/graphein/blob/master/notebooks/subgraphing_tutorial.ipynb)   |

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -6,6 +6,8 @@
 
 # -- Path setup --------------------------------------------------------------
 
+import datetime
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -14,6 +16,9 @@
 import sys
 
 import plotly.io as pio
+import sphinx.ext.autodoc
+
+sphinx.ext.autodoc.NewTypeDataDocumenter.directivetype = "class"
 
 os.environ["PLOTLY_RENDERER"] = "sphinx_gallery"
 
@@ -25,11 +30,11 @@
 # -- Project information -----------------------------------------------------
 
 project = "Graphein"
-copyright = "2022, Arian Jamasb"
 author = "Arian Jamasb"
+copyright = f"{datetime.datetime.now().year}, {author}"
 
 # The full version, including alpha/beta/rc tags
-release = "1.5.2"
+release = "1.6.0dev"
 
 
 # -- General configuration ---------------------------------------------------
@@ -39,6 +44,7 @@
 # ones.
 extensions = [
     "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
     "sphinx.ext.intersphinx",
     "sphinx.ext.viewcode",
     "sphinx_copybutton",
@@ -48,7 +54,11 @@
     "m2r2",
     "nbsphinx",
     "nbsphinx_link",
+    "sphinx.ext.napoleon",
+    # "sphinx_autorun",
 ]
+
+autosummary_generate = True  # Turn on sphinx.ext.autosummary
 nbsphinx_allow_errors = True
 nbsphinx_require_js_path = (
     "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"
@@ -67,16 +77,23 @@
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
+    "networkx": ("https://networkx.github.io/documentation/stable/", None),
+    "nx": ("https://networkx.github.io/documentation/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
-    "xarray": ("https://xarray.pydata.org/en/stable/", None),
+    "np": ("https://numpy.org/doc/stable/", None),
     "pandas": ("https://pandas.pydata.org/docs/", None),
+    "pd": ("https://pandas.pydata.org/docs/", None),
+    "plotly": ("https://plotly.com/python-api-reference/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
     "scikit-learn": ("https://scikit-learn.org/stable/", None),
     "sklearn": ("https://scikit-learn.org/stable/", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
     "Sphinx": ("https://www.sphinx-doc.org/en/stable/", None),
-    "networkx": ("https://networkx.github.io/documentation/stable/", None),
-    "nx": ("https://networkx.github.io/documentation/stable/", None),
     "torch": ("https://pytorch.org/docs/master/", None),
+    "xarray": ("https://xarray.pydata.org/en/stable/", None),
+    "torch_geometric": (
+        "https://pytorch-geometric.readthedocs.io/en/latest/",
+        None,
+    ),
 }
 
 mathjax_path = "https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
@@ -98,7 +115,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
+exclude_patterns = ["_build"]
 source_suffix = [".rst", ".md"]
 
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -45,6 +45,7 @@ The repository can be found at `a-r-j/graphein <https://www.github.com/a-r-j/gra
    :hidden:
    :caption: Machine Learning
 
+   ml_protein_tensors
    datasets
    ml_examples
 
@@ -55,6 +56,7 @@ The repository can be found at `a-r-j/graphein <https://www.github.com/a-r-j/gra
    :caption: API Reference
 
    modules/graphein.protein
+   modules/graphein.protein.tensor
    modules/graphein.molecule
    modules/graphein.rna
    modules/graphein.ppi

diff --git a/docs/source/license.rst b/docs/source/license.rst
@@ -3,7 +3,7 @@ License
 
 MIT License
 
-Copyright (c) 2019-2022 Arian Jamasb
+Copyright (c) 2019-2023 Arian Jamasb
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/docs/source/ml_protein_tensors.rst b/docs/source/ml_protein_tensors.rst
@@ -0,0 +1,13 @@
+===============
+Protein Tensors
+===============
+
+
+Introduction
+---------
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   notebooks/protein_tensors.nblink
+   notebooks/datasets_and_dataloaders.nblink
diff --git a/docs/source/modules/graphein.protein.rst b/docs/source/modules/graphein.protein.rst
@@ -1,8 +1,17 @@
 graphein.protein
 ================
 
+.. currentmodule:: graphein.protein
+
 Config
-------
+---------
+
+.. currentmodule:: graphein.protein.config
+
+
+.. autosummary::
+    :nosignatures:
+
 .. automodule:: graphein.protein.config
     :members:
 

diff --git a/docs/source/modules/graphein.protein.tensor.rst b/docs/source/modules/graphein.protein.tensor.rst
@@ -0,0 +1,77 @@
+graphein.protein.tensor
+=======================
+
+.. currentmodule:: graphein.protein.tensor
+
+Data and Batch Objects
+------------------------
+.. automodule:: graphein.protein.tensor.data
+    :members:
+
+I/O
+------
+.. automodule:: graphein.protein.tensor.io
+    :members:
+
+Representation
+---------------
+.. automodule:: graphein.protein.tensor.representation
+    :members:
+
+
+Geometry
+------
+Geometry Utils
+^^^^^^^^^
+.. automodule:: graphein.protein.tensor.geometry
+    :members:
+
+Angles
+^^^^^^^^^^^^^^^
+.. automodule:: graphein.protein.tensor.angles
+    :members:
+
+
+Reconstruction
+---------
+
+.. automodule:: graphein.protein.tensor.reconstruction
+    :members:
+
+pNERF
+^^^^^^^
+.. automodule:: graphein.protein.tensor.pnerf
+    :members:
+
+Sequence
+---------
+.. automodule:: graphein.protein.tensor.sequence
+    :members:
+
+Plotting
+---------
+.. currentmodule:: graphein.protein.tensor.plot
+
+.. autosummary::
+    :nosignatures:
+
+    graphein.protein.tensor.plot
+
+.. automodule:: graphein.protein.tensor.plot
+    :members:
+
+Types
+---------
+.. automodule:: graphein.protein.tensor.types
+    :members:
+
+
+Testing
+---------
+.. automodule:: graphein.protein.tensor.testing
+    :members:
+
+Constants
+----------
+.. automodule:: graphein.protein.resi_atoms
+    :members:
diff --git a/docs/source/notebooks/datasets_and_dataloaders.nblink b/docs/source/notebooks/datasets_and_dataloaders.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../../../notebooks/datasets_and_dataloaders.ipynb"
+}
diff --git a/docs/source/notebooks/protein_tensors.nblink b/docs/source/notebooks/protein_tensors.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../../../notebooks/protein_tensors.ipynb"
+}