docs: improve structure and add modules

.readthedocs.yaml

@@ -5,9 +5,9 @@ build:
   tools:
     python: "3.11"
 
-# Build from the docs/ directory with Sphinx
+# Build from the docs/source directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
+  configuration: docs/source/conf.py
 
 # Explicitly set the version of Python and its requirements
 python:

CODE_OF_CONDUCT.md

@@ -0,0 +1,43 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+- The use of sexualized language or imagery and unwelcome sexual attention or advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at [email protected]. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 1.4, available at [https://www.contributor-covenant.org/version/1/4/code-of-conduct.html](https://www.contributor-covenant.org/version/1/4/code-of-conduct.html)

CONTRIBUTING.md

@@ -0,0 +1,40 @@
+# Contributing guidelines
+
+We welcome any kind of contribution to our software, from simple comment or question to a full fledged [pull request](https://help.github.com/articles/about-pull-requests/). Please read and follow our [Code of Conduct](https://github.com/DeepRank/deeprank2/blob/main/CODE_OF_CONDUCT.rst).
+
+A contribution can be one of the following cases:
+
+1. you have a question;
+2. you think you may have found a bug (including unexpected behavior);
+3. you want to make some kind of change to the code base (e.g. to fix a bug, to add a new feature, to update documentation).
+
+The sections below outline the steps in each case.
+
+## You have a question
+
+1. use the search functionality [here](https://github.com/DeepRank/deeprank2/issues) to see if someone already filed the same issue;
+2. if your issue search did not yield any relevant results, make a new issue;
+3. apply the "Question" label; apply other labels when relevant.
+
+## You think you may have found a bug
+
+1. use the search functionality [here](https://github.com/DeepRank/deeprank2/issues) to see if someone already filed the same issue;
+2. if your issue search did not yield any relevant results, make a new issue, making sure to provide enough information to the rest of the community to understand the cause and context of the problem. Depending on the issue, you may want to include:
+   - the [SHA hashcode](https://help.github.com/articles/autolinked-references-and-urls/#commit-shas) of the commit that is causing your problem;
+   - some identifying information (name and version number) for dependencies you're using;
+   - information about the operating system;
+3. apply relevant labels to the newly created issue.
+
+## You want to make some kind of change to the code base
+
+1. (**important**) announce your plan to the rest of the community _before you start working_. This announcement should be in the form of a (new) issue;
+2. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
+3. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest main commit. While working on your feature branch, make sure to stay up to date with the main branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions [here](https://help.github.com/articles/configuring-a-remote-for-a-fork/) and [here](https://help.github.com/articles/syncing-a-fork/));
+4. make sure the existing tests still work;
+5. add your own tests (if necessary);
+6. see our [developer's readme](README.dev.md) for detailed information on our style conventions, etc.;
+7. update or expand the documentation;
+8. [push](http://rogerdudler.github.io/git-guide/) your feature branch to (your fork of) the DeepRank2 repository on GitHub;
+9. create the pull request, e.g. following the instructions [here](https://help.github.com/articles/creating-a-pull-request/).
+
+In case you feel like you've made a valuable contribution, but you don't know how to write or run tests for it, or how to generate the documentation: don't let this discourage you from making the pull request; we can help you! Just go ahead and submit the pull request, but keep in mind that you might be asked to append additional commits to your pull request.

deeprank2/query.py

@@ -1,18 +1,19 @@
+from __future__ import annotations
+
 import importlib
 import logging
 import os
 import pickle
 import pkgutil
 import re
 import warnings
-from collections.abc import Iterator
 from dataclasses import MISSING, dataclass, field, fields
 from functools import partial
 from glob import glob
 from multiprocessing import Pool
 from random import randrange
 from types import ModuleType
-from typing import Literal
+from typing import TYPE_CHECKING, Literal
 
 import h5py
 import numpy as np
@@ -21,38 +22,28 @@
 import deeprank2.features
 from deeprank2.domain.aminoacidlist import convert_aa_nomenclature
 from deeprank2.features import components, conservation, contact
-from deeprank2.molstruct.aminoacid import AminoAcid
 from deeprank2.molstruct.residue import Residue, SingleResidueVariant
-from deeprank2.molstruct.structure import PDBStructure
 from deeprank2.utils.buildgraph import get_contact_atoms, get_structure, get_surrounding_residues
 from deeprank2.utils.graph import Graph
 from deeprank2.utils.grid import Augmentation, GridSettings, MapMethod
 from deeprank2.utils.parsing.pssm import parse_pssm
 
+if TYPE_CHECKING:
+    from collections.abc import Iterator
+
+    from deeprank2.molstruct.aminoacid import AminoAcid
+    from deeprank2.molstruct.structure import PDBStructure
+
 _log = logging.getLogger(__name__)
 
 VALID_RESOLUTIONS = ["atom", "residue"]
 
 
 @dataclass(repr=False, kw_only=True)
 class Query:
-    """Represents one entity of interest: a single residue variant (SRV) or a protein-protein interface (PPI).
-
-    :class:`Query` objects are used to generate graphs from structures, and they should be created before any model is loaded.
-    They can have target values associated with them, which will be stored with the resulting graph.
+    """Parent class of :class:`SingleResidueVariantQuery` and :class:`ProteinProteinInterfaceQuery`.
 
-    Args:
-        pdb_path (str): the path to the PDB file to query.
-        resolution (Literal['residue', 'atom']): sets whether each node is a residue or atom.
-        chain_ids (list[str] | str): the chain identifier(s) of the variant residue or interacting interfaces.
-            Note that this does not limit the structure to residues from this/these chain(s).
-        pssm_paths (dict[str, str]): the name of the chain(s) (key) and path to the pssm file(s) (value).
-        targets (dict[str, float]) = Name(s) (key) and target value(s) (value) associated with this query.
-        influence_radius (float | None): all residues within this radius from the variant residue or interacting interfaces
-            will be included in the graph, irrespective of the chain they are on.
-        max_edge_length (float | None): the maximum distance between two nodes to generate an edge connecting them.
-        suppress_pssm_errors (bool): Whether or not to suppress the error raised if the .pssm files do not
-            match the .pdb files. If True, a warning is returned instead.
+    More detailed information about the parameters can be found in :class:`SingleResidueVariantQuery` and :class:`ProteinProteinInterfaceQuery`.
     """
 
     pdb_path: str
@@ -126,7 +117,7 @@ def _check_pssm(self, verbosity: Literal[0, 1, 2] = 0) -> None:  # noqa: C901
                 2 (high): Also list the incorrect residues
 
         Raises:
-            ValueError: Raised if info between pdb file and pssm file doesn't match or if no pssms were provided
+            ValueError: Raised if info between pdb file and pssm file doesn't match or if no pssms were provided.
         """
         if not self.pssm_paths:
             msg = "No pssm paths provided for conservation feature module."
@@ -221,7 +212,7 @@ def get_query_id(self) -> str:
 class SingleResidueVariantQuery(Query):
     """A query that builds a single residue variant graph.
 
-    Args (common for `Query`):
+    Args:
         pdb_path (str): the path to the PDB file to query.
         resolution (Literal['residue', 'atom']): sets whether each node is a residue or atom.
         chain_ids (list[str] | str): the chain identifier of the variant residue (generally a single capital letter).
@@ -231,16 +222,14 @@ class SingleResidueVariantQuery(Query):
         influence_radius (float | None): all residues within this radius from the variant residue
             will be included in the graph, irrespective of the chain they are on.
         max_edge_length (float | None): the maximum distance between two nodes to generate an edge connecting them.
-
         suppress_pssm_errors (bool): Whether or not to suppress the error raised if the .pssm files do not
             match the .pdb files. If True, a warning is returned instead.
-    SRV specific Args:
         variant_residue_number (int): the residue number of the variant residue.
         insertion_code (str | None): the insertion code of the variant residue.
         wildtype_amino_acid (AminoAcid): the amino acid at above position in the wildtype protein.
         variant_amino_acid (AminoAcid): the amino acid at above position in the variant protein.
         radius (float): all Residues within this radius (in Å) from the variant residue will
-            be included in the graph
+            be included in the graph.
     """
 
     variant_residue_number: int

deeprank2/trainer.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import copy
 import inspect
 import logging

deeprank2/utils/grid.py

@@ -1,16 +1,21 @@
 """This module holds the classes that are used when working with a 3D grid."""
 
+from __future__ import annotations
+
 import itertools
 import logging
 from enum import Enum
+from typing import TYPE_CHECKING
 
 import h5py
 import numpy as np
-from numpy.typing import NDArray
 from scipy.interpolate import BSpline
 
 from deeprank2.domain import gridstorage
 
+if TYPE_CHECKING:
+    from numpy.typing import NDArray
+
 _log = logging.getLogger(__name__)
 
 

docs/.gitignore

@@ -0,0 +1 @@
+build/

docs/requirements.txt

@@ -3,3 +3,5 @@ sphinx_rtd_theme==1.1.1
 readthedocs-sphinx-search==0.3.2
 myst-parser
 toml
+typing-extensions
+dill