Ecosyste.ms: Issues

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GitHub / deeprank/deeprank2 issues and pull requests

#543 - Add nucleotides to `aminoacidlist` for protein-nucleic acid graphs

Issue - State: open - Opened by DaniBodor about 1 year ago - 4 comments
Labels: blocking, stale

#542 - Fix Coveralls coverage 0%

Issue - State: closed - Opened by gcroci2 about 1 year ago
Labels: CI

#541 - Change linter to ruff

Issue - State: closed - Opened by gcroci2 about 1 year ago
Labels: docs, blocking, utils

#540 - Fix build for Python 3.11

Issue - State: open - Opened by gcroci2 about 1 year ago - 3 comments
Labels: bug, CI, blocked

#539 - Add GitHub action for testing the latest version released on PyPi

Issue - State: closed - Opened by gcroci2 about 1 year ago
Labels: CI, testing

#538 - docs: implement minor suggestions for JOSS paper

Pull Request - State: closed - Opened by gcroci2 about 1 year ago

#538 - docs: implement minor suggestions for JOSS paper

Pull Request - State: closed - Opened by gcroci2 about 1 year ago
Labels: JOSS

#537 - release: bump the version for the new patch release 2.1.2

Pull Request - State: closed - Opened by gcroci2 about 1 year ago - 1 comment

#537 - release: bump the version for the new patch release 2.1.2

Pull Request - State: closed - Opened by gcroci2 about 1 year ago - 1 comment
Labels: JOSS

#535 - fix: handle cases in which losses are nan during the training

Pull Request - State: closed - Opened by gcroci2 about 1 year ago
Labels: JOSS

#533 - Fix `UnboundLocalError`: local variable 'checkpoint_model' referenced before assignment

Issue - State: closed - Opened by gcroci2 about 1 year ago
Labels: bug, Trainer, JOSS

#533 - Fix `UnboundLocalError`: local variable 'checkpoint_model' referenced before assignment

Issue - State: closed - Opened by gcroci2 about 1 year ago
Labels: bug, priority, Trainer

#532 - including aa residue position along the chain in node features

Issue - State: closed - Opened by aminzia about 1 year ago
Labels: feature

#531 - Update CITATION.cff

Pull Request - State: closed - Opened by DaniBodor about 1 year ago

#530 - docs: fix TOC alignment in README

Pull Request - State: closed - Opened by DaniBodor about 1 year ago - 1 comment

#529 - Fix Dockerfile build and add GitHub action for testing it

Issue - State: closed - Opened by gcroci2 about 1 year ago - 2 comments
Labels: bug, CI

#528 - docs: add `Dockerfile` and `.yml` for building conda env

Pull Request - State: closed - Opened by gcroci2 about 1 year ago - 2 comments
Labels: JOSS

#528 - docs: add `Dockerfile` and `.yml` for building conda env

Pull Request - State: closed - Opened by gcroci2 about 1 year ago - 2 comments

#527 - Add a `Dockerfile` for trying out the package

Issue - State: closed - Opened by gcroci2 about 1 year ago
Labels: docs, JOSS

#527 - Add a `Dockerfile` for trying out the package

Issue - State: closed - Opened by gcroci2 about 1 year ago
Labels: docs, priority

#526 - Improve `test_dataset.py` and `test_trainer.py`

Issue - State: open - Opened by gcroci2 over 1 year ago - 1 comment
Labels: docs, good first issue, nice to have, stale, testing

#526 - Improve `test_dataset.py` and `test_trainer.py`

Issue - State: closed - Opened by gcroci2 over 1 year ago - 1 comment
Labels: docs, good first issue, nice to have, stale, testing

#525 - fix: installation bug due to missing domain files

Pull Request - State: closed - Opened by gcroci2 over 1 year ago - 1 comment
Labels: JOSS

#524 - Bug: Tutorial failing when running deeprank2 as Dockerfile

Issue - State: closed - Opened by abhishektiwari over 1 year ago
Labels: bug, JOSS

#523 - Joss review 5983 jnwei

Pull Request - State: closed - Opened by jnwei over 1 year ago
Labels: JOSS

#523 - Joss review 5983 jnwei

Pull Request - State: closed - Opened by jnwei over 1 year ago

#522 - linting: change linter to ruff

Pull Request - State: closed - Opened by gcroci2 over 1 year ago - 2 comments
Labels: stale

#521 - linting: change linter to ruff

Pull Request - State: closed - Opened by gcroci2 over 1 year ago

#519 - Regenerate class diagrams

Pull Request - State: closed - Opened by gcroci2 over 1 year ago - 2 comments
Labels: docs, class diagram, SS

#518 - Bug: Pytest failure "{parameter} is not cuda" in TestTrainer.test_cuda

Issue - State: closed - Opened by darnells over 1 year ago - 2 comments
Labels: bug

#517 - Evaluate and in case remove Codacy from the CI

Issue - State: closed - Opened by gcroci2 over 1 year ago - 2 comments
Labels: docs, CI, stale

#516 - Make `MapMethod` an attribute of `GridSettings` in deeprank2.grid module

Issue - State: open - Opened by DaniBodor over 1 year ago - 1 comment
Labels: nice to have, stale

#515 - feat: improve `Trainer` and `DeeprankDataset` logic for production testing

Pull Request - State: closed - Opened by gcroci2 over 1 year ago - 4 comments
Labels: stale

#514 - Bug: missing forcefield files with pip installation

Issue - State: closed - Opened by DarioMarzella over 1 year ago - 1 comment
Labels: bug, stale

#513 - docs: add pip install commands for the dependencies listed in the README

Pull Request - State: closed - Opened by DarioMarzella over 1 year ago - 3 comments

#513 - docs: add pip install commands for the dependencies listed in the README

Pull Request - State: closed - Opened by DarioMarzella over 1 year ago - 3 comments

#512 - make `_set_feature_modules` to return `ModuleType` objects

Issue - State: open - Opened by DaniBodor over 1 year ago - 1 comment
Labels: nice to have, stale

#511 - variant residue is only added to atomic graphs, but not residue graphs

Issue - State: open - Opened by DaniBodor over 1 year ago - 1 comment
Labels: bug, stale, needs info

#510 - Improve `Trainer` and `DeeprankDataset` for production testing

Issue - State: closed - Opened by gcroci2 over 1 year ago - 1 comment
Labels: stale

#509 - Integrate PDBprep

Issue - State: open - Opened by DaniBodor over 1 year ago - 2 comments
Labels: stale, feature, tools

#508 - docs: Clarify Pytorch Geometric in README installation

Pull Request - State: closed - Opened by DarioMarzella over 1 year ago

#507 - refactor: unify buildgraph.py and `build_graph` functions for atom and residue level graphs

Pull Request - State: closed - Opened by DaniBodor over 1 year ago - 1 comment
Labels: SS

#506 - Refactor buildgraph module

Issue - State: closed - Opened by DaniBodor over 1 year ago - 3 comments
Labels: stale

#505 - Update prospector and pylint in `pyproject.toml`

Issue - State: closed - Opened by gcroci2 over 1 year ago - 1 comment
Labels: stale

#504 - feature: separate max edge distance from interaction radius throughout

Pull Request - State: closed - Opened by DaniBodor over 1 year ago - 4 comments
Labels: SS

#503 - create amino acid dictionary in deeprank2/domain/aminoacidlist.py

Issue - State: closed - Opened by DaniBodor over 1 year ago - 3 comments
Labels: nice to have, stale

#502 - Remove paper/ folder from distribution

Issue - State: open - Opened by gcroci2 over 1 year ago - 1 comment
Labels: stale

#502 - Remove paper/ folder from distribution

Issue - State: closed - Opened by gcroci2 over 1 year ago - 2 comments

#501 - calculate atom pairwise energies (combination between LJ and Coulomb) using OpenMM

Issue - State: closed - Opened by DaniBodor over 1 year ago - 6 comments
Labels: stale, feature

#500 - Add performances comparisons with previous packages

Issue - State: closed - Opened by gcroci2 over 1 year ago - 4 comments
Labels: docs, stale, disc, framework paper

#499 - Refactor `deeprank2.tools.target.add_targets` function

Issue - State: open - Opened by gcroci2 over 1 year ago - 1 comment
Labels: nice to have, stale

#498 - docs: clarify ppi scoring metrics and add doc strings and tests

Pull Request - State: closed - Opened by gcroci2 over 1 year ago - 9 comments

#498 - docs: clarify ppi scoring metrics and add doc strings and tests

Pull Request - State: closed - Opened by gcroci2 over 1 year ago - 9 comments
Labels: SS

#497 - docs: type hinting and docstrings in molstruct

Pull Request - State: closed - Opened by DaniBodor over 1 year ago - 4 comments

#496 - Joss dani suggestions

Pull Request - State: closed - Opened by DaniBodor over 1 year ago - 4 comments

#495 - Joss paper dani suggestions

Pull Request - State: closed - Opened by DaniBodor over 1 year ago

#494 - ValueErrors raised in Variant tutorials

Issue - State: closed - Opened by DaniBodor over 1 year ago - 6 comments
Labels: bug, duplicate, stale

#493 - docs: add performances table for deeprank2

Pull Request - State: closed - Opened by gcroci2 over 1 year ago - 2 comments

#492 - refactor: `Query` classes and related code

Pull Request - State: closed - Opened by DaniBodor over 1 year ago - 22 comments
Labels: SS

#491 - build: improve installation making use of `pyproject.toml` file only and `setuptools`

Pull Request - State: closed - Opened by gcroci2 over 1 year ago - 1 comment

#491 - build: improve installation making use of `pyproject.toml` file only and `setuptools`

Pull Request - State: closed - Opened by gcroci2 over 1 year ago - 1 comment

#490 - Is `_get_atom_node_key` obsolete?

Issue - State: closed - Opened by DaniBodor over 1 year ago - 5 comments
Labels: stale, needs info

#490 - Is `_get_atom_node_key` obsolete?

Issue - State: open - Opened by DaniBodor over 1 year ago - 3 comments
Labels: stale, needs info

#489 - refactor: Query classes and related code

Pull Request - State: closed - Opened by DaniBodor over 1 year ago - 1 comment

#489 - refactor: Query classes and related code

Pull Request - State: closed - Opened by DaniBodor over 1 year ago - 1 comment

#488 - Class diagram for the new classes

Issue - State: closed - Opened by gcroci2 over 1 year ago - 1 comment
Labels: class diagram, disc, Query

#487 - refactor: query classes and related code

Pull Request - State: closed - Opened by DaniBodor over 1 year ago - 1 comment

#486 - Create feature classes

Issue - State: open - Opened by DaniBodor over 1 year ago - 2 comments
Labels: nice to have, stale

#485 - conflicting PR, will be replaced

Pull Request - State: closed - Opened by DaniBodor over 1 year ago

#485 - conflicting PR, will be replaced

Pull Request - State: closed - Opened by DaniBodor over 1 year ago

#484 - docs: minor improvements to install instructions

Pull Request - State: closed - Opened by DaniBodor over 1 year ago

#483 - style: auto-scrape trailing whitespace upon save in VS code

Pull Request - State: closed - Opened by DaniBodor over 1 year ago

#482 - fix: make scipy 1.11.2 work

Pull Request - State: closed - Opened by cbaakman over 1 year ago - 2 comments

#481 - style: automatically scrape trailing whitespace

Pull Request - State: closed - Opened by DaniBodor over 1 year ago

#480 - Refactor Query classes

Issue - State: closed - Opened by DaniBodor over 1 year ago - 2 comments
Labels: blocking, priority, Query, SS

#480 - Refactor Query classes

Issue - State: closed - Opened by DaniBodor over 1 year ago - 2 comments
Labels: blocking, priority, Query

#479 - remove trailing whitespace in .vscode file

Issue - State: closed - Opened by DaniBodor over 1 year ago
Labels: good first issue

#478 - fix: force scipy version for fixing deeprank2 installation

Pull Request - State: closed - Opened by gcroci2 over 1 year ago

#478 - fix: force scipy version for fixing deeprank2 installation

Pull Request - State: closed - Opened by gcroci2 over 1 year ago

#477 - Investigate scipy 1.11.2 error

Issue - State: closed - Opened by gcroci2 over 1 year ago - 2 comments
Labels: bug

#476 - Add computational performance table

Issue - State: closed - Opened by gcroci2 over 1 year ago

#475 - Cleaning installation

Issue - State: closed - Opened by gcroci2 over 1 year ago - 1 comment

#474 - New release

Issue - State: closed - Opened by gcroci2 over 1 year ago - 1 comment
Labels: priority, stale

#474 - New release

Issue - State: closed - Opened by gcroci2 over 1 year ago - 1 comment
Labels: stale

#473 - Fix installation

Issue - State: closed - Opened by gcroci2 over 1 year ago - 1 comment
Labels: bug, blocking

#472 - fix: readthedocs after deeprank2 renaming

Pull Request - State: closed - Opened by gcroci2 over 1 year ago

#471 - fix readthedocs

Issue - State: closed - Opened by gcroci2 over 1 year ago

#471 - fix readthedocs

Issue - State: closed - Opened by gcroci2 over 1 year ago

#470 - Variant queries requesting redudant inputs

Issue - State: closed - Opened by DaniBodor over 1 year ago - 5 comments
Labels: stale

#469 - refactor: rename deeprankcore to deeprank2

Pull Request - State: closed - Opened by gcroci2 over 1 year ago

#468 - refactor: rename deeprankcore to deeprank2

Pull Request - State: closed - Opened by gcroci2 over 1 year ago

#467 - Rename repository

Issue - State: closed - Opened by gcroci2 over 1 year ago

#467 - Rename repository

Issue - State: closed - Opened by gcroci2 over 1 year ago

#466 - Regarding the use of 'sets' instead of 'lists' to store nodes.

Issue - State: closed - Opened by DTRademaker over 1 year ago - 1 comment
Labels: stale, feature

#465 - fix: cast `hse` feature to float64

Pull Request - State: closed - Opened by DanLep97 over 1 year ago - 1 comment
Labels: bug, stale, Query

#465 - fix: cast `hse` feature to float64

Pull Request - State: closed - Opened by DanLep97 over 1 year ago - 1 comment
Labels: bug, stale, Query

#464 - Investigate the need of both `wildtype_amino_acid` and `residue_number` in the variants' queries

Issue - State: closed - Opened by gcroci2 over 1 year ago
Labels: needs info, Query