Ecosyste.ms: Issues

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GitHub / deeprank/deeprank2 issues and pull requests

#648 - Improvements to PyPi listing/pyproject.toml

Issue - State: open - Opened by DaniBodor about 1 month ago
Labels: docs

#647 - docs: improve dev readme

Pull Request - State: open - Opened by DaniBodor 3 months ago - 2 comments
Labels: stale

#646 - docs: update CHANGELOG.md

Pull Request - State: closed - Opened by gcroci2 5 months ago

#645 - release: v3.1.0

Pull Request - State: closed - Opened by gcroci2 5 months ago - 1 comment

#644 - Question about training

Issue - State: closed - Opened by Tizzzzy 5 months ago - 1 comment

#643 - Dani bodor token

Pull Request - State: closed - Opened by DaniBodor 5 months ago - 1 comment

#642 - ci: move ruff settings to separate toml file

Pull Request - State: closed - Opened by DaniBodor 6 months ago

#641 - Move ruff settings to separate toml file

Issue - State: closed - Opened by DaniBodor 6 months ago
Labels: CI

#640 - ci: add action for releasing new docker image and testing it

Pull Request - State: closed - Opened by gcroci2 6 months ago - 2 comments

#639 - Question about the training data

Issue - State: closed - Opened by Tizzzzy 6 months ago - 1 comment

#638 - Is pretrained model released?

Issue - State: closed - Opened by Tizzzzy 6 months ago - 1 comment
Labels: feature

#637 - fix: dockerfile image build

Pull Request - State: closed - Opened by gcroci2 7 months ago - 1 comment
Labels: stale

#636 - tutorials: avoid error messages in tutorial

Pull Request - State: closed - Opened by DaniBodor 7 months ago - 2 comments
Labels: blocking

#635 - fix SRV notebook

Issue - State: closed - Opened by DaniBodor 7 months ago - 1 comment
Labels: docs, CI, tutorials

#634 - build: fix python 3.11 installation

Pull Request - State: open - Opened by gcroci2 7 months ago - 1 comment
Labels: stale

#633 - re-order `add_feature` arguments

Issue - State: open - Opened by DaniBodor 7 months ago - 3 comments
Labels: stale, disc, covariates

#632 - release: bump2version patch 3.0.5

Pull Request - State: closed - Opened by gcroci2 7 months ago

#631 - release: v3.0.5

Pull Request - State: closed - Opened by gcroci2 7 months ago - 1 comment

#630 - docs: add doc strings to the neural networks architectures

Pull Request - State: closed - Opened by gcroci2 7 months ago - 1 comment

#629 - Migrate kanban boards to new Projects

Issue - State: closed - Opened by DaniBodor 7 months ago - 2 comments

#628 - docs: clean up docstrings

Pull Request - State: closed - Opened by DaniBodor 7 months ago

#627 - Remove types from docstrings

Issue - State: closed - Opened by DaniBodor 8 months ago - 3 comments
Labels: docs

#626 - style: make torch.nn imports more uniform

Pull Request - State: closed - Opened by DaniBodor 8 months ago - 1 comment

#625 - docs: improve structure and add modules

Pull Request - State: closed - Opened by gcroci2 8 months ago - 1 comment

#624 - ci: update ruff and fix linting rules

Pull Request - State: closed - Opened by DaniBodor 8 months ago

#623 - docs: rename paper folder to joss

Pull Request - State: closed - Opened by gcroci2 8 months ago

#622 - Fix linting

Issue - State: closed - Opened by DaniBodor 8 months ago - 1 comment

#621 - ci: improve release workflow

Pull Request - State: closed - Opened by DaniBodor 8 months ago - 15 comments

#620 - docs: clarify tutorials usage

Pull Request - State: closed - Opened by gcroci2 8 months ago - 2 comments

#619 - New release after the sprint

Issue - State: closed - Opened by gcroci2 8 months ago

#618 - docs: clarify usage of `output` column generated by the exporter

Pull Request - State: closed - Opened by gcroci2 8 months ago

#617 - Clarify in docs and tutorials the `output` column in the results' dataset

Issue - State: closed - Opened by rubenalv 8 months ago - 1 comment
Labels: docs

#616 - build: make dependencies versions more reliable

Pull Request - State: closed - Opened by gcroci2 8 months ago - 2 comments

#615 - build: simplify docker installation and improve the manual one

Pull Request - State: closed - Opened by gcroci2 8 months ago - 3 comments

#614 - release: v3.0.4

Pull Request - State: closed - Opened by gcroci2 8 months ago - 1 comment

#613 - Residue not found

Issue - State: closed - Opened by imerelli 8 months ago - 3 comments
Labels: bug, Query

#612 - ci: simplify lint action

Pull Request - State: closed - Opened by DaniBodor 8 months ago

#611 - CI: restore PyPI installation

Pull Request - State: closed - Opened by gcroci2 8 months ago - 8 comments

#610 - release: bump patch 3.0.3

Pull Request - State: closed - Opened by gcroci2 8 months ago - 1 comment

#609 - Bug: OSError: could not get source code

Issue - State: closed - Opened by rubenalv 8 months ago - 10 comments
Labels: docs

#608 - Docs - create descriptions/uses for the neural networks

Issue - State: closed - Opened by rubenalv 8 months ago - 1 comment
Labels: docs

#607 - Manage/set dependencies versions

Issue - State: closed - Opened by gcroci2 9 months ago - 2 comments
Labels: CI

#606 - fix: OSError when retrieving source code for lambda functions

Pull Request - State: closed - Opened by gcroci2 9 months ago - 2 comments

#605 - Add single proteins/molecules class

Issue - State: open - Opened by gcroci2 9 months ago
Labels: stale

#602 - Provide the trained models for various scenarios.

Issue - State: open - Opened by amjjbonvin 11 months ago - 5 comments
Labels: stale, feature

#601 - docs: improve handling pypi packaging contents and add NOTICE

Pull Request - State: closed - Opened by gcroci2 11 months ago

#600 - docs: improve handling pypi packaging contents and add NOTICE

Pull Request - State: closed - Opened by gcroci2 11 months ago - 1 comment

#599 - ci: add python3 to fix the package build

Pull Request - State: closed - Opened by gcroci2 11 months ago - 1 comment

#598 - ci: set default shell for fixing the workflows

Pull Request - State: closed - Opened by gcroci2 11 months ago - 1 comment

#597 - release: 3.0.2 patch

Pull Request - State: closed - Opened by gcroci2 11 months ago - 1 comment

#596 - release: patch 3.0.2

Pull Request - State: closed - Opened by gcroci2 11 months ago

#595 - Release 3.0.2

Issue - State: closed - Opened by gcroci2 11 months ago

#594 - docs: add OPLS ref to the docs

Pull Request - State: closed - Opened by gcroci2 11 months ago

#593 - Add OPLS ref to relevant files

Issue - State: closed - Opened by gcroci2 11 months ago
Labels: docs

#592 - Integrate pdbprep into codebase

Pull Request - State: open - Opened by DaniBodor 11 months ago - 1 comment
Labels: stale

#591 - integrate pdb prep into DR2

Pull Request - State: closed - Opened by DaniBodor 11 months ago - 1 comment

#589 - bug: update requirements.txt

Pull Request - State: closed - Opened by gcroci2 12 months ago - 1 comment

#587 - ci: add action for testing the tutorials' notebooks

Pull Request - State: closed - Opened by gcroci2 12 months ago

#586 - docs: clarify queries' usage

Pull Request - State: closed - Opened by gcroci2 12 months ago - 1 comment

#585 - Clarify usage of PPI and SRV in README.

Issue - State: closed - Opened by DaniBodor 12 months ago
Labels: docs

#584 - style: update ruff

Pull Request - State: closed - Opened by DaniBodor 12 months ago

#583 - merge dev with main

Pull Request - State: closed - Opened by gcroci2 12 months ago

#582 - Bug: Functional group is unknown to the forcefield

Issue - State: closed - Opened by lloydtripp 12 months ago - 12 comments
Labels: bug, Query

#581 - convert PSSM from 3dcons to deeprank

Issue - State: closed - Opened by Lsz-20 12 months ago - 2 comments
Labels: stale, needs info, Query, tools

#580 - paper: add affiliation and corresponding author correction

Pull Request - State: closed - Opened by gcroci2 12 months ago

#579 - docs: update README.md with JOSS badge

Pull Request - State: closed - Opened by gcroci2 12 months ago - 1 comment

#578 - h5x didn't work

Issue - State: closed - Opened by Lsz-20 12 months ago - 3 comments

#577 - Bug: Cannot import modules in data_generation_ppi tutorial

Issue - State: closed - Opened by lloydtripp 12 months ago - 3 comments
Labels: bug

#576 - Add tutorials notebooks testing

Issue - State: closed - Opened by gcroci2 12 months ago
Labels: CI

#575 - dev: merge dev branch with main

Pull Request - State: closed - Opened by gcroci2 12 months ago

#574 - release: patch 3.0.1

Pull Request - State: closed - Opened by gcroci2 12 months ago - 1 comment

#573 - fix: features transform in `Trainer._save_model` internal method

Pull Request - State: closed - Opened by gcroci2 12 months ago - 2 comments

#572 - fix: test_cuda in `test_trainer.py::TestTrainer`

Pull Request - State: closed - Opened by gcroci2 12 months ago - 1 comment

#571 - paper: add minor fixes for acceptance

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

#570 - Fix `features_transform` AttributeError in `Trainer._save_model` method

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

#569 - docs: add RSD badge

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

#568 - fix typo

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

#567 - Bump readthedocs-sphinx-search from 0.1.1 to 0.3.2 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#565 - CI: move PyPI deps installation to conda

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

#564 - docs: fix error message structure

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

#563 - Adapting ruff

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

#562 - release: merge dev with main for release 3.0.0

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

#561 - release: merge dev with main for release 3.0.0

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

#559 - Conda migration

Issue - State: closed - Opened by gcroci2 about 1 year ago - 8 comments
Labels: CI, disc

#557 - New major release (DeepRank 3.0.0)

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

#556 - Create a tutorial for the antibody-antigen docking models use case

Issue - State: open - Opened by gcroci2 about 1 year ago
Labels: blocked

#555 - Create a tutorial for the protein-ligand complexes use case

Issue - State: open - Opened by gcroci2 about 1 year ago
Labels: blocked

#554 - ci: implement ruff

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

#553 - Add example data for antibody-antigen docking models use case

Issue - State: open - Opened by gcroci2 about 1 year ago - 1 comment
Labels: stale, disc, needs info

#552 - Add example data for protein-ligand complexes use case

Issue - State: open - Opened by gcroci2 about 1 year ago - 1 comment
Labels: stale, disc, needs info

#551 - Create tests and docs for multiple-chain graphs

Issue - State: open - Opened by gcroci2 about 1 year ago
Labels: blocked

#550 - Create tests and docs for protein-ligand graphs

Issue - State: open - Opened by gcroci2 about 1 year ago
Labels: blocked

#549 - build: switch to conda dssp installation

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

#548 - Deal with residue features in protein-ligand graphs

Issue - State: open - Opened by DaniBodor about 1 year ago
Labels: blocked

#547 - Allow for multiple-chain graphs

Issue - State: open - Opened by gcroci2 about 1 year ago - 6 comments
Labels: blocking, stale, disc

#546 - Consider allowing mixed resolution graphs for protein-ligand graphs

Issue - State: open - Opened by gcroci2 about 1 year ago
Labels: blocked, disc

#545 - Create tests and docs for protein-nucleic acid graphs

Issue - State: open - Opened by DaniBodor about 1 year ago
Labels: blocked

#544 - Allow for none-residue atom entries for protein-ligand graphs

Issue - State: open - Opened by gcroci2 about 1 year ago - 1 comment
Labels: blocking, stale