Ecosyste.ms: Issues

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GitHub / deeprank/deeprank2 issues and pull requests

#462 - Fix link in TUTORIAL.md

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

#461 - fix: `dataset_train` inheritance warnings

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

#461 - fix: `dataset_train` inheritance warnings

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

#460 - Clarify `distance_cutoff` across different `Query` classes

Issue - State: open - Opened by gcroci2 over 1 year ago - 5 comments
Labels: priority, stale

#460 - Clarify `distance_cutoff` across different `Query` classes

Issue - State: closed - Opened by gcroci2 over 1 year ago - 5 comments
Labels: priority, stale

#459 - docs: add tutorials for variants

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

#459 - docs: add tutorials for variants

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

#458 - Cache CI environment so it doesn't need to be rebuilt each time

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

#456 - Remove h5explorer from package

Issue - State: closed - Opened by DaniBodor over 1 year ago - 2 comments
Labels: tools

#456 - Remove h5explorer from package

Issue - State: closed - Opened by DaniBodor over 1 year ago - 2 comments
Labels: tools

#454 - CI: fewer actions

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

#448 - Add torsion angle feature for residues (calculated from the backbone)

Issue - State: open - Opened by DanLep97 over 1 year ago - 3 comments
Labels: stale, feature

#448 - Add torsion angle feature for residues (calculated from the backbone)

Issue - State: closed - Opened by DanLep97 over 1 year ago - 3 comments
Labels: stale, feature

#444 - Inherit information from training data when `train = False` in `GraphDataset` class

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

#442 - fix: warning messages for invalid data in test_dataset.py

Pull Request - State: closed - Opened by joyceljy over 1 year ago - 13 comments
Labels: stale

#442 - fix: warning messages for invalid data in test_dataset.py

Pull Request - State: closed - Opened by joyceljy over 1 year ago - 13 comments
Labels: stale

#441 - Warnings thrown during standardization

Issue - State: closed - Opened by DaniBodor over 1 year ago - 4 comments
Labels: stale, needs info, Dataset

#441 - Warnings thrown during standardization

Issue - State: closed - Opened by DaniBodor over 1 year ago - 4 comments
Labels: stale, needs info, Dataset

#440 - Evaluate to add a conda release

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

#440 - Evaluate to add a conda release

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

#439 - Remove reduce

Issue - State: closed - Opened by DaniBodor over 1 year ago - 1 comment
Labels: good first issue, priority, stale, MolStruct

#435 - Add tutorials for variants

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

#428 - problem with check_pssm

Issue - State: closed - Opened by rgayatri almost 2 years ago - 7 comments
Labels: bug, stale, Query

#423 - docs: joss paper

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

#417 - Use pathlib or os.join method and global TEST_PATH variable consistently in test modules

Issue - State: closed - Opened by DaniBodor almost 2 years ago - 1 comment
Labels: good first issue, CI, stale, testing

#411 - Creating queries from pdb files with underscore in the filename gives unexpected query ids

Issue - State: closed - Opened by DaniBodor almost 2 years ago - 3 comments
Labels: stale, Query

#410 - 408 interchain energies dbodor

Pull Request - State: closed - Opened by DaniBodor almost 2 years ago

#402 - Bug: No error message when no value calculated for HSE

Issue - State: open - Opened by Max1461 almost 2 years ago - 8 comments
Labels: bug, covariates

#402 - Bug: No error message when no value calculated for HSE

Issue - State: open - Opened by Max1461 almost 2 years ago - 9 comments
Labels: stale, covariates

#396 - docs: create tables for feature documentation

Pull Request - State: closed - Opened by DaniBodor almost 2 years ago - 2 comments
Labels: stale

#396 - docs: create tables for feature documentation

Pull Request - State: closed - Opened by DaniBodor almost 2 years ago - 2 comments
Labels: stale

#395 - Investigate pdb2sql v0.5.3 error

Issue - State: closed - Opened by DaniBodor almost 2 years ago - 3 comments
Labels: stale, needs info, tools

#394 - Unify `get_residue_contact_pairs()` from buildgraph.py by `get_IRCs()` from irc.py

Issue - State: closed - Opened by DaniBodor almost 2 years ago - 1 comment
Labels: good first issue, nice to have, stale, utils

#393 - Use openMM to redefine the forcefield

Issue - State: closed - Opened by DaniBodor almost 2 years ago - 6 comments
Labels: priority, stale, feature, needs info, covariates

#391 - Polarity-pair edge feature

Issue - State: closed - Opened by DaniBodor almost 2 years ago - 1 comment
Labels: nice to have, stale, covariates

#390 - Setting for random seeds

Issue - State: closed - Opened by DaniBodor almost 2 years ago - 1 comment
Labels: stale, feature

#383 - Add skip-grams feature for encoding aminoacids sequences

Issue - State: closed - Opened by gcroci2 almost 2 years ago - 1 comment
Labels: stale, feature, needs info

#382 - Explore options to store hdf5 files used by pytest externally

Issue - State: closed - Opened by DaniBodor almost 2 years ago - 1 comment
Labels: stale, needs info, testing

#381 - Improve package folder structure and add description for it

Issue - State: closed - Opened by gcroci2 almost 2 years ago - 1 comment
Labels: stale

#380 - Fix hydrogens unkown to the forcefield

Issue - State: closed - Opened by Max1461 almost 2 years ago - 3 comments
Labels: bug, stale

#379 - Use actual pairing distances rather than physical distances to define potential energies

Issue - State: closed - Opened by DaniBodor almost 2 years ago - 5 comments
Labels: stale

#373 - Improve `Earlystopping` class

Issue - State: closed - Opened by gcroci2 almost 2 years ago - 1 comment
Labels: stale, Trainer

#371 - Add documentation for Variant queries

Issue - State: closed - Opened by DaniBodor almost 2 years ago - 5 comments
Labels: docs, needs info, Query

#366 - Modify internal `_compute_mean_std` method to be reused in the code

Issue - State: closed - Opened by gcroci2 about 2 years ago - 1 comment
Labels: nice to have, stale, Dataset

#344 - Evaluate storage of grid features values per chain

Issue - State: closed - Opened by cbaakman about 2 years ago - 3 comments
Labels: Query

#325 - Fix usage for multiple GPUs

Issue - State: open - Opened by gcroci2 about 2 years ago - 1 comment
Labels: Trainer

#308 - Check performance warnings of CNNs

Issue - State: closed - Opened by DaniBodor about 2 years ago - 3 comments
Labels: Trainer, tools

#297 - Increase modules rendered by readthedocs

Issue - State: closed - Opened by gcroci2 about 2 years ago - 2 comments
Labels: docs

#297 - Increase modules rendered by readthedocs

Issue - State: open - Opened by gcroci2 about 2 years ago - 2 comments
Labels: docs

#284 - Create unit tests for missing neuralnets

Issue - State: closed - Opened by DaniBodor about 2 years ago - 2 comments
Labels: stale, testing, neuralnets

#275 - Improve speed of queries `process` speed for atomic graphs

Issue - State: closed - Opened by gcroci2 about 2 years ago - 1 comment

#270 - Simplify Interface/Pair usage

Issue - State: closed - Opened by gcroci2 about 2 years ago - 2 comments
Labels: nice to have, MolStruct

#269 - Unify torch imports

Issue - State: closed - Opened by gcroci2 about 2 years ago - 1 comment
Labels: nice to have

#268 - Avoid/check pylint disabled

Issue - State: closed - Opened by gcroci2 about 2 years ago - 1 comment
Labels: nice to have

#259 - Split current test_trainer into test_trainer and test_neuralnets

Issue - State: closed - Opened by DaniBodor about 2 years ago - 1 comment
Labels: nice to have, testing

#257 - Refactor duplicate code

Issue - State: closed - Opened by DaniBodor about 2 years ago - 4 comments
Labels: nice to have

#251 - Regenerate class diagrams

Issue - State: closed - Opened by gcroci2 about 2 years ago - 5 comments
Labels: docs, priority, class diagram, tools

#234 - Reorganize `Trainer` class

Issue - State: closed - Opened by DaniBodor over 2 years ago - 6 comments
Labels: Trainer

#232 - Improve the way in which features are generated

Issue - State: closed - Opened by gcroci2 over 2 years ago - 2 comments
Labels: nice to have, Query

#225 - Include all PDB fields as metafeatures

Issue - State: closed - Opened by KevinVG207 over 2 years ago - 2 comments
Labels: nice to have, covariates

#217 - Visualization module

Issue - State: closed - Opened by gcroci2 over 2 years ago - 3 comments
Labels: nice to have, feature, tools

#198 - Allow for >20 types in `AminoAcid` class

Issue - State: closed - Opened by DTRademaker over 2 years ago - 11 comments
Labels: nice to have, feature

#197 - Add support for categorical targets

Issue - State: closed - Opened by gcroci2 over 2 years ago - 3 comments
Labels: nice to have

#191 - Migrate codebase to PyTorch Lightening

Issue - State: closed - Opened by gcroci2 over 2 years ago - 3 comments
Labels: nice to have

#185 - Using a pdb file containing only one chain gives unexpected results

Issue - State: closed - Opened by DTRademaker over 2 years ago - 14 comments
Labels: bug, stale

#177 - Add package testing for MacOS

Issue - State: closed - Opened by gcroci2 over 2 years ago - 6 comments
Labels: nice to have, CI, testing

#176 - Add relevant badges

Issue - State: closed - Opened by gcroci2 over 2 years ago - 3 comments
Labels: nice to have

#174 - Do a detailed comparison between the actual code base and its original design

Issue - State: closed - Opened by gcroci2 over 2 years ago - 5 comments
Labels: nice to have, stale

#170 - Improve CI workflow for publishing new package version on Github

Issue - State: closed - Opened by gcroci2 over 2 years ago - 6 comments
Labels: CI

#143 - Add gpu testing in CI

Issue - State: closed - Opened by gcroci2 over 2 years ago - 4 comments
Labels: CI

#89 - IndexError when running NeuralNet.train()

Issue - State: closed - Opened by svenvanderburg over 2 years ago - 10 comments

#83 - Use customized HDF5DataSet class

Issue - State: closed - Opened by gcroci2 over 2 years ago - 2 comments
Labels: blocking

#81 - Allow passing our own train/test/split to deeprank-gnn-2 NeuralNet

Issue - State: closed - Opened by gcroci2 over 2 years ago - 4 comments
Labels: duplicate, blocking

#54 - Implement Docking Metrics class

Issue - State: closed - Opened by gcroci2 almost 3 years ago - 8 comments

#54 - Implement Docking Metrics class

Issue - State: closed - Opened by gcroci2 almost 3 years ago - 8 comments

#53 - Implement QueryDataset class

Issue - State: closed - Opened by gcroci2 almost 3 years ago - 2 comments
Labels: class diagram