Jhsmit/PyHDX issues and pull requests

#364 - Bump jinja2 from 3.1.4 to 3.1.5 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 19 days ago
Labels: dependencies, python

#363 - Bump tornado from 6.4.1 to 6.4.2 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 19 days ago
Labels: dependencies, python

#362 - switch to uplot, py310

Pull Request - State: closed - Opened by Jhsmit about 1 month ago

#361 - Enlarge dG limits

Issue - State: open - Opened by Shakrim 3 months ago - 3 comments

#360 - changed default ddG colormap no coverage color to yellow

Pull Request - State: closed - Opened by Jhsmit 4 months ago

#359 - D uptake fit graphs not working

Issue - State: closed - Opened by Neel6164 4 months ago - 1 comment

#358 - Website access problem

Issue - State: closed - Opened by Neel6164 4 months ago - 1 comment

#357 - Bump torch from 2.0.1 to 2.2.0 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 3 comments
Labels: dependencies, python

#356 - Bump zipp from 3.16.2 to 3.19.1 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, python

#355 - Bump certifi from 2023.7.22 to 2024.7.4 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, python

#354 - Bump urllib3 from 2.0.7 to 2.2.2 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#353 - yaml without FD_control

Issue - State: open - Opened by Arthanis58 8 months ago - 2 comments

#352 - Lint

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

#351 - update gitignore

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

#350 - HDExaminer conversion and allow replicates

Pull Request - State: open - Opened by tuttlelm 8 months ago - 2 comments

#349 - HDExaminer data support

Issue - State: open - Opened by Jhsmit 8 months ago - 3 comments

#348 - rfu_residues_sd error

Issue - State: closed - Opened by tuttlelm 8 months ago - 3 comments

#347 - Bump tornado from 6.3.3 to 6.4.1 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#346 - Bump requests from 2.31.0 to 2.32.0 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#345 - Bump jinja2 from 3.1.3 to 3.1.4 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#344 - Bump tqdm from 4.66.1 to 4.66.3 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#343 - Bump idna from 3.4 to 3.7 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies, python

#342 - Bump pillow from 10.2.0 to 10.3.0 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies, python

#341 - Bump pillow from 10.0.1 to 10.2.0 in /requirements

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

#340 - Bump jinja2 from 3.1.2 to 3.1.3 in /requirements

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

#339 - torch performace in dask seems worse

Issue - State: open - Opened by Jhsmit about 1 year ago - 1 comment

#338 - Bump urllib3 from 2.0.6 to 2.0.7 in /requirements

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

#337 - Bump pillow from 10.0.0 to 10.0.1 in /requirements

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

#336 - Bump urllib3 from 2.0.4 to 2.0.6 in /requirements

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

#335 - fix dg color scatter plotting for newer pandas versions

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

#334 - Bump hdxms datasets

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

#333 - Bump hdxms datasets

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

#332 - Bump tornado from 6.3.2 to 6.3.3 in /requirements

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

#331 - Hatch

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

#330 - check lock file

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

#329 - remove downloading datasets on server start

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

#328 - Bump scipy from 1.9.3 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, python

#327 - Add hdxms-datasets

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

#326 - Bump cryptography from 39.0.1 to 41.0.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#325 - colorcet requirement missing for plotting extra

Issue - State: open - Opened by Jhsmit over 1 year ago

#324 - Bump tornado from 6.2 to 6.3.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#323 - Bump requests from 2.28.1 to 2.31.0

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

#322 - Bump mpmath from 1.2.1 to 1.3.0

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

#321 - Bump pymdown-extensions from 9.9.1 to 10.0

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

#320 - fix: reset_index is not an argument

Pull Request - State: closed - Opened by CFisicaro almost 2 years ago - 3 comments

#319 - running pyhdx web should first load local config file before resorting to user dir

Issue - State: closed - Opened by Jhsmit almost 2 years ago
Labels: enhancement

#318 - Rfu file input

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

#317 - docs: Adding measurements

Issue - State: closed - Opened by Jhsmit almost 2 years ago
Labels: documentation

#316 - Bump markdown-it-py from 2.1.0 to 2.2.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, python

#315 - removed the deprecated `Protein` object

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

#314 - move to mkdocs

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

#313 - Bump ipython from 8.7.0 to 8.10.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#312 - Bump cryptography from 39.0.0 to 39.0.1

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, python

#311 - add py3.10

Pull Request - State: closed - Opened by Jhsmit about 2 years ago - 2 comments

#310 - switch to poetry

Pull Request - State: closed - Opened by Jhsmit about 2 years ago

#309 - pdbe nonetype

Issue - State: open - Opened by Jhsmit about 2 years ago

#308 - FutureWarning: pandas indexing

Issue - State: open - Opened by Jhsmit about 2 years ago
Labels: bug

#307 - Fitting with peptide weights

Issue - State: open - Opened by Jhsmit over 2 years ago
Labels: enhancement

#306 - Goodness of fit qualifiers feedback D-uptake fit

Issue - State: open - Opened by Jhsmit over 2 years ago
Labels: enhancement

#305 - Refactor loading data

Pull Request - State: closed - Opened by Jhsmit over 2 years ago - 1 comment

#304 - Refresh c_term n_term defaults when switching experiment state

Issue - State: open - Opened by Jhsmit over 2 years ago - 2 comments

#303 - yaml FD_control

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

#302 - Understanding .yaml file + csv input

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

#301 - Add settings history in web application

Pull Request - State: closed - Opened by Jhsmit over 2 years ago

#300 - Intersection of peptides between HDX measurements

Issue - State: open - Opened by Jhsmit over 2 years ago
Labels: enhancement, GUI

#299 - Residue offset in web application

Issue - State: open - Opened by Jhsmit over 2 years ago
Labels: enhancement, GUI

#298 - Setting values on a copy of dataframe

Issue - State: open - Opened by Jhsmit over 2 years ago

#297 - Add D-uptake fit in web application

Pull Request - State: closed - Opened by Jhsmit over 2 years ago

#296 - Add D-uptake fitting and coverage docs

Pull Request - State: closed - Opened by Jhsmit over 2 years ago

#295 - Deuterium uptake per residue rather than deltaG

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

#294 - Update installation docs

Pull Request - State: closed - Opened by Jhsmit over 2 years ago

#293 - python_requirements.py

Issue - State: closed - Opened by JZbacklife1 over 2 years ago - 2 comments

#292 - new issue

Issue - State: closed - Opened by JZbacklife1 over 2 years ago - 9 comments

#291 - Omegaconf

Pull Request - State: closed - Opened by Jhsmit over 2 years ago

#290 - Add error propagation of uptake stds to rfu stds

Pull Request - State: closed - Opened by Jhsmit over 2 years ago

#289 - Uploading session file does not update graphs

Issue - State: closed - Opened by Jhsmit over 2 years ago
Labels: bug, GUI

#288 - pdb files per protein state; include pdb files in exported session files

Issue - State: open - Opened by Jhsmit over 2 years ago
Labels: enhancement, GUI

#287 - Downsample exported loss in session files

Issue - State: open - Opened by Jhsmit over 2 years ago
Labels: enhancement, GUI

#286 - Single and Batch fit losses result doesnt mix (or can be concatenated)

Issue - State: closed - Opened by Jhsmit over 2 years ago
Labels: bug, GUI

#285 - Peptide viewer

Pull Request - State: closed - Opened by Jhsmit over 2 years ago

#284 - Catch errors when inputting an invalid file in web app

Issue - State: open - Opened by Jhsmit almost 3 years ago
Labels: bug, GUI

#283 - Feature request: export ΔRFU linear bars grouped by state

Issue - State: open - Opened by Jhsmit almost 3 years ago
Labels: enhancement, GUI

#282 - protein viewer highlight color

Issue - State: closed - Opened by Jhsmit almost 3 years ago
Labels: enhancement, GUI

#281 - protein viewer highlight range / single

Issue - State: closed - Opened by Jhsmit almost 3 years ago
Labels: bug, GUI

#280 - Peptide view needs a hover tool

Issue - State: open - Opened by Jhsmit almost 3 years ago
Labels: enhancement, good first issue, GUI

#279 - ddG errorbars (covariance) should be lighter

Issue - State: closed - Opened by Jhsmit almost 3 years ago
Labels: enhancement, GUI

#278 - `rfu_residues.csv` rows arent sorted by index

Issue - State: closed - Opened by Jhsmit almost 3 years ago
Labels: bug, GUI

#277 - state spec yamls do not support relative paths when using the GUI

Issue - State: open - Opened by Jhsmit almost 3 years ago
Labels: bug, GUI

#276 - Proplot pinned requirement

Issue - State: open - Opened by Jhsmit almost 3 years ago
Labels: enhancement

#275 - Web application reference docs superclass info not useful

Issue - State: open - Opened by Jhsmit almost 3 years ago
Labels: documentation

#274 - Align dataframes function should take dicts only

Issue - State: open - Opened by Jhsmit almost 3 years ago

#273 - protein structure does not switch to dG colors

Issue - State: closed - Opened by Jhsmit almost 3 years ago - 1 comment
Labels: bug, GUI

#272 - Catch error when trying to load structure without pdb selected

Issue - State: closed - Opened by Jhsmit almost 3 years ago

#271 - Docstrings and documentation

Pull Request - State: closed - Opened by Jhsmit almost 3 years ago

#270 - Test pickling / weighted averge initial guesses

Issue - State: open - Opened by Jhsmit almost 3 years ago
Labels: enhancement, Fitting

#269 - bump symfit version requirement

Pull Request - State: closed - Opened by Jhsmit almost 3 years ago

#268 - Documentation for `pyhdx process`

Issue - State: open - Opened by Jhsmit almost 3 years ago
Labels: enhancement

#267 - Jobfiles and process from the command line

Pull Request - State: closed - Opened by Jhsmit almost 3 years ago

#266 - Unify fit_result fitresult

Issue - State: open - Opened by Jhsmit almost 3 years ago
Labels: enhancement

#265 - Unify hdx_set and hdxm_set

Issue - State: open - Opened by Jhsmit almost 3 years ago

GitHub / Jhsmit/PyHDX issues and pull requests