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Base branch for new talktorials #74

Merged
merged 329 commits into from
Sep 9, 2021
Merged

Base branch for new talktorials #74

merged 329 commits into from
Sep 9, 2021
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Dec 15, 2020

  1. Remove an usused line of code

    @dominiquesydow
    dominiquesydow committed Dec 15, 2020
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  2. Apply @AndreaVolkamer's suggestions

    @dominiquesydow
    dominiquesydow committed Dec 15, 2020
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  3. Use HTML instead of Markdown format in highlighted boxes

    @dominiquesydow
    dominiquesydow committed Dec 15, 2020
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  4. Add more HTML (still problems with monospaced stuff)

    @dominiquesydow
    dominiquesydow committed Dec 15, 2020
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  5. Fix HTML bugs

    @dominiquesydow
    dominiquesydow committed Dec 15, 2020
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  6. Fix more HTML bugs

    @dominiquesydow
    dominiquesydow committed Dec 15, 2020
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  7. add analysis of interactions.

    @t-kimber
    t-kimber committed Dec 15, 2020
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  8. Refine info boxes

    @dominiquesydow
    dominiquesydow committed Dec 15, 2020
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  9. finalize theory.

    @t-kimber
    t-kimber committed Dec 15, 2020
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  10. Add @AndreaVolkamer's suggestions

    @dominiquesydow
    dominiquesydow committed Dec 15, 2020
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  11. Minor formatting bug

    @dominiquesydow
    dominiquesydow committed Dec 15, 2020
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  12. Merge pull request #85 from volkamerlab/ds-t000-revamp 

    T000 - Talktorial template
    @dominiquesydow
    dominiquesydow authored Dec 15, 2020
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Commits on Dec 16, 2020

  1. AtomicDistance and Hydrogenbond analysis added

    @Mika-Le
    Mika-Le committed Dec 16, 2020
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  2. resize figure.

    @t-kimber
    t-kimber committed Dec 16, 2020
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  3. add YC s suggestions.

    @t-kimber
    t-kimber committed Dec 16, 2020
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Commits on Dec 18, 2020

  1. fix color legend, fix links

    @t-kimber
    t-kimber committed Dec 18, 2020
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  2. fix lint error

    @t-kimber
    t-kimber committed Dec 18, 2020
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  3. html fixes.

    @t-kimber
    t-kimber committed Dec 18, 2020
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  4. change CI to NBVAL in #TODO

    @t-kimber
    t-kimber committed Dec 18, 2020
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  5. nglview rendering.

    @t-kimber
    t-kimber committed Dec 18, 2020
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Commits on Dec 21, 2020

  1. Ready for review

    @Mika-Le
    Mika-Le committed Dec 21, 2020
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  2. Delete T10_MD_simulation_B-Analyze_simulation.ipynb

    @Mika-Le
    Mika-Le authored Dec 21, 2020
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Commits on Dec 23, 2020

  1. started adding pocket detection, dogsitescorer, theory and practical

    @AndreaVolkamer
    AndreaVolkamer committed Dec 23, 2020
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  2. switch to smina

    @schallerdavid
    schallerdavid committed Dec 23, 2020
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  3. Merge pull request #88 from volkamerlab/develop-t014 

    started adding pocket detection, dogsitescorer, theory and practical
    @AndreaVolkamer
    AndreaVolkamer authored Dec 23, 2020
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Commits on Jan 6, 2021

  1. remove installation issue.

    @t-kimber
    t-kimber committed Jan 6, 2021
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Commits on Jan 14, 2021

  1. update references

    @AndreaVolkamer
    AndreaVolkamer committed Jan 14, 2021
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  2. T020 reviewed

    @schallerdavid
    schallerdavid committed Jan 14, 2021
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Commits on Jan 15, 2021

  1. Ready for second review

    @Mika-Le
    Mika-Le committed Jan 15, 2021
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  2. Ready for second review

    @Mika-Le
    Mika-Le committed Jan 15, 2021
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  3. small textual changes, input of functions and automated download of p… 

    …db file
    @AndreaVolkamer
    AndreaVolkamer committed Jan 15, 2021
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  4. Update README.md

    @t-kimber
    t-kimber authored Jan 15, 2021
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  5. Update README.md

    @t-kimber
    t-kimber authored Jan 15, 2021
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  6. Merge remote-tracking branch 'origin/t011-base' into tbk-016-revamp

    @jaimergp
    jaimergp authored Jan 15, 2021
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  7. Merge pull request #75 from volkamerlab/tbk-016-revamp 

    T016 - Protein-ligand interactions
    @jaimergp
    jaimergp authored Jan 15, 2021
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Commits on Jan 17, 2021

  1. polish notebook

    @schallerdavid
    schallerdavid committed Jan 17, 2021
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  2. added theory

    @sakshimisra
    sakshimisra committed Jan 17, 2021
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  3. added figures captions

    @sakshimisra
    sakshimisra committed Jan 17, 2021
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Commits on Jan 18, 2021

  1. added references

    @sakshimisra
    sakshimisra committed Jan 18, 2021
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  2. worked on lint errors

    @sakshimisra
    sakshimisra committed Jan 18, 2021
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  3. worked on lint errors

    @sakshimisra
    sakshimisra committed Jan 18, 2021
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Commits on Jan 20, 2021

  1. added file in talktorial.rst

    @sakshimisra
    sakshimisra committed Jan 20, 2021
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  2. typos

    @sakshimisra
    sakshimisra committed Jan 20, 2021
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  3. added f strings

    @sakshimisra
    sakshimisra committed Jan 20, 2021
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Commits on Jan 21, 2021

  1. typos, worked on suggestions

    @sakshimisra
    sakshimisra committed Jan 21, 2021
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  2. typos

    @sakshimisra
    sakshimisra committed Jan 21, 2021
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Commits on Jan 23, 2021

  1. edited theory

    @sakshimisra
    sakshimisra committed Jan 23, 2021
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  2. edited theory

    @sakshimisra
    sakshimisra committed Jan 23, 2021
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Commits on Jan 24, 2021

  1. very minor textual adaptions

    @AndreaVolkamer
    AndreaVolkamer committed Jan 24, 2021
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  2. added theory on workflow

    @sakshimisra
    sakshimisra committed Jan 24, 2021
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Commits on Jan 25, 2021

  1. added discussion

    @sakshimisra
    sakshimisra committed Jan 25, 2021
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  2. update table of contents and intro

    @jaimergp
    jaimergp committed Jan 25, 2021
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  3. add static file requests section

    @jaimergp
    jaimergp committed Jan 25, 2021
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  4. reword some sections for clarity

    @jaimergp
    jaimergp committed Jan 25, 2021
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  5. add uniprot examples

    @jaimergp
    jaimergp committed Jan 25, 2021
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  6. add last section

    @jaimergp
    jaimergp committed Jan 25, 2021
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  7. add to docs

    @jaimergp
    jaimergp committed Jan 25, 2021
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  8. add gallery thumbnails

    @jaimergp
    jaimergp committed Jan 25, 2021
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  9. edited theory and parctical part

    @sakshimisra
    sakshimisra committed Jan 25, 2021
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  10. ready for review

    @sakshimisra
    sakshimisra committed Jan 25, 2021
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  11. ready for review

    @sakshimisra
    sakshimisra committed Jan 25, 2021
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Commits on Jan 26, 2021

  1. apply code review feedback 

    Co-authored-by: schallerdavid <schallerdavid@users.noreply.github.com>
    @jaimergp @schallerdavid
    jaimergp and schallerdavid committed Jan 26, 2021
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  2. Merge pull request #84 from volkamerlab/jrg-011-revamp 

    T011 - Querying online API webservices
    @jaimergp
    jaimergp authored Jan 26, 2021
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Commits on Jan 28, 2021

  1. Start branch

    @jaimergp
    jaimergp committed Jan 28, 2021
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  2. implements suggestions

    @schallerdavid
    schallerdavid committed Jan 28, 2021
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  3. Merge branch 't011-base' into das-015-revamp

    @jaimergp
    jaimergp committed Jan 28, 2021
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  4. include in collections

    @jaimergp
    jaimergp committed Jan 28, 2021
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  5. ready for review

    @sakshimisra
    sakshimisra committed Jan 28, 2021
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  6. added data readmefile

    @sakshimisra
    sakshimisra committed Jan 28, 2021
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  7. added predicted csv file

    @sakshimisra
    sakshimisra committed Jan 28, 2021
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Commits on Jan 31, 2021

  1. typos

    @sakshimisra
    sakshimisra committed Jan 31, 2021
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  2. minor textual adaptions

    @AndreaVolkamer
    AndreaVolkamer committed Jan 31, 2021
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  3. Merge branch 'sm-021-review' of github.com:volkamerlab/teachopencadd … 

    …into sm-021-review
    @AndreaVolkamer
    AndreaVolkamer committed Jan 31, 2021
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Commits on Feb 1, 2021

  1. typos

    @sakshimisra
    sakshimisra committed Feb 1, 2021
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  2. Update talktorial.ipynb 

    * add introduction of PubChem and PUG-REST,
* refactor the code
    @yonghui-cc
    yonghui-cc committed Feb 1, 2021
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  3. Updata README 

    * Updata README
* fix some syntax in talktorial.ipynb
    @yonghui-cc
    yonghui-cc committed Feb 1, 2021
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  4. Finished intro, added figures and reworked practical part

    @AndreaVolkamer
    AndreaVolkamer committed Feb 1, 2021
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  5. Add matplotlib-venn to environments

    @dominiquesydow
    dominiquesydow committed Feb 1, 2021
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  6. Add nglview pocket visualization

    @dominiquesydow
    dominiquesydow committed Feb 1, 2021
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  7. Visualize pocket with nglview using PDB + residue selection

    @dominiquesydow
    dominiquesydow committed Feb 1, 2021
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  8. added querying ccp4 format, visualization problem not yet solved

    @AndreaVolkamer
    AndreaVolkamer committed Feb 1, 2021
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Commits on Feb 2, 2021

  1. update requirements

    @jaimergp
    jaimergp committed Feb 2, 2021
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  2. Merge pull request #82 from volkamerlab/das-015-revamp 

    T015 - Protein-ligand docking
    @jaimergp
    jaimergp authored Feb 2, 2021
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  3. Merge branch 't011-base' into jrg-017-nglview

    @jaimergp
    jaimergp committed Feb 2, 2021
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  4. Presentation comments implemented. Ready!

    @Mika-Le
    Mika-Le committed Feb 2, 2021
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  5. Presentation comments implemented. Ready!

    @Mika-Le
    Mika-Le committed Feb 2, 2021
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  6. Polished theory part

    @AndreaVolkamer
    AndreaVolkamer committed Feb 2, 2021
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  7. add TOC and first steps

    @jaimergp
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  8. Practical part finished

    @AndreaVolkamer
    AndreaVolkamer committed Feb 2, 2021
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  9. Sections 1.1/2: Sync TOC/headers, fix typos, update KLIFS ref.

    @dominiquesydow
    dominiquesydow committed Feb 2, 2021
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  10. Section 1.3: Fix a few typos (from here on do review with reviewnb)

    @dominiquesydow
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  11. Included review changes.

    @AndreaVolkamer
    AndreaVolkamer committed Feb 2, 2021
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Commits on Feb 3, 2021

  1. Resolve environment conflicts

    @dominiquesydow
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  2. Update nglview volume and DoG table to df conversion

    @dominiquesydow
    dominiquesydow committed Feb 3, 2021
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  3. Correct io.StringIO statement 

    Co-authored-by: jaimergp <jaimergp@users.noreply.github.com>
    @dominiquesydow @jaimergp
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  4. Add io.StringIO documentation link 

    Co-authored-by: jaimergp <jaimergp@users.noreply.github.com>
    @dominiquesydow @jaimergp
    dominiquesydow and jaimergp committed Feb 3, 2021
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  5. Sphinx rendering adaptions.

    @AndreaVolkamer
    AndreaVolkamer committed Feb 3, 2021
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  6. Merge branch 't011-base' into av-t014-revamp

    @jaimergp
    jaimergp committed Feb 3, 2021
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  7. workaround nglview file loading with a memory file

    @jaimergp
    jaimergp committed Feb 3, 2021
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Commits on Feb 4, 2021

  1. Merge pull request #86 from volkamerlab/av-t014-revamp 

    T014 - Binding site detection
    @AndreaVolkamer
    AndreaVolkamer authored Feb 4, 2021
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Commits on Feb 7, 2021

  1. ready for review

    @sakshimisra
    sakshimisra committed Feb 7, 2021
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  2. ready for review

    @sakshimisra
    sakshimisra committed Feb 7, 2021
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Commits on Feb 8, 2021

  1. ready for review

    @sakshimisra
    sakshimisra committed Feb 8, 2021
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  2. cover basic steps

    @jaimergp
    jaimergp committed Feb 8, 2021
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Commits on Feb 11, 2021

  1. add selection language, GUIs, representations

    @jaimergp
    jaimergp committed Feb 11, 2021
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  2. fixed f strings

    @sakshimisra
    sakshimisra committed Feb 11, 2021
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Commits on Feb 12, 2021

  1. minor changes and improved behavior for CI and Colab

    @schallerdavid
    schallerdavid committed Feb 12, 2021
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  2. add links to run talktorial on colab

    @schallerdavid
    schallerdavid committed Feb 12, 2021
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  3. add some js examples

    @jaimergp
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Commits on Feb 14, 2021

  1. small textual adaptions

    @AndreaVolkamer
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Commits on Feb 15, 2021

  1. Add troubleshooting tips

    @jaimergp
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  2. Add some feature requests from Dominique

    @jaimergp
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  3. add theory

    @jaimergp
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  4. polish details

    @jaimergp
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Commits on Feb 17, 2021

  1. Changes in theory.

    @t-kimber
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  2. remove unnecessary files.

    @t-kimber
    t-kimber committed Feb 17, 2021
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  3. Update README.md

    @t-kimber
    t-kimber authored Feb 17, 2021
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  4. Update README.md

    @t-kimber
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  5. Practical: reformulation, typos, simplifications, etc.

    @t-kimber
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Commits on Feb 18, 2021

  1. Most of Jaimes comments addressed. Check simulation output pending

    @Mika-Le
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  2. Add collapsible cell for suppl. material.

    @t-kimber
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Commits on Feb 22, 2021

  1. Theory: typos and links.

    @t-kimber
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  2. pep8 fixes, reformulations, typos.

    @t-kimber
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  3. Update test_env.yml

    @t-kimber
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Commits on Feb 23, 2021

  1. Edit in the suppl.section.

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Commits on Feb 24, 2021

  1. adds visual inspection to docking theory

    @schallerdavid
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Commits on Mar 8, 2021

  1. Andreas comments adressed

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Commits on Apr 1, 2021

  1. Update talktorial.ipynb with V.2 

    add simple example for PubChem API and describe the similar compound searching function with more details.
    @yonghui-cc
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Commits on Apr 13, 2021

  1. Update talktorial.ipynb 

    main change:
- improve the "show the results" part
- check spelling
- add the explain for the PubChem similarity
    @yonghui-cc
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  2. Update talktorial.ipynb 

    main change:
- check the content review and code review.
    @yonghui-cc
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  3. Address review by Dominique Sydow 

    Co-authored-by: dominiquesydow <dominiquesydow@users.noreply.github.com>
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Commits on Apr 23, 2021

  1. Update talktorial.ipynb 

    - split the "query_pubchem_for_similar_compounds" into three parts;
- fix words and grammar
- format the code
    @yonghui-cc
    yonghui-cc committed Apr 23, 2021
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  2. Update talktorial.ipynb 

    - formate the code
    @yonghui-cc
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Commits on Apr 26, 2021

  1. Update talktorial.ipynb 

    - fix the docstrings
    @yonghui-cc
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  2. Final edits after feedback 

    Co-authored-by: Dominique Sydow <dominiquesydow@users.noreply.github.com>
    @jaimergp @dominiquesydow
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  3. Merge pull request #92 from volkamerlab/jrg-017-nglview 

    T017 - Advanced NGLview usage
    @jaimergp
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  4. Merge branch 't011-base' into ml-019-review

    @jaimergp
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  5. rename directory

    @jaimergp
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  6. add some links

    @jaimergp
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  7. add nblinks to docs

    @jaimergp
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  8. Merge pull request #76 from volkamerlab/ml-019-review 

    T020 - Analyzing molecular dynamics simulations
    @jaimergp
    jaimergp authored Apr 26, 2021
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  9. bring sm-019-review with fresh history and cleanup images 

    Co-authored-by: sakshimisra <sakshimisra@users.noreply.github.com>
Co-authored-by: t-kimber <t-kimber@users.noreply.github.com>
Co-authored-by: AndreaVolkamer <AndreaVolkamer@users.noreply.github.com>
Co-authored-by: AndreaVolkamer <AndreaVolkamer@users.noreply.github.com>
    @jaimergp @sakshimisra
    @t-kimber @AndreaVolkamer
    4 people committed Apr 26, 2021
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  10. Merge pull request #99 from volkamerlab/t021-redo 

    bring `sm-019-review` with fresh history and cleanup images
    @jaimergp
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  11. Merge branch 't011-base' into sm-021-review

    @jaimergp
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  12. remove npm stuff??

    @jaimergp
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  13. update other envs

    @jaimergp
    jaimergp committed Apr 26, 2021
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  14. fix images

    @jaimergp
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  15. rename and add to docs

    @jaimergp
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Commits on Apr 27, 2021

  1. Merge branch 't011-base' into ml-018-review

    @jaimergp
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  2. rename 019 -> T019

    @jaimergp
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  3. small style fixes

    @jaimergp
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  4. Merge pull request #56 from volkamerlab/ml-018-review 

    T019 - Molecular dynamics simulation
    @jaimergp
    jaimergp authored Apr 27, 2021
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  5. Rename T018

    @jaimergp
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  6. Update talktorial.ipynb

    @yonghui-cc
    yonghui-cc committed Apr 27, 2021
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  7. minor style fixes

    @jaimergp
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  8. Merge pull request #81 from volkamerlab/yc-013-revamp 

    T013 - Data acquisition from PubChem
    @jaimergp
    jaimergp authored Apr 27, 2021
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Commits on Apr 30, 2021

  1. Merge pull request #95 from volkamerlab/t015-update 

    adds visual inspection to docking theory
    @jaimergp
    jaimergp authored Apr 30, 2021
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Commits on May 3, 2021

  1. fix plots so they are square

    @jaimergp
    jaimergp committed May 3, 2021
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  2. Merge pull request #64 from volkamerlab/sm-021-review 

    T022 - Ligand-based screening: Neural networks
    @jaimergp
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  3. Merge branch 'master' into t011-base

    @jaimergp
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Commits on May 7, 2021

  1. Merge branch 'master' into t011-base

    @jaimergp
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  2. T011: expect exception

    @jaimergp
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  3. T012: disable stderr logging for numexpr

    @jaimergp
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  4. T013: validate some cells

    @jaimergp
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  5. T014: fix nglview screenshots

    @jaimergp
    jaimergp committed May 7, 2021
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  6. T015: deterministic nbval check

    @jaimergp
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  7. T016: minor fixes

    @jaimergp
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  8. T017: check if selection was actually picked (impossible in CI)

    @jaimergp
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  9. T019: add test for topology atoms and trajectory existence

    @jaimergp
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Commits on May 8, 2021

  1. T021: fix imports

    @jaimergp
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  2. T021: fix tested cells and non-pythonic forloops

    @jaimergp
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  3. T022: make nbval checks deterministic

    @jaimergp
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  4. apply black-nb -l 99

    @jaimergp
    jaimergp committed May 8, 2021
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  5. add t014 to docs

    @jaimergp
    jaimergp committed May 8, 2021
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  6. regenerate readmes

    @jaimergp
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Commits on May 11, 2021

  1. T001: regenerate results

    @jaimergp
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  2. T003: fix some depictions

    @jaimergp
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  3. T008: alternative get_ligands workaround

    @jaimergp
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  4. Regenerate outputs T002-T010 after change in T001

    @jaimergp
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Commits on May 12, 2021

  1. Add missing packages from T001-10 to README

    @dominiquesydow
    dominiquesydow committed May 12, 2021
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  2. T011: Replace "?" with NaN in DataFrame (sync Python 3.6 and 3.9 output)

    @dominiquesydow
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  3. Satisfy black-nb

    @dominiquesydow
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  4. T014: Download results when job finishes (add attempts loop)

    @dominiquesydow
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  5. Satisfy black-nb

    @dominiquesydow
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  6. fix python 3.6 error

    @schallerdavid
    schallerdavid committed May 12, 2021
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Commits on May 14, 2021

  1. T010: Use biotite to get PDB IDs matching certain criteria

    @dominiquesydow
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  2. T001-09: Typos; add missing discussions; rm output-dep. values in text

    @dominiquesydow
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  3. Update talktorials' README.md

    @dominiquesydow
    dominiquesydow committed May 14, 2021
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  4. Docs: Remove duplicated nblink

    @dominiquesydow
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  5. T001-T022: Fix typos (special focus on website)

    @dominiquesydow
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  6. Regenerate talktorial READMEs

    @dominiquesydow
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  7. README: Add external packages >T010

    @dominiquesydow
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Commits on May 17, 2021

  1. Add google-colab+condacolab to README

    @dominiquesydow
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  2. T021: Remove duplicated package import

    @dominiquesydow
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  3. T017: do not use cmd lexer - just plain block

    @jaimergp
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  4. T019: adjust dependencies for Linux/MacOS only

    @jaimergp
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  5. docs: fix some 404s and allow-list the rest

    @jaimergp
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  6. README: Add more external resources

    @dominiquesydow
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  7. Merge pull request #102 from volkamerlab/update-package-list 

    Add missing packages from T001-22 to README
    @dominiquesydow
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Commits on May 25, 2021

  1. Add badge for closed issues.

    @t-kimber
    t-kimber authored May 25, 2021
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  2. Update README.md

    @t-kimber
    t-kimber authored May 25, 2021
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  3. Update README.md

    @t-kimber
    t-kimber authored May 25, 2021
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  4. Rearrange badges

    @dominiquesydow
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Commits on May 31, 2021

  1. T008: Use biotite to de-complicate structure selection

    @dominiquesydow
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  2. T008: Update talktorial README

    @dominiquesydow
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Commits on Jun 1, 2021

  1. Edit TOC badge.

    @t-kimber
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Commits on Jun 2, 2021

  1. T010: Cross-reference T008 for pypdb/biotite details; update README

    @dominiquesydow
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Commits on Jun 4, 2021

  1. Update README.md

    @t-kimber
    t-kimber authored Jun 4, 2021
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  2. T011 reviewed

    @AndreaVolkamer
    AndreaVolkamer committed Jun 4, 2021
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  3. T012 reviewed

    @AndreaVolkamer
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Commits on Jun 7, 2021

  1. Merge pull request #104 from volkamerlab/badge 

    Add badges to README top
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  2. T013 reviewed

    @AndreaVolkamer
    AndreaVolkamer committed Jun 7, 2021
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  3. T014 reviewed

    @AndreaVolkamer
    AndreaVolkamer committed Jun 7, 2021
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Commits on Aug 15, 2021

  1. T015 reviewed

    @AndreaVolkamer
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Commits on Aug 17, 2021

  1. T016 reviewed

    @AndreaVolkamer
    AndreaVolkamer committed Aug 17, 2021
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Commits on Aug 18, 2021

  1. T017 reviewed

    @AndreaVolkamer
    AndreaVolkamer committed Aug 18, 2021
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Commits on Aug 25, 2021

  1. T012: Resolve @AndreaVolkamer's review requests

    @dominiquesydow
    dominiquesydow committed Aug 25, 2021
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  2. T013: Resolve @AndreaVolkamer's review requests

    @dominiquesydow
    dominiquesydow committed Aug 25, 2021
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  3. T017: Resolve @AndreaVolkamer's review requests

    @dominiquesydow
    dominiquesydow committed Aug 25, 2021
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Commits on Aug 26, 2021

  1. Address AV's comments.

    @t-kimber
    t-kimber committed Aug 26, 2021
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  2. fix minor typo.

    @t-kimber
    t-kimber committed Aug 26, 2021
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  3. implement suggestions for T015

    @schallerdavid
    schallerdavid committed Aug 26, 2021
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Commits on Aug 27, 2021

  1. T013: Fix typo + table of contents

    @dominiquesydow
    dominiquesydow committed Aug 27, 2021
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  2. T013: Fix typo in "fixed" typo...

    @dominiquesydow
    dominiquesydow committed Aug 27, 2021
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  3. T016: Refer to SI for binding site detection procedure in PLIP

    @dominiquesydow
    dominiquesydow committed Aug 27, 2021
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  4. T016: Fix typo in code comment

    @dominiquesydow
    dominiquesydow committed Aug 27, 2021
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  5. T017: Add comments on RCSB, labels=representations, multimodels

    @dominiquesydow
    dominiquesydow committed Aug 27, 2021
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  6. Merge pull request #106 from volkamerlab/t011-base-review 

    Final round of text reviews for T011-T018
    @dominiquesydow
    dominiquesydow authored Aug 27, 2021
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  7. Fix broken links

    @dominiquesydow
    dominiquesydow committed Aug 27, 2021
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  8. Regenerate READMEs

    @dominiquesydow
    dominiquesydow committed Aug 27, 2021
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  9. Satisfy black-nb (except for 3 cells in T019)

    @dominiquesydow
    dominiquesydow committed Aug 27, 2021
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Commits on Sep 1, 2021

  1. T014: Use new PandasPdb().read_pdb_from_lines method (not private met… 

    …hod)
    @dominiquesydow
    dominiquesydow committed Sep 1, 2021
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  2. Merge branch 'master' into t011-base

    @dominiquesydow
    dominiquesydow authored Sep 1, 2021
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Commits on Sep 2, 2021

  1. Replace broken links

    @dominiquesydow
    dominiquesydow committed Sep 2, 2021
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  2. T007: Regenerate README

    @dominiquesydow
    dominiquesydow committed Sep 2, 2021
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  3. Merge branch 't011-base' into fix-broken-links

    @dominiquesydow
    dominiquesydow authored Sep 2, 2021
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  4. Merge pull request #133 from volkamerlab/fix-broken-links 

    Replace broken links
    @dominiquesydow
    dominiquesydow authored Sep 2, 2021
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Commits on Sep 3, 2021

  1. run T016 with mdanalysis 2.0.0

    @schallerdavid
    schallerdavid committed Sep 3, 2021
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Commits on Sep 8, 2021

  1. CI: Exclude T019 from tests under Windows

    @dominiquesydow
    dominiquesydow committed Sep 8, 2021
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  2. T019: Add link to issue about Windows support

    @dominiquesydow
    dominiquesydow committed Sep 8, 2021
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  3. T001: Freeze final EGFR compounds dataset (add commit hash)

    @dominiquesydow
    dominiquesydow committed Sep 8, 2021
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  4. T001: Rename EGFR bioactivities CSV (used in case database is too slow)

    @dominiquesydow
    dominiquesydow committed Sep 8, 2021
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  5. T001: Remove frozen ChEMBL 27 activities

    @dominiquesydow
    dominiquesydow committed Sep 8, 2021
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  6. T001: Freeze dataset at the end of notebook

    @dominiquesydow
    dominiquesydow committed Sep 8, 2021
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  7. T001+T019: Regenerate READMEs

    @dominiquesydow
    dominiquesydow committed Sep 8, 2021
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  8. README: Update TOC topics image

    @dominiquesydow
    dominiquesydow committed Sep 8, 2021
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  9. README: Update news banner

    @dominiquesydow
    dominiquesydow committed Sep 8, 2021
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  10. CI: Remove ignored file that has been removed

    @dominiquesydow
    dominiquesydow committed Sep 8, 2021
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Commits on Sep 9, 2021

  1. T011: Use utf-8-sig encoding for same results on Windows/Unix

    @dominiquesydow
    dominiquesydow committed Sep 9, 2021
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  2. T016: Remove NBVAL checks for PLIP output bc Windows/Unix diff, see #138

    @dominiquesydow
    dominiquesydow committed Sep 9, 2021
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