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T032: Compound activity: Proteochemometrics #278

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T032: Compound activity: Proteochemometrics #278

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Commits on Oct 7, 2022

  1. Start branch

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Commits on Oct 11, 2022

  1. Start T029 talktorial on proteochemometrics (PCM)

    @gorostiolam
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  2. Add environment file

    @gorostiolam
    gorostiolam committed Oct 11, 2022
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Commits on Oct 12, 2022

  1. Completed Theory draft

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Commits on Oct 13, 2022

  1. Added first practical part to download, read and filter Papyrus dataset

    @gorostiolam
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  2. Added figure with splitting methods

    @gorostiolam
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  3. Add section to download clustalO (Win,Unix,Mac) and perform MSA

    @gorostiolam
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  4. Add libraries for installing ClustalO and visualizing MSA

    @gorostiolam
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Commits on Oct 17, 2022

  1. Update tutorial number to 032

    @gorostiolam
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  2. Add PCM and QSAR training and validation and update tutorial number t… 

    …o 032
    @gorostiolam
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Commits on Oct 18, 2022

  1. Change dependencies to use ClustalO REST API

    @gorostiolam
    gorostiolam committed Oct 18, 2022
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  2. Update code to use ClustalO REST API instead of binary download

    @gorostiolam
    gorostiolam committed Oct 18, 2022
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  3. Add ClustalO REST API client

    @gorostiolam
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  4. Add modelling interpretation and discussion. Make modelling output neat.

    @gorostiolam
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  5. Remove contribution cell and update practical list of contents

    @gorostiolam
    gorostiolam committed Oct 18, 2022
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  6. Update README file with intro from talktorial

    @gorostiolam
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  7. Update data README file

    @gorostiolam
    gorostiolam committed Oct 18, 2022
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  8. Update figures README file

    @gorostiolam
    gorostiolam committed Oct 18, 2022
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  9. Update Papyrus workflow image

    @gorostiolam
    gorostiolam committed Oct 18, 2022
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  10. Update Papyrus workflow image

    @gorostiolam
    gorostiolam committed Oct 18, 2022
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  11. Proofread grammar

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Commits on Oct 20, 2022

  1. Grammar and code revision by Olivier

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Commits on Oct 26, 2022

  1. Theory revision based on Andrea's review.

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  2. Theory contents revision based on Andrea's review.

    @gorostiolam
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Commits on Oct 27, 2022

  1. Run CI unit tests on T032 only (temporarily)

    @dominiquesydow
    dominiquesydow committed Oct 27, 2022
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  2. Add T032 to docs

    @dominiquesydow
    dominiquesydow committed Oct 27, 2022
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  3. Add pytest to tmp env

    @dominiquesydow
    dominiquesydow committed Oct 27, 2022
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  4. Update README

    @dominiquesydow
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  5. CI: Temporarily remove CLI test

    @dominiquesydow
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  6. Add output directory argument

    @gorostiolam
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  7. Add Dominique's comments

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  8. Merge remote-tracking branch 'origin/mgg-032-compound_activity_proteo… 

    …chemometrics' into mgg-032-compound_activity_proteochemometrics

# Conflicts:
#	teachopencadd/talktorials/T032_compound_activity_proteochemometrics/README.md
    @gorostiolam
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Commits on Oct 28, 2022

  1. Add more Dominique's comments

    @gorostiolam
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  2. Move clustalo.py script to /scripts folder and create README

    @gorostiolam
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  3. Resize figures

    @gorostiolam
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  4. CI: Revert back to test_env.yml and CLI tests

    @dominiquesydow
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  5. Env: Add T032 packages + tmp. comment other talktorial packages

    @dominiquesydow
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  6. Add latest Dominique comments

    @gorostiolam
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  7. Merge remote-tracking branch 'origin/mgg-032-compound_activity_proteo… 

    …chemometrics' into mgg-032-compound_activity_proteochemometrics
    @gorostiolam
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  8. Run black-nb

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  9. Automatically generate README file (and correct accents in author's s… 

    …urnames
    @gorostiolam
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  10. Improve aesthetics of outputs

    @gorostiolam
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  11. Update code for new location of ClustalO client

    @gorostiolam
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  12. Update ClustalO client check time

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Commits on Nov 7, 2022

  1. Docs config: Set language to "en" (not None)

    @dominiquesydow
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  2. README: Fix broken conda-forge badge

    @dominiquesydow
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  3. Docs: Add T032 nblink file

    @dominiquesydow
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  4. T032: Add pre-calculated alignments (ClustalO)

    @dominiquesydow
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  5. T032: Set email to None; more formatting

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Commits on Nov 8, 2022

  1. Update HTML formatting to Markdown

    @gorostiolam
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  2. Update conflicting formatting in regression evaluation metrics

    @gorostiolam
    gorostiolam committed Nov 8, 2022
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Commits on Nov 21, 2022

  1. T032: Move pip installs from env file to notebook itself

    @dominiquesydow
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  2. Satisfy black-nb

    @dominiquesydow
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  3. Regenerate READMEs

    @dominiquesydow
    dominiquesydow committed Nov 21, 2022
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  4. T032: Rerun notebook & add NBVAL_CHECK_OUTPUT checks

    @dominiquesydow
    dominiquesydow committed Nov 21, 2022
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  5. T032: Fix typos

    @dominiquesydow
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  6. T032: Remove thumbnail (talktorial has no pure png outputs we can use)

    @dominiquesydow
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  7. T032: Fix typo [skip ci]

    @dominiquesydow
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Commits on Jan 2, 2023

  1. Env: Sync env with latest master

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  2. README: Sync with master README

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  3. CI: Sync with master CI

    @dominiquesydow
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  4. Merge branch 'master' into mgg-032-compound_activity_proteochemometrics

    @dominiquesydow
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  5. CI: Drop T032 under Windows

    @dominiquesydow
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  6. CI: Add env list after T032-specific package installations (tmp)

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Commits on Mar 16, 2023

  1. Merge pull request #327 from volkamerlab/master 

    Merging recent master in mgg-032
    @jesperswillem
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Commits on May 16, 2023

  1. trigger CI

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