From 61d9191a702cc41d2118234a2499dff42dd19cc4 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Wed, 31 Jan 2024 16:06:44 +0530 Subject: [PATCH 01/15] Create devcontainer.json --- .devcontainer/devcontainer.json | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 .devcontainer/devcontainer.json diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 00000000..ad93c14a --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,5 @@ +{ + "image": "mcr.microsoft.com/devcontainers/universal:2", + "features": { + } +} From 9c47fdf17e6c02854e66af5ed807ef6d9ec5392f Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Wed, 31 Jan 2024 16:27:30 +0000 Subject: [PATCH 02/15] fixes --- new-website/.gitignore | 3 +- new-website/utils/tutorials/contents.html | 66 +++++++++++------------ new-website/utils/tutorials/title.html | 2 +- 3 files changed, 34 insertions(+), 37 deletions(-) diff --git a/new-website/.gitignore b/new-website/.gitignore index bc76c665..00337864 100644 --- a/new-website/.gitignore +++ b/new-website/.gitignore @@ -4,4 +4,5 @@ /utils/tutorials/ipynb-notebooks /utils/tutorials/storage /utils/tutorials/website-render-order -/utils/tutorials/notebooks.txt \ No newline at end of file +/utils/tutorials/notebooks.txt +__pycache__ \ No newline at end of file diff --git a/new-website/utils/tutorials/contents.html b/new-website/utils/tutorials/contents.html index ffccb884..fc69a2dd 100644 --- a/new-website/utils/tutorials/contents.html +++ b/new-website/utils/tutorials/contents.html @@ -19,7 +19,7 @@

1. Introduction To Deepchem

  • The Basic Tools of the Deep Life Sciences
  • Working With Datasets
  • An Introduction To MoleculeNet
    • -
  • Molecular Fingerprints
    • +
  • Molecular Fingerprints: Representing Molecules for Deep-Learning
  • Creating Models with TensorFlow and PyTorch
  • Introduction to Graph Convolutions
  • Going Deeper on Molecular Featurizations
    • @@ -33,89 +33,85 @@

    1. Introduction To Deepchem

  • Training a Generative Adversarial Network on MNIST
  • Advanced model training using hyperopt
  • Introduction to Gaussian Processes
    • -
  • PytorchLightning Integration
    • +
  • Pytorch Lightning Integration for DeepChem Models
  • -

    2. Molecular Machine Learning

    +

    2. More Molecular Machine Learning

      -
    1. Molecular Fingerprints -
    2. Going Deeper on Molecular Featurizations -
    3. Learning Unsupervised Embeddings for Molecules -
    4. Atomic Contributions for Molecules -
    5. Interactive Model Evaluation with Trident Chemwidgets -
    6. Transfer Learning With ChemBERTa Transformers -
    7. Training a Normalizing Flow on QM9 -
    8. Large Scale Chemical Screens -
    9. Introduction to Molecular Attention Transformer -
    10. Generating molecules with MolGAN -
    11. Introduction to GROVER +
    12. Going Deeper on Molecular Featurizations
      13. +
    13. Learning Unsupervised Embeddings for Molecules
      14. +
    14. Atomic Contributions for Molecules
      15. +
    15. Interactive Model Evaluation with Trident Chemwidgets
      16. +
    16. Transfer Learning With ChemBERTa Transformers
      17. +
    17. Training a Normalizing Flow on QM9
      18. +
    18. Large Scale Chemical Screens
      19. +
    19. Introduction to Molecular Attention Transformer
      20. +
    20. Generating molecules with MolGAN
      21. +
    21. Introduction to GROVER

  • 3. Modeling Proteins

      -
    1. Protein Deep Learning +
    2. Protein Deep Learning

  • 4. Protein Ligand Modeling

      -
    1. Modeling Protein Ligand Interactions -
    2. Modeling Protein Ligand Interactions With Atomic Convolutions -
    3. DeepChemXAlphafold +
    4. Modeling Protein Ligand Interactions
      5. +
    5. Applications of DeepChem with Alphafold: Docking and protein-ligand interaction from protein sequence

  • 5. Quantum Chemistry

      -
    1. Exploring Quantum Chemistry with GDB1k -
    2. DeepQMC tutorial -
    3. Training an Exchange Correlation Functional using Deepchem +
    4. Exploring Quantum Chemistry with GDB1k
      5. +
    5. DeepQMC integration with DeepChem tutorial
      6. +
    6. Training an Exchange Correlation Functional using Deepchem

  • 6. Bioinformatics

      -
    1. Introduction to Bioinformatics -
    2. Multisequence Alignments -
    3. Deep probabilistic analysis of single-cell omics data +
    4. Introduction to Bioinformatics
      5. +
    5. Multisequence Alignments
      6. +
    6. Deep probabilistic analysis of single-cell omics data

  • 7. Material Sciences

      -
    1. Introduction To Material Science +
    2. Introduction To Material Science

  • 8. Machine Learning Methods

      -
    1. Using Reinforcement Learning to Play Pong -
    2. Introduction to Model Interpretability -
    3. Uncertainty In Deep Learning +
    4. Using Reinforcement Learning to Play Pong
      5. +
    5. Introduction to Model Interpretability
      6. +
    6. Uncertainty In Deep Learning

  • 9. Deep Differential Equations

      -
    1. Physics Informed Neural Networks -
    2. Introducing JaxModel and PINNModel -
    3. About Neural ODE : Using Torchdiffeq with Deepchem +
    4. Physics Informed Neural Networks
      5. +
    5. Introducing JaxModel and PINNModel
      6. +
    6. About Neural ODE : Using Torchdiffeq with Deepchem

  • 10. Equivariance

      -
    1. Introduction to Equivariance -
    2. Modeling Protein Ligand Interactions With Atomic Convolutions -
    3. DeepChemXAlphafold +
    4. Introduction to Equivariance

  • 11. Olfaction

      -
    1. Predict Multi Label Odor Descriptors using OpenPOM +
    2. Predict Multi Label Odor Descriptors using OpenPOM
    • diff --git a/new-website/utils/tutorials/title.html b/new-website/utils/tutorials/title.html index 74910a53..c0d81af9 100644 --- a/new-website/utils/tutorials/title.html +++ b/new-website/utils/tutorials/title.html @@ -21,7 +21,7 @@

    The DeepChem Book

    - Democratizing Deep-Learning for Drug Discovery Quantum Chemistry, Materials Science and Biology + Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

    Bharath Ramsundar From 7905f702fdfa126209c11a969173b649da87051e Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Wed, 31 Jan 2024 16:28:21 +0000 Subject: [PATCH 03/15] build --- new-website/utils/tutorials/build_pdf_book.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/new-website/utils/tutorials/build_pdf_book.py b/new-website/utils/tutorials/build_pdf_book.py index e289939f..abe67414 100644 --- a/new-website/utils/tutorials/build_pdf_book.py +++ b/new-website/utils/tutorials/build_pdf_book.py @@ -48,7 +48,10 @@ def html_to_pdf(): chapter = pd.read_csv(INFO_PATH + "-".join(i)) for j in chapter["File Name"]: print(i, j) - pdfkit.from_file(DATA_PATH + j[:-5] + "html", PDF_PATH + j[:-5] + "pdf") + try: + pdfkit.from_file(DATA_PATH + j[:-5] + "html", PDF_PATH + j[:-5] + "pdf") + except: + pass def merge_pdf(): """Merges the compiled PDFs.""" @@ -86,8 +89,8 @@ def compile_information_pages(): pdfkit.from_file('acknowledgement.html', 'storage/acknowledgement.pdf') if __name__ == "__main__": - os.system("mkdir " + PDF_PATH) - html_to_pdf() + #os.system("mkdir " + PDF_PATH) + #html_to_pdf() merge_pdf() - compile_information_pages() - merge_pdf_pages(['storage/title.pdf', 'storage/acknowledgement.pdf', 'storage/contents.pdf', 'storage/full_pdf.pdf']) + #compile_information_pages() + #merge_pdf_pages(['storage/title.pdf', 'storage/acknowledgement.pdf', 'storage/contents.pdf', 'storage/full_pdf.pdf']) From acbf2a35bcdc190605d4398aa2479ef656012647 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Wed, 31 Jan 2024 16:30:23 +0000 Subject: [PATCH 04/15] Revert "build" This reverts commit 7905f702fdfa126209c11a969173b649da87051e. --- new-website/utils/tutorials/build_pdf_book.py | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/new-website/utils/tutorials/build_pdf_book.py b/new-website/utils/tutorials/build_pdf_book.py index abe67414..e289939f 100644 --- a/new-website/utils/tutorials/build_pdf_book.py +++ b/new-website/utils/tutorials/build_pdf_book.py @@ -48,10 +48,7 @@ def html_to_pdf(): chapter = pd.read_csv(INFO_PATH + "-".join(i)) for j in chapter["File Name"]: print(i, j) - try: - pdfkit.from_file(DATA_PATH + j[:-5] + "html", PDF_PATH + j[:-5] + "pdf") - except: - pass + pdfkit.from_file(DATA_PATH + j[:-5] + "html", PDF_PATH + j[:-5] + "pdf") def merge_pdf(): """Merges the compiled PDFs.""" @@ -89,8 +86,8 @@ def compile_information_pages(): pdfkit.from_file('acknowledgement.html', 'storage/acknowledgement.pdf') if __name__ == "__main__": - #os.system("mkdir " + PDF_PATH) - #html_to_pdf() + os.system("mkdir " + PDF_PATH) + html_to_pdf() merge_pdf() - #compile_information_pages() - #merge_pdf_pages(['storage/title.pdf', 'storage/acknowledgement.pdf', 'storage/contents.pdf', 'storage/full_pdf.pdf']) + compile_information_pages() + merge_pdf_pages(['storage/title.pdf', 'storage/acknowledgement.pdf', 'storage/contents.pdf', 'storage/full_pdf.pdf']) From 8457b3af8ffdef00c040349f96a24724361dfed9 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Wed, 31 Jan 2024 16:30:44 +0000 Subject: [PATCH 05/15] Revert "fixes" This reverts commit 9c47fdf17e6c02854e66af5ed807ef6d9ec5392f. --- new-website/.gitignore | 3 +- new-website/utils/tutorials/contents.html | 66 ++++++++++++----------- new-website/utils/tutorials/title.html | 2 +- 3 files changed, 37 insertions(+), 34 deletions(-) diff --git a/new-website/.gitignore b/new-website/.gitignore index 00337864..bc76c665 100644 --- a/new-website/.gitignore +++ b/new-website/.gitignore @@ -4,5 +4,4 @@ /utils/tutorials/ipynb-notebooks /utils/tutorials/storage /utils/tutorials/website-render-order -/utils/tutorials/notebooks.txt -__pycache__ \ No newline at end of file +/utils/tutorials/notebooks.txt \ No newline at end of file diff --git a/new-website/utils/tutorials/contents.html b/new-website/utils/tutorials/contents.html index fc69a2dd..ffccb884 100644 --- a/new-website/utils/tutorials/contents.html +++ b/new-website/utils/tutorials/contents.html @@ -19,7 +19,7 @@

    1. Introduction To Deepchem

  • The Basic Tools of the Deep Life Sciences
  • Working With Datasets
  • An Introduction To MoleculeNet
    • -
  • Molecular Fingerprints: Representing Molecules for Deep-Learning
    • +
  • Molecular Fingerprints
  • Creating Models with TensorFlow and PyTorch
  • Introduction to Graph Convolutions
  • Going Deeper on Molecular Featurizations
    • @@ -33,85 +33,89 @@

    1. Introduction To Deepchem

  • Training a Generative Adversarial Network on MNIST
  • Advanced model training using hyperopt
  • Introduction to Gaussian Processes
    • -
  • Pytorch Lightning Integration for DeepChem Models
    • +
  • PytorchLightning Integration
  • -

    2. More Molecular Machine Learning

    +

    2. Molecular Machine Learning

      -
    1. Going Deeper on Molecular Featurizations
      2. -
    2. Learning Unsupervised Embeddings for Molecules
      3. -
    3. Atomic Contributions for Molecules
      4. -
    4. Interactive Model Evaluation with Trident Chemwidgets
      5. -
    5. Transfer Learning With ChemBERTa Transformers
      6. -
    6. Training a Normalizing Flow on QM9
      7. -
    7. Large Scale Chemical Screens
      8. -
    8. Introduction to Molecular Attention Transformer
      9. -
    9. Generating molecules with MolGAN
      10. -
    10. Introduction to GROVER
      11. +
    11. Molecular Fingerprints +
    12. Going Deeper on Molecular Featurizations +
    13. Learning Unsupervised Embeddings for Molecules +
    14. Atomic Contributions for Molecules +
    15. Interactive Model Evaluation with Trident Chemwidgets +
    16. Transfer Learning With ChemBERTa Transformers +
    17. Training a Normalizing Flow on QM9 +
    18. Large Scale Chemical Screens +
    19. Introduction to Molecular Attention Transformer +
    20. Generating molecules with MolGAN +
    21. Introduction to GROVER

  • 3. Modeling Proteins

      -
    1. Protein Deep Learning
      2. +
    2. Protein Deep Learning

  • 4. Protein Ligand Modeling

      -
    1. Modeling Protein Ligand Interactions
      2. -
    2. Applications of DeepChem with Alphafold: Docking and protein-ligand interaction from protein sequence
      3. +
    3. Modeling Protein Ligand Interactions +
    4. Modeling Protein Ligand Interactions With Atomic Convolutions +
    5. DeepChemXAlphafold

  • 5. Quantum Chemistry

      -
    1. Exploring Quantum Chemistry with GDB1k
      2. -
    2. DeepQMC integration with DeepChem tutorial
      3. -
    3. Training an Exchange Correlation Functional using Deepchem
      4. +
    4. Exploring Quantum Chemistry with GDB1k +
    5. DeepQMC tutorial +
    6. Training an Exchange Correlation Functional using Deepchem

  • 6. Bioinformatics

      -
    1. Introduction to Bioinformatics
      2. -
    2. Multisequence Alignments
      3. -
    3. Deep probabilistic analysis of single-cell omics data
      4. +
    4. Introduction to Bioinformatics +
    5. Multisequence Alignments +
    6. Deep probabilistic analysis of single-cell omics data

  • 7. Material Sciences

      -
    1. Introduction To Material Science
      2. +
    2. Introduction To Material Science

  • 8. Machine Learning Methods

      -
    1. Using Reinforcement Learning to Play Pong
      2. -
    2. Introduction to Model Interpretability
      3. -
    3. Uncertainty In Deep Learning
      4. +
    4. Using Reinforcement Learning to Play Pong +
    5. Introduction to Model Interpretability +
    6. Uncertainty In Deep Learning

  • 9. Deep Differential Equations

      -
    1. Physics Informed Neural Networks
      2. -
    2. Introducing JaxModel and PINNModel
      3. -
    3. About Neural ODE : Using Torchdiffeq with Deepchem
      4. +
    4. Physics Informed Neural Networks +
    5. Introducing JaxModel and PINNModel +
    6. About Neural ODE : Using Torchdiffeq with Deepchem

  • 10. Equivariance

      -
    1. Introduction to Equivariance
      2. +
    2. Introduction to Equivariance +
    3. Modeling Protein Ligand Interactions With Atomic Convolutions +
    4. DeepChemXAlphafold

  • 11. Olfaction

      -
    1. Predict Multi Label Odor Descriptors using OpenPOM
      2. +
    2. Predict Multi Label Odor Descriptors using OpenPOM
    • diff --git a/new-website/utils/tutorials/title.html b/new-website/utils/tutorials/title.html index c0d81af9..74910a53 100644 --- a/new-website/utils/tutorials/title.html +++ b/new-website/utils/tutorials/title.html @@ -21,7 +21,7 @@

    The DeepChem Book

    - Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology + Democratizing Deep-Learning for Drug Discovery Quantum Chemistry, Materials Science and Biology

    Bharath Ramsundar From 2736ebea34e94b763dffd2db55793ba0a03089ae Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Wed, 31 Jan 2024 16:31:50 +0000 Subject: [PATCH 06/15] Reapply "fixes" This reverts commit 8457b3af8ffdef00c040349f96a24724361dfed9. --- new-website/.gitignore | 3 +- new-website/utils/tutorials/contents.html | 66 +++++++++++------------ new-website/utils/tutorials/title.html | 2 +- 3 files changed, 34 insertions(+), 37 deletions(-) diff --git a/new-website/.gitignore b/new-website/.gitignore index bc76c665..00337864 100644 --- a/new-website/.gitignore +++ b/new-website/.gitignore @@ -4,4 +4,5 @@ /utils/tutorials/ipynb-notebooks /utils/tutorials/storage /utils/tutorials/website-render-order -/utils/tutorials/notebooks.txt \ No newline at end of file +/utils/tutorials/notebooks.txt +__pycache__ \ No newline at end of file diff --git a/new-website/utils/tutorials/contents.html b/new-website/utils/tutorials/contents.html index ffccb884..fc69a2dd 100644 --- a/new-website/utils/tutorials/contents.html +++ b/new-website/utils/tutorials/contents.html @@ -19,7 +19,7 @@

    1. Introduction To Deepchem

  • The Basic Tools of the Deep Life Sciences
  • Working With Datasets
  • An Introduction To MoleculeNet
    • -
  • Molecular Fingerprints
    • +
  • Molecular Fingerprints: Representing Molecules for Deep-Learning
  • Creating Models with TensorFlow and PyTorch
  • Introduction to Graph Convolutions
  • Going Deeper on Molecular Featurizations
    • @@ -33,89 +33,85 @@

    1. Introduction To Deepchem

  • Training a Generative Adversarial Network on MNIST
  • Advanced model training using hyperopt
  • Introduction to Gaussian Processes
    • -
  • PytorchLightning Integration
    • +
  • Pytorch Lightning Integration for DeepChem Models
  • -

    2. Molecular Machine Learning

    +

    2. More Molecular Machine Learning

      -
    1. Molecular Fingerprints -
    2. Going Deeper on Molecular Featurizations -
    3. Learning Unsupervised Embeddings for Molecules -
    4. Atomic Contributions for Molecules -
    5. Interactive Model Evaluation with Trident Chemwidgets -
    6. Transfer Learning With ChemBERTa Transformers -
    7. Training a Normalizing Flow on QM9 -
    8. Large Scale Chemical Screens -
    9. Introduction to Molecular Attention Transformer -
    10. Generating molecules with MolGAN -
    11. Introduction to GROVER +
    12. Going Deeper on Molecular Featurizations
      13. +
    13. Learning Unsupervised Embeddings for Molecules
      14. +
    14. Atomic Contributions for Molecules
      15. +
    15. Interactive Model Evaluation with Trident Chemwidgets
      16. +
    16. Transfer Learning With ChemBERTa Transformers
      17. +
    17. Training a Normalizing Flow on QM9
      18. +
    18. Large Scale Chemical Screens
      19. +
    19. Introduction to Molecular Attention Transformer
      20. +
    20. Generating molecules with MolGAN
      21. +
    21. Introduction to GROVER

  • 3. Modeling Proteins

      -
    1. Protein Deep Learning +
    2. Protein Deep Learning

  • 4. Protein Ligand Modeling

      -
    1. Modeling Protein Ligand Interactions -
    2. Modeling Protein Ligand Interactions With Atomic Convolutions -
    3. DeepChemXAlphafold +
    4. Modeling Protein Ligand Interactions
      5. +
    5. Applications of DeepChem with Alphafold: Docking and protein-ligand interaction from protein sequence

  • 5. Quantum Chemistry

      -
    1. Exploring Quantum Chemistry with GDB1k -
    2. DeepQMC tutorial -
    3. Training an Exchange Correlation Functional using Deepchem +
    4. Exploring Quantum Chemistry with GDB1k
      5. +
    5. DeepQMC integration with DeepChem tutorial
      6. +
    6. Training an Exchange Correlation Functional using Deepchem

  • 6. Bioinformatics

      -
    1. Introduction to Bioinformatics -
    2. Multisequence Alignments -
    3. Deep probabilistic analysis of single-cell omics data +
    4. Introduction to Bioinformatics
      5. +
    5. Multisequence Alignments
      6. +
    6. Deep probabilistic analysis of single-cell omics data

  • 7. Material Sciences

      -
    1. Introduction To Material Science +
    2. Introduction To Material Science

  • 8. Machine Learning Methods

      -
    1. Using Reinforcement Learning to Play Pong -
    2. Introduction to Model Interpretability -
    3. Uncertainty In Deep Learning +
    4. Using Reinforcement Learning to Play Pong
      5. +
    5. Introduction to Model Interpretability
      6. +
    6. Uncertainty In Deep Learning

  • 9. Deep Differential Equations

      -
    1. Physics Informed Neural Networks -
    2. Introducing JaxModel and PINNModel -
    3. About Neural ODE : Using Torchdiffeq with Deepchem +
    4. Physics Informed Neural Networks
      5. +
    5. Introducing JaxModel and PINNModel
      6. +
    6. About Neural ODE : Using Torchdiffeq with Deepchem

  • 10. Equivariance

      -
    1. Introduction to Equivariance -
    2. Modeling Protein Ligand Interactions With Atomic Convolutions -
    3. DeepChemXAlphafold +
    4. Introduction to Equivariance

  • 11. Olfaction

      -
    1. Predict Multi Label Odor Descriptors using OpenPOM +
    2. Predict Multi Label Odor Descriptors using OpenPOM
    • diff --git a/new-website/utils/tutorials/title.html b/new-website/utils/tutorials/title.html index 74910a53..c0d81af9 100644 --- a/new-website/utils/tutorials/title.html +++ b/new-website/utils/tutorials/title.html @@ -21,7 +21,7 @@

    The DeepChem Book

    - Democratizing Deep-Learning for Drug Discovery Quantum Chemistry, Materials Science and Biology + Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

    Bharath Ramsundar From 9a61736fb272e449405cbf94826ff18e805ff67c Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Wed, 31 Jan 2024 16:37:51 +0000 Subject: [PATCH 07/15] Reapply "build" This reverts commit acbf2a35bcdc190605d4398aa2479ef656012647. --- new-website/utils/tutorials/build_pdf_book.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/new-website/utils/tutorials/build_pdf_book.py b/new-website/utils/tutorials/build_pdf_book.py index e289939f..abe67414 100644 --- a/new-website/utils/tutorials/build_pdf_book.py +++ b/new-website/utils/tutorials/build_pdf_book.py @@ -48,7 +48,10 @@ def html_to_pdf(): chapter = pd.read_csv(INFO_PATH + "-".join(i)) for j in chapter["File Name"]: print(i, j) - pdfkit.from_file(DATA_PATH + j[:-5] + "html", PDF_PATH + j[:-5] + "pdf") + try: + pdfkit.from_file(DATA_PATH + j[:-5] + "html", PDF_PATH + j[:-5] + "pdf") + except: + pass def merge_pdf(): """Merges the compiled PDFs.""" @@ -86,8 +89,8 @@ def compile_information_pages(): pdfkit.from_file('acknowledgement.html', 'storage/acknowledgement.pdf') if __name__ == "__main__": - os.system("mkdir " + PDF_PATH) - html_to_pdf() + #os.system("mkdir " + PDF_PATH) + #html_to_pdf() merge_pdf() - compile_information_pages() - merge_pdf_pages(['storage/title.pdf', 'storage/acknowledgement.pdf', 'storage/contents.pdf', 'storage/full_pdf.pdf']) + #compile_information_pages() + #merge_pdf_pages(['storage/title.pdf', 'storage/acknowledgement.pdf', 'storage/contents.pdf', 'storage/full_pdf.pdf']) From 7a2e7ff8a1cfa7893924c847efcf6bbf718f03a2 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Wed, 31 Jan 2024 16:39:32 +0000 Subject: [PATCH 08/15] ignore revert --- new-website/.gitignore | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/new-website/.gitignore b/new-website/.gitignore index 00337864..bc76c665 100644 --- a/new-website/.gitignore +++ b/new-website/.gitignore @@ -4,5 +4,4 @@ /utils/tutorials/ipynb-notebooks /utils/tutorials/storage /utils/tutorials/website-render-order -/utils/tutorials/notebooks.txt -__pycache__ \ No newline at end of file +/utils/tutorials/notebooks.txt \ No newline at end of file From 550f22fc68178fa1e91594aac0700e52336fcc9d Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Wed, 31 Jan 2024 16:57:53 +0000 Subject: [PATCH 09/15] citation --- .../utils/tutorials/acknowledgement.md | 50 ++++++++++++++++++- 1 file changed, 48 insertions(+), 2 deletions(-) diff --git a/new-website/utils/tutorials/acknowledgement.md b/new-website/utils/tutorials/acknowledgement.md index 448e8843..29c15eaa 100644 --- a/new-website/utils/tutorials/acknowledgement.md +++ b/new-website/utils/tutorials/acknowledgement.md @@ -1,2 +1,48 @@ -# Acknowledgement -We acknowledge the DeepChem community for their contributions and support. \ No newline at end of file + + + +

    Acknowledgement

    +

    + We acknowledge the DeepChem community for their contributions and support. +

    +

    +

    Citing This Book:

    +
    + @manual{ +
    + title={The DeepChem Book}, +
    + organization={DeepChem}, +
    + author={Ramsundar, Bharath and DeepChem Community}, +
    + howpublished = {\url{https://deepchem.io/tutorials}}, +
    + year={2024}, +
    + } +

    + + \ No newline at end of file From 08027a240f56cd936852de2fc451a5e1d8585fe3 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Fri, 2 Feb 2024 13:37:57 +0000 Subject: [PATCH 10/15] acknowledgement --- .../utils/tutorials/acknowledgement.html | 27 +++++++ .../utils/tutorials/acknowledgement.md | 48 ------------- new-website/utils/tutorials/contents.md | 71 ------------------- 3 files changed, 27 insertions(+), 119 deletions(-) delete mode 100644 new-website/utils/tutorials/acknowledgement.md delete mode 100644 new-website/utils/tutorials/contents.md diff --git a/new-website/utils/tutorials/acknowledgement.html b/new-website/utils/tutorials/acknowledgement.html index 4c82554a..29c15eaa 100644 --- a/new-website/utils/tutorials/acknowledgement.html +++ b/new-website/utils/tutorials/acknowledgement.html @@ -6,16 +6,43 @@ padding-right: 80px; font-size: 50px; } + h2 { + margin-top: 250px; + padding-right: 80px; + font-size: 20px; + } .general { padding-left: 80px; padding-right: 80px; font-size: 20px; } + .citation { + padding-left: 80px; + padding-right: 80px; + font-size: 15px; + }

    Acknowledgement

    We acknowledge the DeepChem community for their contributions and support.

    +

    +

    Citing This Book:

    +
    + @manual{ +
    + title={The DeepChem Book}, +
    + organization={DeepChem}, +
    + author={Ramsundar, Bharath and DeepChem Community}, +
    + howpublished = {\url{https://deepchem.io/tutorials}}, +
    + year={2024}, +
    + } +

    \ No newline at end of file diff --git a/new-website/utils/tutorials/acknowledgement.md b/new-website/utils/tutorials/acknowledgement.md deleted file mode 100644 index 29c15eaa..00000000 --- a/new-website/utils/tutorials/acknowledgement.md +++ /dev/null @@ -1,48 +0,0 @@ - - - -

    Acknowledgement

    -

    - We acknowledge the DeepChem community for their contributions and support. -

    -

    -

    Citing This Book:

    -
    - @manual{ -
    - title={The DeepChem Book}, -
    - organization={DeepChem}, -
    - author={Ramsundar, Bharath and DeepChem Community}, -
    - howpublished = {\url{https://deepchem.io/tutorials}}, -
    - year={2024}, -
    - } -

    - - \ No newline at end of file diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md deleted file mode 100644 index 8513475f..00000000 --- a/new-website/utils/tutorials/contents.md +++ /dev/null @@ -1,71 +0,0 @@ -# Contents - -### 1. Introduction To Deepchem -1. The Basic Tools of the Deep Life Sciences -2. Working With Datasets -3. An Introduction To MoleculeNet -4. Molecular Fingerprints -5. Creating Models with TensorFlow and PyTorch -6. Introduction to Graph Convolutions -7. Going Deeper on Molecular Featurizations -8. Working With Splitters -9. Advanced Model Training -10. Creating a high fidelity model from experimental data -11. Putting Multitask Learning to Work -12. Modeling Protein Ligand Interactions -13. Modeling Protein Ligand Interactions With Atomic Convolutions -14. Conditional Generative Adversarial Networks -15. Training a Generative Adversarial Network on MNIST -16. Advanced model training using hyperopt -17. Introduction to Gaussian Processes -18. PytorchLightning Integration - -### 2. Molecular Machine Learning -1. Molecular Fingerprints -2. Going Deeper on Molecular Featurizations -3. Learning Unsupervised Embeddings for Molecules -4. Atomic Contributions for Molecules -5. Interactive Model Evaluation with Trident Chemwidgets -6. Transfer Learning With ChemBERTa Transformers -7. Training a Normalizing Flow on QM9 -8. Large Scale Chemical Screens -9. Introduction to Molecular Attention Transformer -10. Generating molecules with MolGAN -11. Introduction to GROVER - -### 3. Modeling Proteins -1. Protein Deep Learning - -### 4. Protein Ligand Modeling -1. Modeling Protein Ligand Interactions -2. Modeling Protein Ligand Interactions With Atomic Convolutions -3. DeepChemXAlphafold - -### 5. Quantum Chemistry -1. Exploring Quantum Chemistry with GDB1k -2. DeepQMC tutorial -3. Training an Exchange Correlation Functional using Deepchem - -### 6. Bioinformatics -1. Introduction to Bioinformatics -2. Multisequence Alignments -3. Deep probabilistic analysis of single-cell omics data - -### 7. Material Sciences -1. Introduction To Material Science - -### 8. Machine Learning Methods -1. Using Reinforcement Learning to Play Pong -2. Introduction to Model Interpretability -3. Uncertainty In Deep Learning - -### 9. Deep Differential Equations -1. Physics Informed Neural Networks -2. Introducing JaxModel and PINNModel -3. About Neural ODE : Using Torchdiffeq with Deepchem - -### 10. Equivariance -1. Introduction to Equivariance - -### 11. Olfaction -1. Predict Multi Label Odor Descriptors using OpenPOM \ No newline at end of file From 8ef3b129ba2e4d1626243ed4cebdd4968ef3e64e Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Mon, 12 Feb 2024 16:12:16 +0000 Subject: [PATCH 11/15] markdown revert --- .../utils/tutorials/acknowledgement.md | 13 ++++ new-website/utils/tutorials/build_pdf_book.py | 8 +-- new-website/utils/tutorials/contents.md | 70 +++++++++++++++++++ 3 files changed, 87 insertions(+), 4 deletions(-) create mode 100644 new-website/utils/tutorials/acknowledgement.md create mode 100644 new-website/utils/tutorials/contents.md diff --git a/new-website/utils/tutorials/acknowledgement.md b/new-website/utils/tutorials/acknowledgement.md new file mode 100644 index 00000000..97b93ee7 --- /dev/null +++ b/new-website/utils/tutorials/acknowledgement.md @@ -0,0 +1,13 @@ +# Acknowledgement + +We acknowledge the DeepChem community for their contributions and support. + +Citing This Book: + +@manual{ +title={The DeepChem Book}, +organization={DeepChem}, +author={Ramsundar, Bharath and DeepChem Community}, +howpublished = {\url{https://deepchem.io/tutorials}}, +year={2024}, +} diff --git a/new-website/utils/tutorials/build_pdf_book.py b/new-website/utils/tutorials/build_pdf_book.py index abe67414..8c1cb400 100644 --- a/new-website/utils/tutorials/build_pdf_book.py +++ b/new-website/utils/tutorials/build_pdf_book.py @@ -89,8 +89,8 @@ def compile_information_pages(): pdfkit.from_file('acknowledgement.html', 'storage/acknowledgement.pdf') if __name__ == "__main__": - #os.system("mkdir " + PDF_PATH) - #html_to_pdf() + os.system("mkdir " + PDF_PATH) + html_to_pdf() merge_pdf() - #compile_information_pages() - #merge_pdf_pages(['storage/title.pdf', 'storage/acknowledgement.pdf', 'storage/contents.pdf', 'storage/full_pdf.pdf']) + compile_information_pages() + merge_pdf_pages(['storage/title.pdf', 'storage/acknowledgement.pdf', 'storage/contents.pdf', 'storage/full_pdf.pdf']) diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md new file mode 100644 index 00000000..ed3163c0 --- /dev/null +++ b/new-website/utils/tutorials/contents.md @@ -0,0 +1,70 @@ + +### 1. Introduction To Deepchem +1. The Basic Tools of the Deep Life Sciences +2. Working With Datasets +3. An Introduction To MoleculeNet +4. Molecular Fingerprints +5. Creating Models with TensorFlow and PyTorch +6. Introduction to Graph Convolutions +7. Going Deeper on Molecular Featurizations +8. Working With Splitters +9. Advanced Model Training +10. Creating a high fidelity model from experimental data +11. Putting Multitask Learning to Work +12. Modeling Protein Ligand Interactions +13. Modeling Protein Ligand Interactions With Atomic Convolutions +14. Conditional Generative Adversarial Networks +15. Training a Generative Adversarial Network on MNIST +16. Advanced model training using hyperopt +17. Introduction to Gaussian Processes +18. PytorchLightning Integration + +### 2. Molecular Machine Learning +1. Molecular Fingerprints +2. Going Deeper on Molecular Featurizations +3. Learning Unsupervised Embeddings for Molecules +4. Atomic Contributions for Molecules +5. Interactive Model Evaluation with Trident Chemwidgets +6. Transfer Learning With ChemBERTa Transformers +7. Training a Normalizing Flow on QM9 +8. Large Scale Chemical Screens +9. Introduction to Molecular Attention Transformer +10. Generating molecules with MolGAN +11. Introduction to GROVER + +### 3. Modeling Proteins +1. Protein Deep Learning + +### 4. Protein Ligand Modeling +1. Modeling Protein Ligand Interactions +2. Modeling Protein Ligand Interactions With Atomic Convolutions +3. DeepChemXAlphafold + +### 5. Quantum Chemistry +1. Exploring Quantum Chemistry with GDB1k +2. DeepQMC tutorial +3. Training an Exchange Correlation Functional using Deepchem + +### 6. Bioinformatics +1. Introduction to Bioinformatics +2. Multisequence Alignments +3. Deep probabilistic analysis of single-cell omics data + +### 7. Material Sciences +1. Introduction To Material Science + +### 8. Machine Learning Methods +1. Using Reinforcement Learning to Play Pong +2. Introduction to Model Interpretability +3. Uncertainty In Deep Learning + +### 9. Deep Differential Equations +1. Physics Informed Neural Networks +2. Introducing JaxModel and PINNModel +3. About Neural ODE : Using Torchdiffeq with Deepchem + +### 10. Equivariance +1. Introduction to Equivariance + +### 11. Olfaction +1. Predict Multi Label Odor Descriptors using OpenPOM \ No newline at end of file From 60c7457384b904a74804207c3841625e4c21dc2f Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Mon, 12 Feb 2024 21:43:26 +0530 Subject: [PATCH 12/15] Update contents.md --- new-website/utils/tutorials/contents.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md index ed3163c0..6a9f8afd 100644 --- a/new-website/utils/tutorials/contents.md +++ b/new-website/utils/tutorials/contents.md @@ -1,3 +1,4 @@ +# Contents ### 1. Introduction To Deepchem 1. The Basic Tools of the Deep Life Sciences @@ -67,4 +68,4 @@ 1. Introduction to Equivariance ### 11. Olfaction -1. Predict Multi Label Odor Descriptors using OpenPOM \ No newline at end of file +1. Predict Multi Label Odor Descriptors using OpenPOM From 40e4a97177c53cd09a6eec677a946ebb6db7f3c1 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Tue, 13 Feb 2024 14:29:23 +0000 Subject: [PATCH 13/15] ci --- .github/workflows/build_check_deploy_gh_pages.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/build_check_deploy_gh_pages.yml b/.github/workflows/build_check_deploy_gh_pages.yml index b9f9baf8..2b852969 100644 --- a/.github/workflows/build_check_deploy_gh_pages.yml +++ b/.github/workflows/build_check_deploy_gh_pages.yml @@ -60,6 +60,13 @@ jobs: npm run lint npm run export + - name: generate and export book + run: | + cd new-website + cd utils/tutorials + python3 build_pdf_book.py + aws s3 cp ./dist/ s3://prithvi-docs/pychiron/${version}/ --recursive --follow-symlinks + # Run the deploy action only if the push is to the main branch - name: Deploy 🚀 if: ${{ github.ref == 'refs/heads/main' }} From 9dc31e6a8634a3735177728241c0e426c250a107 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Tue, 13 Feb 2024 14:35:03 +0000 Subject: [PATCH 14/15] revert ci --- .github/workflows/build_check_deploy_gh_pages.yml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/.github/workflows/build_check_deploy_gh_pages.yml b/.github/workflows/build_check_deploy_gh_pages.yml index 2b852969..b9f9baf8 100644 --- a/.github/workflows/build_check_deploy_gh_pages.yml +++ b/.github/workflows/build_check_deploy_gh_pages.yml @@ -60,13 +60,6 @@ jobs: npm run lint npm run export - - name: generate and export book - run: | - cd new-website - cd utils/tutorials - python3 build_pdf_book.py - aws s3 cp ./dist/ s3://prithvi-docs/pychiron/${version}/ --recursive --follow-symlinks - # Run the deploy action only if the push is to the main branch - name: Deploy 🚀 if: ${{ github.ref == 'refs/heads/main' }} From 5b1fa8030ac063f148e609b8c0a02f78e7ffd3b8 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Tue, 13 Feb 2024 14:41:05 +0000 Subject: [PATCH 15/15] location change --- .../tutorials/__pycache__/utils.cpython-310.pyc | Bin 0 -> 2298 bytes new-website/utils/tutorials/build_pdf_book.py | 6 +++--- 2 files changed, 3 insertions(+), 3 deletions(-) create mode 100644 new-website/utils/tutorials/__pycache__/utils.cpython-310.pyc diff --git a/new-website/utils/tutorials/__pycache__/utils.cpython-310.pyc b/new-website/utils/tutorials/__pycache__/utils.cpython-310.pyc new file mode 100644 index 0000000000000000000000000000000000000000..7eb6c2a675cf27cc54b07ea1026d06e5154fa30e GIT binary patch literal 2298 zcma)7U2o(x6pfQiXF6@CWp_&{5|V|4#AumzwQp2>mnXCW)PfMxPD2{I9d9#9YC9cu zluAg;4{0Cy3;dM4A|CdIH(rW_ICiEVGtk|76nkvn+-u)+?n%0^&~(uLc=tE{Rl{+9 zHIpjLbR9;R83x-P4+8H^sQvj#?=&9WxO8gsXu_S`6FZl;M2 zMWX0QC`FnpnrjgYeM%4VB+??q&Os`v?sKYhok|hLR7Fx`S~Z(n{5Thq4|sxE=T>V{ zG|8JUaV+QSh?rsAY8YqmY~oQrp*wWW2p+d^zI1xcGp``$PT`#sMlSFp&hdHE|O~!zfB6 z6Uiafso4^eDsC^CCH{;RBg~_Lg^i)WzQ~{+kc0QnN{O> zpHqe4oQ>UWah=O#!dK-esLaOxuANSLt!!wRF#3f|k9a~wf*@IFt`{TZILamIyfm4Y zrfb*AnJ~+E!pfS;fN)upVRFbzFXl<La>Mp9lZsV|l@zrf$!JfS&q9o6Mb>uwU zU2d)qQ+cGaFyd;Rah^qeK3F>xx}Wc_iF7^T!_JWJE1~(ip_E#`qK~TPYuRbpLXwf~ zsEQ!x;8?wh&R_INgFGOQ&@YiDaesFI@jcnX)&!Rf{SBWim!9HJ;hftNxNy&iCg(27 zz%9sycSZ`r{8i`NyKv-+Sz7_?3IcZ2Mt|GfqYzHG$zVti#R-xMGz~9oZbOtuEEp9G zR2K*0{=|Tn2}+E;R-}lkm>iA`f_Fx_i!b(2!OfvI%%La3-9-5B1q@3s2`x!5TG-ip z()lp#j6UylgI+}#zpP81#Q?Z;C3vFp{jx3;69BpG%2}klyEJ_QOOC2rfI<0Cr@^$% zd)QD$*XCO-G7pG-B9}3}8(O1o2HFdNW?_XCRIpBiYychu>yQ4tKd|3#JwpNM{(b9x zI?wlkbt=ZILCt0SdNgl58Z1ZkoxR=RuIfos7o*w^4SJ8;KI$Dz&g26u%7^I6TAU8K zyuxs{!UqAT!F%HxJZuIgJsWu4Le~IvtqQuguy!|eCaQLfngcSYszg+s7ybxUviNNA zL3+X!P12+j##uicivo@MP~FIguGP9R8Lfg3=nzVSWtt}p1`u&h4`e#9@_xI1?**tx zsvH~$h#`c2GV|M&5a@oWX~H?f39O_?F%Og1YWmnJs2DQo*?c3$`&V*f@5P}+r>{r| zKCQMe+5e=$=5#c-`@`d6@BL3d-eqmM1Pp-oH38agcWL^{-PYtmr@2tG+us=ceRM4- zv|KfQXUcjIurvySDu5AbTh7uD!`j^PWxgHKDnsL=LCW%&e`3B)%B=fNqu%fuZ#S0b Gm;VL+>0y}w literal 0 HcmV?d00001 diff --git a/new-website/utils/tutorials/build_pdf_book.py b/new-website/utils/tutorials/build_pdf_book.py index 8c1cb400..9913802d 100644 --- a/new-website/utils/tutorials/build_pdf_book.py +++ b/new-website/utils/tutorials/build_pdf_book.py @@ -25,9 +25,9 @@ from typing import List -INFO_PATH = "/workspaces/deepchem.github.io/new-website/utils/tutorials/website-render-order/" -DATA_PATH = "/workspaces/deepchem.github.io/new-website/utils/tutorials/html-notebooks/" -PDF_PATH = "/workspaces/deepchem.github.io/new-website/utils/tutorials/storage/" +INFO_PATH = "./website-render-order/" +DATA_PATH = "./html-notebooks/" +PDF_PATH = "./storage/" files = os.listdir(INFO_PATH) files = sorted(files)