Merge pull request #169 from entelecheia/main

entelecheia · Nov 5, 2024 · dea9f2a · dea9f2a
2 parents d25122d + bded654
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diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -8,51 +8,51 @@ on:
     branches:
       - release*
     paths:
-      - 'src/**'
-      - 'pyproject.toml'
-
-permissions:
-  contents: write
-  issues: write
-  pull-requests: write
+      - "src/**"
+      - "pyproject.toml"
 
 jobs:
-  build:
-    # Name the Job
-    name: semantic-release
-    # Set the agent to run on
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest]
-        python-version: [3.9]
-
-    # Load all steps #
+  release:
+    runs-on: ubuntu-latest
+    concurrency: release
+
+    permissions:
+      id-token: write
+      contents: write
+
     steps:
-      # Checkout the code base #
-      - name: Checkout Code
+      # Note: we need to checkout the repository at the workflow sha in case during the workflow
+      # the branch was updated. To keep PSR working with the configured release branches,
+      # we force a checkout of the desired release branch but at the workflow sha HEAD.
+      - name: Setup | Checkout Repository at workflow sha
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          ref: ${{ github.sha }}
 
-      # set env variable
-      - name: Set env variable
-        run: echo "BRANCH=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
-
-      # install poetry
-      - name: Install poetry
-        run: pipx install poetry>=1.3.2
+      - name: Setup | Force correct release branch on workflow sha
+        run: |
+          git checkout -B ${{ github.ref_name }} ${{ github.sha }}
 
-      # install dependencies
-      - name: Install dependencies
-        run: poetry install --with dev
+      - name: Action | Semantic Version Release
+        id: release
+        # Adjust tag with desired version if applicable.
+        uses: python-semantic-release/[email protected]
+        with:
+          build: true
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          git_committer_name: "github-actions"
+          git_committer_email: "[email protected]"
+
+      - name: Publish | Upload package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        if: steps.release.outputs.released == 'true'
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
 
-      - name: Python Semantic Release to PyPI
-        run: |
-          git config --global user.name "GitHub Actions"
-          git config --global user.email "[email protected]"
-          poetry run semantic-release publish --verbosity=DEBUG --define=branch=${{ env.BRANCH }}
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          REPOSITORY_USERNAME: __token__
-          REPOSITORY_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      - name: Publish | Upload to GitHub Release Assets
+        uses: python-semantic-release/[email protected]
+        if: steps.release.outputs.released == 'true'
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          tag: ${{ steps.release.outputs.tag }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,102 @@
 <!--next-version-placeholder-->
 
+## v0.5.1 (2024-10-29)
+
+### Bug Fixes
+
+* fix(deps): bump python-semantic-release from 7.33.1 to 9.0.0 ([`d921c4e`](https://github.com/entelecheia/intronlp-2024/commit/d921c4eba1d92d99d2d0571ab95dfc77fc934939))
+
+* fix(pyproject): update build-system and semantic release settings ([`30a6dde`](https://github.com/entelecheia/intronlp-2024/commit/30a6dde3cc0a572d051b298f95d3053a979ea25a))
+
+### Chores
+
+* chore(deps): bump huggingface-hub from 0.26.1 to 0.26.2
+
+Bumps [huggingface-hub](https://github.com/huggingface/huggingface_hub) from 0.26.1 to 0.26.2.
+- [Release notes](https://github.com/huggingface/huggingface_hub/releases)
+- [Commits](https://github.com/huggingface/huggingface_hub/compare/v0.26.1...v0.26.2)
+
+---
+updated-dependencies:
+- dependency-name: huggingface-hub
+  dependency-type: direct:production
+  update-type: version-update:semver-patch
+...
+
+Signed-off-by: dependabot[bot] <[email protected]> ([`071cb36`](https://github.com/entelecheia/intronlp-2024/commit/071cb365060500a41f2793def868258299b6d666))
+
+* chore(deps): bump openai from 1.52.1 to 1.52.2
+
+Bumps [openai](https://github.com/openai/openai-python) from 1.52.1 to 1.52.2.
+- [Release notes](https://github.com/openai/openai-python/releases)
+- [Changelog](https://github.com/openai/openai-python/blob/main/CHANGELOG.md)
+- [Commits](https://github.com/openai/openai-python/compare/v1.52.1...v1.52.2)
+
+---
+updated-dependencies:
+- dependency-name: openai
+  dependency-type: direct:production
+  update-type: version-update:semver-patch
+...
+
+Signed-off-by: dependabot[bot] <[email protected]> ([`fff2021`](https://github.com/entelecheia/intronlp-2024/commit/fff2021137d21cb0aa2cfac17324a00a0a76062d))
+
+* chore: typo ([`a8cf015`](https://github.com/entelecheia/intronlp-2024/commit/a8cf015bcb56d8de0a9f485c561c026df6d794b3))
+
+* chore(deps): bump openai from 1.52.0 to 1.52.1
+
+Bumps [openai](https://github.com/openai/openai-python) from 1.52.0 to 1.52.1.
+- [Release notes](https://github.com/openai/openai-python/releases)
+- [Changelog](https://github.com/openai/openai-python/blob/main/CHANGELOG.md)
+- [Commits](https://github.com/openai/openai-python/compare/v1.52.0...v1.52.1)
+
+---
+updated-dependencies:
+- dependency-name: openai
+  dependency-type: direct:production
+  update-type: version-update:semver-patch
+...
+
+Signed-off-by: dependabot[bot] <[email protected]> ([`ab76bfc`](https://github.com/entelecheia/intronlp-2024/commit/ab76bfc72c9d1ee1292a4cc88b5a92bb036e43b8))
+
+### Unknown
+
+* Merge pull request #156 from entelecheia/main ([`8a9a64d`](https://github.com/entelecheia/intronlp-2024/commit/8a9a64d0d3b7b6dc7176f992e1b96edf46893e52))
+
+* Merge pull request #155 from entelecheia/dependabot/pip/huggingface-hub-0.26.2
+
+chore(deps): bump huggingface-hub from 0.26.1 to 0.26.2 ([`60bdc4d`](https://github.com/entelecheia/intronlp-2024/commit/60bdc4d421a6193bf4a80d10ab64571ac62be27f))
+
+* Merge pull request #154 from entelecheia/dependabot/pip/openai-1.52.2
+
+chore(deps): bump openai from 1.52.1 to 1.52.2 ([`7682549`](https://github.com/entelecheia/intronlp-2024/commit/7682549756c9cb744f6307efc47c09dce98944d5))
+
+* Merge pull request #152 from booyuncheol/patch-1
+
+Create research-note-9.md ([`5a4a03e`](https://github.com/entelecheia/intronlp-2024/commit/5a4a03e15e75648cd084f0d7786540e1989725c8))
+
+* Create research-note-9.md
+
+Create research-note-9 ([`3eb3d3e`](https://github.com/entelecheia/intronlp-2024/commit/3eb3d3e029d3a95e14850833f53f273ac48d0da7))
+
+* Merge pull request #153 from entelecheia/dependabot/pip/openai-1.52.1
+
+chore(deps): bump openai from 1.52.0 to 1.52.1 ([`ddd80c6`](https://github.com/entelecheia/intronlp-2024/commit/ddd80c6e06acf3154312b2df57c34b63d35b827a))
+
+* Merge pull request #151 from entelecheia/release
+
+Release ([`a7e6e20`](https://github.com/entelecheia/intronlp-2024/commit/a7e6e20e6d36d473f95ff75706d75e098cb39e90))
+
+
+## v0.5.0 (2024-10-22)
+
+### Feature
+
+* Add research note for week 8 to the table of contents ([`840ddb7`](https://github.com/entelecheia/intronlp-2024/commit/840ddb7cb0695caaeafe0396433661dea979a964))
+* Refactor table of contents to include Week 9 content ([`83ccc5f`](https://github.com/entelecheia/intronlp-2024/commit/83ccc5f6761809045df2a7e4803e723b790c063b))
+* Add Week 9 syllabus and content ([`c40d534`](https://github.com/entelecheia/intronlp-2024/commit/c40d5346a83022101ac5b93dcefbdf3aca354966))
+* Add Week 9 syllabus and content ([`f9bdf7a`](https://github.com/entelecheia/intronlp-2024/commit/f9bdf7abd8a987f56f2636648783fb340bbb272f))
+
 ## v0.4.0 (2024-10-10)
 
 ### Feature

diff --git a/book/en/_toc.yml b/book/en/_toc.yml
@@ -47,6 +47,11 @@ parts:
         sections:
           - file: week09/session1
           - file: week09/session2
+      - file: week10/index
+        sections:
+          - file: week10/session1
+          - file: week10/session2
+          - file: week10/session3
   - caption: Projects
     chapters:
       - file: projects/index

diff --git a/book/en/nobel-chemistry/index.md b/book/en/nobel-chemistry/index.md
@@ -1,4 +1,4 @@
-# Special Lecture - 2024 Nobel Prize in Chemistry
+# Special Lecture: 2024 Nobel Prize in Chemistry
 
 **Computational Protein Design and Protein Structure Prediction**
 

diff --git a/book/en/nobel-chemistry/session1.md b/book/en/nobel-chemistry/session1.md
@@ -1,4 +1,4 @@
-# Session 1 - Computational Protein Design and De Novo Protein Engineering
+# Session 1: Computational Protein Design and De Novo Protein Engineering
 
 The 2024 Nobel Prize in Chemistry was awarded to David Baker for his groundbreaking work in de novo protein engineering. This session explores the revolutionary field of computational protein design, its methods, applications, and broader implications for synthetic biology and biotechnology.
 

diff --git a/book/en/nobel-chemistry/session2.md b/book/en/nobel-chemistry/session2.md
@@ -1,4 +1,4 @@
-# Session 2 - Protein Structure Prediction Using Artificial Intelligence
+# Session 2: Protein Structure Prediction Using Artificial Intelligence
 
 The 2024 Nobel Prize in Chemistry was awarded to Demis Hassabis and John Jumper for their groundbreaking work on AlphaFold2, an artificial intelligence system that revolutionized protein structure prediction. This session explores the journey from traditional methods to AI-powered solutions in understanding protein structures.
 

diff --git a/book/en/nobel-chemistry/session3.md b/book/en/nobel-chemistry/session3.md
@@ -1,4 +1,4 @@
-# Session 3 - Insights from Interviews
+# Session 3: Insights from Interviews
 
 This session explores the personal reflections and insights shared by David Baker, Demis Hassabis, and John Jumper in their first interviews after receiving the news of their Nobel Prize in Chemistry for 2024. These conversations provide valuable perspectives on the impact of their work, the future of AI in science, and the experience of receiving such a prestigious award.
 

diff --git a/book/en/nobel-physics/index.md b/book/en/nobel-physics/index.md
@@ -1,4 +1,4 @@
-# Special Lecture - 2024 Nobel Prize in Physics
+# Special Lecture: 2024 Nobel Prize in Physics
 
 **Foundations of Machine Learning**
 

diff --git a/book/en/nobel-physics/session1.md b/book/en/nobel-physics/session1.md
@@ -1,4 +1,4 @@
-# Session 1 - Foundational Discoveries in Machine Learning with Artificial Neural Networks
+# Session 1: Foundational Discoveries in Machine Learning with Artificial Neural Networks
 
 ![](figs/fig1_fy_24_svartvit.jpeg)
 

diff --git a/book/en/nobel-physics/session2.md b/book/en/nobel-physics/session2.md
@@ -1,4 +1,4 @@
-# Session 2 - Deep Learning Evolution and Advanced Neural Network Architectures
+# Session 2: Deep Learning Evolution and Advanced Neural Network Architectures
 
 This session explores the fascinating journey from foundational neural network models to modern deep learning architectures. We'll focus on the pivotal contributions of Geoffrey Hinton, the development of convolutional neural networks (CNNs), and the groundbreaking introduction of transformer models. This evolution has revolutionized artificial intelligence, enabling machines to process and understand complex data in ways that were once thought impossible.
 

diff --git a/book/en/nobel-physics/session3.md b/book/en/nobel-physics/session3.md
@@ -1,4 +1,4 @@
-# Session 3 - Insights from Interviews
+# Session 3: Insights from Interviews
 
 This session delves into the insights gleaned from interviews with two pioneers in the field of artificial intelligence and neural networks: Geoffrey Hinton and John Hopfield. Their reflections offer a unique perspective on the current state and future of AI, highlighting both its immense potential and the pressing need for safety research and ethical considerations.
 

diff --git a/book/en/week01/index.md b/book/en/week01/index.md
@@ -1,4 +1,4 @@
-# Week 1 - Introduction
+# Week 1: Introduction
 
 Welcome to Week 1 of our course on Natural Language Processing (NLP) and advanced language model technologies. This week, we'll embark on an exciting journey through the world of NLP, exploring its fundamental concepts, historical evolution, and cutting-edge developments.
 

diff --git a/book/en/week01/session1.md b/book/en/week01/session1.md
@@ -1,4 +1,4 @@
-# Week 1 Session 1 - Foundations and Evolution of NLP
+# Week 1 Session 1: Foundations and Evolution of NLP
 
 ## 1. Introduction to Natural Language Processing (NLP)
 

diff --git a/book/en/week01/session2.md b/book/en/week01/session2.md
@@ -1,4 +1,4 @@
-# Week 1 Session 2 - The Revolution in Modern NLP
+# Week 1 Session 2: The Revolution in Modern NLP
 
 ## 6. Evolution Towards Modern NLP
 

diff --git a/book/en/week02/index.md b/book/en/week02/index.md
@@ -1,4 +1,4 @@
-# Week 2 - Basics of Text Preprocessing
+# Week 2: Basics of Text Preprocessing
 
 ## Overview
 

diff --git a/book/en/week02/session1.md b/book/en/week02/session1.md
@@ -1,4 +1,4 @@
-# Week 2 Session 1 - Text Preprocessing Fundamentals
+# Week 2 Session 1: Text Preprocessing Fundamentals
 
 ## Introduction
 

diff --git a/book/en/week02/session2.md b/book/en/week02/session2.md
@@ -1,4 +1,4 @@
-# Week 2 Session 2 - Advanced Text Preprocessing and Representation
+# Week 2 Session 2: Advanced Text Preprocessing and Representation
 
 ## Introduction
 

diff --git a/book/en/week02/session3.md b/book/en/week02/session3.md
@@ -1,4 +1,4 @@
-# Week 2 Session 3 - Korean Text Preprocessing and Tokenization
+# Week 2 Session 3: Korean Text Preprocessing and Tokenization
 
 ## Introduction
 

diff --git a/book/en/week03/index.md b/book/en/week03/index.md
@@ -1,4 +1,4 @@
-# Week 3 - Fundamentals of Language Models
+# Week 3: Fundamentals of Language Models
 
 ## Overview
 

diff --git a/book/en/week03/session1.md b/book/en/week03/session1.md
@@ -1,4 +1,4 @@
-# Week 3 Session 1 - Introduction to Language Models and N-grams
+# Week 3 Session 1: Introduction to Language Models and N-grams
 
 ## 1. Introduction to Language Models
 

diff --git a/book/en/week03/session2.md b/book/en/week03/session2.md
@@ -1,4 +1,4 @@
-# Week 3 Session 2 - Advanced Statistical Language Models
+# Week 3 Session 2: Advanced Statistical Language Models
 
 ## 1. Advanced N-gram Techniques
 

diff --git a/book/en/week04/index.md b/book/en/week04/index.md
@@ -1,4 +1,4 @@
-# Week 4 - Word Embeddings
+# Week 4: Word Embeddings
 
 ## Overview
 

diff --git a/book/en/week04/session1.md b/book/en/week04/session1.md
@@ -1,4 +1,4 @@
-# Week 4 Session 1 - Introduction to Word Embeddings and Word2Vec
+# Week 4 Session 1: Introduction to Word Embeddings and Word2Vec
 
 ## 1. Introduction to Word Embeddings
 

diff --git a/book/en/week04/session2.md b/book/en/week04/session2.md
@@ -1,4 +1,4 @@
-# Week 4 Session 2 -  Advanced Word Embeddings
+# Week 4 Session 2:  Advanced Word Embeddings
 
 ## 1. Introduction to GloVe (Global Vectors for Word Representation)
 

diff --git a/book/en/week05/index.md b/book/en/week05/index.md
@@ -1,4 +1,4 @@
-# Week 5 - Transformers
+# Week 5: Transformers
 
 ## Introduction
 

diff --git a/book/en/week05/session1.md b/book/en/week05/session1.md
@@ -1,4 +1,4 @@
-# Week 5 Session 1 - Introduction to Transformers
+# Week 5 Session 1: Introduction to Transformers
 
 ## Introduction
 

diff --git a/book/en/week05/session2.md b/book/en/week05/session2.md
@@ -1,4 +1,4 @@
-# Week 5 Session 2 - BERT
+# Week 5 Session 2: BERT
 
 ## 1. Introduction to BERT
 

diff --git a/book/en/week05/session3.md b/book/en/week05/session3.md
@@ -1,4 +1,4 @@
-# Week 5 Session 3 - Practical Implementation and Visualization of Transformers
+# Week 5 Session 3: Practical Implementation and Visualization of Transformers
 
 ## Introduction
 

diff --git a/book/en/week06/index.md b/book/en/week06/index.md
@@ -1,4 +1,4 @@
-# Week 6 - Understanding LLM APIs
+# Week 6: Understanding LLM APIs
 
 ## Key Learning Content
 

diff --git a/book/en/week06/session1.md b/book/en/week06/session1.md
@@ -1,4 +1,4 @@
-# Week 6 Session 1 - Introduction to LLM APIs and OpenAI API Usage
+# Week 6 Session 1: Introduction to LLM APIs and OpenAI API Usage
 
 ## 1. Introduction to Large Language Model APIs
 

diff --git a/book/en/week06/session2.md b/book/en/week06/session2.md
@@ -1,4 +1,4 @@
-# Week 6 Session 2 - Sampling Methods and Text Generation
+# Week 6 Session 2: Sampling Methods and Text Generation
 
 ## Overview