From 3c57c5fbbfc14b9f915fc695128135d434d725a3 Mon Sep 17 00:00:00 2001 From: sjin824 Date: Wed, 3 Jul 2024 04:55:43 +0000 Subject: [PATCH 1/9] Update requirements.txt --- paper_recommender/README.md | 6 +++++- paper_recommender/requirements.txt | 3 +-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/paper_recommender/README.md b/paper_recommender/README.md index 93a88ef..bbfc42c 100644 --- a/paper_recommender/README.md +++ b/paper_recommender/README.md @@ -74,4 +74,8 @@ Once all the required packages have been installed, start the app by running `pa - I suggest create a brand new copy of the app and database by following this readme. It serves two purposes: - It helps find out problems in this readme. - There should ideally be two copies of the app and database. One for deployment, another one for development. Only the deployment version should be installed to public channels like the literature channel. The development version can be installed to a new channel dedicated to development. -- I suggest avoid pushing any commits directly into the `main` branch. When developing new features, use the `dev` branch instead, or creating new branches. Then you can submit pull request to merge the changes into the `main ` branch. +- I suggest avoid pushing any commits directly into the `main` branch. When developing new features, use the `dev` branch instead, or creating new branches. Then you can submit pull request to merge the changes into the `main` branch. + +- A VCS line like `-e "git+https://..."` may cause issues when installing dependencies using `pip install -r requirements.txt`. + - I suggest that developers who are not the repository owners but have authentication access create a Personal Access Token (PAT) and insert it properly into that line. Fortunately, this issue won't occur once the repository is set to public. + - Further, ensure that your `pip` is upgraded before installing the dependencies by running `pip install --upgrade pip`. This prevents issues arising from older versions of `pip` that do not support `pyproject.toml`. \ No newline at end of file diff --git a/paper_recommender/requirements.txt b/paper_recommender/requirements.txt index c775eb9..05d84da 100644 --- a/paper_recommender/requirements.txt +++ b/paper_recommender/requirements.txt @@ -68,7 +68,6 @@ pandocfilters==1.5.1 parso==0.8.3 pexpect==4.9.0 pickleshare==0.7.5 -pkg_resources==0.0.0 pkgutil_resolve_name==1.3.10 platformdirs==4.2.0 prometheus-client==0.19.0 @@ -88,7 +87,7 @@ python-json-logger==2.0.7 pytz==2023.4 PyYAML==6.0.1 pyzmq==25.1.2 --e git+https://github.com/Strong-AI-Lab/paper_recommendation.git@cf96ab1fe4b68eba81f1fc2e5e7fe77710d350d0#egg=paper_recommender +-e "git+https://github.com/Strong-AI-Lab/Von.git@a46877f9f34afcbcb986f06241129041a7df7e90#egg=paper_recommender&subdirectory=paper_recommender" referencing==0.33.0 requests==2.31.0 rfc3339-validator==0.1.4 From 7b5e5a263f0faf517103cfb31d129d501bbc0b5a Mon Sep 17 00:00:00 2001 From: sjin824 Date: Wed, 3 Jul 2024 05:24:14 +0000 Subject: [PATCH 2/9] chore: clean up unnecessary dependencies --- paper_recommender/requirements.txt | 130 +++-------------------------- 1 file changed, 12 insertions(+), 118 deletions(-) diff --git a/paper_recommender/requirements.txt b/paper_recommender/requirements.txt index 05d84da..eb8a166 100644 --- a/paper_recommender/requirements.txt +++ b/paper_recommender/requirements.txt @@ -1,119 +1,13 @@ -aiohttp==3.9.3 -aiosignal==1.3.1 -annotated-types==0.6.0 -anyio==4.2.0 -argon2-cffi==23.1.0 -argon2-cffi-bindings==21.2.0 -arxiv==2.1.0 -asttokens==2.4.1 -async-lru==2.0.4 -async-timeout==4.0.3 -attrs==23.2.0 -Babel==2.14.0 -backcall==0.2.0 -beautifulsoup4==4.12.3 -bleach==6.1.0 -certifi==2023.11.17 -cffi==1.16.0 -charset-normalizer==3.3.2 -comm==0.2.1 -cryptography==42.0.5 -debugpy==1.8.0 -decorator==5.1.1 -defusedxml==0.7.1 -distro==1.9.0 -dnspython==2.5.0 -exceptiongroup==1.2.0 -executing==2.0.1 -fastjsonschema==2.19.1 -feedparser==6.0.10 -frozenlist==1.4.1 -h11==0.14.0 -httpcore==1.0.2 -httpx==0.26.0 -idna==3.6 -importlib-metadata==7.0.1 -importlib-resources==6.1.1 -ipykernel==6.29.0 -ipython==8.12.3 -jedi==0.19.1 -Jinja2==3.1.3 -json5==0.9.14 -jsonlines==4.0.0 -jsonschema==4.21.1 -jsonschema-specifications==2023.12.1 -jupyter-events==0.9.0 -jupyter-lsp==2.2.2 -jupyter_client==8.6.0 -jupyter_core==5.7.1 -jupyter_server==2.12.5 -jupyter_server_terminals==0.5.2 -jupyterlab==4.0.12 -jupyterlab_pygments==0.3.0 -jupyterlab_server==2.25.2 -MarkupSafe==2.1.4 -matplotlib-inline==0.1.6 -mistune==3.0.2 -multidict==6.0.5 -nbclient==0.9.0 -nbconvert==7.14.2 -nbformat==5.9.2 -nest-asyncio==1.6.0 -notebook==7.0.7 -notebook_shim==0.2.3 -openai==1.10.0 -overrides==7.7.0 -packaging==23.2 -pandocfilters==1.5.1 -parso==0.8.3 -pexpect==4.9.0 -pickleshare==0.7.5 -pkgutil_resolve_name==1.3.10 -platformdirs==4.2.0 -prometheus-client==0.19.0 -prompt-toolkit==3.0.43 -psutil==5.9.8 -ptyprocess==0.7.0 -pure-eval==0.2.2 -pycparser==2.21 -pydantic==2.6.0 -pydantic_core==2.16.1 -Pygments==2.17.2 -pymongo==4.6.1 -PyMuPDF==1.24.0 -PyMuPDFb==1.24.0 -python-dateutil==2.8.2 -python-json-logger==2.0.7 -pytz==2023.4 -PyYAML==6.0.1 -pyzmq==25.1.2 -e "git+https://github.com/Strong-AI-Lab/Von.git@a46877f9f34afcbcb986f06241129041a7df7e90#egg=paper_recommender&subdirectory=paper_recommender" -referencing==0.33.0 -requests==2.31.0 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rpds-py==0.17.1 -Send2Trash==1.8.2 -sgmllib3k==1.0.0 -six==1.16.0 -slack-bolt==1.18.1 -slack_sdk==3.26.2 -sniffio==1.3.0 -soupsieve==2.5 -stack-data==0.6.3 -terminado==0.18.0 -tinycss2==1.2.1 -tomli==2.0.1 -tornado==6.4 -tqdm==4.66.1 -traitlets==5.14.1 -types-beautifulsoup4==4.12.0.20240229 -types-html5lib==1.1.11.20240228 -types-requests==2.31.0.20240218 -typing_extensions==4.9.0 -urllib3==2.2.0 -wcwidth==0.2.13 -webencodings==0.5.1 -websocket-client==1.7.0 -yarl==1.9.4 -zipp==3.17.0 +bs4==0.0.2 +bson==0.5.10 +configparser==7.0.0 +dataclasses==0.6 +DateTime==5.5 +feedparser==6.0.11 +openai==1.35.9 +pathlib==1.0.1 +pymongo==4.8.0 +requests==2.32.3 +slack_bolt==1.19.1 +typing==3.7.4.3 \ No newline at end of file From 290bc6159c9ae414e68c9c6f235204538f44d467 Mon Sep 17 00:00:00 2001 From: sjin824 Date: Wed, 3 Jul 2024 05:35:45 +0000 Subject: [PATCH 3/9] chore: add dependencies.txt for visualizing dependency tree --- paper_recommender/dependencies.txt | 54 ++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 paper_recommender/dependencies.txt diff --git a/paper_recommender/dependencies.txt b/paper_recommender/dependencies.txt new file mode 100644 index 0000000..962df7a --- /dev/null +++ b/paper_recommender/dependencies.txt @@ -0,0 +1,54 @@ +bs4==0.0.2 +└── beautifulsoup4 [required: Any, installed: 4.12.3] + └── soupsieve [required: >1.2, installed: 2.5] +bson==0.5.10 +├── python-dateutil [required: >=2.4.0, installed: 2.9.0.post0] +│ └── six [required: >=1.5, installed: 1.16.0] +└── six [required: >=1.9.0, installed: 1.16.0] +configparser==7.0.0 +dataclasses==0.6 +DateTime==5.5 +├── pytz [required: Any, installed: 2024.1] +└── zope.interface [required: Any, installed: 6.4.post2] + └── setuptools [required: Any, installed: 50.3.2] +feedparser==6.0.11 +└── sgmllib3k [required: Any, installed: 1.0.0] +openai==1.35.9 +├── anyio [required: >=3.5.0,<5, installed: 4.4.0] +│ ├── exceptiongroup [required: >=1.0.2, installed: 1.2.1] +│ ├── idna [required: >=2.8, installed: 3.7] +│ ├── sniffio [required: >=1.1, installed: 1.3.1] +│ └── typing_extensions [required: >=4.1, installed: 4.12.2] +├── distro [required: >=1.7.0,<2, installed: 1.9.0] +├── httpx [required: >=0.23.0,<1, installed: 0.27.0] +│ ├── anyio [required: Any, installed: 4.4.0] +│ │ ├── exceptiongroup [required: >=1.0.2, installed: 1.2.1] +│ │ ├── idna [required: >=2.8, installed: 3.7] +│ │ ├── sniffio [required: >=1.1, installed: 1.3.1] +│ │ └── typing_extensions [required: >=4.1, installed: 4.12.2] +│ ├── certifi [required: Any, installed: 2024.6.2] +│ ├── httpcore [required: ==1.*, installed: 1.0.5] +│ │ ├── certifi [required: Any, installed: 2024.6.2] +│ │ └── h11 [required: >=0.13,<0.15, installed: 0.14.0] +│ ├── idna [required: Any, installed: 3.7] +│ └── sniffio [required: Any, installed: 1.3.1] +├── pydantic [required: >=1.9.0,<3, installed: 2.8.0] +│ ├── annotated-types [required: >=0.4.0, installed: 0.7.0] +│ ├── pydantic_core [required: ==2.20.0, installed: 2.20.0] +│ │ └── typing_extensions [required: >=4.6.0,!=4.7.0, installed: 4.12.2] +│ └── typing_extensions [required: >=4.6.1, installed: 4.12.2] +├── sniffio [required: Any, installed: 1.3.1] +├── tqdm [required: >4, installed: 4.66.4] +└── typing_extensions [required: >=4.7,<5, installed: 4.12.2] +paper_recommender==0.1.0 +pathlib==1.0.1 +pymongo==4.8.0 +└── dnspython [required: >=1.16.0,<3.0.0, installed: 2.6.1] +requests==2.32.3 +├── certifi [required: >=2017.4.17, installed: 2024.6.2] +├── charset-normalizer [required: >=2,<4, installed: 3.3.2] +├── idna [required: >=2.5,<4, installed: 3.7] +└── urllib3 [required: >=1.21.1,<3, installed: 2.2.2] +slack_bolt==1.19.1 +└── slack_sdk [required: >=3.25.0,<4, installed: 3.30.0] +typing==3.7.4.3 From 9c7bace74f1b3e3e1b997de87f5c0c6a9d7a1765 Mon Sep 17 00:00:00 2001 From: Michael Witbrock Date: Thu, 11 Jul 2024 22:00:25 +1200 Subject: [PATCH 4/9] Update README.md Less hope, more intent. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9404b73..014e545 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ This is an open source set of projects to enhance and enrich the tasks and capabilities of academic researchers using AI. Initially, there are two (sub) projects: tell_von which helps organize notes and files, and paper_recommender which organizes and distributes paper recommendations and references. -Hopefully this will become a family of Agents for Assisted Science and beyond. +We intend that this will become a family of Agents for Assisted Science and beyond.     From 798b89f8cd709ee65301d47904fd218417317766 Mon Sep 17 00:00:00 2001 From: syc <166462538+ysu132@users.noreply.github.com> Date: Mon, 15 Jul 2024 10:20:01 +1200 Subject: [PATCH 5/9] Create python-publish.yml Publish vonlib to PyPI --- tell_von/workflows/python-publish.yml | 1 + 1 file changed, 1 insertion(+) create mode 100644 tell_von/workflows/python-publish.yml diff --git a/tell_von/workflows/python-publish.yml b/tell_von/workflows/python-publish.yml new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/tell_von/workflows/python-publish.yml @@ -0,0 +1 @@ + From dfb2d39af3e8f575b6c9f786e83f7fdab619563b Mon Sep 17 00:00:00 2001 From: syc <166462538+ysu132@users.noreply.github.com> Date: Mon, 15 Jul 2024 10:42:02 +1200 Subject: [PATCH 6/9] Update python-publish.yml --- tell_von/workflows/python-publish.yml | 39 +++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/tell_von/workflows/python-publish.yml b/tell_von/workflows/python-publish.yml index 8b13789..48054be 100644 --- a/tell_von/workflows/python-publish.yml +++ b/tell_von/workflows/python-publish.yml @@ -1 +1,40 @@ +name: Publish Python Package +on: + push: + branches: + - main + - master + pull_request: + branches: + - main + - master + +jobs: + publish: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: '3.x' + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install setuptools wheel + + - name: Build package + run: python setup.py sdist bdist_wheel + + - name: Publish package to PyPI + env: + TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} + TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} + run: | + python -m pip install --upgrade twine + twine upload dist/* From 216bee7641ae59fe0ac880dbb5a8d1a0907a5a47 Mon Sep 17 00:00:00 2001 From: syc <166462538+ysu132@users.noreply.github.com> Date: Mon, 22 Jul 2024 23:22:48 +1200 Subject: [PATCH 7/9] Create python-publish.yml --- workflows/python-publish.yml | 1 + 1 file changed, 1 insertion(+) create mode 100644 workflows/python-publish.yml diff --git a/workflows/python-publish.yml b/workflows/python-publish.yml new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/workflows/python-publish.yml @@ -0,0 +1 @@ + From 9c152b458142e86567eb7f640ad2e46ed4f91773 Mon Sep 17 00:00:00 2001 From: syc <166462538+ysu132@users.noreply.github.com> Date: Tue, 23 Jul 2024 02:46:31 +1200 Subject: [PATCH 8/9] Update python-publish.yml --- workflows/python-publish.yml | 40 ++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/workflows/python-publish.yml b/workflows/python-publish.yml index 8b13789..3004027 100644 --- a/workflows/python-publish.yml +++ b/workflows/python-publish.yml @@ -1 +1,41 @@ +name: Publish +on: + release: + types: + - created + +jobs: + publish: + runs-on: ubuntu-latest + strategy: + matrix: + package: + - vonlib + permissions: + id-token: write + steps: + - name: Dump GitHub context + env: + GITHUB_CONTEXT: ${{ toJson(github) }} + run: echo "$GITHUB_CONTEXT" + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.10" + # Issue ref: https://github.com/actions/setup-python/issues/436 + # cache: "pip" + # cache-dependency-path: pyproject.toml + - name: Install build dependencies + run: pip install build + - name: Build distribution + env: + TIANGOLO_BUILD_PACKAGE: ${{ matrix.package }} + run: python -m build + - name: Publish + uses: pypa/gh-action-pypi-publish@v1.8.14 + - name: Dump GitHub context + env: + GITHUB_CONTEXT: ${{ toJson(github) }} + run: echo "$GITHUB_CONTEXT" From f1067d30cf02bf4cd5335dcde85c1fe5755a9dec Mon Sep 17 00:00:00 2001 From: Yuchen Su Date: Mon, 22 Jul 2024 17:30:09 -0700 Subject: [PATCH 9/9] delete workflows in TellVon --- tell_von/workflows/python-publish.yml | 40 --------------------------- 1 file changed, 40 deletions(-) delete mode 100644 tell_von/workflows/python-publish.yml diff --git a/tell_von/workflows/python-publish.yml b/tell_von/workflows/python-publish.yml deleted file mode 100644 index 48054be..0000000 --- a/tell_von/workflows/python-publish.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: Publish Python Package - -on: - push: - branches: - - main - - master - pull_request: - branches: - - main - - master - -jobs: - publish: - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v2 - - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: '3.x' - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install setuptools wheel - - - name: Build package - run: python setup.py sdist bdist_wheel - - - name: Publish package to PyPI - env: - TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} - TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} - run: | - python -m pip install --upgrade twine - twine upload dist/*