From 268ff8f2ae960b8063c67d7ea2154128197f680f Mon Sep 17 00:00:00 2001 From: EhsanBitaraf Date: Mon, 12 Feb 2024 09:29:53 +0330 Subject: [PATCH] Repacking --- .github/workflows/test-poetry-action.yml | 4 +- CHANGELOG.md | 7 +- poetry.lock | 3529 ++++++++++++++-------- pyproject.toml | 35 +- requirements1.txt | 105 + 5 files changed, 2415 insertions(+), 1265 deletions(-) create mode 100644 requirements1.txt diff --git a/.github/workflows/test-poetry-action.yml b/.github/workflows/test-poetry-action.yml index faa0f9a..8a64c5d 100644 --- a/.github/workflows/test-poetry-action.yml +++ b/.github/workflows/test-poetry-action.yml @@ -5,8 +5,8 @@ name: Testing on: pull_request: branches: [main] - # push: - # branches: [main] + push: + branches: [main] jobs: test: diff --git a/CHANGELOG.md b/CHANGELOG.md index 7ae3e4b..a2276a3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,12 +5,6 @@ All notable changes to this project will be documented in this file. ### Task - RIS Parser -- pip install from source: - - ModuleNotFoundError: No module named 'pydantic_settings' - - ModuleNotFoundError: No module named 'langchain' - - ModuleNotFoundError: No module named 'langchain_openai' - - ModuleNotFoundError: No module named 'PyPDF2' - - ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. triplea 0.0.5 requires pydantic<2.0.0,>=1.10.4, but you have pydantic 2.6.1 which is incompatible. - Expose `get_article_by_arxiv_id` to cli - Article.Published must be fixed in pubmed and is string in Arxiv - Data Extraction from Unstructured PDFs @@ -40,6 +34,7 @@ All notable changes to this project will be documented in this file. ### Bug Fixes +- Repackaing pyproject.toml - Fix parsing_details_pubmed.py", line 214 : `abstract_all = abstract_all + " " + abstract_part["#text"]` - Fix `triplea/config/settings.py`, line 27 - FileNotFoundError: [Errno 2] No such file or directory: 'pyproject.toml' - Fix `print_error()` diff --git a/poetry.lock b/poetry.lock index 4a4257c..b3bbc8f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,195 +1,277 @@ # This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +[[package]] +name = "aiohttp" +version = "3.9.3" +description = "Async http client/server 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python_version >= "3.10" and python_version < "4.0" +jsonpatch==1.33 ; python_version >= "3.10" and python_version < "4.0" +jsonpointer==2.4 ; python_version >= "3.10" and python_version < "4.0" +jupyter-client==8.6.0 ; python_version >= "3.10" and python_version < "4.0" +jupyter-core==5.7.1 ; python_version >= "3.10" and python_version < "4.0" +jupyterlab-widgets==3.0.10 ; python_version >= "3.10" and python_version < "4.0" +kiwisolver==1.4.5 ; python_version >= "3.10" and python_version < "4.0" +langchain-community==0.0.19 ; python_version >= "3.10" and python_version < "4.0" +langchain-core==0.1.22 ; python_version >= "3.10" and python_version < "4.0" +langchain-openai==0.0.5 ; python_version >= "3.10" and python_version < "4.0" +langchain==0.1.6 ; python_version >= "3.10" and python_version < "4.0" +langsmith==0.0.87 ; python_version >= "3.10" and python_version < "4.0" +marshmallow==3.20.2 ; python_version >= "3.10" and python_version < "4.0" +matplotlib-inline==0.1.6 ; python_version >= "3.10" and python_version < "4.0" +matplotlib==3.8.2 ; python_version >= "3.10" and python_version < "4.0" +more-itertools==10.2.0 ; python_version >= "3.10" and python_version < "4.0" +multidict==6.0.5 ; python_version >= "3.10" and python_version < "4.0" +mypy-extensions==1.0.0 ; python_version >= "3.10" and python_version < "4.0" +nest-asyncio==1.6.0 ; python_version >= "3.10" and python_version < "4.0" +networkx==3.2.1 ; python_version >= "3.10" and python_version < "4.0" +netwulf==0.1.5 ; python_version >= "3.10" and python_version < "4.0" +numpy==1.26.4 ; python_version >= "3.10" and python_version < "4.0" +nxviz==0.7.4 ; python_version >= "3.10" and python_version < "4.0" +openai==1.12.0 ; python_version >= "3.10" and python_version < "4.0" +packaging==23.2 ; python_version >= "3.10" and python_version < "4.0" +palettable==3.3.3 ; python_version >= "3.10" and python_version < "4.0" +pandas==2.2.0 ; python_version >= "3.10" and python_version < "4.0" +parso==0.8.3 ; python_version >= "3.10" and python_version < "4.0" +pexpect==4.9.0 ; python_version >= "3.10" and python_version < "4.0" and sys_platform != "win32" +pillow==10.2.0 ; python_version >= "3.10" and python_version < "4.0" +platformdirs==4.2.0 ; python_version >= "3.10" and python_version < "4.0" +prompt-toolkit==3.0.43 ; python_version >= "3.10" and python_version < "4.0" +psutil==5.9.8 ; python_version >= "3.10" and python_version < "4.0" +ptyprocess==0.7.0 ; python_version >= "3.10" and python_version < "4.0" and sys_platform != "win32" +pure-eval==0.2.2 ; python_version >= "3.10" and python_version < "4.0" +pycparser==2.21 ; python_version >= "3.10" and python_version < "4.0" and implementation_name == "pypy" +pydantic-core==2.16.2 ; python_version >= "3.10" and python_version < "4.0" +pydantic-settings==2.1.0 ; python_version >= "3.10" and python_version < "4.0" +pydantic==2.6.1 ; python_version >= "3.10" and python_version < "4.0" +pygments==2.17.2 ; python_version >= "3.10" and python_version < "4.0" +pymongo==4.6.1 ; python_version >= "3.10" and python_version < "4.0" +pyparsing==3.1.1 ; python_version >= "3.10" and python_version < "4.0" +pypdf2==3.0.1 ; python_version >= "3.10" and python_version < "4.0" +python-dateutil==2.8.2 ; python_version >= "3.10" and python_version < "4.0" +python-dotenv==1.0.1 ; python_version >= "3.10" and python_version < "4.0" +pytz==2024.1 ; python_version >= "3.10" and python_version < "4.0" +pywin32==306 ; sys_platform == "win32" and platform_python_implementation != "PyPy" and python_version >= "3.10" and python_version < "4.0" +pyyaml==6.0.1 ; python_version >= "3.10" and python_version < "4.0" +pyzmq==25.1.2 ; python_version >= "3.10" and python_version < "4.0" +regex==2023.12.25 ; python_version >= "3.10" and python_version < "4.0" +requests==2.31.0 ; python_version >= "3.10" and python_version < "4.0" +seaborn==0.13.2 ; python_version >= "3.10" and python_version < "4.0" +simplejson==3.19.2 ; python_version >= "3.10" and python_version < "4.0" +six==1.16.0 ; python_version >= "3.10" and python_version < "4.0" +sniffio==1.3.0 ; python_version >= "3.10" and python_version < "4.0" +sqlalchemy==2.0.26 ; python_version >= "3.10" and python_version < "4.0" +stack-data==0.6.3 ; python_version >= "3.10" and python_version < "4.0" +tenacity==8.2.3 ; python_version >= "3.10" and python_version < "4.0" +tiktoken==0.5.2 ; python_version >= "3.10" and python_version < "4.0" +tinydb==4.8.0 ; python_version >= "3.10" and python_version < "4.0" +tomli==2.0.1 ; python_version >= "3.10" and python_version < "4.0" +tornado==6.4 ; python_version >= "3.10" and python_version < "4.0" +tqdm==4.66.2 ; python_version >= "3.10" and python_version < "4.0" +traitlets==5.14.1 ; python_version >= "3.10" and python_version < "4.0" +typing-extensions==4.9.0 ; python_version >= "3.10" and python_version < "4.0" +typing-inspect==0.9.0 ; python_version >= "3.10" and python_version < "4.0" +tzdata==2024.1 ; python_version >= "3.10" and python_version < "4.0" +urllib3==2.2.0 ; python_version >= "3.10" and python_version < "4.0" +wcwidth==0.2.13 ; python_version >= "3.10" and python_version < "4.0" +widgetsnbextension==4.0.10 ; python_version >= "3.10" and python_version < "4.0" +xmltodict==0.13.0 ; python_version >= "3.10" and python_version < "4.0" +yarl==1.9.4 ; python_version >= "3.10" and python_version < "4.0"