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remove deprecated pyproject group definitions
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adbX committed Dec 5, 2024
1 parent c79375d commit 55ca3cb
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290 changes: 146 additions & 144 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,144 +1,146 @@
.DS_Store
.vscode/
.idea/

site/
sphinxdocs/

case-studies/individual/
case-studies/arxiv-corpus/gold_standard_old/
case-studies/arxiv-corpus/gold_standard_test/
client_secrets.json

outputs/
doc/

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock

# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/
.DS_Store
.vscode/
.idea/
poetry.lock*

site/
sphinxdocs/

case-studies/individual/
case-studies/arxiv-corpus/gold_standard_old/
case-studies/arxiv-corpus/gold_standard_test/
client_secrets.json

outputs/
doc/

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock

# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/
.aider*
2 changes: 1 addition & 1 deletion docs/installation.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ All you need is to pip install `reproscreener`!
pip install reproscreener
```

=== "pyenv"
=== ["pyenv"](https://github.com/pyenv/pyenv-virtualenv)

``` bash
pyenv install {{ versions.python }}
Expand Down
13 changes: 6 additions & 7 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ arxiv = "^1.4.7"
transformers = "^4.30.2"
adapter-transformers = "^3.2.1"


[tool.poetry.group.dev.dependencies]
pytest = "^7.3.1"
pytest-cov = "^4.0.0"
Expand All @@ -52,7 +53,6 @@ rank-bm25 = "^0.2.2"
faiss-gpu = "^1.7.2"
torch = {version = "^2.1.0.dev20230708+cu121", allow-prereleases = true}


[tool.poetry.group.extras.dependencies]
pydrive2 = "^1.15.3"
black = {extras = ["jupyter"], version = "^23.3.0"}
Expand All @@ -70,15 +70,14 @@ pylint = "^2.17.4"
ipywidgets = "^8.0.6"
shtab = "^1.6.1"
openai = "^0.27.7"
langchain = "^0.0.189"
nltk = "^3.8.1"
# langchain = "^0.0.189"
# nltk = "^3.8.1"


[[tool.poetry.source]]
name = "nightly"
url = "https://download.pytorch.org/whl/nightly/cu121"
default = false
secondary = false
name = "torch-nightly"
url = "https://download.pytorch.org/whl/nightly/cpu"
priority = "explicit"

[build-system]
requires = ["poetry-core>=1.0.0"]
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