scitex-dataset 0.1.0__tar.gz

scitex_dataset-0.1.0/.env.example

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+# scitex-dataset environment variables
+# Copy to .env and modify as needed
+
+# Cache directory for local database (default: ~/.cache/scitex-dataset/)
+# SCITEX_DATASET_CACHE_DIR=/path/to/cache
+
+# Debug mode (set to 1 to enable verbose logging)
+# SCITEX_DATASET_DEBUG=0
+
+# API timeout in seconds (default: 30)
+# SCITEX_DATASET_TIMEOUT=30

scitex_dataset-0.1.0/.github/workflows/test.yml

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+name: Tests
+
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev,mcp]"
+
+      - name: Run linter
+        run: |
+          ruff check src/
+
+      - name: Run tests
+        run: |
+          pytest tests/ -v --tb=short
+
+      - name: Run tests with coverage
+        if: matrix.python-version == '3.11'
+        run: |
+          pytest tests/ --cov=src/scitex_dataset --cov-report=xml
+
+      - name: Upload coverage
+        if: matrix.python-version == '3.11'
+        uses: codecov/codecov-action@v4
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false

scitex_dataset-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+dist/
+build/
+*.egg-info/
+*.egg
+
+# Virtual environments
+.venv/
+venv/
+ENV/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+
+# Session outputs
+*_out/
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Custom/Specific.gitignore ###
+# Please add files here
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Custom/Claude.gitignore ###
+docs/to_claude
+docs/from_agents
+docs/from_user
+CLAUDE.md
+.claude
+mgmt
+.mcp.json
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Custom/Secrets.gitignore ###
+.git-crypt/keys
+**/*secret*
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Custom/Development.gitignore ###
+# old directories as trash bin
+*old*
+**/*old*
+.old
+**/.old
+.dev
+**/.dev
+.playground
+**/.playground
+**/.dev
+.dev
+**/.legacy
+.legacy
+
+# Backup
+**/*_back
+**/*_backup
+**/*_backups
+
+# Renaming
+**/.rename_backups
+**/.rename_backups
+
+# Logs
+*.log
+**/*.log
+**RUNNING**
+**FINISHED**
+**/RUNNING
+**/FINISHED
+**/202?Y-*
+
+# TODO
+**/TODO.md
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Custom/MyEmacs.gitignore ###
+**/*~undo-tree~
+**/undohist/*
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Custom/Apptainer.gitignore ###
+**/*.log
+**/*.sandbox/*
+**/*.sif
+**/build-temp-*
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Custom/Django.gitignore ###
+./staticfiles*
+./static/bootstrap*
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Custom/LargeFiles.gitignore ###
+data/*
+
+**/*.csv
+**/*.mat
+**/*.mp4
+**/*.npy
+**/*.pdf
+**/*.pkl
+**/*.png
+**/*.pth
+**/*.pt
+**/*.chk
+**/*.model
+**/*.tiff
+**/*.wav
+**/*.jpg
+**/*.jpeg
+**/*.h5
+**/*.zip
+**/*.tar
+**/*.gz
+**/*.rar
+**/*.7z
+**/*.hdf5
+**/*.npz
+**/*.fits
+**/*.avi
+**/*.mov
+**/*.mkv
+**/*.gif
+**/*.bmp
+**/*.svg
+**/*.psd
+**/*.tif
+**/*.raw
+**/*.nii
+**/*.dicom
+**/*.xls
+**/*.xlsx
+**/*.doc
+**/*.docx
+**/*.ppt
+**/*.pptx
+**/*.txt
+**/*.log
+**/*.db
+**/*.sqlite
+**/*.xml
+**/*.JNB
+**/*.jnb
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Python.gitignore ###
+# 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/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Django.gitignore ###
+
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/TeX.gitignore ###
+## Core latex/pdflatex auxiliary files:
+*.aux
+*.lof
+*.log
+*.lot
+*.fls
+*.out
+*.toc
+*.fmt
+*.fot
+*.cb
+*.cb2
+.*.lb
+
+## Intermediate documents:
+*.dvi
+*.xdv
+*-converted-to.*
+# these rules might exclude image files for figures etc.
+# *.ps
+# *.eps
+# *.pdf
+
+## Generated if empty string is given at "Please type another file name for output:"
+.pdf
+
+## Bibliography auxiliary files (bibtex/biblatex/biber):
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.run.xml
+
+## Build tool auxiliary files:
+*.fdb_latexmk
+*.synctex
+*.synctex(busy)
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+*.rubbercache
+rubber.cache
+
+## Build tool directories for auxiliary files
+# latexrun
+latex.out/
+
+## Auxiliary and intermediate files from other packages:
+# algorithms
+*.alg
+*.loa
+
+# achemso
+acs-*.bib
+
+# amsthm
+*.thm
+
+# beamer
+*.nav
+*.pre
+*.snm
+*.vrb
+
+# changes
+*.soc
+
+# comment
+*.cut
+
+# cprotect
+*.cpt
+
+# elsarticle (documentclass of Elsevier journals)
+*.spl
+
+# endnotes
+*.ent
+
+# fixme
+*.lox
+
+# feynmf/feynmp
+*.mf
+*.mp
+*.t[1-9]
+*.t[1-9][0-9]
+*.tfm
+
+#(r)(e)ledmac/(r)(e)ledpar
+*.end
+*.?end
+*.[1-9]
+*.[1-9][0-9]
+*.[1-9][0-9][0-9]
+*.[1-9]R
+*.[1-9][0-9]R
+*.[1-9][0-9][0-9]R
+*.eledsec[1-9]
+*.eledsec[1-9]R
+*.eledsec[1-9][0-9]
+*.eledsec[1-9][0-9]R
+*.eledsec[1-9][0-9][0-9]
+*.eledsec[1-9][0-9][0-9]R
+
+# glossaries
+*.acn
+*.acr
+*.glg
+*.glo
+*.gls
+*.glsdefs
+*.lzo
+*.lzs
+*.slg
+*.slo
+*.sls
+
+# uncomment this for glossaries-extra (will ignore makeindex's style files!)
+# *.ist
+
+# gnuplot
+*.gnuplot
+*.table
+
+# gnuplottex
+*-gnuplottex-*
+
+# gregoriotex
+*.gaux
+*.glog
+*.gtex
+
+# htlatex
+*.4ct
+*.4tc
+*.idv
+*.lg
+*.trc
+*.xref
+
+# hypdoc
+*.hd
+
+# hyperref
+*.brf
+
+# knitr
+*-concordance.tex
+# TODO Uncomment the next line if you use knitr and want to ignore its generated tikz files
+# *.tikz
+*-tikzDictionary
+
+# listings
+*.lol
+
+# luatexja-ruby
+*.ltjruby
+
+# makeidx
+*.idx
+*.ilg
+*.ind
+
+# minitoc
+*.maf
+*.mlf
+*.mlt
+*.mtc[0-9]*
+*.slf[0-9]*
+*.slt[0-9]*
+*.stc[0-9]*
+
+# minted
+_minted*
+*.pyg
+
+# morewrites
+*.mw
+
+# newpax
+*.newpax
+
+# nomencl
+*.nlg
+*.nlo
+*.nls
+
+# pax
+*.pax
+
+# pdfpcnotes
+*.pdfpc
+
+# sagetex
+*.sagetex.sage
+*.sagetex.py
+*.sagetex.scmd
+
+# scrwfile
+*.wrt
+
+# svg
+svg-inkscape/
+
+# sympy
+*.sout
+*.sympy
+sympy-plots-for-*.tex/
+
+# pdfcomment
+*.upa
+*.upb
+
+# pythontex
+*.pytxcode
+pythontex-files-*/
+
+# tcolorbox
+*.listing
+
+# thmtools
+*.loe
+
+# TikZ & PGF
+*.dpth
+*.md5
+*.auxlock
+
+# titletoc
+*.ptc
+
+# todonotes
+*.tdo
+
+# vhistory
+*.hst
+*.ver
+
+# easy-todo
+*.lod
+
+# xcolor
+*.xcp
+
+# xmpincl
+*.xmpi
+
+# xindy
+*.xdy
+
+# xypic precompiled matrices and outlines
+*.xyc
+*.xyd
+
+# endfloat
+*.ttt
+*.fff
+
+# Latexian
+TSWLatexianTemp*
+
+## Editors:
+# WinEdt
+*.bak
+*.sav
+
+# Texpad
+.texpadtmp
+
+# LyX
+*.lyx~
+
+# Kile
+*.backup
+
+# gummi
+.*.swp
+
+# KBibTeX
+*~[0-9]*
+
+# TeXnicCenter
+*.tps
+
+# auto folder when using emacs and auctex
+./auto/*
+*.el
+
+# expex forward references with \gathertags
+*-tags.tex
+
+# standalone packages
+*.sta
+
+# Makeindex log files
+*.lpz
+
+# xwatermark package
+*.xwm
+
+# REVTeX puts footnotes in the bibliography by default, unless the nofootinbib
+# option is specified. Footnotes are the stored in a file with suffix Notes.bib.
+# Uncomment the next line to have this generated file ignored.
+#*Notes.bib
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Global/Emacs.gitignore ###
+# -*- mode: gitignore; -*-
+*~
+\#*\#
+/.emacs.desktop
+/.emacs.desktop.lock
+*.elc
+auto-save-list
+tramp
+.\#*
+
+# Org-mode
+.org-id-locations
+*_archive
+
+# flymake-mode
+*_flymake.*
+
+# eshell files
+/eshell/history
+/eshell/lastdir
+
+# elpa packages
+/elpa/
+
+# reftex files
+*.rel
+
+# AUCTeX auto folder
+/auto/
+
+# cask packages
+.cask/
+dist/
+
+# Flycheck
+flycheck_*.el
+
+# server auth directory
+/server/
+
+# projectiles files
+.projectile
+
+# directory configuration
+.dir-locals.el
+
+# network security
+/network-security.data
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Custom/SQL.gitignore ###
+**/*.db
+**/*.sqlite3
+*.db-shm
+*.db-wal
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Custom/GitKeep.gitignore ###
+!.gitkeep
+!**/.gitkeep
+
+### Source: /home/ywatanabe/.git-templates/.gitignore-templates/Custom/SLURM.gitignore ###
+slurm_logs
+/.coverage
+/dataset