pymorgan 0.8.260814.dev1__tar.gz

pymorgan-0.8.260814.dev1/.gitattributes

@@ -0,0 +1,64 @@
+# Line-ending policy for PyMORGAN.
+#
+# Text files are stored with LF in the repository and checked out with the
+# platform's native endings (CRLF on Windows). Without this, editors and tools
+# that rewrite a whole file with the other convention make it look entirely
+# modified in `git status`.
+#
+# After adding this file once, run:
+#     git add --renormalize .
+# and commit the result; from then on line endings stay out of the diffs.
+
+* text=auto
+
+# Source and configuration (explicit, so they are never guessed as binary)
+*.py      text diff=python
+*.pyi     text diff=python
+*.md      text diff=markdown
+*.txt     text
+*.toml    text
+*.json    text
+*.cfg     text
+*.ini     text
+*.yml     text
+*.yaml    text
+*.m       text
+*.tex     text diff=tex
+*.bib     text diff=bibtex
+*.mplstyle text
+*.ui      text
+*.csv     text
+*.CSV     text
+*.dat     text
+*.pdat    text
+*.p2dat   text
+.gitattributes text
+.gitignore     text
+LICENSE        text
+
+# Shell / PowerShell scripts keep the endings their interpreter expects
+*.sh      text eol=lf
+*.ps1     text eol=crlf
+*.bat     text eol=crlf
+*.cmd     text eol=crlf
+
+# Binary assets: never touched, never diffed as text
+*.png     binary
+*.jpg     binary
+*.jpeg    binary
+*.gif     binary
+*.ico     binary
+*.pdf     binary
+*.ttf     binary
+*.otf     binary
+*.woff    binary
+*.woff2   binary
+*.xlsx    binary
+*.h5      binary
+*.hdf5    binary
+*.npy     binary
+*.npz     binary
+*.mat     binary
+
+# uv resolves this itself; keep it LF so it is stable across platforms
+uv.lock   text eol=lf linguist-generated=true

pymorgan-0.8.260814.dev1/.github/workflows/python-publish.yml

@@ -0,0 +1,54 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:  # This adds a "Run workflow" button in the Actions tab
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      id-token: write
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pymorgan
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

pymorgan-0.8.260814.dev1/.gitignore

@@ -0,0 +1,254 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+local/
+.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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# 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
+.envrc
+.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/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# AI guidelines (kept out of the published repo)
+CLAUDE.md
+ANTIGRAVITY.md
+.agents/
+.gemini/
+.claude/
+walkthrough.md
+implementation_plan.md
+
+# Archived / superseded code (kept locally, excluded from repo)
+old_code/
+/old_code/
+
+
+
+
+
+# Roadmap and TODO files
+TODO.md
+todo_twoD_routines.md
+todo_calibration_routines.md
+gui_redesign_prompt.md
+
+# Custom user-added calibration reference spectra (shipped ones & README remain tracked)
+src/pymorgan/cal/ref_spectra/*
+!src/pymorgan/cal/ref_spectra/README.md
+!src/pymorgan/cal/ref_spectra/FTIR-DCM_2cm-1.csv
+!src/pymorgan/cal/ref_spectra/FTIR-DioxaneRAL_2cm-1.csv
+!src/pymorgan/cal/ref_spectra/FTIR-Dioxane_2cm-1.csv
+!src/pymorgan/cal/ref_spectra/FTIR-PS_38+76µm_RAL_2cm-1.csv
+!src/pymorgan/cal/ref_spectra/FTIR-PS_38µm_RAL_2cm-1.csv
+!src/pymorgan/cal/ref_spectra/FTIR-PS_76µm_RAL_2cm-1.csv
+!src/pymorgan/cal/ref_spectra/FTIR-PolystyreneFilm_2cm-1.csv
+!src/pymorgan/cal/ref_spectra/FTIR-PolystyreneRAL(1.5mil)_2cm-1.csv
+!src/pymorgan/cal/ref_spectra/FTIR-PolystyreneRAL(3mil)_2cm-1.csv
+!src/pymorgan/cal/ref_spectra/FTIR_PS50µm_2cm-1.CSV
+!src/pymorgan/cal/ref_spectra/Hoya-HY1.csv
+!src/pymorgan/cal/ref_spectra/Hoya-V11.csv
+!src/pymorgan/cal/ref_spectra/NIR-Holmium.csv
+!src/pymorgan/cal/ref_spectra/UVVis-Holmium.csv
+
+# Local user settings (settings.default.toml provides the template)
+settings.toml
+/settings.toml
+

pymorgan-0.8.260814.dev1/.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "docwriter.style": "Auto-detect"
+}