Refactor to standard Python package structure

[Copilot]

Repository Organization Refactoring - Complete ✅

This PR successfully refactors the pyDIWASP repository to follow traditional Python package structure, making it deployable, maintainable, and ready for PyPI distribution.

✅ Completed Tasks

• Analyze current repository structure
• Create proper package directory pydiwasp/
• Move main modules into package directory
• Update private/ as a subpackage
• Create package __init__.py files
• Update all import statements in tests
• Update all import statements in main modules
• Update setup.py configuration
• Add modern packaging files (pyproject.toml, MANIFEST.in)
• Update documentation and examples
• Verify tests still pass (28/28 ✓)
• Verify package builds successfully
• Run security scan (0 vulnerabilities)
• Address review feedback (remove duplicate imports, cleanup dependencies)

📦 Package Structure Changes

Before:

pyDIWASP/
├── dirspec.py
├── infospec.py
├── plotspec.py
├── writespec.py
├── interpspec.py
├── private/
│   ├── hsig.py
│   └── ...
└── tests/

After (Traditional Python Package):

pyDIWASP/
├── pydiwasp/              # Main package
│   ├── __init__.py       # Package exports
│   ├── dirspec.py
│   ├── infospec.py
│   ├── plotspec.py
│   ├── writespec.py
│   ├── interpspec.py
│   └── private/          # Subpackage
│       ├── __init__.py
│       └── ...
├── tests/
├── setup.py
├── pyproject.toml        # Modern packaging (PEP 518)
└── MANIFEST.in           # Distribution manifest

🔄 Import Changes

Before:

from dirspec import dirspec
from private.hsig import hsig

After:

from pydiwasp import dirspec
from pydiwasp.private.hsig import hsig

📝 Key Benefits

1. Standard Package Structure: Follows Python packaging best practices
2. Pip Installable: pip install -e . or pip install pyDIWASP (when published)
3. Clean Imports: from pydiwasp import dirspec instead of direct file imports
4. PyPI Ready: Can be published to PyPI with python -m build and twine upload
5. Modern Standards: Uses pyproject.toml (PEP 518) for build configuration
6. Better Isolation: Package code isolated from repository root
7. CI/CD Compatible: Existing GitHub Actions workflows work without changes

✅ Verification

• All 28 tests pass
• Package builds successfully as source distribution
• Package installs correctly in editable mode
• No security vulnerabilities detected (CodeQL)
• Documentation updated with new import patterns
• Example notebook updated to use new structure
• Review feedback addressed

Original prompt

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This section details on the original issue you should resolve

<issue_title>organize repository</issue_title>
<issue_description>refactor organization to make more deployable and traditional </issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes organize repository #18

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[SBFRF]

Lgtm

[Copilot]

Pull request overview

Refactors the repo into an installable Python package (pydiwasp) with updated imports, packaging metadata, and documentation/examples so users can pip install and import via pydiwasp.

Changes:

• Introduces pydiwasp/ package + pydiwasp.private/ subpackage and updates internal imports to be package-relative.
• Updates tests/examples/docs to import via pydiwasp instead of root-level modules.
• Adds/updates packaging files (pyproject.toml, MANIFEST.in, setup.py) to support building/installing the package.

Reviewed changes

Copilot reviewed 15 out of 35 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/test_integration.py	Updates integration test imports to use pydiwasp.
tests/test_core.py	Updates core test imports to use pydiwasp.private paths.
tests/test_api.py	Updates API tests to import public functions from pydiwasp.
setup.py	Restricts package discovery to pydiwasp packages.
pyproject.toml	Adds PEP 518/621 project/build metadata for packaging.
MANIFEST.in	Adds sdist include/exclude rules for key repo files.
README.md	Updates installation and import examples for installed package usage.
examples/pyDIWASP_example.ipynb	Removes sys.path manipulation; imports from pydiwasp.
pydiwasp/init.py	Defines package public API re-exports.
pydiwasp/dirspec.py	Switches to relative imports for package modules.
pydiwasp/infospec.py	Updates internal import to use package-relative private.
pydiwasp/interpspec.py	Updates internal imports to use package-relative private.
pydiwasp/plotspec.py	Updates internal import to use package-relative private.
pydiwasp/writespec.py	Adds writespec module under package.
pydiwasp/private/init.py	Defines private as a subpackage (docstring only).
pydiwasp/private/accs.py	Adds transfer functions for acceleration measurements.
pydiwasp/private/BDM.py	Adds Bayesian Directional Method implementation.
pydiwasp/private/check_data.py	Adds DIWASP data structure validation/utilities.
pydiwasp/private/DFTM.py	Adds Direct Fourier Transform Method implementation.
pydiwasp/private/diwasp_csd.py	Adds cross-spectral density helper.
pydiwasp/private/elev.py	Adds elevation transfer function.
pydiwasp/private/EMEP.py	Adds EMEP estimation method implementation.
pydiwasp/private/EMLM.py	Adds EMLM estimation method implementation.
pydiwasp/private/hsig.py	Adds significant wave height helper.
pydiwasp/private/IMLM.py	Adds IMLM estimation method implementation.
pydiwasp/private/pres.py	Adds pressure transfer function.
pydiwasp/private/slpx.py	Adds x-direction surface slope transfer function.
pydiwasp/private/slpy.py	Adds y-direction surface slope transfer function.
pydiwasp/private/smoothspec.py	Adds spectrum smoothing helper.
pydiwasp/private/spectobasis.py	Adds spectral unit conversion helper.
pydiwasp/private/vels.py	Updates import to be relative within private subpackage.
pydiwasp/private/velx.py	Adds x-velocity transfer function.
pydiwasp/private/vely.py	Adds y-velocity transfer function.
pydiwasp/private/velz.py	Adds vertical velocity transfer function.
pydiwasp/private/wavenumber.py	Adds wave number calculation helper.

Comments suppressed due to low confidence (9)

pydiwasp/dirspec.py:19

• dirspec selects the estimation algorithm via eval(EP['method']), but only IMLM and EMEP are imported in this module. If a caller sets EP['method'] to one of the other allowed values (DFTM, EMLM, BDM per check_data), this will raise NameError. Import the missing methods into this module (or replace eval with an explicit dispatch map).
  pydiwasp/dirspec.py:9
• Import of 'velx' is not used.
  pydiwasp/dirspec.py:10
• Import of 'vely' is not used.
  pydiwasp/dirspec.py:11
• Import of 'pres' is not used.
  pydiwasp/dirspec.py:12
• Import of 'elev' is not used.
  pydiwasp/dirspec.py:13
• Import of 'vels' is not used.
  pydiwasp/dirspec.py:14
• Import of 'accs' is not used.
  Import of 'accz' is not used.
  pydiwasp/dirspec.py:16
• Import of 'IMLM' is not used.
  pydiwasp/dirspec.py:17
• Import of 'EMEP' is not used.

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[SBFRF]

@copilot fix based on review comments

[SBFRF]

Lgtm. @Thesser