traitly 0.1.2__tar.gz → 0.2.1__tar.gz

{traitly-0.1.2/traitly_test/lib/python3.13/site-packages/pymdown_extensions-10.21.2.dist-info → traitly-0.2.1/.docs_venv/lib/python3.12/site-packages/pymdown_extensions-10.7.dist-info}/licenses/LICENSE.md

@@ -4,7 +4,7 @@
 
 The MIT License (MIT)
 
-Copyright (c) 2014 - 2025 Isaac Muse
+Copyright (c) 2014 - 2023 Isaac Muse
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -34,7 +34,7 @@ Fenced Code Extension for Python Markdown
 This extension adds Fenced Code Blocks to Python-Markdown.
 See <https://python-markdown.github.io/extensions/fenced_code_blocks/>
 for documentation.
-Original code Copyright 2007-2008 [Waylan Limberg](https://github.com/waylan).
+Original code Copyright 2007-2008 [Waylan Limberg](http://achinghead.com/).
 All changes Copyright 2008-2014 The Python Markdown Project
 License: [BSD](http://www.opensource.org/licenses/bsd-license.php)
 ```
@@ -49,28 +49,11 @@ CodeHilite Extension for Python-Markdown
 Adds code/syntax highlighting to standard Python-Markdown code blocks.
 See <https://python-markdown.github.io/extensions/code_hilite/>
 for documentation.
-Original code Copyright 2006-2008 [Waylan Limberg](https://github.com/waylan).
+Original code Copyright 2006-2008 [Waylan Limberg](http://achinghead.com/).
 All changes Copyright 2008-2014 The Python Markdown Project
 License: [BSD](http://www.opensource.org/licenses/bsd-license.php)
 ```
 
-## FancyLists
-
-`fancylists.py` is derived from Python Markdown's list handler.
-
-```
-Started by Manfred Stienstra (http://www.dwerg.net/).
-Maintained for a few years by Yuri Takhteyev (http://www.freewisdom.org).
-Currently maintained by Waylan Limberg (https://github.com/waylan),
-Dmitry Shachnev (https://github.com/mitya57) and Isaac Muse (https://github.com/facelessuser).
-
-Copyright 2007-2023 The Python Markdown Project (v. 1.7 and later)
-Copyright 2004, 2005, 2006 Yuri Takhteyev (v. 0.2-1.6b)
-Copyright 2004 Manfred Stienstra (the original version)
-
-License: [BSD](http://www.opensource.org/licenses/bsd-license.php)
-```
-
 ## Gemoji Index
 
 `gemoji_db.py` is generated from Gemoji's source code: @github/gemoji.

{traitly-0.1.2 → traitly-0.2.1}/.gitignore

@@ -7,10 +7,14 @@ __pycache__/
 .Python
 
 # python environments
-.traitly_test/*
+traitly_test/*
+dev_venv
+venv_traitly
+docs_tests
 
 # Cache
 .cache/
+.DS_Store
 
 # Build
 build/
@@ -25,14 +29,30 @@ requirements.txt
 requirements-dev.txt
 
 # test results
-tests/**/Results
 tests/**/Images_from_PDF/
 tests/**/*.txt
-
+tests/color_correction/18-26*
 .coverage
+tests/data
+
 
 # notebooks
 Untitled*
 
 # HF files
-./traitly/
+./traitly/traitly
+
+# Notes
+scripts/
+
+# Logs
+*.log
+
+
+# extra files
+*.jpg
+*.png
+*.pt
+*.ipynb
+
+traitly_app_hf

{traitly-0.1.2 → traitly-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: traitly
-Version: 0.1.2
+Version: 0.2.1
 Summary: Computer vision toolkit for high-throughput fruit phenotyping.
 Project-URL: Repository, https://github.com/mariameraz/traitly
 Project-URL: Documentation, https://traitly.readthedocs.io/en/latest/
@@ -16,14 +16,14 @@ Classifier: Environment :: Console
 Classifier: Environment :: Web Environment
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Image Processing
-Requires-Python: >=3.9
+Requires-Python: >=3.10
+Requires-Dist: colour-science
 Requires-Dist: easyocr
 Requires-Dist: ipython
 Requires-Dist: matplotlib
@@ -32,6 +32,7 @@ Requires-Dist: opencv-contrib-python
 Requires-Dist: pandas
 Requires-Dist: psutil
 Requires-Dist: rich-argparse
+Requires-Dist: scikit-learn
 Requires-Dist: scipy
 Requires-Dist: tqdm
 Requires-Dist: ultralytics
@@ -48,8 +49,8 @@ Description-Content-Type: text/markdown
 <div align="center">
 <h1>Traitly</h1>
 
-
-[![Python 3.9+](https://github.com/mariameraz/traitly/actions/workflows/python_compatibility.yml/badge.svg)](https://github.com/mariameraz/traitly/actions/workflows/python_compatibility.yml)
+[![PyPI](https://img.shields.io/pypi/v/traitly?logo=pypi&logoColor=white&cacheSeconds=300)](https://pypi.org/project/traitly)
+[![Python 3.10+](https://github.com/mariameraz/traitly/actions/workflows/python_compatibility.yml/badge.svg)](https://github.com/mariameraz/traitly/actions/workflows/python_compatibility.yml)
 [![Testing](https://github.com/mariameraz/traitly/actions/workflows/pytest.yml/badge.svg?branch=main)](https://github.com/mariameraz/traitly/actions/workflows/pytest.yml)
 [![codecov](https://codecov.io/gh/mariameraz/traitly/graph/badge.svg?token=ZDT6RBAGZJ)](https://codecov.io/gh/mariameraz/traitly)
 [![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-green?logo=gnu&logoColor=white)](https://github.com/mariameraz/traitly/blob/main/LICENSE)
@@ -64,7 +65,7 @@ Description-Content-Type: text/markdown
 
 <br>
 
-Página disponible en: [![Spanish](https://img.shields.io/badge/Idioma-Espa%C3%B1ol-pink)](https://github.com/mariameraz/traitly/blob/main/README_ES.md)
+ Disponible en: [![Spanish](https://img.shields.io/badge/Idioma-Espa%C3%B1ol-pink)](https://github.com/mariameraz/traitly/blob/main/README_ES.md)
 
 
 **Traitly** is an open-source Python tool for automated, high-throughput fruit phenotyping from digital images. Using computer vision methods, it quantifies morphological, symmetry, and color traits across both internal structures and the external appearance of the fruit.
@@ -102,6 +103,7 @@ Traitly can be used from Python, the command line (CLI), or as a web application
 Posters related to Traitly can be found in this folder:
 
 - [Posters](https://drive.google.com/drive/folders/1AvlHWKcDvoE9m9QcmCJ5o-ma9W-LNQMe?usp=share_link) ★ˎˊ˗
+- [Presentations](https://drive.google.com/file/d/1OwLi9_24Be9-VKDPo0dshGsbO3_rUtUb/view?usp=sharing) ★ˎˊ˗
 
 These materials provide additional methodological details and results from research derived from our package.
 
@@ -120,7 +122,7 @@ We are working on a manuscript describing this software and its applications, ex
 
 For questions or comments about the project, feel free to reach out to:
 
-* [ma.meraz@proton.me](mailto:ma.meraz@proton.me)
+* [ma.torresmeraz@gmail.com](mailto:ma.torresmeraz@gmail.com)
 * [torresmeraz@wisc.edu](mailto:torresmeraz@wisc.edu)
 
 We are open to collaborations, including adding new traits, and creating tutorials or workflows for specific crops or plant tissues.
@@ -134,7 +136,7 @@ Inspired by [All Contributors](https://allcontributors.org/), we recognize all k
 <!-- CONTRIBUTORS-START -->
 | Contributor | Role |
 |-------------|------|
-| [<img src="https://github.com/mariameraz.png" width="44" height="44" valign="middle">&nbsp;María Meraz](https://github.com/mariameraz) | 💻 📆 🚧 📓 ✅ 🐛 📖 ⚠️ 🤔 🌍 |
+| [<img src="https://github.com/mariameraz.png" width="44" height="44" valign="middle">&nbsp;María Meraz](https://github.com/mariameraz) | 💻 🚧 📓 ✅ 🐛 📖 ⚠️ 💬 👀 🌍 |
 | [<img src="https://github.com/hector-LM.png" width="44" height="44" valign="middle">&nbsp;Héctor López](https://github.com/hector-LM) | 📖 📓 ✅ 🤔 🐛 🔣 🌍 |
 | Juan Zalapa | 🔣 |
 | [<img src="https://github.com/AlvaroGuerrero.png" width="44" height="44" valign="middle">&nbsp;Álvaro Guerrero](https://github.com/AlvaroGuerrero) | 🐛 |

{traitly-0.1.2 → traitly-0.2.1}/README.md

@@ -1,8 +1,8 @@
 <div align="center">
 <h1>Traitly</h1>
 
-
-[![Python 3.9+](https://github.com/mariameraz/traitly/actions/workflows/python_compatibility.yml/badge.svg)](https://github.com/mariameraz/traitly/actions/workflows/python_compatibility.yml)
+[![PyPI](https://img.shields.io/pypi/v/traitly?logo=pypi&logoColor=white&cacheSeconds=300)](https://pypi.org/project/traitly)
+[![Python 3.10+](https://github.com/mariameraz/traitly/actions/workflows/python_compatibility.yml/badge.svg)](https://github.com/mariameraz/traitly/actions/workflows/python_compatibility.yml)
 [![Testing](https://github.com/mariameraz/traitly/actions/workflows/pytest.yml/badge.svg?branch=main)](https://github.com/mariameraz/traitly/actions/workflows/pytest.yml)
 [![codecov](https://codecov.io/gh/mariameraz/traitly/graph/badge.svg?token=ZDT6RBAGZJ)](https://codecov.io/gh/mariameraz/traitly)
 [![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-green?logo=gnu&logoColor=white)](https://github.com/mariameraz/traitly/blob/main/LICENSE)
@@ -17,7 +17,7 @@
 
 <br>
 
-Página disponible en: [![Spanish](https://img.shields.io/badge/Idioma-Espa%C3%B1ol-pink)](https://github.com/mariameraz/traitly/blob/main/README_ES.md)
+ Disponible en: [![Spanish](https://img.shields.io/badge/Idioma-Espa%C3%B1ol-pink)](https://github.com/mariameraz/traitly/blob/main/README_ES.md)
 
 
 **Traitly** is an open-source Python tool for automated, high-throughput fruit phenotyping from digital images. Using computer vision methods, it quantifies morphological, symmetry, and color traits across both internal structures and the external appearance of the fruit.
@@ -55,6 +55,7 @@ Traitly can be used from Python, the command line (CLI), or as a web application
 Posters related to Traitly can be found in this folder:
 
 - [Posters](https://drive.google.com/drive/folders/1AvlHWKcDvoE9m9QcmCJ5o-ma9W-LNQMe?usp=share_link) ★ˎˊ˗
+- [Presentations](https://drive.google.com/file/d/1OwLi9_24Be9-VKDPo0dshGsbO3_rUtUb/view?usp=sharing) ★ˎˊ˗
 
 These materials provide additional methodological details and results from research derived from our package.
 
@@ -73,7 +74,7 @@ We are working on a manuscript describing this software and its applications, ex
 
 For questions or comments about the project, feel free to reach out to:
 
-* [ma.meraz@proton.me](mailto:ma.meraz@proton.me)
+* [ma.torresmeraz@gmail.com](mailto:ma.torresmeraz@gmail.com)
 * [torresmeraz@wisc.edu](mailto:torresmeraz@wisc.edu)
 
 We are open to collaborations, including adding new traits, and creating tutorials or workflows for specific crops or plant tissues.
@@ -87,7 +88,7 @@ Inspired by [All Contributors](https://allcontributors.org/), we recognize all k
 <!-- CONTRIBUTORS-START -->
 | Contributor | Role |
 |-------------|------|
-| [<img src="https://github.com/mariameraz.png" width="44" height="44" valign="middle">&nbsp;María Meraz](https://github.com/mariameraz) | 💻 📆 🚧 📓 ✅ 🐛 📖 ⚠️ 🤔 🌍 |
+| [<img src="https://github.com/mariameraz.png" width="44" height="44" valign="middle">&nbsp;María Meraz](https://github.com/mariameraz) | 💻 🚧 📓 ✅ 🐛 📖 ⚠️ 💬 👀 🌍 |
 | [<img src="https://github.com/hector-LM.png" width="44" height="44" valign="middle">&nbsp;Héctor López](https://github.com/hector-LM) | 📖 📓 ✅ 🤔 🐛 🔣 🌍 |
 | Juan Zalapa | 🔣 |
 | [<img src="https://github.com/AlvaroGuerrero.png" width="44" height="44" valign="middle">&nbsp;Álvaro Guerrero](https://github.com/AlvaroGuerrero) | 🐛 |

{traitly-0.1.2 → traitly-0.2.1}/pyproject.toml

@@ -4,10 +4,10 @@ build-backend = "hatchling.build"
 
 [project]
 name = "traitly"
-version = "0.1.2"
+version = "0.2.1"
 description = "Computer vision toolkit for high-throughput fruit phenotyping."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = { text = "AGPL-3.0-or-later" }
 license-files = ["LICENSE*"]
 
@@ -27,11 +27,11 @@ dependencies = [
   "easyocr",
   "ultralytics",
   "rich-argparse",
-  "ipython"
+  "ipython",
+  "scikit-learn",
+  "colour-science"
 ]
 
-
-
 keywords = [
   "plant-phenotyping",
   "fruit-morphology",
@@ -43,7 +43,6 @@ classifiers = [
   "Operating System :: OS Independent",
   "Environment :: Console",
   "Environment :: Web Environment",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",

{traitly-0.1.2 → traitly-0.2.1}/src/traitly/cli.py

@@ -13,6 +13,8 @@ Usage
 
     traitly --fruit_internal -i PATH [-o PATH] [--json PATH] [--num_cores N]
     traitly --fruit_external -i PATH [-o PATH] [--json PATH] [--num_cores N]
+    traitly --info
+    traitly --version
 
 For folder inputs, delegates to
 :meth:`~traitly.fruit_phenotyping.internal_analysis.FruitInternalAnalyzer.analyze_folder`
@@ -20,18 +22,32 @@ or
 :meth:`~traitly.fruit_phenotyping.external_analysis.FruitExternalAnalyzer.analyze_folder`.
 For single images, delegates to
 :meth:`~traitly.fruit_phenotyping.internal_analysis.FruitInternalAnalyzer.process_single_file`.
+or
+:meth:`~traitly.fruit_phenotyping.external_analysis.FruitExternalAnalyzer.process_single_file`.
 """
 
+# ============================================================================
+# STANDARD LIBRARY
+# ============================================================================
 import argparse
 import sys
 import os
 from pathlib import Path
+import importlib.metadata
 from rich_argparse import RawDescriptionRichHelpFormatter
-from traitly import __version__
 
 # ============================================================================
-# Parser
+# INTERNAL
 # ============================================================================
+from traitly.utils.environment import (
+    get_session_metadata,
+    get_package_versions,
+    get_system_metadata
+)
+
+###########
+# Parser ##
+###########
 
 def _fmt_examples(rows):
     return "\n".join(f"  {r[0]}" for r in rows)
@@ -60,90 +76,97 @@ def create_parser() -> argparse.ArgumentParser:
             "",
             "Examples:",
             _fmt_examples([
+                ("  # Get traitly fruit_internal and fruit_external parameters info",),
+                ("  traitly fruit_internal --help",),
+                ("  traitly fruit_external --help",),
+                ("",),
                 ("  # Internal structure analysis (single image or folder)",),
-                ("  traitly --fruit_internal -i tests/sample_data/",),
-                ("  traitly --fruit_internal -i tests/sample_data/ -o results/ --num_cores 4",),
-                ("  traitly --fruit_internal -i tests/sample_data/ --json config.json",),
+                ("  traitly fruit_internal -i tests/sample_data/",),
+                ("  traitly fruit_internal -i tests/sample_data/ -o results/ --num_cores 4",),
+                ("  traitly fruit_internal -i tests/sample_data/ --json config.json",),
                 ("",),
                 ("  # External analysis (single image or folder)",),
-                ("  traitly --fruit_external -i tests/sample_data/",),
-                ("  traitly --fruit_external -i tests/sample_data/ -o results/ --json config.json --num_cores 4",),
+                ("  traitly fruit_external -i tests/sample_data/",),
+                ("  traitly fruit_external -i tests/sample_data/ -o results/ --json config.json --num_cores 4",),
+                ("",),
+                ("  # Get traitly and system metadata",),
+                ("  traitly info",),
+                ("",),
+                ("  # Get traitly version",),
+                ("  traitly --version",),
             ]),
             "",
             "="*70,
             "For more details ->",
             "   - GitHub Repository: https://github.com/mariameraz/traitly \n"
             "   - Documentation: https://traitly.readthedocs.io/ ",
+            "   - Contact: ma.torresmeraz@gmail.com",
             "="*70,
             "",
         ])
     )
 
-    # Mode (mutually exclusive)
-    mode_group = parser.add_mutually_exclusive_group(required=True)
-    mode_group.add_argument(
-        '--fruit_internal',
-        action='store_true',
-        help='Analyze internal fruit structure (locules, pericarp, symmetry)'
-    )
-    mode_group.add_argument(
-        '--fruit_external',
-        action='store_true',
-        help='Analyze external fruit structure (morphology, color)'
-    )
-
-    # Required
-    parser.add_argument(
-        '-i', '--input',
-        type=str,
-        required=True,
-        metavar='PATH',
-        help='Path to image file or folder'
-    )
-
-    # Optional
-    parser.add_argument(
-        '-o', '--output',
-        type=str,
-        default=None,
-        metavar='PATH',
-        help='Output directory (default: <input>/Results/)'
-    )
-
-    parser.add_argument(
-        '--json',
-        type=str,
-        default=None,
-        metavar='PATH',
-        help='Path to JSON config file with analysis parameters'
-    )
-
-    parser.add_argument(
-        '--num_cores',
-        type=int,
-        default=1,
-        metavar='N',
-        help='Number of CPU cores for parallel processing (default: 1)'
-    )
-
-    parser.add_argument(
-        '--no_morphology',
-        action='store_true',
-        help='Skip morphology analysis'
+    subparsers = parser.add_subparsers(dest='command', required=True)
+
+    def _add_common_args(subparser):
+        subparser.add_argument(
+            '-i', '--input',
+            type=str,
+            required=True,
+            metavar='PATH',
+            help='Path to image file or folder'
+        )
+        subparser.add_argument(
+            '-o', '--output',
+            type=str,
+            default=None,
+            metavar='PATH',
+            help='Output directory (default: <input>/Results/)'
+        )
+        subparser.add_argument(
+            '--json',
+            type=str,
+            default=None,
+            metavar='PATH',
+            help='Path to JSON config file with analysis parameters'
+        )
+        subparser.add_argument(
+            '--num_cores',
+            type=int,
+            default=1,
+            metavar='N',
+            help='Number of CPU cores for parallel processing (default: 1)'
+        )
+        subparser.add_argument(
+            '--no_morphology',
+            action='store_true',
+            help='Skip morphology analysis'
+        )
+        subparser.add_argument(
+            '--no_color',
+            action='store_true',
+            help='Skip color analysis'
+        )
+
+    fruit_internal = subparsers.add_parser(
+        'fruit_internal',
+        help='Analyze internal fruit structure (locules, pericarp, symmetry)',
+        formatter_class=RawDescriptionRichHelpFormatter,
     )
+    _add_common_args(fruit_internal)
 
-    parser.add_argument(
-        '--no_color',
-        action='store_true',
-        help='Skip color analysis'
+    fruit_external = subparsers.add_parser(
+        'fruit_external',
+        help='Analyze external fruit structure (morphology, color)',
+        formatter_class=RawDescriptionRichHelpFormatter,
     )
+    _add_common_args(fruit_external)
 
-    parser.add_argument(
-        '--version',
-        action='version',
-        version=f'%(prog)s {__version__}'
+    subparsers.add_parser(
+        'info',
+        help='Print traitly and system metadata',
+        formatter_class=RawDescriptionRichHelpFormatter,
     )
-
     return parser
 
 
@@ -371,14 +394,22 @@ def main() -> None:
     parser = create_parser()
     args   = parser.parse_args()
 
-    if args.fruit_internal:
+    if args.command == 'fruit_internal':
         run_internal(args)
-    elif args.fruit_external:
+    elif args.command == 'fruit_external':
         run_external(args)
+    elif args.command == 'info':
+        for line in get_session_metadata():
+            print(line)
+        print("\nsystem:")
+        for line in get_system_metadata():
+            print(f"    {line}")
+        print("\ndependencies:")
+        for pkg, version in get_package_versions().items():
+            print(f"    {pkg}: {version}")
     else:
         parser.print_help()
         sys.exit(0)
 
-
 if __name__ == '__main__':
     main()

traitly-0.2.1/src/traitly/color_correction/__init__.py

@@ -0,0 +1 @@
+from .color_correction import ColorCorrection