autogaita 1.5.4__tar.gz → 1.5.6__tar.gz

{autogaita-1.5.4 → autogaita-1.5.6}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: autogaita
-Version: 1.5.4
+Version: 1.5.6
 Summary: Automated Gait (and more!) Analysis in Python
 Author-email: Mahan Hosseini <autogaita@fz-juelich.de>
-License: GPLv3
+License-Expression: GPL-3.0-only
 Project-URL: Homepage, https://github.com/mahan-hosseini/AutoGaitA/
 Project-URL: Documentation, https://docs.google.com/document/d/1iQxSwqBW3VdIXHm-AtV4TGlgpJPDldogVx6qzscsGxA/edit?tab=t.0
 Project-URL: YouTube, https://youtube.com/playlist?list=PLCn5T7K_H8K56NIcEsfDK664OP7cN_Bad&si=JBEYuzDDRe7qz5Qd
@@ -18,7 +18,7 @@ Requires-Dist: matplotlib>=3.7
 Requires-Dist: scikit-learn>=1.2
 Requires-Dist: pingouin>=0.5
 Requires-Dist: scipy>=1.11
-Requires-Dist: scikit-bio>=0.7.1
+Requires-Dist: scikit-bio>=0.7.1; sys_platform == "darwin"
 Requires-Dist: statsmodels>=0.14
 Requires-Dist: ffmpeg-python>=0.2
 Requires-Dist: openpyxl>=3.1

{autogaita-1.5.4 → autogaita-1.5.6}/autogaita/group/group_3_PCA.py

@@ -2,11 +2,11 @@
 from autogaita.resources.utils import bin_num_to_percentages, write_issues_to_textfile
 from autogaita.group.group_utils import save_figures
 import os
+import sys
 import pandas as pd
 import numpy as np
 from sklearn.preprocessing import StandardScaler
 from sklearn.decomposition import PCA
-from skbio.stats.distance import DistanceMatrix, permanova
 from scipy.spatial.distance import pdist, squareform
 from statsmodels.stats.multitest import multipletests
 import openpyxl
@@ -14,6 +14,14 @@ import seaborn as sns
 import matplotlib.pyplot as plt
 from matplotlib.animation import FuncAnimation, FFMpegWriter
 
+# skbio throws some error on windows during build
+skbio_available = sys.platform == "darwin"
+if skbio_available:
+    try:
+        from skbio.stats.distance import DistanceMatrix, permanova
+    except ImportError:
+        skbio_available = False
+
 # %% constants
 from autogaita.resources.constants import (
     ID_COL,
@@ -50,8 +58,13 @@ def PCA_main(avg_dfs, folderinfo, cfg, plot_panel_instance):
     PCA_df, features = create_PCA_df(avg_dfs, folderinfo, cfg)
     # run the PCA
     PCA_df, PCA_info = run_PCA(PCA_df, features, folderinfo, cfg)
-    # run the PERMANOVA
-    run_PCA_PERMANOVA(PCA_df, folderinfo, cfg)
+    # run the PERMANOVA - only on mac
+    if skbio_available:
+        run_PCA_PERMANOVA(PCA_df, folderinfo, cfg)
+    else:
+        write_issues_to_textfile(
+            "\nSkipping PCA PERMANOVA (skbio is broken on Windows).", folderinfo
+        )
     # save PCA info to xlsx files
     PCA_info_to_xlsx(PCA_df, PCA_info, folderinfo, cfg)
     if PCA_info["number_of_PCs"] < 2:

{autogaita-1.5.4 → autogaita-1.5.6}/autogaita.egg-info/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: autogaita
-Version: 1.5.4
+Version: 1.5.6
 Summary: Automated Gait (and more!) Analysis in Python
 Author-email: Mahan Hosseini <autogaita@fz-juelich.de>
-License: GPLv3
+License-Expression: GPL-3.0-only
 Project-URL: Homepage, https://github.com/mahan-hosseini/AutoGaitA/
 Project-URL: Documentation, https://docs.google.com/document/d/1iQxSwqBW3VdIXHm-AtV4TGlgpJPDldogVx6qzscsGxA/edit?tab=t.0
 Project-URL: YouTube, https://youtube.com/playlist?list=PLCn5T7K_H8K56NIcEsfDK664OP7cN_Bad&si=JBEYuzDDRe7qz5Qd
@@ -18,7 +18,7 @@ Requires-Dist: matplotlib>=3.7
 Requires-Dist: scikit-learn>=1.2
 Requires-Dist: pingouin>=0.5
 Requires-Dist: scipy>=1.11
-Requires-Dist: scikit-bio>=0.7.1
+Requires-Dist: scikit-bio>=0.7.1; sys_platform == "darwin"
 Requires-Dist: statsmodels>=0.14
 Requires-Dist: ffmpeg-python>=0.2
 Requires-Dist: openpyxl>=3.1

{autogaita-1.5.4 → autogaita-1.5.6}/autogaita.egg-info/SOURCES.txt

@@ -74,6 +74,7 @@ autogaita/universal3D/universal3D_constants.py
 autogaita/universal3D/universal3D_datafile_preparation.py
 autogaita/universal3D/universal3D_main.py
 autogaita/universal3D/universal3D_utils.py
+autogaita_backup/backup_setup.py
 autogaita_backup/common2D_run_and_done_gui.py
 autogaita_backup/dlc_1_preparation.py
 autogaita_backup/dlc_2_sc_extraction.py

autogaita-1.5.6/autogaita_backup/backup_setup.py

@@ -0,0 +1,44 @@
+# import
+from setuptools import setup, find_packages
+
+# list of across-platform dependencies
+install_requires = [
+    "customtkinter>=5.2",
+    "pandas>=2.0,<3.0",
+    "numpy>=1.24",
+    "seaborn>=0.13",
+    "matplotlib>=3.7",
+    "scikit-learn>=1.2",
+    "pingouin>=0.5",
+    "scipy>=1.11",
+    "scikit-bio>=0.7.1",
+    "statsmodels>=0.14",
+    "ffmpeg-python>=0.2",
+    "openpyxl>=3.1",
+    "pillow>=10.3",
+    "h5py>=3.11",
+    "pyobjc; sys_platform == 'darwin'",  # Only on macOS
+]
+
+# call setup function
+setup(
+    name="autogaita",
+    python_requires=">=3.10",
+    version="1.5.3",  # rc == release candidate (before release is finished)
+    author="Mahan Hosseini",
+    description="Automatic Gait Analysis in Python.",
+    long_description="A toolbox to streamline and standardise the analysis of kinematics across species after ML-based body posture tracking. Despite being optimised for gait analyses, AutoGaitA has the potential to be used for any kind of kinematic analysis.",
+    long_description_content_type="text/plain",
+    entry_points={
+        "console_scripts": [
+            "autogaita = autogaita.gui.main_gui:run_gui",
+        ],
+    },
+    packages=find_packages(),
+    include_package_data=True,
+    package_data={"": ["*.txt", "*.rst", "*.png", "*.icns", "*.ico", "*.json"]},
+    install_requires=install_requires,
+    extras_require={"dev": ["pytest", "hypothesis"]},
+    license="GPLv3",
+    url="https://github.com/mahan-hosseini/AutoGaitA/",
+)

{autogaita-1.5.4 → autogaita-1.5.6}/pyproject.toml

@@ -4,12 +4,12 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "autogaita"
-version = "1.5.4"  # rc == release candidate
+version = "1.5.6"  # rc == release candidate
 authors = [{name = "Mahan Hosseini", email = "autogaita@fz-juelich.de"}]
 description = "Automated Gait (and more!) Analysis in Python"
 readme = "README.md"
 requires-python = ">=3.10"
-license = {text = "GPLv3"}
+license = "GPL-3.0-only"
 dependencies = [
     "customtkinter>=5.2",
     "pandas>=2.0,<3.0",
@@ -19,7 +19,7 @@ dependencies = [
     "scikit-learn>=1.2",
     "pingouin>=0.5",
     "scipy>=1.11",
-    "scikit-bio>=0.7.1",
+    "scikit-bio>=0.7.1; sys_platform == 'darwin'",
     "statsmodels>=0.14",
     "ffmpeg-python>=0.2",
     "openpyxl>=3.1",

{autogaita-1.5.4 → autogaita-1.5.6}/autogaita.egg-info/requires.txt

@@ -6,7 +6,6 @@ matplotlib>=3.7
 scikit-learn>=1.2
 pingouin>=0.5
 scipy>=1.11
-scikit-bio>=0.7.1
 statsmodels>=0.14
 ffmpeg-python>=0.2
 openpyxl>=3.1
@@ -14,6 +13,7 @@ pillow>=10.3
 h5py>=3.11
 
 [:sys_platform == "darwin"]
+scikit-bio>=0.7.1
 pyobjc
 
 [dev]