Merge branch '0.0.X' into main

conda/conda_build_config.yaml

@@ -1,2 +1,4 @@
 python:
-  - 3.9
+  - 3.9
+  - 3.8
+  - 3.7

conda/meta.yaml

@@ -19,15 +19,15 @@ requirements:
     - flake8
   run:
     - python
-    - ete3>=3.*
+    - ete3>=3.1.2
     - biopython>=1.78
     - tqdm>=4.62.3
     - numpy>=1.19
-    - pandas>=1.3.5
+    - pandas>=1.1.0
     - pillow>=8.4.0
     - seaborn>=0.11.2
     - matplotlib>=3.5.0
-    - pyqt>=5.*
+    - pyqt>=5.9.2
     - jupyter>=1.0.0
 
 test:

pyiwe/__init__.py

@@ -5,7 +5,7 @@
 See README.md for complete documentation.
 """
 
-__version__ = '0.0.6'
+__version__ = '0.0.7'
 
 import sys
 import traceback
@@ -18,7 +18,7 @@
     from .utils import visualize
     from .config import pyiw_config
 except ModuleNotFoundError:
-    print('ModuleNotFoundError happened. Check your dependencies.')
+    print('ModuleNotFoundError happened. Check your dependencies. Ignore during packaging.')
     traceback.print_exc(file=sys.stdout)
 
 TNTSetup().setup()

pyiwe/config.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import os
 import sys
 
@@ -12,10 +13,13 @@ def __init__(self):
         self.correct_platfrom = self.platform in self.available_platforms
 
     def get_tnt_path(self) -> str:
-        tnt_path = {
-            'linux': os.environ.get('TNT_PATH'),
-        }
-        return tnt_path.get(self.platform)
+        split_symb = {'linux': ":", 'win32': ";"}
+        found_path = None
+        for p in os.environ["PATH"].split(split_symb.get(self.platform)):
+            if "TNT" in p:
+                found_path = p
+                break
+        return found_path
 
 
 pyiw_config = PyIWConfig()

pyiwe/iwe.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import glob
 import itertools
 import os

pyiwe/utils/common.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import datetime as dt
 
 

pyiwe/utils/processing.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import io
 import re
 
@@ -32,7 +33,7 @@ def check_tree_formats_selection(tree_format: str):
     Returns:
 
     """
-    _tree_formats = list(supported_formats.keys())
+    _tree_formats = tuple(supported_formats.keys())
     if tree_format not in _tree_formats:
         raise AssertionError(f'Tree format is not recognized: {tree_format}\n Available: {_tree_formats}')
 
@@ -121,15 +122,15 @@ def buffer_convert(trees, out_format: str, **kwargs) -> io.StringIO:
 
 
 def get_tnt_trees(tree_path: str, output_format: str = 'newick',
-                  verbose: bool = True) -> tuple[list[ph.BaseTree.Tree], str]:
+                  verbose: bool = True) -> list[list[ph.BaseTree.Tree], str]:
     """
     Read TNT tree and return it in format `output_format`.
     Args:
         tree_path:     str, the path to a tree
         output_format: str, possible formats: 'newick', 'nexus', 'nexml', 'phyloxml', newick is default
         verbose:       bool, verbosity for trees reading
 
-    Returns: tuple[list[ph.BaseTree.Tree], str]
+    Returns: list[list[ph.BaseTree.Tree], str]
 
     """
     check_tree_formats_selection(output_format)

pyiwe/utils/visualize.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import os
 
 import matplotlib.pyplot as plt

requirements.txt

@@ -0,0 +1,10 @@
+ete3>=3.1.2
+biopython>=1.78
+tqdm>=4.62.3
+numpy>=1.19
+pandas>=1.1.0
+pillow>=8.4.0
+seaborn>=0.11.2
+matplotlib>=3.5.0
+PyQt5>=5.15.6
+jupyter>=1.0.0

setup.py

@@ -1,5 +1,4 @@
 import os
-
 from setuptools import setup, find_packages
 from setuptools.command.install import install
 
@@ -32,15 +31,15 @@ def run(self):
     description="Python wrapper for TNT (Tree analysis using New Technology) implied weighting with clades support",
     long_description=long_description,
     install_requires=[
-        'ete3>=3.*',
+        'ete3>=3.1.2',
         'biopython>=1.78',
         'tqdm>=4.62.3',
         'numpy>=1.19',
-        'pandas>=1.3.5',
+        'pandas>=1.1.0',
         'pillow>=8.4.0',
         'seaborn>=0.11.2',
         'matplotlib>=3.5.0',
-        'PyQt5>=5.*',
+        'PyQt5>=5.15.6',
         'jupyter>=1.0.0',
     ],
     package_data={'pyiwe': ['tests/testdata/bryocorini/*',
@@ -50,7 +49,7 @@ def run(self):
                             ]},
     setup_requires=['flake8'],
     tests_require=['pytest'],
-    python_requires='>=3.9',
+    python_requires='>=3.7',
     cmdclass={
         'install': _TNTSetup,
     },
@@ -61,6 +60,8 @@ def run(self):
         "Operating System :: Unix",
         "Operating System :: Microsoft :: Windows",
         "Programming Language :: Python",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
     ],
     url="https://github.com/alexander-pv/pyiwe",

tutorial/pyiwe_runner.py

@@ -111,7 +111,12 @@ def runner(args: argparse.Namespace):
     with open(os.path.join(args.output_folder, 'final_tree_newick.txt'), 'w') as f:
         f.write(majority_tree.format(format='newick'))
     open_ete_browser(tree=ETree(majority_tree.format(format='newick')))
-    df_tree_flat = df.explode(column=['k_vals'])
+
+    if int(pd.__version__.split('.')[1]) < 3:
+        df_tree_flat = df.explode('k_vals')
+    else:
+        df_tree_flat = df.explode(column=['k_vals'])
+
     tree_vis.make_k_stripplot(df=df_tree_flat, x='clade_id', y='k_vals', save=False)