split pytorch dependence

xenonpy/__init__.py

@@ -3,7 +3,7 @@
 # license that can be found in the LICENSE file.
 
 __version__ = '0.1.0'
-__release__ = 'b6'
+__release__ = 'b7'
 __short_description__ = "material descriptor library"
 __license__ = "BSD (3-clause)"
 __author__ = "TsumiNa"
@@ -12,7 +12,9 @@
 __maintainer_email__ = "liu.chang.1865@gmail.com"
 __github_username__ = "yoshida-lab"
 
-__pkg_cfg_root__ = '.' + __name__
+cfg_root = '.' + __name__
+
+dataset_ver = 'v0.1.0b6'
 
 
 def get_conf(key: str = None):
@@ -33,7 +35,7 @@ def get_conf(key: str = None):
     import yaml
     from pathlib import Path
     home = Path.home()
-    dir_ = home / __pkg_cfg_root__
+    dir_ = home / cfg_root
     cfg_file = dir_ / 'conf.yml'
     with open(cfg_file) as f:
         conf = yaml.load(f)
@@ -61,7 +63,7 @@ def _get_dataset_url(fname: str):
     return 'https://github.com/' + \
            __github_username__ + '/' + \
            __name__ + '/releases/download/' + \
-           __version__ + __release__ + '/' + \
+           dataset_ver + '/' + \
            fname + '.pkl'
 
 
@@ -80,7 +82,7 @@ def _init_cfg_file(force=False):
     from shutil import rmtree, copyfile
     from pathlib import Path
     home = Path.home()
-    dir_ = home / __pkg_cfg_root__
+    dir_ = home / cfg_root
     cfg_file = dir_ / 'conf.yml'
 
     dataset_dir = dir_ / 'dataset'
@@ -107,8 +109,8 @@ def _init_cfg_file(force=False):
 _init_cfg_file()
 
 from . import descriptor
-from . import model
 # from .pipeline import *
 # from .preprocess import *
 from . import utils
 from . import visualization
+from . import model

xenonpy/model/__init__.py

@@ -2,5 +2,6 @@
 # Use of this source code is governed by a BSD-style
 # license that can be found in the LICENSE file.
 
-from xenonpy.model.nn.checkpoint import CheckPoint
-from .nn import *
+from . import nn
+
+from . import extern

xenonpy/model/nn/__init__.py

@@ -2,5 +2,14 @@
 # Use of this source code is governed by a BSD-style
 # license that can be found in the LICENSE file.
 
-from .base_model import *
-from .layer import *
+import warnings as warnings
+
+with warnings.catch_warnings():
+    # warnings.simplefilter('default')
+    try:
+        import torch
+    except ImportError:
+        warnings.warn("Can't fing pytorch, will not load Neorul Network modules.", RuntimeWarning)
+    else:
+        from .base_model import *
+        from .layer import *

xenonpy/utils/datatools.py

@@ -15,7 +15,7 @@
 import requests
 from sklearn.externals import joblib as jl
 
-from .. import __pkg_cfg_root__
+from .. import cfg_root
 from .. import _get_dataset_url
 
 
@@ -155,19 +155,19 @@ def __init__(self,
             'electron_density', 'sample_A', 'mp_structure'
         ]
         self.chunk_size = chunk_size
-        self.dataset_dir = Path().home() / __pkg_cfg_root__ / 'dataset'
-        self.user_data_dir = Path().home() / __pkg_cfg_root__ / 'userdata'
-        self.cached_dir = Path().home() / __pkg_cfg_root__ / 'cached'
+        self.dataset_dir = Path().home() / cfg_root / 'dataset'
+        self.user_data_dir = Path().home() / cfg_root / 'userdata'
+        self.cached_dir = Path().home() / cfg_root / 'cached'
 
-    def _fetch_data(self, url):
+    def _fetch_data(self, url, save_to=None):
         schemes = {'http', 'https'}
         scheme = urlparse(url).scheme
         if 'http' in scheme:
-            return self._http_data(url)
+            return self._http_data(url, save_to)
         else:
             raise ValueError("Only can access [{}] data but you send {}. :(".format(schemes, scheme))
 
-    def _http_data(self, url):
+    def _http_data(self, url, save_to=None):
         r = requests.get(url, stream=True)
         r.raise_for_status()
 
@@ -176,7 +176,7 @@ def _http_data(self, url):
         else:
             filename = url.split('/')[-1]
 
-        save_to = str(self.cached_dir / filename)
+        save_to = str(self.cached_dir / filename) if not save_to else str(save_to)
         with open(save_to, 'wb') as f:
             for chunk in r.iter_content(chunk_size=self.chunk_size):
                 if chunk:  # filter out keep-alive new chunks
@@ -304,7 +304,7 @@ def __init__(self, dataset=None):
             The dir to save and load data
         """
         self.dataset = dataset
-        self._path = Path.home() / __pkg_cfg_root__ / 'userdata' / dataset
+        self._path = Path.home() / cfg_root / 'userdata' / dataset
         if not self._path.exists():
             self._path.mkdir(parents=True)
         self._files = None

xenonpy/visualization/heatmap.py

@@ -54,7 +54,7 @@ def fit(self, desc):
         self.desc = pd.DataFrame(minmax_scale(desc_), index=desc.index, columns=desc.columns)
         return self
 
-    def draw(self, y):
+    def draw(self, y=None):
         ax = sb.clustermap(
             self.desc,
             cmap="RdBu",
@@ -64,15 +64,19 @@ def draw(self, y):
             col_cluster=self.col_cluster,
             **self.kwargs)
         ax.cax.set_visible(False)
-        ax.ax_heatmap.set_position((0.1, 0.2, 0.84, 0.6))
         ax.ax_heatmap.yaxis.set_ticks_position('left')
         ax.ax_heatmap.yaxis.set_label_position('left')
-        ax.ax_col_dendrogram.set_position((0.1, 0.8, 0.83, 0.1))
 
-        ax = plt.axes([0.95, 0.2, 0.05, 0.6])
-        ax.plot(y.values, lw=4)
-        ax.spines['top'].set_visible(False)
-        ax.spines['right'].set_visible(False)
-        ax.set_xlabel('{:s}\n(property)'.format(y.name), fontsize=20)
+        if y is None:
+            ax.ax_col_dendrogram.set_position((0.1, 0.8, 0.9, 0.1))
+            ax.ax_heatmap.set_position((0.1, 0.2, 0.9, 0.6))
+        else:
+            ax.ax_col_dendrogram.set_position((0.1, 0.8, 0.83, 0.1))
+            ax.ax_heatmap.set_position((0.1, 0.2, 0.84, 0.6))
+            ax = plt.axes([0.95, 0.2, 0.05, 0.6])
+            ax.plot(y.values, lw=4)
+            ax.spines['top'].set_visible(False)
+            ax.spines['right'].set_visible(False)
+            ax.set_xlabel('{:s}\n(property)'.format(y.name), fontsize=20)
         if self.save:
             plt.savefig(**self.save)