prepare to release 0.5.2

yoshida-lab · Jun 4, 2021 · e8484ff · e8484ff
1 parent e36ca0e
commit e8484ff
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Showing 4 changed files with 37 additions and 34 deletions.
diff --git a/README.md b/README.md
@@ -114,8 +114,8 @@ the following command:
 docker run --rm -it \
   --runtime=nvidia \
   --ipc=host \
-  --publish="8888:8888"
-  --volume=$Home/.xenonpy:/home/user/.xenonpy \
+  --publish="8888:8888" \
+  --volume=$HOME/.xenonpy:/home/user/.xenonpy \
   --volume=<path/to/your/workspace>:/workspace \
   -e NVIDIA_VISIBLE_DEVICES=0 \
   yoshidalab/xenonpy

diff --git a/setup.py b/setup.py
@@ -18,6 +18,12 @@
 
 
 class PackageInfo(object):
+    """
+    Appendix
+    --------
+    classifiers: https://pypi.python.org/pypi?%3Aaction=list_classifiers
+    """
+
     def __init__(self, conf_file):
         yaml = YAML(typ='safe')
         yaml.indent(mapping=2, sequence=4, offset=2)
@@ -101,8 +107,7 @@ def __getattr__(self, item: str):
     # It's a directory style package
     if os.path.exists(__file__[:-8] + PKG_NAME):
         # Include all sub packages in package directory
-        PACKAGES = find_packages(
-            exclude=["*.tests", "*.tests.*", "tests.*", "tests"])
+        PACKAGES = find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests"])
 
         # Include everything in package directory
         INCLUDE_PACKAGE_DATA = True
@@ -121,8 +126,7 @@ def __getattr__(self, item: str):
     # Use todays date as GitHub release tag
     RELEASE_TAG = 'v' + VERSION
     # Source code download url
-    DOWNLOAD_URL = "https://github.com/{0}/{1}/archive/{2}.tar.gz".format(
-        GITHUB_USERNAME, PKG_NAME, RELEASE_TAG)
+    DOWNLOAD_URL = "https://github.com/{0}/{1}/archive/{2}.tar.gz".format(GITHUB_USERNAME, PKG_NAME, RELEASE_TAG)
 
     LICENSE = package.license or "'__license__' not found in '%s.__init__.py'!" % PKG_NAME
 
@@ -148,30 +152,24 @@ def __getattr__(self, item: str):
     INSTALL_REQUIRES = PackageInfo.requirements()
     SETUP_REQUIRES = ['pytest-runner', 'ruamel.yaml']
     TESTS_REQUIRE = ['pytest']
-    setup(
-        python_requires='~=3.6',
-        name=PKG_NAME,
-        description=SHORT_DESCRIPTION,
-        long_description=LONG_DESCRIPTION,
-        version=VERSION,
-        author=AUTHOR,
-        author_email=AUTHOR_EMAIL,
-        maintainer=MAINTAINER,
-        maintainer_email=MAINTAINER_EMAIL,
-        packages=PACKAGES,
-        include_package_data=INCLUDE_PACKAGE_DATA,
-        package_data=PACKAGE_DATA,
-        py_modules=PY_MODULES,
-        url=GITHUB_URL,
-        download_url=DOWNLOAD_URL,
-        classifiers=CLASSIFIERS,
-        platforms=PLATFORMS,
-        license=LICENSE,
-        setup_requires=SETUP_REQUIRES,
-        install_requires=INSTALL_REQUIRES,
-        tests_require=TESTS_REQUIRE)
-"""
-Appendix
---------
-classifiers: https://pypi.python.org/pypi?%3Aaction=list_classifiers
-"""
+    setup(python_requires='~=3.6',
+          name=PKG_NAME,
+          description=SHORT_DESCRIPTION,
+          long_description=LONG_DESCRIPTION,
+          version=VERSION,
+          author=AUTHOR,
+          author_email=AUTHOR_EMAIL,
+          maintainer=MAINTAINER,
+          maintainer_email=MAINTAINER_EMAIL,
+          packages=PACKAGES,
+          include_package_data=INCLUDE_PACKAGE_DATA,
+          package_data=PACKAGE_DATA,
+          py_modules=PY_MODULES,
+          url=GITHUB_URL,
+          download_url=DOWNLOAD_URL,
+          classifiers=CLASSIFIERS,
+          platforms=PLATFORMS,
+          license=LICENSE,
+          setup_requires=SETUP_REQUIRES,
+          install_requires=INSTALL_REQUIRES,
+          tests_require=TESTS_REQUIRE)
diff --git a/xenonpy/conf.yml b/xenonpy/conf.yml
@@ -9,9 +9,11 @@ short_description: "material descriptor library"
 license: "BSD (3-clause)"
 author:
   - "TsumiNa"
+  - "stewu5"
 author_email: "liu.chang.1865@gmail.com"
 maintainer:
   - "TsumiNa"
+  - "stewu5"
 maintainer_email: "liu.chang.1865@gmail.com"
 github_username: "yoshida-lab"
 

diff --git a/xenonpy/model/sequential.py b/xenonpy/model/sequential.py
@@ -19,8 +19,8 @@ class LinearLayer(nn.Module):
     def __init__(self,
                  in_features: int,
                  out_features: int,
-                 bias: bool = True,
                  *,
+                 bias: bool = True,
                  dropout: float = 0.,
                  activation_func: Callable = nn.ReLU(),
                  normalizer: Union[float, None] = .1):
@@ -31,6 +31,9 @@ def __init__(self,
             Size of each input sample.
         out_features:
             Size of each output sample
+        bias:
+            If set to ``False``, the layer will not learn an additive bias.
+            Default: ``True``
         dropout: float
             Probability of an element to be zeroed. Default: 0.5
         activation_func: func