Formatting and update the binder related stuff

.github/workflows/ci.yml

@@ -31,4 +31,4 @@ jobs:
       - name: Test with pytest
         shell: bash -el {0}
         run: |
-          pytest
+          pytest

.gitignore

@@ -1,3 +1,3 @@
 *.egg-info
 *.pyc
-*.bak
+*.bak

.gitlab-ci.yml

@@ -42,7 +42,7 @@ build_docker:
   services:
     - docker:dind
   before_script:
-    - echo '0. Installing dependencies...' 
+    - echo '0. Installing dependencies...'
     - apk add --no-cache pigz python3
     - python3 -m venv venv
     - . venv/bin/activate

.pre-commit-config.yaml

@@ -1,9 +1,44 @@
+exclude: '^(doc)|(cookiecutters)'
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.5.0
+  hooks:
+  - id: trailing-whitespace
+    exclude: (example)
+  - id: end-of-file-fixer
+    exclude: (example)
+  - id: check-yaml
+    exclude: (example)
+    args: ['--unsafe']
+  - id: check-json
+    exclude: (example)
+  - id: check-added-large-files
+    exclude: (example|tests/test_data/PROCAR.mgo)
+  - id: double-quote-string-fixer
+    exclude: (example)
+  - id: forbid-new-submodules
+    exclude: (example)
+
+- repo: https://github.com/psf/black
+  rev: 23.3.0
+  hooks:
+    - id: black
+      # It is recommended to specify the latest version of Python
+      # supported by your project here, or alternatively use
+      # pre-commit's default_language_version, see
+      # https://pre-commit.com/#top_level-default_language_version
+      language_version: python3.9
+
 - repo: local
   hooks:
-  # yapf = yet another python formatter
-  - id: yapf
-    name: yapf
-    entry: yapf
-    language: system
+  - id: pylint
+    name: pylint
+    entry: pylint
     types: [python]
-    args: ["-i"]
+    language: system
+    exclude: |
+      (?x)(
+      ^tutorials/|
+      ^examples/|
+      ^tests
+      )

README.md

@@ -6,7 +6,7 @@ airsspy
 A package to help working with the Ab initio Random Structure Searching ([AIRSS](https://www.mtg.msm.cam.ac.uk/Codes/AIRSS))
 using Atomic simulation environment ([ase](https://wiki.fysik.dtu.dk/ase/)).
 Supports building a search seed for AIRSS in a interactive python environments.
-One of the important steps for performing a successful search with AIRSS is to have sensible seed for generating 
+One of the important steps for performing a successful search with AIRSS is to have sensible seed for generating
 random structures, which are subsequently relaxed using the method of choice.
 In general, AIRSS only relies on a few simple parameters to generate random structure, such as numbers of atoms,
 numbers of species and cell volume.
@@ -15,7 +15,7 @@ tedious or impossible job to do.
 ASE has a suite of tools for manipulate atomic structure which can be very helpful for building structures,
 and here, for building search seeds.
 
-AIRSS is a open source code licensed under GPLv2, 
+AIRSS is a open source code licensed under GPLv2,
 this package does not contain any source code of AIRSS nor links to it.
 
 
@@ -97,6 +97,6 @@ Limitations
 -----------
 
 Due to the lack of `timeout` argument of `Popen.communicate` in python 2.7,
-communication with the `buildcell` is not available. Hence, direct generation and 
-retrieval of the random structure are not supported in python. However, it is 
+communication with the `buildcell` is not available. Hence, direct generation and
+retrieval of the random structure are not supported in python. However, it is
 still possible to write the seed out and call the program externally.

airsspy/build.py

@@ -71,7 +71,7 @@ def generate(self, timeout=10, write_cell=None):
 
         # Write the output from buildcell
         if write_cell:
-            with open(write_cell + ".cell", "w") as output:
+            with open(write_cell + ".cell", "w", encoding="utf-8") as output:
                 output.write(self.bc_out)
 
         # Process the result
@@ -80,7 +80,7 @@ def generate(self, timeout=10, write_cell=None):
         parser.parse()
         cellout = CellInput()
         for k, value in parser.get_dict().items():
-            cellout.__setitem__(k, value)
+            cellout[k] = value
 
         cell = cellout.get_cell()
         elements, positions, _ = cellout.get_positions()

airsspy/common.py

@@ -23,4 +23,4 @@
 
 
 class BuildcellError(RuntimeError):
-    """Exception for not been able to build the random cell"""
+    """Exception for not been able to build the random cell"""

binder/environment.yml

@@ -0,0 +1,8 @@
+name: airsspy
+channels:
+  - conda-forge
+dependencies:
+  - airss
+  - ase
+  - pip:
+      - castepinput

pyproject.toml

@@ -0,0 +1,22 @@
+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+
+[project]
+name = "airsspy"
+version = "0.1.4"
+description = "A wrapper for using AIRSS with python and ase."
+authors = [{name = "Bonan Zhu", email = "zhubonan@outlook.com"}]
+readme = "README.md"
+license = {file = "LICENSE"}
+
+dependencies = ['ase~=3.17', 'castepinput~=0.1']
+
+[project.urls]
+"Homepage" = "https://github.com/zhubonan/airsspy"
+
+[project.optional-dependencies]
+
+testing = ['pytest']
+"pre-commit" = ['pre-commit']

setup.py

@@ -20,9 +20,10 @@
 ###########################################################################
 
 from setuptools import setup, find_packages
-version = '0.1.4'
 
-if __name__ == '__main__':
+version = "0.1.4"
+
+if __name__ == "__main__":
     from os import path
     import os
 
@@ -31,24 +32,24 @@
         long_description = fh.read()
 
     setup(
-        name='airsspy',
+        name="airsspy",
         version=version,
-        url='https://github.com/zhubonan/airsspy',
+        url="https://github.com/zhubonan/airsspy",
         packages=find_packages(),
         install_requires=[
-            'ase~=3.17',
-            'castepinput~=0.1',
+            "ase~=3.17",
+            "castepinput~=0.1",
         ],
-        description='A wrapper for using AIRSS with python and ase.',
+        description="A wrapper for using AIRSS with python and ase.",
         extras_require={
-            'testing': ['pytest'],
+            "testing": ["pytest"],
             "pre-commit": [
                 "pre-commit>=1,<2",
                 "black",
-            ]
+            ],
         },
-        maintainer='Bonan Zhu',
-        maintainer_email='zhubonan@outlook.com',
+        maintainer="Bonan Zhu",
+        maintainer_email="zhubonan@outlook.com",
         long_description=long_description,
-        long_description_content_type='text/markdown',
+        long_description_content_type="text/markdown",
     )