Merge pull request #19 from fjhheras/develop

Merging develop into master. Preparing v. 0.3.2

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,80 @@
+# trajectorytools Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to make participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies within all project spaces, and it also applies when
+an individual is representing the project or its community in public spaces.
+Examples of representing a project or community include using an official
+project e-mail address, posting via an official social media account, or acting
+as an appointed representative at an online or offline event. Representation of
+a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting any member of the core project team:
+
+- francisco.heras@neuro.fchampalimaud.org (Francisco J. H. Heras)
+- francisco.romero@neuro.fchampalimaud.org (Francisco Romero Ferrero)
+
+All complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

.github/CONTRIBUTING.md

@@ -0,0 +1,32 @@
+# Contributing to trajectorytools
+
+## Reporting issues
+
+When reporting issues please include as much detail as possible about your
+operating system, trajectorytools version and python version. Whenever 
+possible, please also include a brief, self-contained code example 
+demonstrating the problem.
+
+## Contributing code
+
+Thanks for your interest in contributing code to trajectorytools!
+
+We gladly welcome pull requests, normally to the develop branch. 
+
+We try very hard to follow good coding practices. This includes:
+
++ We do not add commits directly to master and develop, only pull requests
++ We follow [PEP 8 recommendations](https://www.python.org/dev/peps/pep-0008/),
+including the line length limit of 79 for python code and 72 for docs/comments.
++ We use an autoformatter called [black](https://github.com/psf/black) to have
+a uniform code look. Before submitting pull requests, we would appreciate if 
+you autoformat the code using the following command: `black -l 79 .`
++ Whenever possible, we create tests for any new code.
+
+If you are like us some years ago and have problems following these rules,
+we are happy to help you implement them during the pull request process.
+
+## Attribution
+
+This CONTRIBUTING file is highly influenced by the contributing guidelines in
+[numpy](https://github.com/numpy/numpy/edit/master/.github/CONTRIBUTING.md)

.github/workflows/pythonpackage_coverage.yml

@@ -26,15 +26,23 @@ jobs:
     - name: Install
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov
+        pip install black flake8 pytest pytest-cov
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install .
+    - name: Check format with black 
+      run: |
+        black -l 79 --check .
     - name: Lint with flake8
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        # stop the build if there are Python syntax errors, deprecations or undefined names
+        # our line length is 79 (72 for docstrings), and we are strict (stop) if above 88
+        flake8 . --count --select=E5,E9,W6,F63,F7,F82 --max-line-length=88 --show-source --statistics
+        # exit-zero treats all errors as warnings.
+        # ignoring when clashing with black:
+        # - W503 line break before binary operator
+        # - E203 whitespace before ':'
+        # - C0330 Wrong hanging indentation before block
+        flake8 . --count --exit-zero --max-complexity=10 --statistics --ignore=E203,W503,C0330
     - name: Generate coverage report
       run: |
         pip install pytest

.gitignore

@@ -54,3 +54,6 @@ docs/_build
 .vscode
 
 \.idea/
+
+# Type checking stuff
+.mypy_cache/

README.rst

@@ -117,7 +117,11 @@ Francisco Romero Ferrero (2017-)
 Contribute
 ==========
 
-Please.
+We welcome contributions. The preferred way to report problems is by creating an issue. The best way to propose changes in the code is to create a pull request. Please, check our `contribution guidelines`_ and our `code of conduct`_. 
+
+.. _contribution guidelines: .github/CONTRIBUTING.md
+.. _code of conduct: .github/CODE_OF_CONDUCT.md
+
 
 License
 =======

setup.py

@@ -1,34 +1,28 @@
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 with open("README.rst", "r") as fh:
     long_description = fh.read()
 
-setup(name='trajectorytools',
-      version='0.3.1-alpha',
-      description='A tool to study 2D trajectories',
-      long_description=long_description,
-      url='http://github.com/fjhheras/trajectorytools',
-      author='Francisco J.H. Heras',
-      author_email='fjhheras@gmail.com',
-      license='GPL',
-
-      install_requires=['MiniballCpp',
-                        'matplotlib',
-                        'scikit-learn',
-                        'scipy'],
-
-      packages=find_packages(),
-      package_data={'trajectorytools': ['data/*.npy']},
-      include_package_data=True,
-      zip_safe=False,
-
-      classifiers=[
-          'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
-          'Programming Language :: Python',
-          'Topic :: Scientific/Engineering',
-          'Topic :: Scientific/Engineering :: Physics',
-          'Topic :: Software Development :: Libraries',
-          'Topic :: Utilities'
-      ],
-
-      )
+setup(
+    name="trajectorytools",
+    version="0.3.2-alpha",
+    description="A tool to study 2D trajectories",
+    long_description=long_description,
+    url="http://github.com/fjhheras/trajectorytools",
+    author="Francisco J.H. Heras, Francisco Romero Ferrero",
+    author_email="fjhheras@gmail.com",
+    license="GPL",
+    install_requires=["MiniballCpp", "matplotlib", "scikit-learn", "scipy"],
+    packages=find_packages(),
+    package_data={"trajectorytools": ["data/*.npy"]},
+    include_package_data=True,
+    zip_safe=False,
+    classifiers=[
+        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+        "Programming Language :: Python",
+        "Topic :: Scientific/Engineering",
+        "Topic :: Scientific/Engineering :: Physics",
+        "Topic :: Software Development :: Libraries",
+        "Topic :: Utilities",
+    ],
+)

tests/collective_test.py

@@ -1,17 +1,16 @@
-import pytest
 import numpy as np
+import pytest
 
+import trajectorytools as tt
 import trajectorytools.constants as cons
-from trajectorytools.collective import (angular_momentum,
-                                        polarization)
+from trajectorytools.collective import angular_momentum, polarization
 from trajectorytools.geometry import center_in_trajectory
-import trajectorytools as tt
 
 
-class TestExtremeCases():
+class TestExtremeCases:
     def setup_class(self):
         v = np.random.randn(50, 2)
-        self.v_same = np.stack([v]*10, axis=1)
+        self.v_same = np.stack([v] * 10, axis=1)
         self.v_antiparallel = self.v_same.copy()
         self.v_antiparallel[:, ::2, :] *= -1
 
@@ -23,17 +22,18 @@ def test_pol_antiparallel(self):
         pol = tt.norm(polarization(self.v_antiparallel))
         assert pytest.approx(pol, 1e-16) == 0
 
-    @pytest.mark.parametrize('num_dims_point', [2, 1])
+    @pytest.mark.parametrize("num_dims_point", [2, 1])
     def test_ang_mom_antiparallel(self, num_dims_point):
         # Random point to measure angular momentum
         if num_dims_point == 2:
             point = np.random.randn(2)
         elif num_dims_point == 1:
             point = np.random.randn(50, 2)
         # Random locations (but all in the same point)
-        locations = np.stack([np.random.randn(50, 2)]*10, axis=1)
-        ang_momentum = tt.norm(angular_momentum(
-            self.v_antiparallel, locations))
+        locations = np.stack([np.random.randn(50, 2)] * 10, axis=1)
+        ang_momentum = tt.norm(
+            angular_momentum(self.v_antiparallel, locations, center=point)
+        )
         assert pytest.approx(ang_momentum, 1e-16) == 0
 
     @pytest.fixture(autouse=True)
@@ -46,7 +46,7 @@ def run_around_tests(self):
         assert np.all(v_antiparallel == self.v_antiparallel)
 
 
-class TestAngularMomentum():
+class TestAngularMomentum:
     def setup_class(self):
         self.v = np.random.randn(50, 10, 2)
         self.s = np.random.randn(50, 10, 2)
@@ -70,9 +70,8 @@ def test_theorem_center_of_mass(self):
         np.testing.assert_almost_equal(L_1, L_1_b)
 
         L_2 = num_individuals * angular_momentum(
-            V[:, np.newaxis, :],
-            S[:, np.newaxis, :],
-            self.p)
+            V[:, np.newaxis, :], S[:, np.newaxis, :], self.p
+        )
 
         # angular momentum around a point is the sum of the angular
         # momentum around the center of mass and the angular momentum