dynsight 2023.11.16__tar.gz

dynsight-2023.11.16/.github/pull_request_template.md

@@ -0,0 +1,43 @@
+Related Issues: <!-- Add related issues here, e.g. #121 #341 -->
+Requested Reviewers: @andrewtarzia <!-- Add other reviewers here -->
+*Note for Reviewers: If you accept the review request add a :+1: to this post*
+
+<!--
+Talk about what a user would see (a big, a new feature) and what
+user goals weren't being met. If the commit fixes a bug, describe how
+the bug was discovered and steps to reproduce it, unless this is
+already covered by the related issues. If this is a bug fix, what was
+the mistake in the application logic? Be precise. Act like a detective
+and report your findings.
+-->
+
+<!--
+Why did you make the change this way? What other ways did you consider
+but reject? Explain how amazing your work is.
+-->
+
+<!--
+What risks are associated with making the changes in the commit? Will
+anything else break? Are the changes backwards-compatible? Is there
+any "tech debt"?
+-->
+
+<!--
+Explain the source code changes. Changes that are fully explained in
+code comments or the above paragraphs don't need to be repeated here.
+Use bullet points, e.g.
+
+* `src/dynsight/_internal/lens/lens.py:Lens.get_lens()`: The method
+  parameters were updated because <some reason>. The places where
+  the method was called were also updated.
+-->
+
+<!--
+Give evidence that the commit works. Did you visually inspect any
+changes to molecular structures yourself?
+-->
+
+<!--
+The suggested PR outline is taken from
+https://joshuatauberer.medium.com/write-joyous-git-commit-messages-2f98891114c4
+-->

dynsight-2023.11.16/.github/workflows/publish_release.yaml

@@ -0,0 +1,23 @@
+name: Publish release
+on:
+  push:
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+jobs:
+  publish-release:
+    runs-on: ubuntu-22.04
+    env:
+      VERSION: ${{ github.ref_name }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - run: pip install -e '.[dev]'
+      - run: python -m build
+      - run:
+          twine upload
+          -u __token__
+          -p ${{ secrets.PYPI_API_TOKEN }}
+          dist/*

dynsight-2023.11.16/.github/workflows/tests.yaml

@@ -0,0 +1,58 @@
+name: Tests
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+jobs:
+  ruff:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - run: pip install -e '.[dev]'
+      - run: ruff .
+  mypy:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - run: pip install -e '.[dev]'
+      - run: mypy .
+  ruff-format:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - run: pip install -e '.[dev]'
+      - run: ruff format --check .
+  pytest:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - run: pip install -e '.[dev]'
+      - run: pytest --cov=src --cov-report term-missing
+  doctest:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - run: pip install -e '.[dev]'
+      - run: make -C docs doctest

dynsight-2023.11.16/.gitignore

@@ -0,0 +1,7 @@
+__pycache__
+*.egg-info
+/.coverage
+/dist
+/build
+docs/build
+docs/source/_autosummary

dynsight-2023.11.16/.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: 2
+
+build:
+    os: ubuntu-22.04
+    tools:
+      python: "3.11"
+
+sphinx:
+    configuration: docs/source/conf.py
+
+python:
+    install:
+        - method: pip
+          path: .
+          extra_requirements:
+            - dev

dynsight-2023.11.16/LICENSE

@@ -0,0 +1,19 @@
+iCopyright (c) 2023 Andrew Tarzia, GMPavanLab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

dynsight-2023.11.16/PKG-INFO

@@ -0,0 +1,54 @@
+Metadata-Version: 2.1
+Name: dynsight
+Version: 2023.11.16
+Summary: Simplifies analysis of Molecular Dynamics simulations.
+Maintainer-email: Andrew Tarzia <andrew.tarzia@gmail.com>
+Project-URL: github, https://github.com/GMPavanLab/dynsight
+Project-URL: documentation, https://dynsight.readthedocs.io/en/latest/
+Requires-Python: >=3.7
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Provides-Extra: dev
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: sphinx-copybutton; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: furo; extra == "dev"
+
+:maintainers:
+    `andrewtarzia <https://github.com/andrewtarzia/>`_
+:documentation: https://dynsight.readthedocs.io
+
+Installation
+============
+
+To get ``dynsight``, you can install it with pip::
+
+    $ pip install dynsight
+
+How To Cite
+===========
+
+If you use ``dynsight`` please cite
+
+    https://github.com/GMPavanLab/dynsight
+
+
+
+Publications
+============
+
+* people need to add PRs to mention these.
+
+
+Acknowledgements
+================
+
+Developed in GMP
+ERC
+NextGenEU
+Danielle Rappeti

dynsight-2023.11.16/README.rst

@@ -0,0 +1,33 @@
+:maintainers:
+    `andrewtarzia <https://github.com/andrewtarzia/>`_
+:documentation: https://dynsight.readthedocs.io
+
+Installation
+============
+
+To get ``dynsight``, you can install it with pip::
+
+    $ pip install dynsight
+
+How To Cite
+===========
+
+If you use ``dynsight`` please cite
+
+    https://github.com/GMPavanLab/dynsight
+
+
+
+Publications
+============
+
+* people need to add PRs to mention these.
+
+
+Acknowledgements
+================
+
+Developed in GMP
+ERC
+NextGenEU
+Danielle Rappeti

dynsight-2023.11.16/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?= -W --keep-going
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

dynsight-2023.11.16/docs/source/_templates/class.rst

@@ -0,0 +1,31 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+      :nosignatures:
+   {% for item in methods %}
+      {%- if not item.startswith('_') and item not in inherited_members %}
+      ~{{ name }}.{{ item }}
+      {%- endif -%}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

dynsight-2023.11.16/docs/source/_templates/module.rst

@@ -0,0 +1,68 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: class.rst
+      :nosignatures:
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :template: module.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

dynsight-2023.11.16/docs/source/conf.py

@@ -0,0 +1,45 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+from __future__ import annotations
+
+project = "dynsight"
+project_copyright = "2023, Andrew Tarzia"
+author = "Andrew Tarzia"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.doctest",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx_copybutton",
+]
+
+autosummary_imported_members = True
+
+autodoc_typehints = "description"
+autodoc_member_order = "groupwise"
+autoclass_content = "class"
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+}
+
+
+templates_path = ["_templates"]
+exclude_patterns: list[str] = []
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "furo"
+html_static_path = ["_static"]

dynsight-2023.11.16/docs/source/index.rst

@@ -0,0 +1,65 @@
+.. dynsight documentation master file, created by
+   sphinx-quickstart on Thu Oct 19 15:55:32 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+
+.. toctree::
+  :hidden:
+  :maxdepth: 2
+  :caption: Modules:
+
+  Modules <modules>
+
+============
+Introduction
+============
+
+| GitHub: https://www.github.com/GMPavanLab/dynsight
+
+
+:mod:`.dynsight` is a Python library aimed at simplifying the analysis of Molecular
+Dynamics simulations.
+
+
+
+Previously in `cpctools`_.
+
+.. _`cpctools`: https://github.com/GMPavanLab/cpctools
+
+
+Installation
+------------
+
+To get :mod:`.dynsight`, you can install it with pip::
+
+  $ pip install dynsight
+
+Developer Setup
+...............
+
+#. Install `just`_.
+#. In a new virtual environment run::
+
+    $ just dev
+
+
+#. Run code checks::
+
+    $ just check
+
+
+.. _`just`: https://github.com/casey/just
+
+
+Overview
+--------
+
+To be written.
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

dynsight-2023.11.16/docs/source/modules.rst

@@ -0,0 +1,9 @@
+Modules
+=======
+
+.. autosummary::
+  :toctree: _autosummary
+  :template: module.rst
+  :recursive:
+
+  dynsight

dynsight-2023.11.16/justfile

@@ -0,0 +1,46 @@
+# List all commands.
+default:
+  @just --list
+
+# Build docs.
+docs:
+  rm -rf docs/source/_autosummary
+  make -C docs html
+  echo Docs are in $PWD/docs/build/html/index.html
+
+# Do a dev install.
+dev:
+  pip install -e '.[dev]'
+
+# Run code checks.
+check:
+  #!/usr/bin/env bash
+
+  error=0
+  trap error=1 ERR
+
+  echo
+  (set -x; ruff . )
+
+  echo
+  ( set -x; ruff format --check . )
+
+  echo
+  ( set -x; mypy . )
+
+  echo
+  ( set -x; pytest --cov=src --cov-report term-missing )
+
+  echo
+  ( set -x; make -C docs doctest )
+
+  test $error = 0
+
+# Auto-fix code issues.
+fix:
+  ruff format .
+  ruff --fix .
+
+# Build a release.
+build:
+  python -m build

dynsight-2023.11.16/pyproject.toml

@@ -0,0 +1,73 @@
+[build-system]
+requires = ["setuptools", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "dynsight"
+maintainers = [
+  { name = "Andrew Tarzia", email = "andrew.tarzia@gmail.com" },
+]
+
+dependencies = []
+requires-python = ">=3.7"
+dynamic = ["version"]
+readme = "README.rst"
+description = "Simplifies analysis of Molecular Dynamics simulations."
+
+[project.optional-dependencies]
+dev = [
+  "ruff",
+  "mypy",
+  "pytest",
+  "pytest-cov",
+  "sphinx",
+  "sphinx-copybutton",
+  "build",
+  "twine",
+  "furo",
+]
+
+[project.urls]
+github = "https://github.com/GMPavanLab/dynsight"
+documentation = "https://dynsight.readthedocs.io/en/latest/"
+
+[tool.setuptools_scm]
+
+[tool.ruff]
+line-length = 79
+select = ["ALL"]
+ignore = ["ANN101", "ANN401", "COM812", "ISC001"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = [
+  "D100",
+  "D101",
+  "D102",
+  "D103",
+  "D104",
+  "D105",
+  "D106",
+  "D107",
+  "S101",
+  "INP001",
+]
+"docs/source/conf.py" = ["D100", "INP001"]
+
+[tool.mypy]
+show_error_codes = true
+implicit_optional = false
+warn_no_return = true
+strict_optional = true
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+check_untyped_defs = true
+disallow_untyped_decorators = true
+warn_unreachable = true
+disallow_any_generics = true
+
+[[tool.mypy.overrides]]
+module = []
+ignore_missing_imports = true

dynsight-2023.11.16/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

dynsight-2023.11.16/src/dynsight/__init__.py

@@ -0,0 +1,8 @@
+"""dynsight package."""
+from dynsight import hdf5er, lens, soapify
+
+__all__ = [
+    "soapify",
+    "lens",
+    "hdf5er",
+]

dynsight-2023.11.16/src/dynsight/_internal/hdf5er/__init__.py

@@ -0,0 +1,10 @@
+def foo1(a: int) -> str:
+    """Do stuff.
+
+    Parameters:
+        a: A number.
+
+    Returns:
+        A message for you.
+    """
+    return f"Hello, World! Also: {a}"

dynsight-2023.11.16/src/dynsight/_internal/lens/__init__.py

@@ -0,0 +1,10 @@
+def foo2(a: int) -> str:
+    """Do stuff.
+
+    Parameters:
+        a: A number.
+
+    Returns:
+        A message for you.
+    """
+    return f"Hello, World! Also: {a}"

dynsight-2023.11.16/src/dynsight/_internal/soapify/__init__.py

@@ -0,0 +1,10 @@
+def foo3(a: int) -> str:
+    """Do stuff.
+
+    Parameters:
+        a: A number.
+
+    Returns:
+        A message for you.
+    """
+    return f"Hello, World! Also: {a}"

dynsight-2023.11.16/src/dynsight/hdf5er.py

@@ -0,0 +1,6 @@
+"""hdf5er package."""
+from dynsight._internal.hdf5er import foo1
+
+__all__ = [
+    "foo1",
+]

dynsight-2023.11.16/src/dynsight/lens.py

@@ -0,0 +1,6 @@
+"""LENS package."""
+from dynsight._internal.lens import foo2
+
+__all__ = [
+    "foo2",
+]

dynsight-2023.11.16/src/dynsight/soapify.py

@@ -0,0 +1,6 @@
+"""SOAPify package."""
+from dynsight._internal.soapify import foo3
+
+__all__ = [
+    "foo3",
+]

dynsight-2023.11.16/src/dynsight.egg-info/PKG-INFO

@@ -0,0 +1,54 @@
+Metadata-Version: 2.1
+Name: dynsight
+Version: 2023.11.16
+Summary: Simplifies analysis of Molecular Dynamics simulations.
+Maintainer-email: Andrew Tarzia <andrew.tarzia@gmail.com>
+Project-URL: github, https://github.com/GMPavanLab/dynsight
+Project-URL: documentation, https://dynsight.readthedocs.io/en/latest/
+Requires-Python: >=3.7
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Provides-Extra: dev
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: sphinx-copybutton; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: furo; extra == "dev"
+
+:maintainers:
+    `andrewtarzia <https://github.com/andrewtarzia/>`_
+:documentation: https://dynsight.readthedocs.io
+
+Installation
+============
+
+To get ``dynsight``, you can install it with pip::
+
+    $ pip install dynsight
+
+How To Cite
+===========
+
+If you use ``dynsight`` please cite
+
+    https://github.com/GMPavanLab/dynsight
+
+
+
+Publications
+============
+
+* people need to add PRs to mention these.
+
+
+Acknowledgements
+================
+
+Developed in GMP
+ERC
+NextGenEU
+Danielle Rappeti

dynsight-2023.11.16/src/dynsight.egg-info/SOURCES.txt

@@ -0,0 +1,31 @@
+.gitignore
+.readthedocs.yaml
+LICENSE
+README.rst
+justfile
+pyproject.toml
+.github/pull_request_template.md
+.github/workflows/publish_release.yaml
+.github/workflows/tests.yaml
+docs/Makefile
+docs/source/conf.py
+docs/source/index.rst
+docs/source/modules.rst
+docs/source/_static/empty
+docs/source/_templates/class.rst
+docs/source/_templates/module.rst
+src/dynsight/__init__.py
+src/dynsight/hdf5er.py
+src/dynsight/lens.py
+src/dynsight/py.typed
+src/dynsight/soapify.py
+src/dynsight.egg-info/PKG-INFO
+src/dynsight.egg-info/SOURCES.txt
+src/dynsight.egg-info/dependency_links.txt
+src/dynsight.egg-info/requires.txt
+src/dynsight.egg-info/top_level.txt
+src/dynsight/_internal/__init__.py
+src/dynsight/_internal/hdf5er/__init__.py
+src/dynsight/_internal/lens/__init__.py
+src/dynsight/_internal/soapify/__init__.py
+tests/test_foo.py

dynsight-2023.11.16/src/dynsight.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

dynsight-2023.11.16/src/dynsight.egg-info/requires.txt

@@ -0,0 +1,11 @@
+
+[dev]
+ruff
+mypy
+pytest
+pytest-cov
+sphinx
+sphinx-copybutton
+build
+twine
+furo

dynsight-2023.11.16/src/dynsight.egg-info/top_level.txt

@@ -0,0 +1 @@
+dynsight

dynsight-2023.11.16/tests/test_foo.py

@@ -0,0 +1,13 @@
+import dynsight
+
+
+def test_foo1() -> None:
+    assert dynsight.hdf5er.foo1(3) == "Hello, World! Also: 3"
+
+
+def test_foo2() -> None:
+    assert dynsight.soapify.foo3(11) == "Hello, World! Also: 11"
+
+
+def test_foo3() -> None:
+    assert dynsight.lens.foo2(13) == "Hello, World! Also: 13"