cookiecutter: untracked files (#149)

* untracked files

* [pre-commit.ci] auto fixes from pre-commit hooks

* update LICENSE.rst

* update AUTHORS.rst and remove AUTHORS.txt

* tipping our hat

* Remove BSD 3-Clause, leaving Columbia copyright

* remove README from requirements

* replace requirements

* adding wxpython back

* adding back freezegun

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Simon Billinge <[email protected]>

.isort.cfg

@@ -0,0 +1,4 @@
+[settings]
+line_length = 115
+multi_line_output = 3
+include_trailing_comma = True

AUTHORS.txt → AUTHORS.rst

@@ -1,3 +1,16 @@
+Authors
+=======
+
+DiffPy was initiated as part of the Distributed Data Analysis of Neutron
+Scattering Experiments (DANSE) project, funded by the National Science
+Foundation under grant DMR-0520547.  More information on DANSE can be
+found at http://danse.us.  Any opinions, findings, and conclusions or
+recommendations expressed in this material are those of the author(s)
+and do not necessarily reflect the views of the NSF.
+
+Main Contributors
+-----------------
+
 This code was developed as part of the DiffPy project to create python
 modules for structure investigations from diffraction data.  The main
 contributors to this package were
@@ -7,33 +20,31 @@ contributors to this package were
     Pavol Juhas
     Dmitriy Bryndin
 
-The DiffPy team is located in the Billinge-group at the Applied Physics
-and Applied Mathematics Department of the Columbia University in New York.
-Currently the team consists of
+Other current and former contributors of the DiffPy project include
 
     Simon Billinge
-    Pavol Juhas
     Chris Farrow
     Emil Bozin
     Wenduo Zhou
     Peng Tian
-    Timur Dykhne
 
+The DiffPy team is part of the Billinge Group at Columbia University in New York,
+within the Department of Applied Physics and Applied Mathematics.
+
+Contributors
+------------
 Please see the header of each source file for a detailed list of
 contributors.  This is an open-source project and we hope and expect
 that the list of contributors will expand with time.  Many thanks to
 all current and future contributors!
 
 For more information on the DiffPy project email [email protected]
 
-DiffPy was initiated as part of the Distributed Data Analysis of Neutron
-Scattering Experiments (DANSE) project, funded by the National Science
-Foundation under grant DMR-0520547.  More information on DANSE can be
-found at http://danse.us.  Any opinions, findings, and conclusions or
-recommendations expressed in this material are those of the author(s)
-and do not necessarily reflect the views of the NSF.
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.pdfgui/graphs/contributors
 
-Acknowledgments:
+Acknowledgments
+---------------
 
 We are truly grateful to all the people who have contributed, in all
 different ways, to this project:  Thomas Proffen, Xiangyun Qiu, Pete

CODE_OF_CONDUCT.rst

@@ -0,0 +1,133 @@
+=====================================
+ Contributor Covenant Code of Conduct
+=====================================
+
+Our Pledge
+----------
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+Our Standards
+-------------
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+Enforcement Responsibilities
+----------------------------
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders 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, and will communicate reasons for moderation
+decisions when appropriate.
+
+Scope
+-----
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+Enforcement
+-----------
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[email protected]. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+Enforcement Guidelines
+----------------------
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+1. Correction
+****************
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+2. Warning
+*************
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+3. Temporary Ban
+******************
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+4. Permanent Ban
+******************
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+Attribution
+-----------
+
+This Code of Conduct is adapted from the `Contributor Covenant <https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>`_.
+
+Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder <https://github.com/mozilla/inclusion>`_.
+
+For answers to common questions about this code of conduct, see the `FAQ <https://www.contributor-covenant.org/faq>`_. `Translations are available <https://www.contributor-covenant.org/translations>`_

LICENSE.txt → LICENSE.rst

@@ -1,3 +1,7 @@
+Copyright (c) 2024, The Trustees of Columbia University
+in the City of New York.
+All rights reserved.
+
 This software was originally developed by the Billinge group as part
 of the Distributed Data Analysis of Neutron Scattering Experiments
 (DANSE) project funded by the US National Science Foundation under
@@ -47,32 +51,26 @@ For more information please visit the project web-page:
 or email Prof. Simon Billinge at [email protected]
 
 Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions
-are met:
+modification, are permitted provided that the following conditions are met:
 
-  * Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimer.
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
 
-  * Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in the
-    documentation and/or other materials provided with the distribution.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
 
-  * Neither the name of the copyright holder nor the names of its
-    contributors may be used to endorse or promote products derived from
-    this software without specific prior written permission.
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY COPYRIGHT HOLDER "AS IS".  COPYRIGHT HOLDER
-EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES AND CONDITIONS, EITHER
-EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY, TITLE, FITNESS, ADEQUACY OR SUITABILITY
-FOR A PARTICULAR PURPOSE, AND ANY WARRANTIES OF FREEDOM FROM
-INFRINGEMENT OF ANY DOMESTIC OR FOREIGN PATENT, COPYRIGHTS, TRADE
-SECRETS OR OTHER PROPRIETARY RIGHTS OF ANY PARTY.  IN NO EVENT SHALL
-COPYRIGHT HOLDER BE LIABLE TO ANY PARTY FOR ANY DIRECT, INDIRECT,
-INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
-NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
-USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
-THIS SOFTWARE OR RELATING TO THIS AGREEMENT, EVEN IF ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

requirements/build.txt

@@ -0,0 +1,2 @@
+python
+setuptools

requirements/docs.txt

@@ -0,0 +1,4 @@
+sphinx
+sphinx_rtd_theme
+doctr
+m2r

requirements/run.txt

@@ -1,5 +1,5 @@
-numpy==1.26
-wxpython
-diffpy.pdffit2
-diffpy.utils
-matplotlib-base
+numpy==1.26
+wxpython
+diffpy.pdffit2
+diffpy.utils
+matplotlib-base

requirements/test.txt

@@ -1,4 +1,6 @@
-pytest
+flake8
 freezegun
-coverage
+pytest
 codecov
+coverage
+pytest-env

src/diffpy/pdfgui/control/calculation.py

@@ -19,11 +19,7 @@
 import copy
 import math
 
-from diffpy.pdfgui.control.controlerrors import (
-    ControlConfigError,
-    ControlKeyError,
-    ControlValueError,
-)
+from diffpy.pdfgui.control.controlerrors import ControlConfigError, ControlKeyError, ControlValueError
 from diffpy.pdfgui.control.pdfcomponent import PDFComponent
 from diffpy.pdfgui.utils import pickle_loads, safeCPickleDumps
 
@@ -124,10 +120,7 @@ def setRGrid(self, rmin=None, rstep=None, rmax=None):
 
     def start(self):
         """entry function for calculation"""
-        from diffpy.pdfgui.control.fitting import (
-            getEngineExceptions,
-            handleEngineException,
-        )
+        from diffpy.pdfgui.control.fitting import getEngineExceptions, handleEngineException
 
         try:
             self.calculate()

src/diffpy/pdfgui/control/fitting.py

@@ -18,11 +18,7 @@
 import threading
 import time
 
-from diffpy.pdfgui.control.controlerrors import (
-    ControlError,
-    ControlStatusError,
-    ControlValueError,
-)
+from diffpy.pdfgui.control.controlerrors import ControlError, ControlStatusError, ControlValueError
 from diffpy.pdfgui.control.organizer import Organizer
 from diffpy.pdfgui.utils import pickle_loads, safeCPickleDumps
 

src/diffpy/pdfgui/control/pdfguicontrol.py

@@ -24,11 +24,7 @@
 import six.moves.cPickle as pickle
 
 from diffpy.pdfgui.control.calculation import Calculation
-from diffpy.pdfgui.control.controlerrors import (
-    ControlError,
-    ControlFileError,
-    ControlTypeError,
-)
+from diffpy.pdfgui.control.controlerrors import ControlError, ControlFileError, ControlTypeError
 from diffpy.pdfgui.control.fitdataset import FitDataSet
 from diffpy.pdfgui.control.fitstructure import FitStructure
 from diffpy.pdfgui.control.fitting import Fitting

src/diffpy/pdfgui/tests/conftest.py

@@ -0,0 +1,19 @@
+import json
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture
+def user_filesystem(tmp_path):
+    base_dir = Path(tmp_path)
+    home_dir = base_dir / "home_dir"
+    home_dir.mkdir(parents=True, exist_ok=True)
+    cwd_dir = base_dir / "cwd_dir"
+    cwd_dir.mkdir(parents=True, exist_ok=True)
+
+    home_config_data = {"username": "home_username", "email": "[email protected]"}
+    with open(home_dir / "diffpyconfig.json", "w") as f:
+        json.dump(home_config_data, f)
+
+    yield tmp_path

src/diffpy/pdfgui/tests/testphaseconfigurepanel.py

@@ -23,13 +23,7 @@
 
 from diffpy.pdfgui.gui.mainframe import MainFrame
 from diffpy.pdfgui.gui.phaseconfigurepanel import PhaseConfigurePanel
-from diffpy.pdfgui.tests.testutils import (
-    GUITestCase,
-    clickcell,
-    datafile,
-    overrideclipboard,
-    tooltiptext,
-)
+from diffpy.pdfgui.tests.testutils import GUITestCase, clickcell, datafile, overrideclipboard, tooltiptext
 
 # ----------------------------------------------------------------------------