Merge pull request #112 from sbillinge/sp3

sp3

Author: sbillinge

.codecov.yml

@@ -1,33 +1,14 @@
-# codecov can find this file anywhere in the repo, so we don't need to clutter
-# the root folder.
-#comment: false
-
-codecov:
-  notify:
-    require_ci_to_pass: no
-
 coverage:
   status:
-    patch:
+    project: # more options at https://docs.codecov.com/docs/commit-status
       default:
-        target: "80"
-        if_no_uploads: error
-        if_not_found: success
-        if_ci_failed: failure
-    project:
-      default: false
-      library:
-        target: auto
-        if_no_uploads: error
-        if_not_found: success
-        if_ci_failed: failure
-        paths: "!*/tests/.*"
-
-      tests:
-        target: 97.9%
-        paths: "*/tests/.*"
-
-flags:
-  tests:
-    paths:
-      - tests/
+        target: auto # use the coverage from the base commit, fail if coverage is lower
+        threshold: 0% # allow the coverage to drop by
+
+comment:
+  layout: " diff, flags, files"
+  behavior: default
+  require_changes: false
+  require_base: false # [true :: must have a base report to post]
+  require_head: false # [true :: must have a head report to post]
+  hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage]

.coveragerc

@@ -0,0 +1,10 @@
+Authors
+=======
+
+Christopher Farrow, Pavol Juhas, Simon J. L. Billinge, and members of the Billinge Group
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.srfit/graphs/contributors

.gitarchive.cfg

@@ -0,0 +1,36 @@
+=============
+Release notes
+=============
+
+.. current developments
+
+Version 3.0.0 – 2019-03-14
+==========================
+
+**Added:**
+
+* Support for Python 3.7, 3.6, 3.5 in addition to 2.7.
+
+**Changed:**
+
+* Always use lower-case imports from `diffpy.structure`.
+* Use numeric-value sort to order variables in `PrintFitHook`.
+
+**Deprecated:**
+
+* Variable `__gitsha__` in the `version` module renamed to `__git_commit__`.
+
+**Removed:**
+
+* Optional upper and lower-bound arguments in `Parameter.setValue`.
+  The bounds can be set with `Parameter.boundRange` instead.
+* Unused classes `ListOperator`, `SetOperator`.
+
+**Fixed:**
+
+* Metadata retrieval from `PDFContribution` hierarchy.
+* Refresh `PDFGenerator` when its `rgrid` is changed in-place.
+* Zero division in the `nppdfsas.py` example.
+* Crash in `ellipsoidsas.py` example because of bug in `Parameter.setValue`.
+* Pickling of `ProfileGenerator` objects and of bound class methods.
+* Invalid escape sequences in string values.

.gitattributes

@@ -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, socioeconomic 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>`_

AUTHORS.rst

@@ -9,9 +9,10 @@ Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP")
 Copyright (c) 2006-2007, Board of Trustees of Michigan State University
 Copyright (c) 2008-2012, The Trustees of Columbia University in the City
     of New York
-
 Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National
     Laboratory
+Copyright (c) 2020-2025, The Trustees of Columbia University in the City
+    of New York
 
 
 The "DiffPy-CMI" is distributed subject to the following license conditions:

AUTHORS.txt

@@ -1,16 +1,14 @@
-recursive-include src *
-include AUTHORS.txt LICENSE*.txt README.rst
-recursive-exclude src *.pyc
-global-exclude .gitattributes .gitignore .gitarchive.cfg
-global-exclude .DS_Store
+graft src
+graft tests
+graft requirements
 
-# Avoid user content in setup.cfg to make distribution reproducible.
-exclude setup.cfg
+include AUTHORS.rst LICENSE*.rst README.rst
 
-# Exclude git-tracked files spuriously added by setuptools_scm
+# Exclude all bytecode files and __pycache__ directories
+global-exclude *.py[cod]  # Exclude all .pyc, .pyo, and .pyd files.
+global-exclude .DS_Store  # Exclude Mac filesystem artifacts.
+global-exclude __pycache__  # Exclude Python cache directories.
+global-exclude .git*  # Exclude git files and directories.
+global-exclude .idea  # Exclude PyCharm project settings.
 exclude .codecov.yml
 exclude .coveragerc
-exclude .travis*
-prune conda-recipe
-prune devutils
-prune doc