Running cookiecutter on labpdfproc

.codecov.yml

@@ -1,10 +1,34 @@
-# show coverage in CI status, not as a comment.
-comment: off
+# 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:
-    project:
-      default:
-        target: auto
     patch:
       default:
+        target: '70'
+        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: error
+        paths: '!*/tests/.*'
+
+      tests:
+        target: 97.9%
+        paths: '*/tests/.*'
+        if_not_found: success
+
+flags:
+  tests:
+    paths:
+      - tests/

.coveragerc

@@ -1,7 +1,6 @@
 [run]
 source =
-    src
-
+    diffpy.labpdfproc
 [report]
 omit =
     */python?.?/*

.flake8

@@ -4,9 +4,8 @@ exclude =
     __pycache__,
     build,
     dist,
-    versioneer.py,
-    labpdfproc/_version.py,
-    doc/manual/source/conf.py
+    doc/source/conf.py
 max-line-length = 115
 # Ignore some style 'errors' produced while formatting by 'black'
-ignore = E203, W503
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
+extend-ignore = E203

.gitattributes

@@ -1 +1 @@
-labpdfproc/_version.py export-subst
+diffpy.labpdfproc/_version.py export-subst

.github/workflows/docs.yml

@@ -34,10 +34,10 @@ jobs:
         run: python -m pip install . --no-deps
 
       - name: build documents
-        run: make -C doc/manual html
+        run: make -C doc html
 
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./doc/manual/build/html
+          publish_dir: ./doc/build/html

.github/workflows/testing.yml → .github/workflows/main.yml

@@ -42,14 +42,13 @@ jobs:
           conda config --set always_yes yes --set changeps1 no
           conda config --add channels conda-forge
           conda activate test
-          conda install --file requirements/requirements.txt
-          conda install --file requirements/requirements-dev.txt
+          conda install --file requirements/run.txt
+          conda install --file requirements/test.txt
           pip install .
-
       - name: Validate diffpy.labpdfproc
         shell: bash -l {0}
         run: |
           conda activate test
-          coverage run -m pytest -s
+          coverage run -m pytest -vv -s
           coverage report -m
           codecov

.github/workflows/pre-commit.yml

@@ -14,8 +14,6 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
-      - name: Make prevent_commit_to_main.sh executable
-        run: chmod +x ./prevent_commit_to_main.sh
       - uses: pre-commit/[email protected]
         with:
           extra_args: --all-files

.gitignore

@@ -24,6 +24,10 @@ venv/
 *.egg-info/
 .installed.cfg
 *.egg
+bin/
+temp/
+tags/
+errors.err
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -34,6 +38,7 @@ venv/
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
+MANIFEST
 
 # Unit test / coverage reports
 htmlcov/
@@ -50,6 +55,11 @@ coverage.xml
 *.mo
 *.pot
 
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
 # Django stuff:
 *.log
 
@@ -80,3 +90,10 @@ target/
 
 # Ipython Notebook
 .ipynb_checkpoints
+
+# version information
+setup.cfg
+/src/diffpy/*/version.cfg
+
+# Rever
+rever/

AUTHORS.rst

@@ -1,13 +1,10 @@
+Authors
 =======
-Credits
-=======
-
-Maintainer
-----------
 
-* diffpy <[email protected]>
+Billinge Group and community contibutors.
 
 Contributors
 ------------
 
-None yet. Why not be the first? See: CONTRIBUTING.rst
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.labpdfproc/graphs/contributors

CHANGELOG.rst

@@ -0,0 +1,7 @@
+=============
+Release Notes
+=============
+
+.. current developments
+
+Initial release of labPDFproc.  Please see README and documentation for details

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.rst

@@ -0,0 +1,30 @@
+BSD 3-Clause License
+
+Copyright (c) 2024, The Trustees of Columbia University
+in the City of New York.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+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.
+
+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 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.

MANIFEST.in

@@ -1,17 +1,16 @@
 include AUTHORS.rst
-include CONTRIBUTING.rst
 include LICENSE
 include README.rst
 include requirements.txt
-include docs/examples/*
+include doc/examples/*
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
 recursive-include docs *.rst conf.py Makefile make.bat
 
-include versioneer.py
-include labpdfproc/_version.py
+
+include diffpy.labpdfproc/version.py
 
 # If including data files in the package, add them like:
 # include path/to/data_file