merging cookiecut main

.codecov.yml

@@ -1,34 +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/.*'
-        if_not_found: success
-
-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]

.codespell/ignore_lines.txt

@@ -0,0 +1,2 @@
+;; Please include filenames and explanations for each ignored line.
+;; See https://docs.openverse.org/meta/codespell.html for docs.

.codespell/ignore_words.txt

@@ -0,0 +1,27 @@
+;; Please include explanations for each ignored word (lowercase).
+;; See https://docs.openverse.org/meta/codespell.html for docs.
+
+;; abbreviation for "materials" often used in a journal title
+mater
+
+;; alternative use of socioeconomic
+socio-economic
+
+;; Frobenius norm used in np.linalg.norm
+fro
+
+;; variable names
+stati
+convertor
+dploy
+pres
+Ond
+
+;; package name
+rever
+
+;; people.rst manually allows 'programer' as a variation of 'programmer'
+programer
+
+;; suffix for dates
+nd

.flake8

@@ -0,0 +1,11 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    doc/source/conf.py
+max-line-length = 115
+# Ignore some style 'errors' produced while formatting by 'black'
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
+extend-ignore = E203

.github/ISSUE_TEMPLATE/bug_feature.md

@@ -0,0 +1,16 @@
+---
+name: Bug Report or Feature Request
+about: Report a bug or suggest a new feature!
+title: ""
+labels: ""
+assignees: ""
+---
+
+### Problem
+
+<!--
+For a bug report, please copy and paste any error messages from the application or command-line here.
+For a feature request, please state how the new functionality could benefit the community.
+-->
+
+### Proposed solution

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -0,0 +1,28 @@
+---
+name: Release
+about: Checklist and communication channel for PyPI and GitHub release
+title: "Ready for <version-number> PyPI/GitHub release"
+labels: "release"
+assignees: ""
+---
+
+### Release checklist for GitHub contributors
+
+- [ ] All PRs/issues attached to the release are merged.
+- [ ] All the badges on the README are passing.
+- [ ] License information is verified as correct. If you are unsure, please comment below.
+- [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
+  missing), tutorials, and other human written text is up-to-date with any changes in the code.
+- [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) updated.
+- [ ] Successfully run any tutorial examples or do functional testing with the latest Python version
+- [ ] Grammar and writing quality have been checked (no typos).
+
+Please mention @sbillinge when you are ready for release. Include any additional comments necessary, such as
+version information and details about the pre-release here:
+
+### Post-release checklist
+
+Before closing this issue, please complete the following:
+
+- [ ]  Run tutorial examples and conduct functional testing using the installation guide in the README.
+- [ ]  Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.

.github/workflows/build-wheel-release-upload.yml

@@ -0,0 +1,16 @@
+name: Release (GitHub/PyPI) and Deploy Docs
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - '*'  # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
+
+jobs:
+  release:
+    uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
+    with:
+      project: regolith
+    secrets:
+      PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+      PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

.github/workflows/check-news-item.yml

@@ -0,0 +1,12 @@
+name: Check for News
+
+on:
+  pull_request_target:
+    branches:
+    - main
+
+jobs:
+  check-news-item:
+    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
+    with:
+      project: regolith

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -0,0 +1,21 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - prereleased
+      - published
+  workflow_dispatch:
+
+jobs:
+  matrix-coverage:
+    uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    with:
+      project: regolith
+      c_extension: false
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/publish-docs-on-release.yml

@@ -0,0 +1,16 @@
+name: Deploy Documentation on Release
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  docs:
+    permissions:
+      contents: write
+    uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
+    with:
+      project: regolith
+      c_extension: false
+      headless: false

.github/workflows/tests-on-pr.yml

@@ -0,0 +1,59 @@
+name: Tests on PR
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  validate:
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out regolith repository
+        uses: actions/checkout@v4
+
+      - name: Initialize miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test
+          auto-update-conda: true
+          environment-file: environment.yml
+          auto-activate-base: false
+          python-version: 3.11
+
+      - name: Conda config
+        run: >-
+          conda config --set always_yes yes
+          --set changeps1 no
+
+      - name: Install libgtk for Linux
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgtk-3-dev
+
+      - name: Install regolith and requirements
+        run: |
+          conda install --file requirements/test.txt
+          conda install --file requirements/conda.txt
+          pip install gooey
+          python -m pip install . --no-deps
+
+
+      - name: Validate regolith
+        run: |
+          pytest --cov
+          coverage report -m
+          codecov
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          verbose: true
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -1,6 +1,7 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
+*$py.class
 
 # C extensions
 *.so
@@ -19,10 +20,14 @@ lib64/
 parts/
 sdist/
 var/
+venv/
 *.egg-info/
 .installed.cfg
 *.egg
-.idea
+bin/
+temp/
+tags/
+errors.err
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -33,6 +38,7 @@ var/
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
+MANIFEST
 
 # Unit test / coverage reports
 htmlcov/
@@ -43,20 +49,52 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *,cover
+.hypothesis/
 
 # Translations
 *.mo
 *.pot
 
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
 # Django stuff:
 *.log
 
 # Sphinx documentation
-docs/_build/
+docs/build/
+docs/source/generated/
+
+# pytest
+.pytest_cache/
 
 # PyBuilder
 target/
 
+# Editor files
+# mac
+.DS_Store
+*~
+
+# vim
+*.swp
+*.swo
+
+# pycharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Ipython Notebook
+.ipynb_checkpoints
+
+# version information
+setup.cfg
+/src/regro/*/version.cfg
+
 # Rever
 rever/
 
@@ -70,8 +108,3 @@ docs/collections/people.rst
 docs/collections/projects.rst
 docs/collections/proposals.rst
 docs/collections/students.rst
-
-# Idea
-.idea/
-
-.DS_Store

.isort.cfg

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