Merge pull request #47 from Tieqiong/cookie

Refactor: Cookiecut (merge the other ones first)

.codecov.yml

@@ -1,2 +1,14 @@
-fixes:
-  - ".*/site-packages/::src/"
+coverage:
+  status:
+    project: # more options at https://docs.codecov.com/docs/commit-status
+      default:
+        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_words.txt

@@ -10,15 +10,6 @@ socio-economic
 ;; Frobenius norm used in np.linalg.norm
 fro
 
-;; abbreviation for "structure"
-struc
-
-;; method name within JournalPanel class
-onText
-
-;; a method name within JournalPanel class
-delt
-
 ;; structure file format
 discus
 

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

@@ -0,0 +1,18 @@
+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: diffpy.srreal
+      c_extension: true
+      github_admin_username: sbillinge
+    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: diffpy.srreal

.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: diffpy.srreal
+      c_extension: true
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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

@@ -0,0 +1,12 @@
+name: Deploy Documentation on Release
+
+on:
+  workflow_dispatch:
+
+jobs:
+  docs:
+    uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
+    with:
+      project: diffpy.srreal
+      c_extension: true
+      headless: false

.gitignore

@@ -1,52 +1,92 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
 *.py[cod]
+*$py.class
 
 # C extensions
 *.so
 
-# Packages
-*.egg
-*.egg-info
-dist
-build
-eggs
-parts
-bin
-var
-sdist
-temp
-develop-eggs
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+venv/
+*.egg-info/
 .installed.cfg
-lib
-lib64
-tags
+*.egg
+bin/
+temp/
+tags/
 errors.err
 
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
 # Installer logs
 pip-log.txt
+pip-delete-this-directory.txt
 MANIFEST
 
 # Unit test / coverage reports
+htmlcov/
+.tox/
 .coverage
-.tox
+.coverage.*
+.cache
 nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
 
 # Translations
 *.mo
+*.pot
 
 # Mr Developer
 .mr.developer.cfg
 .project
 .pydevproject
-.settings
-
-# SCons build files
-.gdb_history
-.sconf_temp/
-.sconsign.dblite
-config.log
-/sconscript.local
-/sconsvars.py
-
-# version information
-setup.cfg
-/src/diffpy/*/version.cfg
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+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

AUTHORS.rst

@@ -0,0 +1,12 @@
+Authors
+=======
+
+Pavol Juhas,
+Chris Farrow,
+Simon J.L. Billinge
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.srreal/graphs/contributors

CHANGELOG.rst

@@ -0,0 +1,47 @@
+=============
+Release Notes
+=============
+
+.. current developments
+
+
+Version 1.3.0  2019-03-13
+=========================
+
+Main differences from version 1.2.
+
+**Added:**
+
+* Support for Python 3.7, 3.6, 3.5 in addition to 2.7.
+* Validation of compiler options from `python-config`.
+* Make scons scripts compatible with Python 3 and Python 2.
+* `ConstantPeakWidth` attributes `uisowidth`, `bisowidth` to ease
+  PDF simulation with uniform isotropic atom displacements.
+
+**Changed:**
+
+* Require libdiffpy 1.4 or later.
+* Build Anaconda package with Anaconda C++ compiler.
+* Allow language standard c++11.
+* Pickle format for `PDFCalculator`, `DebyePDFCalculator`,
+  `OverlapCalculator`, `PeakWidthModel`, `PeakProfile`, `PDFEnvelope`,
+  `PDFBaseline`, and `ScatteringFactorTable` objects.
+
+**Deprecated:**
+
+* Variable `__gitsha__` in the `version` module renamed to `__git_commit__`.
+* `libdiffpy_version_info` attribute `git_sha` renamed to `git_commit`.
+
+**Removed**
+
+* Unused method `BVParam.__hash__`.
+* Disable pickling of `BasePairQuantity` as it is in effect abstract.
+* Pickling of Python-added attributes to exported C++ classes.
+* Function `get_libdiffpy_version_info` from the `version` module.
+
+**Fixed**
+
+* Return value conversion of `CrystalStructureAdapter` methods
+  `expandLatticeAtom` and `getEquivalentAtoms` methods.
+  Make them return a `list` of `Atom` objects.
+* Name suffix resolution of `boost_python` shared library.