Merge pull request #123 from sbillinge/cr2

PDFmorph cookiecuttered!  passing tests.

Author: sbillinge

Diff for: .codecov.yml

@@ -20,7 +20,7 @@ coverage:
         target: auto
         if_no_uploads: error
         if_not_found: success
-        if_ci_failed: failure
+        if_ci_failed: error
         paths: '!*/tests/.*'
 
       tests:

Diff for: .coveragerc

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

Diff for: .flake8

@@ -7,4 +7,5 @@ exclude =
     doc/source/conf.py
 max-line-length = 115
 # Ignore some style 'errors' produced while formatting by 'black'
-ignore = W503
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
+extend-ignore = E203

Diff for: .gitattributes

@@ -0,0 +1 @@
+diffpy.pdfmorph/_version.py export-subst

Diff for: .github/workflows/docs.yml

@@ -6,7 +6,6 @@ on:
       - main
   release:
 
-
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -35,10 +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@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./doc/manual/build/html
+          publish_dir: ./doc/build/html

Diff for: .github/workflows/main.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - main
+      - CI
   pull_request:
   workflow_dispatch:
 
@@ -19,9 +20,8 @@ jobs:
         uses: actions/checkout@v3
         with:
           repository: diffpy/diffpy.pdfmorph
-          # for bookkeeping have diffpy.pdfmorph at the same level as everything else in the
-          # directory tree
           path: .
+          fetch-depth: 0  # avoid shallow clone with no tags
 
       - name: initialize miniconda
         # this uses a marketplace action that sets up miniconda in a way that makes
@@ -36,7 +36,7 @@ jobs:
           python-version: 3
           auto-activate-base: false
 
-      - name: install pdfmorph requirements
+      - name: install diffpy.pdfmorph requirements
         shell: bash -l {0}
         run: |
           conda config --set always_yes yes --set changeps1 no
@@ -45,12 +45,10 @@ jobs:
           conda install --file requirements/run.txt
           conda install --file requirements/test.txt
           pip install .
-
-      - name: Validate pdfmorph
+      - name: Validate diffpy.pdfmorph
         shell: bash -l {0}
         run: |
           conda activate test
-          pdfmorph --help  # Check run on command line
-          python -m coverage run run_tests.py  # use `python -m` to search for modules within env
+          coverage run -m pytest -vv -s
           coverage report -m
           codecov

Diff for: .github/workflows/pre-commit.yml

@@ -0,0 +1,19 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+  workflow_dispatch:
+
+jobs:
+  pre-commit:
+    # pull requests are a duplicate of a branch push if within the same repo.
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --all-files

Diff for: .gitignore

@@ -20,9 +20,14 @@ lib64/
 parts/
 sdist/
 var/
+venv/
 *.egg-info/
 .installed.cfg
 *.egg
+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/
@@ -49,48 +55,45 @@ coverage.xml
 *.mo
 *.pot
 
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
 # Django stuff:
 *.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
 
 # Sphinx documentation
-docs/_build/
+docs/build/
+docs/source/generated/
+
+# pytest
+.pytest_cache/
 
 # PyBuilder
 target/
 
-# IPython Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
+# Editor files
+# mac
+.DS_Store
+*~
 
-# celery beat schedule file
-celerybeat-schedule
+# vim
+*.swp
+*.swo
 
-# dotenv
-.env
+# pycharm
+.idea/
 
-# virtualenv
-venv/
-ENV/
+# VSCode
+.vscode/
 
-# Spyder project settings
-.spyderproject
+# Ipython Notebook
+.ipynb_checkpoints
 
-# Rope project settings
-.ropeproject
+# version information
+setup.cfg
+/src/diffpy/*/version.cfg
 
-# pycharm
-.idea/
-# Mac
-.DS_Store
 # Rever
 rever/

Diff for: .pre-commit-config.yaml

@@ -11,27 +11,27 @@ ci:
     submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
         exclude: '\.(rst|txt)$'
-  - repo: https://github.com/ambv/black
-    rev: 23.3.0
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/pre-commit/pre-commit-hooks

Diff for: AUTHORS.rst

@@ -1,11 +1,10 @@
 Authors
-====================
+=======
 
-Christopher L. Farrow, Christopher James Wright, Pavol Juhas,
-Chia-Hao (Timothy) Liu, Timur Davis, S. Matthew Román, Simon J.L. 
-Billinge
+Billinge Group and community contibutors.
 
 Contributors
 ------------
-For a list of contributors, visit 
+
+For a list of contributors, visit
 https://github.com/diffpy/diffpy.pdfmorph/graphs/contributors

Diff for: CHANGELOG.rst

@@ -1,6 +1,6 @@
-==========================
+=============
 Release Notes
-==========================
+=============
 
 .. current developments