update base package with merged cookie edits

.codecov.yml

@@ -1,2 +1,34 @@
-fixes:
-  - ".*/site-packages/::src/"
+# 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:
+      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

@@ -1,22 +1,13 @@
-# Configuration of the coverage.py tool for reporting test coverage.
-
-[report]
-# RE patterns for lines to be excluded from consideration.
-exclude_lines =
-    ## Have to re-enable the standard pragma
-    pragma: no cover
-    ## Don't complain if tests don't hit defensive assertion code:
-    raise AssertionError
-    raise NotImplementedError
-    ^[ ]*assert False
-
-    ## Don't complain if non-runnable code isn't run:
-    ^[ ]*@unittest.skip\b
-    ^[ ]{4}unittest.main()
-    if __name__ == .__main__.:
-
-
 [run]
+source =
+    diffpy.pdfgui
+[report]
 omit =
-    ## exclude debug.py from codecov report
-    */tests/debug.py
+    */python?.?/*
+    */site-packages/nose/*
+    # ignore _version.py and versioneer.py
+    .*version.*
+    *_version.py
+
+exclude_lines =
+    if __name__ == '__main__':

.gitattributes

@@ -1,7 +1 @@
-/.gitattributes  export-ignore
-/.gitignore  export-ignore
-/.travis.yml  export-ignore
-/conda-recipe/  export-ignore
-/devutils  export-ignore
-.gitarchive.cfg  export-subst
-*.bat  text eol=crlf
+diffpy.pdfgui/_version.py export-subst

.github/workflows/docs.yml

@@ -0,0 +1,43 @@
+name: Build Documentation
+
+on:
+  push:
+    branches:
+      - main
+  release:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: build
+          auto-update-conda: true
+
+      - name: install requirements
+        run: >-
+          conda install -n build -c conda-forge
+          --file requirements/build.txt
+          --file requirements/run.txt
+          --file requirements/docs.txt
+          --quiet --yes
+
+      - name: install the package
+        run: python -m pip install . --no-deps
+
+      - name: build documents
+        run: make -C doc html
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc/build/html

.github/workflows/main.yml

@@ -0,0 +1,53 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - CI
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  miniconda:
+    name: Miniconda ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: ["ubuntu-latest"]
+    steps:
+      - name: check out diffpy.pdfgui
+        uses: actions/checkout@v3
+        with:
+          repository: diffpy/diffpy.pdfgui
+          path: .
+          fetch-depth: 0  # avoid shallow clone with no tags
+
+      - name: Install Mamba
+        run: |
+          wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh" -O mambaforge.sh
+          bash mambaforge.sh -b -p $HOME/mambaforge
+          echo "$HOME/mambaforge/bin" >> $GITHUB_PATH
+          source $HOME/mambaforge/etc/profile.d/conda.sh
+          conda init bash
+
+      - name: Create conda environment
+        run: |
+          source $HOME/mambaforge/etc/profile.d/conda.sh
+          conda create -n test_env python=3.12 xonsh regolith -c conda-forge -y
+          conda activate test_env
+          pip install case_insensitive_dict
+
+      - name: Install dependencies
+        run: |
+          source $HOME/mambaforge/etc/profile.d/conda.sh
+          conda activate test_env
+          mamba install --file requirements/run.txt
+          mamba install --file requirements/test.txt
+          pip install -e .
+
+      - name: Use Xvfb Action
+        uses: GabrielBB/xvfb-action@v1
+        with:
+          run: |
+            bash -c "source $HOME/mambaforge/etc/profile.d/conda.sh && conda activate test_env && python -m run_tests.py"

.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

.gitignore

@@ -1,44 +1,99 @@
+# 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
-.idea
+
+# 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
 
+# 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
+
 # version information
 setup.cfg
 /src/diffpy/*/version.cfg
+
+# Rever
+rever/

.isort.cfg

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

AUTHORS.txt → AUTHORS.rst

@@ -1,3 +1,16 @@
+Authors
+=======
+
+DiffPy was initiated as part of the Distributed Data Analysis of Neutron
+Scattering Experiments (DANSE) project, funded by the National Science
+Foundation under grant DMR-0520547.  More information on DANSE can be
+found at http://danse.us.  Any opinions, findings, and conclusions or
+recommendations expressed in this material are those of the author(s)
+and do not necessarily reflect the views of the NSF.
+
+Main Contributors
+-----------------
+
 This code was developed as part of the DiffPy project to create python
 modules for structure investigations from diffraction data.  The main
 contributors to this package were
@@ -7,33 +20,31 @@ contributors to this package were
     Pavol Juhas
     Dmitriy Bryndin
 
-The DiffPy team is located in the Billinge-group at the Applied Physics
-and Applied Mathematics Department of the Columbia University in New York.
-Currently the team consists of
+Other current and former contributors of the DiffPy project include
 
     Simon Billinge
-    Pavol Juhas
     Chris Farrow
     Emil Bozin
     Wenduo Zhou
     Peng Tian
-    Timur Dykhne
 
+The DiffPy team is part of the Billinge Group at Columbia University in New York,
+within the Department of Applied Physics and Applied Mathematics.
+
+Contributors
+------------
 Please see the header of each source file for a detailed list of
 contributors.  This is an open-source project and we hope and expect
 that the list of contributors will expand with time.  Many thanks to
 all current and future contributors!
 
 For more information on the DiffPy project email [email protected]
 
-DiffPy was initiated as part of the Distributed Data Analysis of Neutron
-Scattering Experiments (DANSE) project, funded by the National Science
-Foundation under grant DMR-0520547.  More information on DANSE can be
-found at http://danse.us.  Any opinions, findings, and conclusions or
-recommendations expressed in this material are those of the author(s)
-and do not necessarily reflect the views of the NSF.
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.pdfgui/graphs/contributors
 
-Acknowledgments:
+Acknowledgments
+---------------
 
 We are truly grateful to all the people who have contributed, in all
 different ways, to this project:  Thomas Proffen, Xiangyun Qiu, Pete

CHANGELOG.rst

@@ -1,6 +1,6 @@
-=========================
-Diffpy.pdfgui Change Log
-=========================
+=============
+Release Notes
+=============
 
 .. current developments