cookiecutter: modified files pt1

.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/main.yml

@@ -23,31 +23,32 @@ jobs:
           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: initialize miniconda
+        # this uses a marketplace action that sets up miniconda in a way that makes
+        # it easier to use.  I tried setting it up without this and it was a pain
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test
+          # environment.yml file is needed by this action.  Because I don't want
+          # maintain this but rather maintain the requirements files it just has
+          # basic things in it like conda and pip
+          environment-file: ./environment.yml
+          python-version: 3
+          auto-activate-base: false
 
-      - name: Create conda environment
+      - name: install diffpy.pdfgui requirements
+        shell: bash -l {0}
         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
+          conda config --set always_yes yes --set changeps1 no
+          conda config --add channels conda-forge
+          conda activate test
+          conda install --file requirements/run.txt
+          conda install --file requirements/test.txt
+          pip install .
+      - name: Validate diffpy.pdfgui
+        shell: bash -l {0}
         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"
+          conda activate test
+          coverage run -m pytest -vv -s
+          coverage report -m
+          codecov

.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/

CHANGELOG.rst

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

MANIFEST.in

@@ -1,23 +1,14 @@
-recursive-include src *
-recursive-exclude src *.py[co]
-include AUTHORS.txt LICENSE*.txt README*
-recursive-include doc *
-prune doc/epydoc
-prune doc/manual/images/originals
-exclude doc/manual/images/*.pdf
-recursive-exclude doc/manual Makefile *.py *.texinfo
-recursive-exclude doc/manual *.aux *.cp *.cps *.err *.log *.toc *.vr *.vrs
-recursive-include icons *.png *.ico
-recursive-exclude icons *.m *.xcf
-global-exclude .gitattributes .gitignore .gitarchive.cfg
-global-exclude .DS_Store
+include AUTHORS.rst
+include LICENSE
+include README.rst
+include requirements.txt
 
-# Avoid user content in setup.cfg to make distribution reproducible.
-exclude setup.cfg
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
 
-# Exclude git-tracked files spuriously added by setuptools_scm
-exclude .coveragerc
-exclude .travis*
-prune conda-recipe
-prune devutils
-#prune doc
+recursive-include docs *.rst conf.py Makefile make.bat
+
+include diffpy.pdfgui/version.py
+
+# If including data files in the package, add them like:
+# include path/to/data_file