Cookie (#179)

* copy .github directory

* nest inside .github

* update for pdfgui

* test tests (#131)

* pin numpy to 1.x for now

* add environment.yml

* test tests

* trigger

* try again with requirements

* try again with requirements

* now update test reqs

* try and handle xwindow display issue

* try using xfvb action

* refactor xvfb action commands

* source activate?

* different tack, generate error and work on test?

* again

* again

* chatgpt method

* supress running qc of meta.yaml in conda-forge by renaming

* try new pyproject.toml

* again2

* forgot to install diffpy.pdfgui!

* back to setup.py

* copyright fixes (#134)

* Flake8v1 (#137)

* move modules to top

* remove extra #s

* line length and extra #s

* extra #s

* modules to top

* replace lambda function and line length

* add # noqa: E501

* modules to top

* fix lambda func

* Flake8v2 (#138)

* fix not in

* fix lambda functions

* remove #

* remove lambda func

* modules to top

* mod to top

* line length and import and #s

* fix line length and #s

* comment unused var, fix imports and #s

* modules to top and inline comment fix

* def functions within function to pass tests

* move functions outside of class

* Flake8v4 (#140)

* capitalize Trustees

* Exception on errorwrapper

* wx.PyObjectError in except

* ValueError and Exception

* Exception

* remove import

* pre-commit errors in comments (#141)

* wx12 and bonlengthdialog (#142)

* wx12 and bonlengthdialog

* devutils/makedist import order

* news (#143)

* cookiecutter: untracked files (#149)

* untracked files

* [pre-commit.ci] auto fixes from pre-commit hooks

* update LICENSE.rst

* update AUTHORS.rst and remove AUTHORS.txt

* tipping our hat

* Remove BSD 3-Clause, leaving Columbia copyright

* remove README from requirements

* replace requirements

* adding wxpython back

* adding back freezegun

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Simon Billinge <sbillinge@users.noreply.github.com>

* Files in doc directory (#157)

* move images to _static

* move files in .../doc/manual into doc/source

* move .gitignore file

* move rest of files to doc/

* move makefile from doc/source to doc/

* remove Makefile from doc/source

* update Makefile in doc

* add rest of cookiecutter files into doc/source

* add make.bat file

* moving .py files into doc/manual

* move files into manual

* moving images into manual

* add TUTORIAL.rst

* convert .txt to .rst in TUTORIAL

* fix formating

* formating

* formating

* reference formating

* move TUTORIAL.rst to manual

* move tutorial.rst from manual to source

* rm extra tutorial.rst

* add tutorial section to index.rst

* index.rst formating

* files (#158)

* Replace Caden's PR (#160)

Minor copyright fixes and news update

* try workflow for testing (#161)

* workflow for testing

* test unittest

* try Xvfb

* try to remove no test ran line

* [pre-commit.ci] auto fixes from pre-commit hooks

* try to remove no test ran line

* try pytest

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* remove unused files (#166)

* update requirements/run.txt (#165)

* update requirements/run.txt, include right package

* use matplotlib-base

* remove dependency tests (#169)

* fix deprecation warning when test (#170)

* fix pkg_resources deprecation warning

* use __name__

* daemon deprecation

* rst file changes (#171)

* Use the original license

* other file changes

* add a bit more in readme

* remove epydoc (#173)

* build doc (#174)

* build doc

* pre commit

* Apply the new workflow (#168)

* Apply the new workflow

* remove prerelease from docs workflow

* rename to main

---------

Co-authored-by: Caden Myers <cjm2304@columbia.edu>
Co-authored-by: Caden Myers <158210249+cadenmyers13@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Tieqiong <123656525+Tieqiong@users.noreply.github.com>

.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/codecov.yml

@@ -0,0 +1,62 @@
+name: Gather coverage report and upload to codecov
+
+on:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - prereleased
+      - published
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  coverage:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out diffpy.pdfgui
+        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
+
+      - name: Conda config
+        run: >-
+          conda config --set always_yes yes
+          --set changeps1 no
+
+      - name: Install diffpy.pdfgui and requirements
+        run: |
+          conda install --file requirements/run.txt
+          conda install --file requirements/test.txt
+          python -m pip install -r requirements/pip.txt
+          python -m pip install . --no-deps
+
+      - name: Install Xvfb
+        run: sudo apt-get install -y xvfb
+
+      - name: Start Xvfb
+        run: |
+          export DISPLAY=:99
+          Xvfb :99 -screen 0 1024x768x16 &
+
+      - name: Validate diffpy.pdfgui
+        run: |
+          export DISPLAY=:99
+          coverage run -m pytest -vv -s
+          coverage report -m
+          codecov
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/docs.yml

@@ -0,0 +1,48 @@
+name: Build and Deploy Documentation
+
+on:
+  release:
+    types:
+      - published
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out diffpy.pdfgui
+        uses: actions/checkout@v4
+
+      - name: Initialize miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: build
+          auto-update-conda: true
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: Conda config
+        run: >-
+          conda config --set always_yes yes
+          --set changeps1 no
+
+      - name: Install diffpy.pdfgui and build requirements
+        run: |
+          conda install --file requirements/build.txt
+          conda install --file requirements/run.txt
+          conda install --file requirements/docs.txt
+          python -m pip install -r requirements/pip.txt
+          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 +1,52 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out diffpy.pdfgui
+        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
+
+      - name: Conda config
+        run: >-
+          conda config --set always_yes yes
+          --set changeps1 no
+
+      - name: Install diffpy.pdfgui and requirements
+        run: |
+          conda install --file requirements/run.txt
+          conda install --file requirements/test.txt
+          python -m pip install -r requirements/pip.txt
+          python -m pip install . --no-deps
+
+      - name: Install Xvfb
+        run: sudo apt-get install -y xvfb
+
+      - name: Start Xvfb
+        run: |
+          export DISPLAY=:99
+          Xvfb :99 -screen 0 1024x768x16 &
+
+      - name: Validate diffpy.pdfgui
+        run: |
+          export DISPLAY=:99
+          python -m pytest

.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