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be6c14a
pre-commit run with no manual change
stevenhua0320 Aug 11, 2024
58a94de
Merge pull request #70 from stevenhua0320/c1
sbillinge Aug 11, 2024
3dfe3b4
ValueError to TypeError for two test functions
bobleesj Aug 19, 2024
0540413
Run black . without any manual modification
bobleesj Aug 19, 2024
68d57e4
Merge pull request #73 from bobleesj/cookie-black
sbillinge Aug 19, 2024
6be7651
Merge pull request #71 from bobleesj/cookie-pass-test
sbillinge Aug 19, 2024
b64fe12
Remove the usage of l in adding literal
bobleesj Aug 20, 2024
cc2bd12
Change l to error message
bobleesj Aug 20, 2024
e5adc96
Rename lambda l to calculate_pr
bobleesj Aug 20, 2024
92c5493
Rename l to lattice
bobleesj Aug 20, 2024
5d7a65d
Rename l to l_parameter
bobleesj Aug 20, 2024
ad545e4
Rename l to lattice
bobleesj Aug 20, 2024
95483ef
Fix multiple # into a single #
bobleesj Aug 20, 2024
c61ba23
Import modules at the top
bobleesj Aug 20, 2024
baaf54e
Move doc module at the top
bobleesj Aug 20, 2024
bf1fcaf
Move module at the top, fix format for if-stmt
bobleesj Aug 20, 2024
a0e5fa5
Merge pull request #74 from bobleesj/cookie-flake8
sbillinge Aug 20, 2024
e373508
Merge branch 'cookie' into cookie-flake8-E266
sbillinge Aug 20, 2024
12507e8
Merge pull request #75 from bobleesj/cookie-flake8-E266
sbillinge Aug 20, 2024
0927c7a
Merge pull request #76 from bobleesj/cookie-flake8-E402
sbillinge Aug 20, 2024
a4f99b4
Fix unambiguous label name from I to intensity
bobleesj Aug 21, 2024
82f18b8
Use 'not in' instead of not xxx in
bobleesj Aug 21, 2024
e19a955
Do not use not in and use black fix cond lines
bobleesj Aug 21, 2024
91835f7
Replace not xxx in to not in, make variables clear
bobleesj Aug 21, 2024
563de3f
Merge pull request #77 from bobleesj/cookie-flake8-rest
sbillinge Aug 21, 2024
b478b10
Move lambda directly into funcs
bobleesj Aug 21, 2024
02ce549
Use noqa for clear ladmbda in test builder
bobleesj Aug 21, 2024
a05b3f1
Replace erf to erfc by importing the func
bobleesj Aug 21, 2024
bf0244a
Merge pull request #79 from bobleesj/cookie-lambda-direct
sbillinge Aug 22, 2024
15d57bd
Merge pull request #81 from bobleesj/cookie-lambda-func2
sbillinge Aug 22, 2024
312c34d
Use nested func instead of lambda in builder.py
bobleesj Aug 24, 2024
4f724d7
Insert lambda into map in prcalcualtor.py
bobleesj Aug 24, 2024
e649789
Use noqa #731 for a test function in testcontribution.py
bobleesj Aug 24, 2024
7ea0fa9
Merge pull request #82 from bobleesj/flake8-lambda-3
sbillinge Aug 25, 2024
2ac6bfb
Add noqa: E731 with flake8
bobleesj Sep 10, 2024
f1162a6
Merge pull request #84 from bobleesj/cookie-lambda
sbillinge Sep 14, 2024
50ad60b
Add minimal pyproject
bobleesj Sep 26, 2024
876f895
Move tests and rename test files
bobleesj Sep 26, 2024
faed7be
Add github CI and change conda-recipe files to .txt
bobleesj Sep 26, 2024
d50dd9d
Add test.txt, run.txt
bobleesj Sep 26, 2024
52c4b80
[pre-commit.ci] auto fixes from pre-commit hooks
pre-commit-ci[bot] Sep 26, 2024
2fafe83
Add env.yml file
bobleesj Sep 26, 2024
5798f0c
Merge pull request #89 from bobleesj/cookie-py312
sbillinge Sep 30, 2024
d39431e
Add doc
bobleesj Sep 30, 2024
8af2e9b
Add src
bobleesj Sep 30, 2024
bc92906
Add license
bobleesj Sep 30, 2024
78d1048
Add tests, iosrt, flake8, codecov
bobleesj Sep 30, 2024
99265fe
Add requirements
bobleesj Sep 30, 2024
2183645
Auhors, changelog, code of conduct
bobleesj Sep 30, 2024
0c8e78b
Delete older files
bobleesj Sep 30, 2024
f64b601
Add coveragerc
bobleesj Sep 30, 2024
a9c853c
Add limited license
bobleesj Sep 30, 2024
7224746
Add diffpy.structure under run-ext
bobleesj Sep 30, 2024
89ddff4
[pre-commit.ci] auto fixes from pre-commit hooks
pre-commit-ci[bot] Sep 30, 2024
6fe1508
Change news name to cookie
bobleesj Sep 30, 2024
dca1ca7
merge
bobleesj Sep 30, 2024
f0debb9
Update citation and fix being developed at columbia
bobleesj Oct 1, 2024
2836264
Merge pull request #91 from bobleesj/cookie-recut
sbillinge Oct 1, 2024
061f4a9
Add conda-forge release chceklist to GitHub Issue template
bobleesj Nov 9, 2024
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5 changes: 3 additions & 2 deletions .codecov.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ coverage:
status:
patch:
default:
target: '80'
target: '70'
if_no_uploads: error
if_not_found: success
if_ci_failed: failure
Expand All @@ -20,12 +20,13 @@ coverage:
target: auto
if_no_uploads: error
if_not_found: success
if_ci_failed: failure
if_ci_failed: error
paths: '!*/tests/.*'

tests:
target: 97.9%
paths: '*/tests/.*'
if_not_found: success

flags:
tests:
Expand Down
31 changes: 11 additions & 20 deletions .coveragerc
Original file line number Diff line number Diff line change
@@ -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.srfit
[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__':
11 changes: 11 additions & 0 deletions .flake8
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
[flake8]
exclude =
.git,
__pycache__,
build,
dist,
doc/source/conf.py
max-line-length = 115
# Ignore some style 'errors' produced while formatting by 'black'
# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
extend-ignore = E203
5 changes: 0 additions & 5 deletions .gitarchive.cfg

This file was deleted.

7 changes: 0 additions & 7 deletions .gitattributes

This file was deleted.

35 changes: 35 additions & 0 deletions .github/ISSUE_TEMPLATE
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
---
name: Release
about: Checklist and communication channel for PyPI and GitHub release
title: "Ready for <version-number> PyPI/GitHub release"
labels: "release"
assignees: ""
---

### PyPI/GitHub release checklist:

- [ ] All PRs/issues attached to the release are merged.
- [ ] All the badges on the README are passing.
- [ ] License information is verified as correct. If you are unsure, please comment below.
- [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
missing), tutorials, and other human written text is up-to-date with any changes in the code.
- [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) are updated.
- [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
- [ ] Grammar and writing quality are checked (no typos).

Please mention @sbillinge here when you are ready for PyPI/GitHub release. Include any additional comments necessary, such as
version information and details about the pre-release here:

### conda-forge release checklist:

<!-- After @sbillinge releases the PyPI package, please check the following when creating a PR for conda-forge release.-->

- [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock.
- [ ] All relevant issues in the feedstock are addressed in the release PR.

### Post-release checklist

<!-- Before closing this issue, please complete the following: -->

- [ ] Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
- [ ] Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.
12 changes: 12 additions & 0 deletions .github/workflows/check-news-item.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
name: Check for News

on:
pull_request_target:
branches:
- main

jobs:
build:
uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
with:
project: diffpy.srfit
21 changes: 21 additions & 0 deletions .github/workflows/matrix-and-codecov-on-merge-to-main.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
name: CI

on:
push:
branches:
- main
release:
types:
- prereleased
- published
workflow_dispatch:

jobs:
coverage:
uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
with:
project: diffpy.srfit
c_extension: false
headless: false
secrets:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
14 changes: 14 additions & 0 deletions .github/workflows/publish-docs-on-release.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
name: Build and Deploy Docs

on:
release:
types:
- published
workflow_dispatch:

jobs:
docs:
uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
with:
project: diffpy.srfit
c_extension: false
16 changes: 16 additions & 0 deletions .github/workflows/tests-on-pr.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
name: Tests on PR

on:
push:
branches:
- main
pull_request:
workflow_dispatch:

jobs:
validate:
uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
with:
project: diffpy.srfit
c_extension: false
headless: false
89 changes: 72 additions & 17 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -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

# 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

# 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/
8 changes: 0 additions & 8 deletions .idea/.gitignore

This file was deleted.

4 changes: 4 additions & 0 deletions .isort.cfg
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
[settings]
line_length = 115
multi_line_output = 3
include_trailing_comma = True
46 changes: 46 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
default_language_version:
python: python3
ci:
autofix_commit_msg: |
[pre-commit.ci] auto fixes from pre-commit hooks
autofix_prs: true
autoupdate_branch: 'pre-commit-autoupdate'
autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
autoupdate_schedule: monthly
skip: [no-commit-to-branch]
submodules: false
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.6.0
hooks:
- id: check-yaml
- id: end-of-file-fixer
- id: trailing-whitespace
- id: check-case-conflict
- id: check-merge-conflict
- id: check-toml
- id: check-added-large-files
- repo: https://github.com/psf/black
rev: 24.4.2
hooks:
- id: black
- repo: https://github.com/pycqa/flake8
rev: 7.0.0
hooks:
- id: flake8
- repo: https://github.com/pycqa/isort
rev: 5.13.2
hooks:
- id: isort
args: ["--profile", "black"]
- repo: https://github.com/kynan/nbstripout
rev: 0.7.1
hooks:
- id: nbstripout
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.4.0
hooks:
- id: no-commit-to-branch
name: Prevent Commit to Main Branch
args: ["--branch", "main"]
stages: [pre-commit]
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