Merge pull request #73 from diffpy/cookie

Cookie

Author: sbillinge

.coveragerc

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

.flake8

@@ -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

.gitattributes

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

.github/workflows/docs.yml

@@ -0,0 +1,59 @@
+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
+          environment-file: ./environment.yml
+          python-version: 3
+          auto-update-conda: true
+
+      - name: install requirements
+        run: |
+          conda config --set always_yes yes --set changeps1 no
+          conda config --add channels conda-forge
+          conda create -n build python=3.12
+          conda activate build
+          conda install --file requirements/build.txt
+          conda install --file requirements/run.txt
+          conda install --file requirements/test.txt
+          conda install --file requirements/docs.txt
+          python -m pip install . --no-deps
+
+      - name: build documents
+        run: make -C doc html
+
+      - name: Run tests and upload coverage
+        shell: bash -l {0}
+        run: |
+          conda activate build
+          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 }}
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc/build/html

.github/workflows/documentation.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.snmf
-          # for bookkeeping have diffpy.snmf 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
@@ -50,10 +50,6 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate test
-          coverage run run_tests.py
+          coverage run -m pytest -vv -s
           coverage report -m
-
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3
-#        with:
-#          token: ${{ secrets.CODECOV_TOKEN }}
+          codecov

.github/workflows/main.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

.github/workflows/pre-commit.yml

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

.isort.cfg

@@ -0,0 +1,43 @@
+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
+        exclude: '\.(rst|txt)$'
+  - 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]

.pre-commit-config.yaml

@@ -1,9 +1,10 @@
 Authors
-====================
+=======
 
-Ran Gu, Adeolu Ajayi, Qiang Du,  Simon J.L. Billinge
+Billinge Group and community contibutors.
 
 Contributors
 ------------
-For a full list of contributors, visit
+
+For a list of contributors, visit
 https://github.com/diffpy/diffpy.snmf/graphs/contributors