cookiecut src/regolith, no migration for doc/dir files yet

.codecov.yml

@@ -20,7 +20,7 @@ coverage:
         target: auto
         if_no_uploads: error
         if_not_found: success
-        if_ci_failed: failure
+        if_ci_failed: error
         paths: '!*/tests/.*'
 
       tests:

.flake8

@@ -4,11 +4,10 @@ exclude =
     __pycache__,
     build,
     dist,
-    versioneer.py,
-    doc/manual/source/conf.py
+    doc/source/conf.py
 max-line-length = 115
-# Ignore some style 'errors' produced while formatting by 'black' (see link below)
+# 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
 per-file-ignores =
-    tests/test_helpers.py: E501
+    src/regolith/tests/test_helpers.py: E501

.gitattributes

@@ -0,0 +1 @@
+regolith/_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@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc/build/html

.github/workflows/main.yml

@@ -0,0 +1,54 @@
+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 regolith
+        uses: actions/checkout@v3
+        with:
+          repository: regro/regolith
+          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
+        # 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: install regolith requirements
+        shell: bash -l {0}
+        run: |
+          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 regolith
+        shell: bash -l {0}
+        run: |
+          conda activate test
+          coverage run -m pytest -vv -s
+          coverage report -m
+          codecov

.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/action@v3.0.0
+        with:
+          extra_args: --all-files

.gitignore

@@ -1,6 +1,7 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
+*$py.class
 
 # C extensions
 *.so
@@ -19,10 +20,15 @@ lib64/
 parts/
 sdist/
 var/
+venv/
 *.egg-info/
 .installed.cfg
 *.egg
 .idea
+bin/
+temp/
+tags/
+errors.err
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -33,6 +39,7 @@ var/
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
+MANIFEST
 
 # Unit test / coverage reports
 htmlcov/
@@ -43,20 +50,52 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *,cover
+.hypothesis/
 
 # Translations
 *.mo
 *.pot
 
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
 # Django stuff:
 *.log
 
 # Sphinx documentation
-docs/_build/
+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/regro/*/version.cfg
+
 # Rever
 rever/
 

.isort.cfg

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

AUTHORS.rst

@@ -0,0 +1,10 @@
+Authors
+=======
+
+Billinge Group and community contibutors.
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/regro/regolith/graphs/contributors