Merge pull request #6 from EricaCMitchell/dipoles

v0.2.0

.codecov.yml

@@ -0,0 +1,14 @@
+# Codecov configuration to make it a bit less noisy
+coverage:
+  status:
+    patch: false
+    project:
+      default:
+        threshold: 50%
+comment:
+  layout: "header"
+  require_changes: false
+  branches: null
+  behavior: default
+  flags: null
+  paths: null

.gitattributes

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

.github/CONTRIBUTING.md

@@ -0,0 +1,42 @@
+# How to contribute
+
+We welcome contributions from external contributors, and this document
+describes how to merge code changes into this Quax. 
+
+## Getting Started
+
+* Make sure you have a [GitHub account](https://github.com/signup/free).
+* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub.
+* On your local machine,
+  [clone](https://help.github.com/articles/cloning-a-repository/) your fork of
+  the repository.
+
+## Making Changes
+
+* Add some really awesome code to your local fork.  It's usually a [good
+  idea](http://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/)
+  to make changes on a
+  [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
+  with the branch name relating to the feature you are going to add.
+* When you are ready for others to examine and comment on your new feature,
+  navigate to your fork of {{cookiecutter.repo_name}} on GitHub and open a [pull
+  request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
+  after you launch a PR from one of your fork's branches, all
+  subsequent commits to that branch will be added to the open pull request
+  automatically.  Each commit added to the PR will be validated for
+  mergability, compilation and test suite compliance; the results of these tests
+  will be visible on the PR page.
+* If you're providing a new feature, you must add test cases and documentation.
+* When the code is ready to go, make sure you run the test suite using pytest.
+* When you're ready to be considered for merging, check the "Ready to go"
+  box on the PR page to let the Quax devs know that the changes are complete.
+  The code will not be merged until this box is checked, the continuous
+  integration returns checkmarks,
+  and multiple core developers give "Approved" reviews.
+
+# Additional Resources
+
+* [General GitHub documentation](https://help.github.com/)
+* [PR best practices](http://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/)
+* [A guide to contributing to software packages](http://www.contribution-guide.org)
+* [Thinkful PR example](http://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR)

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,12 @@
+## Description
+Provide a brief description of the PR's purpose here.
+
+## Todos
+Notable points that this PR has either accomplished or will accomplish.
+  - [ ] TODO 1
+
+## Questions
+- [ ] Question1
+
+## Status
+- [ ] Ready to go

.github/workflows/continuous_integration.yml

@@ -7,30 +7,67 @@ on:
   pull_request:
     branches:
       - master
+  schedule:
+    # Weekly tests run on main by default:
+    #   Scheduled workflows run on the latest commit on the default or base branch.
+    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+    - cron: "0 0 * * 0"
+    #   Scheduled workflows are automatically disabled when no repository activity has occurred in 60 day.
 
 jobs:
-  build-linux:
-    runs-on: ubuntu-latest
+  test:
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.7
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install dependencies
-      shell: bash -l {0}
-      run: |
-        conda install python=3.7
-        conda install -c psi4 psi4
-        conda install -c conda-forge jax
-        conda install -c conda-forge jaxlib
-        conda install -c conda-forge h5py
-        pip install -e .
-    - name: Test with pytest
-      run: |
-        conda install pytest
-        pytest
+      - uses: actions/checkout@v4
+
+      - name: Additional info about the build
+        shell: bash
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+
+      - name: Create Environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: devtools/conda-envs/test_env.yaml
+          environment-name: test
+          condarc: | 
+            channels:
+              - conda-forge
+          create-args: >- 
+            python=${{ matrix.python-version }}
+
+      - name: Build integrals
+        shell: bash -l {0}
+        run: |
+          cd $GITHUB_WORKSPACE/quax/integrals
+          make
+          cd $GITHUB_WORKSPACE
+
+      - name: Install package
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          python -m pip install .
+          micromamba list
+
+      - name: Run tests
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          pytest -v --cov=quax --cov-report=xml --color=yes tests/
+
+      - name: CodeCov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+

.gitignore

@@ -1,5 +1,3 @@
-localtests/
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -8,11 +6,6 @@ __pycache__/
 # C extensions
 *.so
 
-# Psi4, HdF5, molecule file disk junk
-*.dat
-*.h5
-*.xyz
-
 # Distribution / packaging
 .Python
 env/
@@ -22,6 +15,7 @@ dist/
 downloads/
 eggs/
 .eggs/
+lib/
 lib64/
 parts/
 sdist/
@@ -30,7 +24,6 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-benchmarks/
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -48,6 +41,7 @@ htmlcov/
 .coverage
 .coverage.*
 .cache
+.pytest_cache
 nosetests.xml
 coverage.xml
 *.cover
@@ -101,11 +95,31 @@ ENV/
 # Rope project settings
 .ropeproject
 
+# Pycharm settings
+.idea
+*.iml
+*.iws
+*.ipr
+
+# Ignore devcontainer
+/.devcontainer
+
+# Ignore VSCode settings
+/.vscode
+
+# Ignore Sublime Text settings
+*.sublime-workspace
+*.sublime-project
+
+# vim swap
+*.swp
+
 # mkdocs documentation
 /site
 
 # mypy
 .mypy_cache/
 
-#misc files
-project_notes.txt
+# profraw files from LLVM? Unclear exactly what triggers this
+# There are reports this comes from LLVM profiling, but also Xcode 9.
+*profraw

CODE_OF_CONDUCT.md

@@ -0,0 +1,77 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age,
+body size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+Moreover, project maintainers will strive to offer feedback and advice to
+ensure quality and consistency of contributions to the code.  Contributions
+from outside the group of project maintainers are strongly welcomed but the
+final decision as to whether commits are merged into the codebase rests with
+the team of project maintainers.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event. Representation of a
+project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at '{{cookiecutter.author_email}}'. The project team will
+review and investigate all complaints, and will respond in a way that it deems
+appropriate to the circumstances. The project team is obligated to maintain
+confidentiality with regard to the reporter of an incident. Further details of
+specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.4, available at
+[http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

MANIFEST.in

@@ -0,0 +1,6 @@
+include CODE_OF_CONDUCT.md
+include MANIFEST.in
+include LICENSE
+
+graft quax
+global-exclude *.py[cod] __pycache__ *.so