Updated setup.py -> pyproject.toml with poetry build backend. Fully d…

…efined package dependencies.

Removed --validate tests.

Added scripts/build_docs.sh and removed Makefile for /docs. Flattened docs directory.

Removed setup.py in favor of pyproject.toml and poetry build system.

Removed LGTM and travis-ci code.

.github/PULL_REQUEST_TEMPLATE.md

@@ -7,6 +7,6 @@
 <!-- Provide a brief single sentence for the changelog. -->
 
 ## Status
-<!-- Please `pip install .[lint]; make format` in the base folder. -->
+<!-- Please `poetry install; bash scripts/format.sh` in the base folder. -->
 - [ ] Code base linted
 - [ ] Ready to go

.github/workflows/CI.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.11]
+        python-version: ["3.7", "3.11"]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
@@ -20,12 +20,12 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Checkout Code
         uses: actions/checkout@v3
-      - name: Install QCElemental
-        run: python -m pip install '.[tests]'
+      - name: Install poetry
+        run: pip install poetry
+      - name: Install repo
+        run: poetry install --no-interaction --no-ansi
       - name: Run tests
-        run: pytest -rws -v --cov=qcelemental --color=yes --cov-report=xml qcelemental
-      - name: Run pytest validate
-        run: pytest -rws -v --color=yes --validate qcelemental
+        run: poetry run pytest -rws -v --cov=qcelemental --color=yes --cov-report=xml
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3 # NEEDS UPDATE TO v3 https://github.com/codecov/codecov-action
       - name: QCSchema Examples Deploy
@@ -47,14 +47,15 @@ jobs:
         name: Set up Python
         with:
           python-version: "3.7"
+      - name: Install poetry
+        run: pip install poetry
+      - name: Install repo
+        run: poetry install --no-interaction --no-ansi
       - name: Build Documentation
-        run: |
-          python -m pip install '.[docs]'
-          cd docs
-          make html
+        run: bash scripts/build_docs.sh
       - name: GitHub Pages Deploy
         uses: JamesIves/github-pages-deploy-action@4.1.1
         if: github.event_name == 'push' && github.repository == 'MolSSI/QCElemental' && ( startsWith( github.ref, 'refs/tags/' ) || github.ref == 'refs/heads/master' )
         with:
           branch: gh-pages
-          folder: docs/build/html
+          folder: build/docs/

.github/workflows/Lint.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Install black
         run: pip install black
       - name: Check code formatting with black
-        run: black --check qcelemental devtools
+        run: black --check .
 
   isort:
     runs-on: ubuntu-latest
@@ -28,10 +28,12 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.7"
+      - name: Install poetry
+        run: pip install poetry
       - name: Install repo
-        run: pip install -e '.[lint]'
+        run: poetry install --no-interaction --no-ansi
       - name: Check import formatting with isort
-        run: isort --check-only --diff qcelemental devtools
+        run: poetry run isort --check-only --diff .
 # TODO: Support flake8 when the repo is ready :)
 # flake8:
 #   runs-on: ubuntu-latest
@@ -44,7 +46,7 @@ jobs:
 #     - name: Install flake8
 #       run: pip install flake8
 #     - name: Flake8
-#       run: flake8 --count qcelemental devtools
+#       run: flake8 --count .
 
 # TODO: Support mypy when the repo is ready
 # mypy:

.gitignore

@@ -64,8 +64,7 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/build/
-docs/source/api/
+docs/api/
 
 # PyBuilder
 target/
@@ -120,6 +119,7 @@ runinfo/*
 .vscode/
 raw_data/**/*_blob.py
 
-# autogen
+# QCElemental Specific ignores
 qcschema/*.schema
 qcelemental/tests/qcschema_instances/*/*.json
+poetry.lock

.pre-commit-config.yaml

@@ -24,7 +24,7 @@ repos:
       - id: black
   # TODO: Support flake8 when the repo is ready
   # - repo: https://github.com/PyCQA/flake8
-  #   rev: 6.0.0
+  #   rev: 5.0.4
   #   hooks:
   #     - id: flake8
   # TODO: Support mypy when the repo is ready

CONTRIBUTING.md

@@ -16,24 +16,26 @@ We welcome contributions from external contributors, and this document describes
   git clone https://github.com/{YOUR-GITHUB-USERNAME}/QCElemental.git
   cd QCElemental
   ```
-- Create a virtual environment into which you can install QCElemental. Make sure to use Python3.7+. Source this environment to use it for development.
+- Install [poetry](https://python-poetry.org/) if you do not have it on your system. Poetry will manage package dependencies and virtual environments for you.
+  ```sh
+  curl -sSL https://install.python-poetry.org | python3 -
+  ```
+- Install QCElemental.
 
   ```sh
-  python -m venv env
-  source env/bin/activate
+  poetry install
   ```
 
-- Install `QCElemental` into this virtual environment and then source the new command line tools. The command below installs QCElemental in "editable" mode--meaning all changes to the code will be instantly available to the python interpreter--and with all associated development tools.
+- Activate your new virtual environment. Many editors--like VS Code--will do this for you automatically when you open a directory that has been installed with `poetry`.
 
   ```sh
-  pip install -e '.[docs,tests,align,viz,lint]'
-  source env/bin/activate
+  poetry shell
   ```
 
 - Check your installation by running the tests.
 
   ```sh
-  bash devtools/scripts/test.sh
+  bash scripts/test.sh
   ```
 
 - Look at the code coverage by opening the newly created `htmlcov/index.html` in your browser. This can help you evaluate the test coverage of new code that you add.
@@ -64,13 +66,32 @@ We welcome contributions from external contributors, and this document describes
 - Make changes to the code and commit your changes using git. You can lint your code (make sure it adheres to our code guidelines by standardizing code format, import ordering, spacing, etc.) without needing to deal with these details yourself by running:
 
   ```sh
-  bash devtools/scripts/format.sh
+  bash scripts/format.sh
   ```
 
 - If you're providing a new feature, you must add test cases and documentation.
 
 - Push to your repo. When you are ready to submit your changes open a [Pull Request](https://github.com/MolSSI/QCElemental/pulls) on the MolSSI/QCElemental repo from your fork into the QCElemental `master` branch. When you're ready to be considered for merging, check the "Ready to go" box on the PR page to let the QCElemental developers know that the changes are complete. The code will not be merged until this box is checked, the continuous integration returns check marks, and multiple core developers give "Approved" reviews.
 
+## Building Docs and Packaging for Distribution
+
+- Build Docs:
+
+  ```sh
+  bash scripts/build_docs.sh
+  ```
+
+- Build packages for distribution. Build artifacts will be in `dist/`:
+
+  ```sh
+  poetry build
+  ```
+
+- Distribute built packages to PyPi:
+  ```sh
+  poetry publish --username {pypi_username} --password {pypi_password}
+  ```
+
 ## Additional Resources
 
 - [General GitHub documentation](https://help.github.com/)

README.md

@@ -2,24 +2,45 @@
 
 [![Build Status](https://github.com/MolSSI/QCElemental/workflows/CI/badge.svg?branch=master)](https://github.com/MolSSI/QCElemental/actions?query=workflow%3ACI)
 [![codecov](https://img.shields.io/codecov/c/github/MolSSI/QCElemental.svg?logo=Codecov&logoColor=white)](https://codecov.io/gh/MolSSI/QCElemental)
-[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/MolSSI/QCElemental.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/MolSSI/QCElemental/context:python)
 [![Documentation Status](https://img.shields.io/github/workflow/status/MolSSI/QCElemental/CI/master?label=docs&logo=readthedocs&logoColor=white)](http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/)
 [![Chat on Slack](https://img.shields.io/badge/chat-on_slack-green.svg?longCache=true&style=flat&logo=slack)](https://join.slack.com/t/qcarchive/shared_invite/enQtNDIzNTQ2OTExODk0LTE3MWI0YzBjNzVhNzczNDM0ZTA5MmQ1ODcxYTc0YTA1ZDQ2MTk1NDhlMjhjMmQ0YWYwOGMzYzJkZTM2NDlmOGM)
-![python](https://img.shields.io/badge/python-3.6+-blue.svg)
+![python](https://img.shields.io/badge/python-3.7+-blue.svg)
 
-QCElemental is a resource module for quantum chemistry containing physical
-constants and periodic table data from NIST and molecule handlers.
+**Documentation:** [Read The Docs](http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/index.html)
 
-Periodic Table and Physical Constants data are pulled from NIST srd144 and
-srd121, respectively ([details](raw_data/README.md)) in a renewable manner
-(class around NIST-published JSON file).
+Core data structures for Quantum Chemistry. QCElemental also contains physical constants and periodic table data from NIST and molecule handlers.
 
-This project also contains a generator, validator, and translator for [Molecule
-QCSchema](https://molssi-qc-schema.readthedocs.io/en/latest/auto_topology.html).
+Periodic Table and Physical Constants data are pulled from NIST srd144 and srd121, respectively ([details](raw_data/README.md)) in a renewable manner (class around NIST-published JSON file).
 
-It is intended to keep the QCElemental code compatible with Python 3.7+
-as long as dependencies allow. Packages are assured for Python 3.8+.
+This project also contains a generator, validator, and translator for [Molecule QCSchema](https://molssi-qc-schema.readthedocs.io/en/latest/auto_topology.html).
 
+## ✨ Getting Started
+
+- Installation. QCElemental supports Python 3.7+.
+
+  ```sh
+  python -m pip install qcelemental
+  ```
+
+- To install QCElemental with molecule visualization capabilities (useful in iPython or Jupyter notebook environments):
+
+  ```sh
+  python -m pip install 'qcelemental[viz]`
+  ```
+
+- To install QCElemental with various alignment capabilities using `networkx`
+
+  ```sh
+  python -m pip install 'qcelemental[align]`
+  ```
+
+- Or install both:
+
+  ```sh
+  python -m pip install 'qcelemental[viz,align]`
+  ```
+
+- See [documentation](http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/index.html)
 
 ### Periodic Table
 
@@ -77,6 +98,7 @@ conversion factors can be obtained:
 ### Covalent Radii
 
 Covalent radii are accessible for most of the periodic table from [Alvarez, Dalton Transactions (2008) doi:10.1039/b801115j](https://doi.org/10.1039/b801115j) ([details](qcelemental/data/alvarez_2008_covalent_radii.py.py)).
+
 ```python
 >>> import qcelemental as qcel
 >>> qcel.covalentradii.get('I')
@@ -96,6 +118,7 @@ qcelemental.exceptions.DataUnavailableError: ('covalent radius', 'Lv')
 ### van der Waals Radii
 
 Van der Waals radii are accessible for tmost of the periodic table from [Mantina, J. Phys. Chem. A (2009) doi: 10.1021/jp8111556](https://pubs.acs.org/doi/10.1021/jp8111556) ([details](qcelemental/data/mantina_2009_vanderwaals_radii.py)).
+
 ```python
 >>> import qcelemental as qcel
 >>> qcel.vdwradii.get('I')