Merge pull request #22 from maximilianvz/sphinx_docs

Create Sphinx Documentation Site

.editorconfig

@@ -0,0 +1,16 @@
+root = true
+
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+indent_style = space
+indent_size = 4
+max_line_length = 100
+
+[Makefile]
+indent_style = tab
+
+[{*.json,*.yml,*.yaml}]
+indent_style = space
+indent_size = 2

.github/workflows/website.yaml

@@ -0,0 +1,52 @@
+name: build_website
+
+on:
+  push:
+    branches:
+      - master
+
+permissions:
+  contents: write
+  deployments: write
+  pages: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      deployments: write
+      pages: write
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Install development and distributions version
+      run: |
+        pip install --upgrade pip
+        pip install .[doc]
+        pip install pypandoc_binary
+
+    - name: Setup pandoc
+      uses: siacodelabs/setup-pandoc@v1
+      with:
+        xelatex: true.
+
+    # didn't need to change anything here, but had to add sphinx.ext.githubpages
+    # to my conf.py extensions list. that fixes the broken uploads
+    - name: Building documentation
+      run: |
+        sphinx-apidoc -a -o ./docs/source/pyapi/ ./atomdb/ ./atomdb/test/ ./atomdb/data/ ./atomdb/datasets/ --separate
+        sphinx-build -M html docs/source _build 
+
+    # still need to build and set the PAT to get a rebuild on the pages job,
+    # apart from that quite clean and nice
+    - name: GitHub Pages Action
+      #if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: _build/html
+        publish_branch: gh-pages
+        cname: atomdb.qcdevs.org

.pre-commit-config.yaml

@@ -0,0 +1,40 @@
+files: "atomdb/"
+exclude: "examples/"
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+    - id: check-added-large-files                   # prevents giant files from being commit
+    - id: check-ast                                 # Check whether files parse as valid python.
+    - id: check-case-conflict                       # Checks conflict case-insensitive
+    - id: check-executables-have-shebangs
+    - id: check-json
+    - id: check-merge-conflict
+    - id: check-symlinks                            # Check for symlinks which don't point
+    - id: check-toml
+    - id: check-vcs-permalinks
+    - id: debug-statements                          # Check for debugger imports and py37 breakpt
+    - id: detect-private-key                        # Checks for the existence of private keys.
+    - id: destroyed-symlinks
+    - id: end-of-file-fixer                         # Makes sure files end in a newline
+    - id: fix-byte-order-marker                     # Removes UTF-8 byte order marker
+    - id: mixed-line-ending                         # Replaces or checks mixed line ending.
+    - id: pretty-format-json                        # Checks JSON are pretty
+      args: ["--autofix", "--no-sort-keys"]
+    - id: trailing-whitespace                       # Trims trailing whitespace.
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+  rev: v1.5.4
+  hooks:
+    - id: remove-crlf
+- repo: https://github.com/psf/black
+  rev: 24.1.1
+  hooks:
+    - id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: 'v0.1.14'
+  hooks:
+    - id: ruff
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: 0.27.3
+  hooks:
+    - id: check-github-workflows

MANIFEST.in

@@ -1,5 +1,4 @@
 include LICENSE
 include README.rst
 
-include atomdb/datasets/*/data/*
-include atomdb/datasets/*/raw_data/*
+include atomdb/datasets/*/db/*

atomdb/__init__.py

@@ -24,6 +24,8 @@
 
 from atomdb.promolecule import *
 
+from atomdb.periodic import *
+
 
 __version__ = version
 r"""AtomDB version string."""

atomdb/__main__.py

@@ -24,18 +24,12 @@
 
 
 # Initialize command line argument parser
-parser = ArgumentParser(
-    prog="python -m atomdb", description="Compile and/or query an AtomDB entry"
-)
+parser = ArgumentParser(prog="python -m atomdb", description="Compile and/or query an AtomDB entry")
 
 
 # Specify positional arguments and options
-parser.add_argument(
-    "-c", action="store_true", default=False, help="compile the specified entry"
-)
-parser.add_argument(
-    "-q", action="store_true", default=False, help="query the specified entry"
-)
+parser.add_argument("-c", action="store_true", default=False, help="compile the specified entry")
+parser.add_argument("-q", action="store_true", default=False, help="query the specified entry")
 parser.add_argument("dataset", type=str, help="name of dataset")
 parser.add_argument("elem", type=str, help="element symbol")
 parser.add_argument("charge", type=int, help="charge")
@@ -57,11 +51,7 @@
     if args.c:
         atomdb.compile(args.elem, args.charge, args.mult, args.e, args.dataset)
     if args.q:
-        print(
-            atomdb.load(
-                args.elem, args.charge, args.mult, args.e, args.dataset
-            ).to_json()
-        )
+        print(atomdb.load(args.elem, args.charge, args.mult, args.e, args.dataset).to_json())
 
     # Exit successfully
     exit(0)