Add docs.

.github/workflows/testing.yml

@@ -41,8 +41,10 @@ jobs:
       - name: pytest
         run: |
           pytest --cov=package tests --color=yes
-#      - name: Coveralls
-#        uses: coverallsapp/github-action@v2
+#      - name: Upload coverage reports to Codecov
+#        uses: codecov/codecov-action@v3
+#        env:
+#          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   build:
     needs: test

.gitignore

@@ -24,6 +24,7 @@ setuptools*
 .*_cache
 # VS Code
 .vscode/*
+_site
 
 # Environments
 .env

README.md

@@ -1,4 +1,13 @@
+[![GitHub license](https://img.shields.io/github/license/materialsvirtuallab/python_template)](https://github.com/materialsvirtuallab/python_template/blob/main/LICENSE)
+[![Linting](https://github.com/materialsvirtuallab/python_template/workflows/Linting/badge.svg)](https://github.com/materialsvirtuallab/python_template/workflows/Linting/badge.svg)
+[![Testing](https://github.com/materialsvirtuallab/python_template/workflows/Testing/badge.svg)](https://github.com/materialsvirtuallab/python_template/workflows/Testing/badge.svg)
+<!--
+[![Downloads](https://pepy.tech/badge/python_template)](https://pepy.tech/project/python_template)
+[![codecov](https://codecov.io/gh/materialsvirtuallab/python_template/branch/main/graph/badge.svg?token=3V3O79GODQ)]
+(https://codecov.io/gh/materialsvirtuallab/python_template)
+-->
+
 # Introduction
 
-This is a template for setting up Python packages in the Materials Virtual Lab. It comes with the standard Github 
-workflows, pyproject and linting.
+This is a template for setting up Python packages in the Materials Virtual Lab. It comes with the standard Github
+workflows, pyproject and linting.

docs/Gemfile

@@ -0,0 +1,35 @@
+source "https://rubygems.org"
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+# gem "jekyll", "~> 4.3.2"
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+gem "minima", "~> 2.5"
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+gem "github-pages", group: :jekyll_plugins
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "jekyll-feed", "~> 0.12"
+end
+
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library.
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", ">= 1", "< 3"
+  gem "tzinfo-data"
+end
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
+
+# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem
+# do not have a Java counterpart.
+gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]
+
+gem "webrick", "~> 1.8"

docs/_config.yml

@@ -0,0 +1,21 @@
+title: MVL template
+email: ongsp@ucsd.edu
+description: >- # this means to ignore newlines until "baseurl:"
+  This is the template for MAVRL repos.
+# twitter_username: jekyllrb
+github_username:  materialsvirtuallab
+
+# Build settings
+remote_theme: just-the-docs/just-the-docs
+plugins:
+  - jekyll-feed
+
+# favicon_ico: "/assets/favicon.ico"
+
+nav_external_links:
+  - title: "GitHub"
+    url: "https://github.com/materialsvirtuallab/python_template"
+
+aux_links:
+  "Materials Virtual Lab":
+    - "https://materialsvirtuallab.org"

docs/_includes/footer_custom.html

@@ -0,0 +1 @@
+<small>&copy; Copyright 2022, Materials Virtual Lab</small>

docs/_includes/nav_footer_custom.html

@@ -0,0 +1 @@
+<span class="site-footer">&copy; Copyright 2022, Materials Virtual Lab</span>

docs/index.md

@@ -0,0 +1,13 @@
+[![GitHub license](https://img.shields.io/github/license/materialsvirtuallab/python_template)](https://github.com/materialsvirtuallab/python_template/blob/main/LICENSE)
+[![Linting](https://github.com/materialsvirtuallab/python_template/workflows/Linting/badge.svg)](https://github.com/materialsvirtuallab/python_template/workflows/Linting/badge.svg)
+[![Testing](https://github.com/materialsvirtuallab/python_template/workflows/Testing/badge.svg)](https://github.com/materialsvirtuallab/python_template/workflows/Testing/badge.svg)
+<!-- 
+[![Downloads](https://pepy.tech/badge/python_template)](https://pepy.tech/project/python_template)
+[![codecov](https://codecov.io/gh/materialsvirtuallab/python_template/branch/main/graph/badge.svg?token=3V3O79GODQ)]
+(https://codecov.io/gh/materialsvirtuallab/python_template) 
+-->
+
+# Introduction
+
+This is a template for setting up Python packages in the Materials Virtual Lab. It comes with the standard Github 
+workflows, pyproject.toml, docs, and linting.

pyproject.toml

@@ -76,23 +76,6 @@ isort.split-on-trailing-comma = false
 [tool.pytest.ini_options]
 addopts = "--durations=30 --quiet -r xXs --color=yes -p no:warnings --import-mode=importlib"
 
-[tool.coverage.run]
-omit = ["pymatgen/cli"]
-relative_files = true
-
-[tool.coverage.report]
-exclude_lines = [
-  "@deprecated",
-  "def __repr__",
-  "if 0:",
-  "if __name__ == .__main__.:",
-  "if self.debug:",
-  "if settings.DEBUG",
-  "pragma: no cover",
-  "raise AssertionError",
-  "raise NotImplementedError",
-]
-
 [tool.mypy]
 ignore_missing_imports = true
 namespace_packages = true
@@ -109,3 +92,22 @@ titel,alls,ans,nd,mater,nwo,te,hart,ontop,ist,ot,fo,nax,coo,coul,ser,leary,thre,
 fase,rute,reson,titels,ges,scalr,strat,struc,hda,nin,ons,pres,kno,loos,lamda,lew
 """
 check-filenames = true
+
+[tool.coverage.run]
+relative_files = true
+
+[tool.coverage.report]
+exclude_lines = [
+  "@deprecated",
+  "def __repr__",
+  "if 0:",
+  "if __name__ == .__main__.:",
+  "if self.debug:",
+  "if settings.DEBUG",
+  "pragma: no cover",
+  "raise AssertionError",
+  "raise NotImplementedError",
+  "input",
+  "if TYPE_CHECKING:",
+  "except PackageNotFoundError:"
+]