Merge pull request #41 from molssi-seamm/dev

Added handler for XYZ files and added properties

.github/workflows/CodeQL.yaml

@@ -0,0 +1,13 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main" ]
+
+jobs:
+  codeql:
+    name: CodeQL
+    uses: molssi-seamm/devops/.github/workflows/CodeQL.yaml@main

.gitignore

@@ -14,13 +14,6 @@ tramp
 .org-id-locations
 *_archive
 
-# VStudio
-.vscode
-
-# MOPAC
-*.arc
-*.out
-
 # flymake-mode
 *_flymake.*
 

HISTORY.rst

@@ -2,9 +2,26 @@
 History
 =======
 
+2023.1.24 -- Added handler for XYZ files and added properties
+
+  * Added a custom handler for XYZ files to cope with some of the variant formats.
+
+    * Supports files with no atom count on the first line
+
+    * Supports the variant used in the Minnesota Solubility database, which has 3 header
+      lines.
+
+  * Add capability to store properties into the database for formats such as MOPAC and
+    SDF that can handle properties. Also can output the properties when writing the
+    files.
+
+  * Fixed bugs if the system name or configuration name is not a string, but rather a number.
+
 2022.10.28 -- Fixed bug reading cif and mmcif files
+
   * There was a bug that caused a crash when reading cif and mmcif files, and potentially
     some other formats. It has been fixed throughout.
+
   * The standard error for properties were missing a commma in the property name. The
     comma is standard elsewhere in SEAMM so add it here: '<prop>, stderr'
 
@@ -13,8 +30,11 @@ History
   issue, and printing any other messages as warnings.
 
 2021.2.12 (12 February 2021)
+
   * Updated the README file to give a better description.
+
   * Updated the short description in setup.py to work with the new installer.
+
   * Added keywords for better searchability.
 
 2021.2.4 (4 February 2021)
@@ -30,9 +50,10 @@ History
   Removed leftover debug print statements.
 
 0.9 (15 April 2020)
+
   * General bug fixing and code cleanup.
-  * Part of release of all modules.
 
+  * Part of release of all modules.
 
 0.7.1 (23 November 2019)
   First release on PyPI.

Makefile

@@ -1,6 +1,9 @@
 MODULE := read_structure_step
-.PHONY: clean clean-test clean-pyc clean-build docs help
+.PHONY: help clean clean-build clean-docs clean-pyc clean-test lint format typing test
+.PHONY: dependencies test-all coverage html docs servedocs release check-release
+.PHONY: dist install uninstall
 .DEFAULT_GOAL := help
+
 define BROWSER_PYSCRIPT
 import os, webbrowser, sys
 try:
@@ -10,6 +13,7 @@ except:
 
 webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
 endef
+
 export BROWSER_PYSCRIPT
 
 define PRINT_HELP_PYSCRIPT
@@ -21,7 +25,9 @@ for line in sys.stdin:
 		target, help = match.groups()
 		print("%-20s %s" % (target, help))
 endef
+
 export PRINT_HELP_PYSCRIPT
+
 BROWSER := python -c "$$BROWSER_PYSCRIPT"
 
 help:
@@ -53,34 +59,31 @@ lint: ## check style with black and flake8
 	black --extend-exclude '_version.py' --check --diff $(MODULE) tests
 	flake8 --color never $(MODULE) tests
 
-format: ## reformat with with black
+format: ## reformat with with yapf and isort
 	black --extend-exclude '_version.py' $(MODULE) tests
 
-typing: ## check typing
-	pytype $(MODULE)
-
 test: ## run tests quickly with the default Python
-	py.test -rP
-
-dependencies:
-	pur -r requirements_dev.txt
-	pip install -r requirements_dev.txt
-
-test-all: ## run tests on every Python version with tox
-	tox
+	pytest tests/
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source $(MODULE) -m pytest
-	coverage report -m
-	coverage html
+	pytest -v --cov=$(MODULE) --cov-report term --color=yes tests/
+
+coverage-html: ## check code coverage quickly with the default Python, showing as html
+	pytest -v --cov=$(MODULE) --cov-report=html:htmlcov --cov-report term --color=yes tests/
 	$(BROWSER) htmlcov/index.html
 
-docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/developer/$(MODULE).rst
-	rm -f docs/developer/modules.rst
-	sphinx-apidoc -o docs/developer $(MODULE)
+clean-docs: ## remove files associated with building the docs
+	rm -f docs/api/$(MODULE).rst
+	rm -f docs/api/modules.rst
 	$(MAKE) -C docs clean
+
+html: clean-docs ## generate Sphinx HTML documentation, including API docs
+	sphinx-apidoc -o docs/api $(MODULE)
 	$(MAKE) -C docs html
+	rm -f docs/api/$(MODULE).rst
+	rm -f docs/api/modules.rst
+
+docs: html ## Make the html docs and show in the browser
 	$(BROWSER) docs/_build/html/index.html
 
 servedocs: docs ## compile the docs watching for changes

README.rst

@@ -14,11 +14,11 @@ SEAMM Read Structure Plug-in
    :target: https://codecov.io/gh/molssi-seamm/read_structure_step
    :alt: Code Coverage
 
-.. image:: https://img.shields.io/lgtm/grade/python/g/molssi-seamm/read_structure_step.svg?logo=lgtm&logoWidth=18
-   :target: https://lgtm.com/projects/g/molssi-seamm/read_structure_step/context:python
+.. image:: https://github.com/molssi-seamm/quickmin_step/workflows/CodeQL/badge.svg
+   :target: https://github.com/molssi-seamm/quickmin_step/security/code-scanning
    :alt: Code Quality
 
-.. image:: https://github.com/molssi-seamm/read_structure_step/workflows/Documentation/badge.svg
+.. image:: https://github.com/molssi-seamm/read_structure_step/workflows/Release/badge.svg
    :target: https://molssi-seamm.github.io/read_structure_step/index.html
    :alt: Documentation Status
 

devtools/conda-envs/test_env.yaml

@@ -19,11 +19,10 @@ dependencies:
   - pytest-cov
 
   # Documentation
-  - pygments
-
+  - pydata-sphinx-theme
+  - sphinx-design
+
   # Pip-only installs
   - pip:
     # Documentation
-    - rinohtype
-    - sphinx-rtd-theme
-    - pystemmer
+    - sphinx-copybutton

docs/_static/css/custom.css

@@ -1,24 +1,73 @@
-/* Make the page wider so e.g. the status table can be seen fully */
-.wy-nav-content {
-    max-width: 1200px !important;
+@import "../basic.css";
+
+html[data-theme="light"] {
+    --pst-color-primary: #ed1c24;
+	--pst-color-warning: #ed1c24;
+	--pst-color-primary-highlight: #bc151b;
+	--pst-color-secondary: #1d35e7;
+	--pst-color-secondary-highlight: #3e51e3;
+
+}
+
+html[data-theme="dark"] {
+    --pst-color-primary: #ed1c24;
+	--pst-color-warning: #ed1c24;
+	--pst-color-primary-highlight: #bc151b;
+	--pst-color-background: #1A1A1A;
+	--pst-color-secondary: #1d35e7;
+	--pst-color-secondary-highlight: #3e51e3;
+
+
+}
+
+html[data-theme="light"] a:hover {
+	color: #1A1A1A;
+}
+
+html[data-theme="dark"] h1, html[data-theme="dark"] h2, html[data-theme="dark"] h3, html[data-theme="dark"] h4, html[data-theme="dark"] h5, html[data-theme="dark"] h6 {
+	color: #ffffff;
+}
+
+
+html[data-theme="dark"] a {
+	color: #ffffff;
+}
+
+html[data-theme="dark"] .reference.external {
+	text-decoration: underline;
+
+}
+
+html[data-theme="dark"] p .reference.internal {
+	text-decoration: underline;
+
+}
+
+html[data-theme="dark"] a:hover {
+	color: #ed1c24;
+}
+
+html[data-theme="dark"] .prev-next-area a p.prev-next-title {
+    color: white;
 }
-.column_left {
-  display: table-cell;
-  width: 60px;
-  vertical-align: middle;
+
+html[data-theme="dark"] .prev-next-area:hover a:hover p.prev-next-title:hover {
+    color: #ed1c24;
 }
-.column {
-  display: table-cell;
+
+html[data-theme="dark"] dt:target {
+    background-color: #000000;
 }
-.column_right {
-  display: table-cell;
-  width: 60px;
-  vertical-align: middle;
+
+html .toctree-wrapper li[class^=toctree-l] {
+	list-style: circle;
 }
 
-/* Clear floats after the columns */
-.row:after {
-  content: "";
-  display: table;
-  clear: both;
+img:not(.logo__image, .footer_logo) {
+	padding: 20px;
+}
+
+
+.footer_logo {
+	max-height: 60px;
 }

docs/user/index.rst → docs/api/index.rst

@@ -1,15 +1,17 @@
-User Documentation
-==================
+API Documentation
+=================
 
 Contents:
 
 .. toctree::
    :maxdepth: 2
 
-   overview
+   modules
+
 
 Indices and tables
 ------------------
 
 * :ref:`genindex`
+* :ref:`modindex`
 * :ref:`search`

docs/api/read_structure_step.formats.cif.rst

@@ -0,0 +1,29 @@
+read\_structure\_step.formats.cif package
+=========================================
+
+Submodules
+----------
+
+read\_structure\_step.formats.cif.cif module
+--------------------------------------------
+
+.. automodule:: read_structure_step.formats.cif.cif
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+read\_structure\_step.formats.cif.mmcif module
+----------------------------------------------
+
+.. automodule:: read_structure_step.formats.cif.mmcif
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: read_structure_step.formats.cif
+   :members:
+   :undoc-members:
+   :show-inheritance: